blastx_gbnr_files/1152925_blastx.Z


BLASTX 2.0a19MP-WashU [05-Feb-1998] [Build sol2.5-ultra 01:47:30 05-Feb-1998]

Reference:  Gish, Warren (1994-1997).  unpublished.
Gish, Warren and David J. States (1993).  Identification of protein coding
regions by database similarity search.  Nat. Genet. 3:266-72.

Notice:  statistical significance is estimated under the assumption that the
equivalent of one entire reading frame in the query sequence codes for protein
and that significant alignments will involve only coding reading frames.

Query=  1152925
        (283 letters)

  Translating both strands of query sequence in all 6 reading frames

Database:  /usr/local/db/others/blast/nrdb
           322,836 sequences; 97,797,364 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
  Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N

A gi|2266931           (AF008443) RNA polymerase II subu... +2   397  3.3e-36   1
A sp|P19387|RPB3_HUMAN DNA-DIRECTED RNA POLYMERASE II 33... +2   387  3.7e-35   1
A sp|P97760|RPB3_MOUSE DNA-DIRECTED RNA POLYMERASE II 33... +2   360  2.7e-32   1
A gnl|PID|e348526      (Z80215) C36B1.3 [Caenorhabditis ... +2   338  5.8e-30   1
A gi|172213            (M27496) RNA polymerase II (EC 2.... +2   224  7.0e-18   1
A sp|P16370|RPB3_YEAST DNA-DIRECTED RNA POLYMERASE II 45... +2   218  3.0e-17   1
A sp|P37382|RPB3_SCHPO DNA-DIRECTED RNA POLYMERASE II 33... +2   208  3.5e-16   1
A gnl|PID|d1009957     (D50661) RNA polymerase II subuni... +2   208  3.5e-16   1
A gnl|PID|d1009958     (D50662) RNA polymerase II subuni... +2   208  3.5e-16   1
A dbj||D15070_1        (D15070) polymerase II third larg... +2   208  3.5e-16   1
A pir||S71176          RNA polymerase II third largest c... +2   162  7.7e-11   1
A pir||S71177          RNA polymerase II third largest c... +2   150  1.7e-09   1
A gi|514322            (L34772) RNA polymerase subunit [... +2   107  0.00012   1
A gi|514324            (L34773) RNA polymerase subunit [... +2   107  0.00013   1
A gnl|PID|d1028743     (AB009521) 261aa long hypothetica... +2   102  0.00022   1
A sp|O26144|RPOD_METTH DNA-DIRECTED RNA POLYMERASE SUBUN... +2   101  0.00029   1
A sp|P16925|CNJC_TETTH CONJUGATION STAGE-SPECIFIC PROTEI... +2   102  0.00031   1
A sp|Q57648|RPOD_METJA DNA-DIRECTED RNA POLYMERASE SUBUN... +2    96  0.00046   1
A gi|3335138           (AF047441) RNA polymerase I 40kD ... +2    93  0.0034    1
A gi|2266929           (AF008442) RNA polymerase I subun... +2    93  0.0035    1
A sp|P52432|RPA5_MOUSE DNA-DIRECTED RNA POLYMERASE I 40 ... +2    87  0.016     1
A sp|O28002|RPOD_ARCFU DNA-DIRECTED RNA POLYMERASE SUBUN... +2    84  0.021     1
A gnl|PID|e298589      (Y10542) homologous to 40kD subun... +2    83  0.042     1
A sp|Q00813|RPOD_HALMA DNA-DIRECTED RNA POLYMERASE SUBUN... +2    79  0.071     1
A sp|P07703|RPC5_YEAST DNA-DIRECTED RNA POLYMERASES I AN... +2    79  0.10      1
A sp|P39471|RPOD_SULAC DNA-DIRECTED RNA POLYMERASE SUBUN... +2    68  0.71      1
A sp|P95989|RPOD_SULSO DNA-DIRECTED RNA POLYMERASE SUBUN... +2    68  0.71      1
A gi|995989            (X87584) pid:g995989 [Coxsackievi... +2    55  0.997     1



>gi|2266931 (AF008443) RNA polymerase II subunit hRPB33 [Homo sapiens]
            >gi|3252823 (AC004382) RNA polymerase II subunit hRPB33 [Homo
            sapiens]
            Length = 275

  Plus Strand HSPs:

 Score = 397 (139.8 bits), Expect = 3.3e-36, P = 3.3e-36
 Identities = 72/92 (78%), Positives = 78/92 (84%), Frame = +2

Query:     8 VGQESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHTFLHKPEE 187
             V Q+ ILIVK+RKGQ L+LRA AKKGFGKEHAKWNPTAGV FEYDPDNALRHT   KPEE
Sbjct:   143 VEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEE 202

Query:   188 WPRSEYSTLPENEHQAPYDPTGKPNRFYXNIE 283
             WP+SEYS L E+E QAPYDP GKP RFY N+E
Sbjct:   203 WPKSEYSELDEDESQAPYDPNGKPERFYYNVE 234


>sp|P19387|RPB3_HUMAN DNA-DIRECTED RNA POLYMERASE II 33 KD POLYPEPTIDE (RPB3)
            (RPB33) (RPB31) >pir||A36264 DNA-directed RNA polymerase (EC
            2.7.7.6) II 33K chain - human >gi|337497 (J05448) RNA polymerase
            subunit hRPB 33 [Homo sapiens] >gnl|PID|e1254208 (AJ224143) RNA
            polymerase II subunit [Homo sapiens] >gnl|PID|e1254210 (AJ224144)
            RNA polymerase subunit [Homo sapiens]
            Length = 275

  Plus Strand HSPs:

 Score = 387 (136.2 bits), Expect = 3.7e-35, P = 3.7e-35
 Identities = 71/92 (77%), Positives = 77/92 (83%), Frame = +2

Query:     8 VGQESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHTFLHKPEE 187
             V Q+ ILIVK+RKGQ L+LRA AKKGFGKEHAKWNPTAGV FEYDPDNALR T   KPEE
Sbjct:   143 VEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRTTVYPKPEE 202

Query:   188 WPRSEYSTLPENEHQAPYDPTGKPNRFYXNIE 283
             WP+SEYS L E+E QAPYDP GKP RFY N+E
Sbjct:   203 WPKSEYSELDEDESQAPYDPNGKPERFYYNVE 234


>sp|P97760|RPB3_MOUSE DNA-DIRECTED RNA POLYMERASE II 33 KD POLYPEPTIDE (RPB3)
            (RPB33) (RPB31) >gnl|PID|d1012880 (D83999) the third largest RNA
            polymerase II subunit [Mus musculus]
            Length = 275

  Plus Strand HSPs:

 Score = 360 (126.7 bits), Expect = 2.7e-32, P = 2.7e-32
 Identities = 67/92 (72%), Positives = 73/92 (79%), Frame = +2

Query:     8 VGQESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHTFLHKPEE 187
             V Q+ ILIVK+RKGQ L+LRA  KK  GKEHAKWNPTAGV FEYDPDN LRHT   KPEE
Sbjct:   143 VEQDDILIVKLRKGQELRLRAYVKKRSGKEHAKWNPTAGVAFEYDPDNGLRHTVYPKPEE 202

Query:   188 WPRSEYSTLPENEHQAPYDPTGKPNRFYXNIE 283
              P+SEYS L E+E QAPYDP GKP RFY N+E
Sbjct:   203 GPKSEYSELDEDESQAPYDPNGKPERFYYNVE 234


>gnl|PID|e348526 (Z80215) C36B1.3 [Caenorhabditis elegans]
            Length = 402

  Plus Strand HSPs:

 Score = 338 (119.0 bits), Expect = 5.8e-30, P = 5.8e-30
 Identities = 61/92 (66%), Positives = 74/92 (80%), Frame = +2

Query:    14 QESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHTFLHKPEEWP 193
             +E ILIVK+RKGQ L L+A  KKGFGKEHAKWNPT GV FEYDPDNALRHT     EEWP
Sbjct:   151 REEILIVKLRKGQELNLKAYVKKGFGKEHAKWNPTCGVAFEYDPDNALRHTIYPNVEEWP 210

Query:   194 RSEYSTLPEN--EHQAPYDPTGKPNRFYXNIE 283
             RS++S+LPE+  E +AP++P  KPN+F+ +IE
Sbjct:   211 RSDHSSLPEDSTEKEAPFEPDNKPNKFWFSIE 242


>gi|172213 (M27496) RNA polymerase II (EC 2.7.7.6) [Saccharomyces cerevisiae]
           Length = 318

  Plus Strand HSPs:

 Score = 224 (78.9 bits), Expect = 7.0e-18, P = 7.0e-18
 Identities = 47/92 (51%), Positives = 61/92 (66%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHT-FLHKPE---EW 190
             +LI K+RKGQ LKL  +AKKG  KEHAKW P AG+ FEYDP N L+HT + ++ +   EW
Sbjct:   142 VLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAGIEFEYDPWNKLKHTDYWYEQDSAKEW 201

Query:   191 PRS---EYSTLPENEHQAPYDPTGKPNRFYXNIE 283
             P+S   EY   P NE   P+D   + + FY N+E
Sbjct:   202 PQSKNCEYED-PPNEGD-PFDYKAQADTFYMNVE 233


>sp|P16370|RPB3_YEAST DNA-DIRECTED RNA POLYMERASE II 45 KD POLYPEPTIDE (B44.5)
            >pir||S49961 DNA-directed RNA polymerase (EC 2.7.7.6) II chain RPB3
            - yeast (Saccharomyces cerevisiae) >gi|599978 (Z46881) RNA
            polymerase II [Saccharomyces cerevisiae] >gi|763325 (Z47047) DNA
            polymerase II [Saccharomyces cerevisiae]
            Length = 318

  Plus Strand HSPs:

 Score = 218 (76.7 bits), Expect = 3.0e-17, P = 3.0e-17
 Identities = 46/92 (50%), Positives = 60/92 (65%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHT-FLHKPE---EW 190
             +LI K+RKGQ LKL  +AKKG  KEHAKW P A + FEYDP N L+HT + ++ +   EW
Sbjct:   142 VLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEW 201

Query:   191 PRS---EYSTLPENEHQAPYDPTGKPNRFYXNIE 283
             P+S   EY   P NE   P+D   + + FY N+E
Sbjct:   202 PQSKNCEYED-PPNEGD-PFDYKAQADTFYMNVE 233


>sp|P37382|RPB3_SCHPO DNA-DIRECTED RNA POLYMERASE II 33 KD POLYPEPTIDE (RNA
            POLYMERASE II SUBUNIT 3) >pir||S43201 DNA-directed RNA polymerase
            (EC 2.7.7.6) II chain 3 - fission yeast (Schizosaccharomyces pombe)
            (fragment)
            Length = 296

  Plus Strand HSPs:

 Score = 208 (73.2 bits), Expect = 3.5e-16, P = 3.5e-16
 Identities = 43/91 (47%), Positives = 59/91 (64%), Frame = +2

Query:    26 LIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHT---FLHKPE-EWP 193
             LI K+RK Q + LR IAKKG  KEHAKW+PT+ V FEYDP N L+HT   F +  + EWP
Sbjct:   144 LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWP 203

Query:   194 RSEYSTLPENEHQA-PYDPTGKPNRFYXNIE 283
             +S+ +   E   +  P++   +P RFY ++E
Sbjct:   204 KSKNADWEEPPREGEPFNFQEEPRRFYMDVE 234


>gnl|PID|d1009957 (D50661) RNA polymerase II subunit 3 [Schizosaccharomyces
            pombe]
            Length = 296

  Plus Strand HSPs:

 Score = 208 (73.2 bits), Expect = 3.5e-16, P = 3.5e-16
 Identities = 43/91 (47%), Positives = 59/91 (64%), Frame = +2

Query:    26 LIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHT---FLHKPE-EWP 193
             LI K+RK Q + LR IAKKG  KEHAKW+PT+ V FEYDP N L+HT   F +  + EWP
Sbjct:   144 LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWP 203

Query:   194 RSEYSTLPENEHQA-PYDPTGKPNRFYXNIE 283
             +S+ +   E   +  P++   +P RFY ++E
Sbjct:   204 KSKNADWEEPPREGEPFNFQEEPRRFYMDVE 234


>gnl|PID|d1009958 (D50662) RNA polymerase II subunit 3 [Schizosaccharomyces
            pombe]
            Length = 296

  Plus Strand HSPs:

 Score = 208 (73.2 bits), Expect = 3.5e-16, P = 3.5e-16
 Identities = 43/91 (47%), Positives = 59/91 (64%), Frame = +2

Query:    26 LIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHT---FLHKPE-EWP 193
             LI K+RK Q + LR IAKKG  KEHAKW+PT+ V FEYDP N L+HT   F +  + EWP
Sbjct:   144 LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWP 203

Query:   194 RSEYSTLPENEHQA-PYDPTGKPNRFYXNIE 283
             +S+ +   E   +  P++   +P RFY ++E
Sbjct:   204 KSKNADWEEPPREGEPFNFQEEPRRFYMDVE 234


>dbj||D15070_1 (D15070) polymerase II third largest subunit (subunit 3)
            [Schizosaccharomyces pombe]
            Length = 297

  Plus Strand HSPs:

 Score = 208 (73.2 bits), Expect = 3.5e-16, P = 3.5e-16
 Identities = 43/91 (47%), Positives = 59/91 (64%), Frame = +2

Query:    26 LIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHT---FLHKPE-EWP 193
             LI K+RK Q + LR IAKKG  KEHAKW+PT+ V FEYDP N L+HT   F +  + EWP
Sbjct:   144 LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWP 203

Query:   194 RSEYSTLPENEHQA-PYDPTGKPNRFYXNIE 283
             +S+ +   E   +  P++   +P RFY ++E
Sbjct:   204 KSKNADWEEPPREGEPFNFQEEPRRFYMDVE 234


>pir||S71176 RNA polymerase II third largest chain RPB35.5A - Arabidopsis
            thaliana >gi|514318 (L34770) RNA polymerase II third largest
            subunit [Arabidopsis thaliana]
            Length = 319

  Plus Strand HSPs:

 Score = 162 (57.0 bits), Expect = 7.7e-11, P = 7.7e-11
 Identities = 29/44 (65%), Positives = 37/44 (84%), Frame = +2

Query:    17 ESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPD 148
             + I+IVK+R+GQ LKLRAIA+KG GK+HAKW+P A V F Y+PD
Sbjct:   150 KGIIIVKLRRGQELKLRAIARKGIGKDHAKWSPAATVTFMYEPD 193


>pir||S71177 RNA polymerase II third largest chain - Arabidopsis thaliana
            >gi|514320 (L34771) RNA polymerase II third largest subunit
            [Arabidopsis thaliana]
            Length = 319

  Plus Strand HSPs:

 Score = 150 (52.8 bits), Expect = 1.7e-09, P = 1.7e-09
 Identities = 25/44 (56%), Positives = 36/44 (81%), Frame = +2

Query:    17 ESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPD 148
             + I+I K+R+GQ LKL+A+A+KG GK+HAKW+P A V + Y+PD
Sbjct:   150 KGIIIAKLRRGQELKLKALARKGIGKDHAKWSPAATVTYMYEPD 193


>gi|514322 (L34772) RNA polymerase subunit [Arabidopsis thaliana]
           >prf||2204246A RNA polymerase [Arabidopsis thaliana]
           Length = 375

  Plus Strand HSPs:

 Score = 107 (37.7 bits), Expect = 0.00012, P = 0.00012
 Identities = 21/46 (45%), Positives = 27/46 (58%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALR 160
             ILI K+  GQ ++L A A KG GK HAKW+P     +   P+  LR
Sbjct:   232 ILIAKLAPGQEIELEAHAVKGIGKTHAKWSPVGTAWYRMHPEVVLR 277


>gi|514324 (L34773) RNA polymerase subunit [Arabidopsis thaliana] >gi|2462755
           (AC002292) RNA polymerase subunit (isoform B) [Arabidopsis thaliana]
           >prf||2204246B RNA polymerase [Arabidopsis thaliana]
           Length = 385

  Plus Strand HSPs:

 Score = 107 (37.7 bits), Expect = 0.00013, P = 0.00013
 Identities = 24/57 (42%), Positives = 31/57 (54%), Frame = +2

Query:    17 ESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHTFLHKPEE 187
             + ILI K+  GQ ++L A A KG GK HAKW+P A   +   P+  L   F  K  E
Sbjct:   237 KDILIAKLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEVVLLKEFEGKHAE 293


>gnl|PID|d1028743 (AB009521) 261aa long hypothetical DNA-directed RNA
            polymerase subunit D [Pyrococcus horikoshii] >gnl|PID|d1031692
            (AP000006) 261aa long hypothetical DNA-directed RNA polymerase
            subunit D [Pyrococcus horikoshii]
            Length = 261

  Plus Strand HSPs:

 Score = 102 (35.9 bits), Expect = 0.00022, P = 0.00022
 Identities = 23/39 (58%), Positives = 25/39 (64%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEY 139
             I IVK+ KGQRL   A AK G GK+HAKW P    GF Y
Sbjct:   120 IPIVKLAKGQRLVFNAYAKLGRGKDHAKWQP----GFTY 154


>sp|O26144|RPOD_METTH DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|2621073
            (AE000796) DNA-dependent RNA polymerase, subunit D
            [Methanobacterium thermoautotrophicum]
            Length = 264

  Plus Strand HSPs:

 Score = 101 (35.6 bits), Expect = 0.00029, P = 0.00029
 Identities = 18/41 (43%), Positives = 26/41 (63%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDP 145
             I +VK+     L+L A+A+ G G+EHAKW PT    ++Y P
Sbjct:   125 IPLVKLGDDDELELEAVAQLGVGREHAKWEPTTACAYKYYP 165


>sp|P16925|CNJC_TETTH CONJUGATION STAGE-SPECIFIC PROTEIN >pir||S12807 cnjC
            protein, conjugation-specific - Tetrahymena thermophila (SGC5)
            >gnl|PID|e1192685 (X62317) RNA polymerase subunit [Tetrahymena
            thermophila]
            Length = 310

  Plus Strand HSPs:

 Score = 102 (35.9 bits), Expect = 0.00031, P = 0.00031
 Identities = 21/48 (43%), Positives = 29/48 (60%), Frame = +2

Query:     5 EVGQESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPD 148
             EVG   I I+K+ KGQ++     A+KG GK H+KWNP     F  +P+
Sbjct:   146 EVG---IPIIKLSKGQQIHFECEAQKGIGKMHSKWNPVCISTFSVEPE 190


>sp|Q57648|RPOD_METJA DNA-DIRECTED RNA POLYMERASE SUBUNIT D >pir||A64324
            DNA-directed RNA polymerase (EC 2.7.7.6) subunit D - Methanococcus
            jannaschii >gi|1590937 (U67475) DNA-directed RNA polymerase,
            subunit D (rpoD) [Methanococcus jannaschii]
            Length = 191

  Plus Strand HSPs:

 Score = 96 (33.8 bits), Expect = 0.00046, P = 0.00046
 Identities = 20/41 (48%), Positives = 26/41 (63%), Frame = +2

Query:     5 EVGQESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGV 127
             EV  ++I IVK+ KGQR+++   A  G GK HAKW P   V
Sbjct:   103 EVAFKNIPIVKLGKGQRIQIECEAIPGIGKVHAKWQPCNAV 143


>gi|3335138 (AF047441) RNA polymerase I 40kD subunit [Homo sapiens]
            Length = 342

  Plus Strand HSPs:

 Score = 93 (32.7 bits), Expect = 0.0034, P = 0.0034
 Identities = 19/47 (40%), Positives = 27/47 (57%), Frame = +2

Query:    17 ESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNAL 157
             + ILI ++R GQ + L     KG GK+HAK++P A   +   PD  L
Sbjct:   195 DDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDITL 241


>gi|2266929 (AF008442) RNA polymerase I subunit hRPA39 [Homo sapiens]
            Length = 346

  Plus Strand HSPs:

 Score = 93 (32.7 bits), Expect = 0.0035, P = 0.0035
 Identities = 19/47 (40%), Positives = 27/47 (57%), Frame = +2

Query:    17 ESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNAL 157
             + ILI ++R GQ + L     KG GK+HAK++P A   +   PD  L
Sbjct:   195 DDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDITL 241


>sp|P52432|RPA5_MOUSE DNA-DIRECTED RNA POLYMERASE I 40 KD POLYPEPTIDE (RPA40)
            >pir||A55082 DNA-directed RNA polymerase (EC 2.7.7.6) 40k chain -
            mouse >gnl|PID|d1007308 (D31966) mouse RNA polymerase I 40kD
            subunit [Mus musculus]
            Length = 355

  Plus Strand HSPs:

 Score = 87 (30.6 bits), Expect = 0.016, P = 0.016
 Identities = 17/43 (39%), Positives = 25/43 (58%), Frame = +2

Query:    17 ESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDP 145
             + ILI ++R GQ + L     KG GK+HAK++P A   +   P
Sbjct:   204 DDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSPVATASYRLLP 246


>sp|O28002|RPOD_ARCFU DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gi|2648239
            (AE000947) DNA-directed RNA polymerase, subunit D (rpoD)
            [Archaeoglobus fulgidus]
            Length = 264

  Plus Strand HSPs:

 Score = 84 (29.6 bits), Expect = 0.022, P = 0.021
 Identities = 15/44 (34%), Positives = 31/44 (70%), Frame = +2

Query:    17 ESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPD 148
             ++I ++++ +GQ+L L A+A+ G G+EHAK+ P +   ++  P+
Sbjct:   123 DNIPVLELFEGQQLMLEAVARLGTGREHAKFQPVSVCVYKIIPE 166


>gnl|PID|e298589 (Y10542) homologous to 40kD subunit of RNA-polymerase I and
            III [Cricetulus griseus]
            Length = 347

  Plus Strand HSPs:

 Score = 83 (29.2 bits), Expect = 0.043, P = 0.042
 Identities = 16/41 (39%), Positives = 25/41 (60%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDP 145
             I++ K+R GQ + L A A  G G++HAK++P A   +   P
Sbjct:   197 IVVAKLRPGQEIDLEAHAILGIGQDHAKFSPVATASYRLLP 237


>sp|Q00813|RPOD_HALMA DNA-DIRECTED RNA POLYMERASE SUBUNIT D >pir||D44126
            DNA-directed RNA polymerase II chain RpB3 homolog Rp-alpha -
            Haloarcula marismortui >gi|148773 (M87833) ribosomal protein
            HmaRp-alpha subunit [Halobacterium marismortui]
            Length = 259

  Plus Strand HSPs:

 Score = 79 (27.8 bits), Expect = 0.074, P = 0.071
 Identities = 16/45 (35%), Positives = 27/45 (60%), Frame = +2

Query:     5 EVGQESILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEY 139
             E   ++I I+ +++GQRL++ A A    G+EHAK      VG+ +
Sbjct:   109 EAADDNIPIIDLKEGQRLEVEADAVLDTGREHAKHQGGVAVGYRH 153


>sp|P07703|RPC5_YEAST DNA-DIRECTED RNA POLYMERASES I AND III 40 KD POLYPEPTIDE
            (AC40) >pir||A25968 DNA-directed RNA polymerase (EC 2.7.7.6) 40K
            chain - yeast (Saccharomyces cerevisiae) >gi|172474 (M15499) RNA
            polymerase C-40 [Saccharomyces cerevisiae] >gi|914981 (U32445) RNA
            Polymerases I and III 40 kD subunit (Swiss Prot. accession number
            P07703) [Saccharomyces cerevisiae]
            Length = 335

  Plus Strand HSPs:

 Score = 79 (27.8 bits), Expect = 0.11, P = 0.10
 Identities = 17/47 (36%), Positives = 27/47 (57%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPD-NALR 160
             IL+ K+R GQ + L+A    G G +HAK++P +   +   P  N L+
Sbjct:   191 ILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQ 237


>sp|P39471|RPOD_SULAC DNA-DIRECTED RNA POLYMERASE SUBUNIT D >pir||S47023
            DNA-directed RNA polymerase (EC 2.7.7.6) chain D - Sulfolobus
            acidocaldarius >gi|517290 (X80194) RNA polymerase subunit D
            [Sulfolobus acidocaldarius]
            Length = 264

  Plus Strand HSPs:

 Score = 68 (23.9 bits), Expect = 1.2, P = 0.71
 Identities = 15/42 (35%), Positives = 24/42 (57%), Frame = +2

Query:    20 SILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDP 145
             +I IV +   Q++ L A  + G+GKEH K++P +     Y P
Sbjct:   127 AIPIVLLGSKQKISLEARLRLGYGKEHIKYSPVSVSIVRYYP 168


>sp|P95989|RPOD_SULSO DNA-DIRECTED RNA POLYMERASE SUBUNIT D >gnl|PID|e283852
            (Y08257) DNA-directed RNA polymerase subunit D [Sulfolobus
            solfataricus]
            Length = 265

  Plus Strand HSPs:

 Score = 68 (23.9 bits), Expect = 1.2, P = 0.71
 Identities = 16/41 (39%), Positives = 23/41 (56%), Frame = +2

Query:    23 ILIVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDP 145
             I IV +   Q++ L A  + G+GKEHAK+ P +     Y P
Sbjct:   128 IPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYP 168


>gi|995989 (X87584) pid:g995989 [Coxsackievirus A1]
           Length = 70

  Plus Strand HSPs:

 Score = 55 (19.4 bits), Expect = 5.7, P = 1.0
 Identities = 13/29 (44%), Positives = 14/29 (48%), Frame = +2

Query:   185 EWPRSEYSTLPENEHQAPYDPTGKPNRFY 271
             EWP S  S    N   AP +P    NRFY
Sbjct:    41 EWP-SFLSDKEANPVDAPTEPDASSNRFY 68


Parameters:
  matrix=/usr/local/src/bio/blast/blast2/matrix/aa/BLOSUM62
  W=3
  T=1000

  ctxfactor=5.93
  E=10

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   Std.    0   BLOSUM62                                 0.318   0.135   0.401  
   +3      0   BLOSUM62        0.318   0.135   0.401    0.357   0.160   0.519  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   +2      0   BLOSUM62        0.315   0.136   0.423    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   +1      0   BLOSUM62        0.318   0.135   0.401    0.373   0.164   0.686  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -1      0   BLOSUM62        0.318   0.135   0.401    0.364   0.164   0.706  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -2      0   BLOSUM62        0.318   0.135   0.401    0.346   0.153   0.537  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -3      0   BLOSUM62        0.318   0.135   0.401    0.340   0.151   0.496  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W    T  X   E2     S2
   +3      0       93        92       10.  63 3 1000 22  0.095   32
                                                     28  0.12    33
   +2      0       94        93       10.  63 3 1000 23  0.11    32
                                                     28  0.12    33
   +1      0       94        93       10.  63 3 1000 22  0.096   32
                                                     28  0.12    33
   -1      0       94        93       10.  63 3 1000 22  0.096   32
                                                     28  0.12    33
   -2      0       94        93       10.  63 3 1000 22  0.096   32
                                                     28  0.12    33
   -3      0       93        92       10.  63 3 1000 22  0.095   32
                                                     28  0.12    33


Statistics:

  Database:  /usr/local/db/others/blast/nrdb
    Title:  /usr/local/db/others/blast/nrdb
    Release date:  unknown
    Posted date:  9:16 PM EDT Aug 19, 1998
    Format:  BLAST
  # of letters in database:  97,797,364
  # of sequences in database:  322,836
  # of database sequences satisfying E:  28
  No. of states in DFA:  316 (31 KB)
  Total size of DFA:  38 KB (64 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t  Elapsed: 00:00:00
  No. of threads or processors used:  6
  Search cpu time:  20.52u 1.30s 21.82t  Elapsed: 00:00:08
  Total cpu time:  20.57u 3.20s 23.77t  Elapsed: 00:00:10
  Start:  Sat Sep 26 04:05:22 1998   End:  Sat Sep 26 04:05:32 1998

Date: 16:23:55 on Sun 17 Dec 117.