BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 005638
(686 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 221 bits (562), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 128/364 (35%), Positives = 195/364 (53%), Gaps = 17/364 (4%)
Query: 325 KPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRY 384
+PW +++G L ++L++ + +D+ S + P H SF ++
Sbjct: 469 QPWPLPVQMELGKLLAEMLVQATQMPCSLDKPHRSS-RLVPVLYHVY-SFRNV----QQI 522
Query: 385 GVIECDPLVRKGLEKTGRHMII---PYMPMLVPPLNWRGYNRGGHFFLPSYVMRT-HGAR 440
G+++ P + LEK + +PML PPL W + G P+ +MRT GA
Sbjct: 523 GILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLSPTKLMRTVEGAT 582
Query: 441 QQRETIKMTPRSQLEPVFQALDTLGSTKWRVNKRILGVIDRMWASGGC--LAGLVDQEDV 498
Q +E ++ P + L AL LG+ WRVN R+L ++ +++ + GC L +
Sbjct: 583 QHQELLETCPPTALHGALDALTQLGNCAWRVNGRVLDLVLQLFQAKGCPQLGVPAPPSEA 642
Query: 499 PLPEK---PNTDDETEIXXXXXXXXXXXXQNSEKHSQRCDIELKLSVARKMKDEEGFYYP 555
P P + P++ E HS R + +LS+A+ ++D F+ P
Sbjct: 643 PQPPEAHLPHSAAPARKAELRRELAHCQKVAREMHSLRAEALYRLSLAQHLRDRV-FWLP 701
Query: 556 HNLDFRGRAYPMHPYLNHLGSDLCRGVLEFEEGHPLGKAGLHWLKIHLANLYAGGVDKLS 615
HN+DFRGR YP P+ NHLGSD+ R +LEF +G PLG GL WLKIHL NL G +
Sbjct: 702 HNMDFRGRTYPCPPHFNHLGSDVARALLEFAQGRPLGPHGLDWLKIHLVNL-TGLKKREP 760
Query: 616 YEGRVAFTENHLDDIFDSADRPLEGRRWWLGAEDPFQCLATCINLSEALRSPSPESTISH 675
R+AF E +DDI DSAD+PL GR+WW+GAE+P+Q LA C+ ++ A+R+ P + +SH
Sbjct: 761 LRKRLAFAEEVMDDILDSADQPLTGRKWWMGAEEPWQTLACCMEVANAVRASDPAAYVSH 820
Query: 676 IPVH 679
+PVH
Sbjct: 821 LPVH 824
>pdb|2PI4|A Chain A, T7rnap Complexed With A Phi10 Protein And Initiating Gtps.
pdb|2PI5|A Chain A, T7 Rna Polymerase Complexed With A Phi10 Promoter
Length = 878
Score = 145 bits (366), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 138/554 (24%), Positives = 236/554 (42%), Gaps = 99/554 (17%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 27 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 86
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ + K T + + + +A IT+ + L T+A V A
Sbjct: 87 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 135
Query: 250 IGEAIENEAR---IQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EAR I+ KKN + RV +
Sbjct: 136 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 173
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ----L 356
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q +
Sbjct: 174 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVV 232
Query: 357 GDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPL 416
G I L EA+ R + P+ + P +VPP
Sbjct: 233 GQDSETIE------LAPEYAEAIATRAGALAGISPM---------------FQPCVVPPK 271
Query: 417 NWRGYNRGGHFF---LPSYVMRTHG--ARQQRETIKMTPRSQLEPVFQALDTLGSTKWRV 471
W G GG++ P ++RTH A + E + M V++A++ +T W++
Sbjct: 272 PWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPE------VYKAINIAQNTAWKI 325
Query: 472 NKRILGVIDRMWASGGCLAG---LVDQEDVPL-PEKPNTDDETEIXXXXXXXXXXXXQNS 527
NK++L V + + C +++E++P+ PE + + E + ++
Sbjct: 326 NKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEA-LTAWKRAAAAVYRKDK 384
Query: 528 EKHSQRCDIELKLSVARKMKDEEGFYYPHNLDFRGRAYPMHPYLNHLGSDLCRGVLEFEE 587
+ S+R +E L A K + + ++P+N+D+RGR Y + + N G+D+ +G+L +
Sbjct: 385 ARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKGLLTLAK 443
Query: 588 GHPLGKAGLHWLKIHLANLYAGGVDKLSYEGRVAFTENHLDDIFDSADRPLEGRRWWLGA 647
G P+GK G +WLKIH AN GVDK+ + R+ F E + ++I A PLE WW
Sbjct: 444 GKPIGKEGYYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLEN-TWWAEQ 500
Query: 648 EDPFQCLATCINLS 661
+ PF LA C +
Sbjct: 501 DSPFCFLAFCFEYA 514
>pdb|4RNP|A Chain A, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|B Chain B, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|C Chain C, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|1CEZ|A Chain A, Crystal Structure Of A T7 Rna Polymerase-T7 Promoter
Complex
pdb|1QLN|A Chain A, Structure Of A Transcribing T7 Rna Polymerase Initiation
Complex
pdb|1H38|A Chain A, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|B Chain B, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|C Chain C, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|D Chain D, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1MSW|D Chain D, Structural Basis For The Transition From Initiation To
Elongation Transcription In T7 Rna Polymerase
pdb|1S0V|A Chain A, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|B Chain B, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|C Chain C, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|D Chain D, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S76|D Chain D, T7 Rna Polymerase Alpha Beta Methylene Atp Elongation
Complex
pdb|1S77|D Chain D, T7 Rnap Product Pyrophosphate Elongation Complex
Length = 883
Score = 145 bits (366), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 138/554 (24%), Positives = 237/554 (42%), Gaps = 99/554 (17%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 32 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 91
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ + K T + + + +A IT+ + L T+A V A
Sbjct: 92 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 140
Query: 250 IGEAIENEAR---IQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EAR I+ KKN + RV +
Sbjct: 141 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 178
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ----L 356
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q +
Sbjct: 179 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVV 237
Query: 357 GDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPL 416
G I A + EA+ R + P+ + P +VPP
Sbjct: 238 GQDSETIELAPEYA------EAIATRAGALAGISPM---------------FQPCVVPPK 276
Query: 417 NWRGYNRGGHFF---LPSYVMRTHG--ARQQRETIKMTPRSQLEPVFQALDTLGSTKWRV 471
W G GG++ P ++RTH A + E + M V++A++ +T W++
Sbjct: 277 PWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPE------VYKAINIAQNTAWKI 330
Query: 472 NKRILGVIDRMWASGGCLAG---LVDQEDVPL-PEKPNTDDETEIXXXXXXXXXXXXQNS 527
NK++L V + + C +++E++P+ PE + + E + ++
Sbjct: 331 NKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEA-LTAWKRAAAAVYRKDK 389
Query: 528 EKHSQRCDIELKLSVARKMKDEEGFYYPHNLDFRGRAYPMHPYLNHLGSDLCRGVLEFEE 587
+ S+R +E L A K + + ++P+N+D+RGR Y + + N G+D+ +G+L +
Sbjct: 390 ARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKGLLTLAK 448
Query: 588 GHPLGKAGLHWLKIHLANLYAGGVDKLSYEGRVAFTENHLDDIFDSADRPLEGRRWWLGA 647
G P+GK G +WLKIH AN GVDK+ + R+ F E + ++I A PLE WW
Sbjct: 449 GKPIGKEGYYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLEN-TWWAEQ 505
Query: 648 EDPFQCLATCINLS 661
+ PF LA C +
Sbjct: 506 DSPFCFLAFCFEYA 519
>pdb|3E2E|A Chain A, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 7nt Of Rna
pdb|3E3J|C Chain C, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
pdb|3E3J|B Chain B, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
Length = 889
Score = 144 bits (363), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 135/553 (24%), Positives = 235/553 (42%), Gaps = 97/553 (17%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 38 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 97
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ + K T + + + +A IT+ + L T+A V A
Sbjct: 98 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 146
Query: 250 IGEAIENEAR---IQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EAR I+ KKN + RV +
Sbjct: 147 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 184
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSP 360
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q
Sbjct: 185 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQ----- 238
Query: 361 PDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMI---IPYMPMLVPPLN 417
+ G+ IE P + + + + + P +VPP
Sbjct: 239 ---------------NAGVVGQDSETIELAPEYAEAIATRAGALAGISLMFQPCVVPPKP 283
Query: 418 WRGYNRGGHFF---LPSYVMRTHG--ARQQRETIKMTPRSQLEPVFQALDTLGSTKWRVN 472
W G GG++ P ++RTH A + E + M V++A++ +T W++N
Sbjct: 284 WTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPE------VYKAINIAQNTAWKIN 337
Query: 473 KRILGVIDRMWASGGCLAG---LVDQEDVPL-PEKPNTDDETEIXXXXXXXXXXXXQNSE 528
K++L V + + C +++E++P+ PE + + E + ++
Sbjct: 338 KKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEA-LTAWKRAAAAVYRKDKA 396
Query: 529 KHSQRCDIELKLSVARKMKDEEGFYYPHNLDFRGRAYPMHPYLNHLGSDLCRGVLEFEEG 588
+ S+R +E L A K + + ++P+N+D+RGR Y + + N G+D+ +G+L +G
Sbjct: 397 RKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKGLLTLAKG 455
Query: 589 HPLGKAGLHWLKIHLANLYAGGVDKLSYEGRVAFTENHLDDIFDSADRPLEGRRWWLGAE 648
P+GK G +WLKIH AN GVDK+ + R+ F E + ++I A PLE WW +
Sbjct: 456 KPIGKEGYYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLEN-TWWAEQD 512
Query: 649 DPFQCLATCINLS 661
PF LA C +
Sbjct: 513 SPFCFLAFCFEYA 525
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 144 bits (362), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 141/560 (25%), Positives = 232/560 (41%), Gaps = 111/560 (19%)
Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189
L R Q+ +E E++E ++ + +AD K + LP + + WFE
Sbjct: 32 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 91
Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249
++ + K T + + + +A IT+ + L T+A V A
Sbjct: 92 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 140
Query: 250 IGEAIENEAR---IQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306
IG AIE+EAR I+ KKN + RV +
Sbjct: 141 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 178
Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ----L 356
KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q +
Sbjct: 179 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVV 237
Query: 357 GDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPL 416
G I L EA+ R + P+ + P +VPP
Sbjct: 238 GQDSETIE------LAPEYAEAIATRAGALAGISPM---------------FQPCVVPPK 276
Query: 417 NWRGYNRGGHFF---LPSYVMRTHG--ARQQRETIKMTPRSQLEPVFQALDTLGSTKWRV 471
W G GG++ P ++RTH A + E + M V++A++ +T W++
Sbjct: 277 PWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPE------VYKAINIAQNTAWKI 330
Query: 472 NKRILGVIDRM--WASGGCLAGLVDQEDVP------LPEKPNTDDET--EIXXXXXXXXX 521
NK++L V + + W ED+P LP KP D +
Sbjct: 331 NKKVLAVANVITKWKHSPV-------EDIPAIEREELPMKPEDIDMNPEALTAWKRAAAA 383
Query: 522 XXXQNSEKHSQRCDIELKLSVARKMKDEEGFYYPHNLDFRGRAYPMHPYLNHLGSDLCRG 581
++ + S+R +E L A K + + ++P+N+D+RGR Y + + N G+D+ +G
Sbjct: 384 VYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKG 442
Query: 582 VLEFEEGHPLGKAGLHWLKIHLANLYAGGVDKLSYEGRVAFTENHLDDIFDSADRPLEGR 641
+L +G P+GK G +WLKIH AN GVDK+ + R+ F E + ++I A PLE
Sbjct: 443 LLTLAKGKPIGKEGYYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLEN- 499
Query: 642 RWWLGAEDPFQCLATCINLS 661
WW + PF LA C +
Sbjct: 500 TWWAEQDSPFCFLAFCFEYA 519
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,339,807
Number of Sequences: 62578
Number of extensions: 782138
Number of successful extensions: 1590
Number of sequences better than 100.0: 128
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 123
Number of HSP's that attempted gapping in prelim test: 1558
Number of HSP's gapped (non-prelim): 132
length of query: 686
length of database: 14,973,337
effective HSP length: 105
effective length of query: 581
effective length of database: 8,402,647
effective search space: 4881937907
effective search space used: 4881937907
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)