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= 036741
(1030 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 = 495 bits (1274), Expect = e-140, Method: Compositional matrix adjust.
Identities = 281/687 (40%), Positives = 398/687 (57%), Gaps = 51/687 (7%)
Query: 374 KPWGQDARAKVGSRVIELLTQTAYIQSPADQLADAPPDIFPAFTH--ALRTVSKETKGGS 431
+PW + ++G + E+L Q + D+ + P H + R V
Sbjct: 469 QPWPLPVQMELGKLLAEMLVQATQMPCSLDK-PHRSSRLVPVLYHVYSFRNV-------- 519
Query: 432 KKYGVIECNPLVLKGLERTARHMVI---PYMPMLVPPVKWTGYDKGAHFFLPSYVMRT-H 487
++ G+++ +P ++ LE+ A + +PML PP+ WT GA P+ +MRT
Sbjct: 520 QQIGILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLSPTKLMRTVE 579
Query: 488 GAKQQRDTVKRTPKKQLEPVFEALDTLGNTKWRVNNRVLSVLDRIWSCGG--RLADLVDR 545
GA Q ++ ++ P L +AL LGN WRVN RVL ++ +++ G +L
Sbjct: 580 GATQHQELLETCPPTALHGALDALTQLGNCAWRVNGRVLDLVLQLFQAKGCPQLGVPAPP 639
Query: 546 NDVP------LPEKPETEDEAQLRKWQWKVRNVKKENRERHSQRCDIELKLSVARKMKDE 599
++ P LP +A+LR+ ++ + +K RE HS R + +LS+A+ ++D
Sbjct: 640 SEAPQPPEAHLPHSAAPARKAELRR---ELAHCQKVAREMHSLRAEALYRLSLAQHLRDR 696
Query: 600 EGFYYPHNVDFRGRAYPMHPYLNHLGSDLCRGILEFAEGRTLGKSGLHWLKIHLANLYAG 659
F+ PHN+DFRGR YP P+ NHLGSD+ R +LEFA+GR LG GL WLKIHL NL G
Sbjct: 697 V-FWLPHNMDFRGRTYPCPPHFNHLGSDVARALLEFAQGRPLGPHGLDWLKIHLVNL-TG 754
Query: 660 GVDKLSHEGRLAFTENHLDDIFDSADKPLEGRRWWLKAEDPFQCLAVCINLTEALRSSSP 719
+ RLAF E +DDI DSAD+PL GR+WW+ AE+P+Q LA C+ + A+R+S P
Sbjct: 755 LKKREPLRKRLAFAEEVMDDILDSADQPLTGRKWWMGAEEPWQTLACCMEVANAVRASDP 814
Query: 720 ETFISHIPVHQDGSCNGLQHYAALGRDTLGAAAVNLVAREKPADVYSGIAARVLVIIQRD 779
++SH+PVHQDGSCNGLQHYAALGRD++GAA+VNL + P DVYSG+AA+V V ++D
Sbjct: 815 AAYVSHLPVHQDGSCNGLQHYAALGRDSVGAASVNLEPSDVPQDVYSGVAAQVEVFRRQD 874
Query: 780 AQRDPAVFPDALRAKLLLSQVDRKLVKQTVMTSVYGVTYIGARDQIKRRLKERGAPMEEA 839
AQR V A++L + RK+VKQTVMT VYGVT G R QI++RL+E +E
Sbjct: 875 AQRGMRV------AQVLEGFITRKVVKQTVMTVVYGVTRYGGRLQIEKRLRELSDFPQEF 928
Query: 840 ELFGASCYAAKVTLTALGEMFQAARGIMSWLGECAKIIASENQPVRWTTPLGLPVVQPYR 899
++ AS Y + +L EMF R I WL E A++I+ V W TPLG+PV+QPYR
Sbjct: 929 -VWEASHYLVRQVFKSLQEMFSGTRAIQHWLTESARLISHMGSVVEWVTPLGVPVIQPYR 987
Query: 900 KLGR-HTVKTSLQILTLQRE---TEKVMVKRQRTAFPPNFVHSLDGSHMMMTAVACRKAG 955
+ + +Q +T + K ++Q+ FPPNF+HSLD SHMM+TA+ C + G
Sbjct: 988 LDSKVKQIGGGIQSITYTHNGDISRKPNTRKQKNGFPPNFIHSLDSSHMMLTALHCYRKG 1047
Query: 956 LTFAGVHDSYWTHACDVDEMNRILREKFVELYEMPIFENLLDSFQKSFP----------- 1004
LTF VHD YWTHA DV MN++ RE+FV L+ PI ++L K F
Sbjct: 1048 LTFVSVHDCYWTHAADVSVMNQVCREQFVRLHSEPILQDLSRFLVKRFCSEPQKILEASQ 1107
Query: 1005 -KLVFPPLPERGDFDLREVLGSPYFFN 1030
K +P+ G FDL +V S YFF+
Sbjct: 1108 LKETLQAVPKPGAFDLEQVKRSTYFFS 1134
>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 = 284 bits (727), Expect = 1e-76, Method: Compositional matrix adjust.
Identities = 248/915 (27%), Positives = 409/915 (44%), Gaps = 147/915 (16%)
Query: 184 MGSGKYRMLKMRQVKIETEAWEKAANEYRELLMDMCEQKLAPNLPYMKSLFLGWFEPLRD 243
MG ++R + RQ+K A E A N + L+ LP M + WFE ++
Sbjct: 41 MGEARFRKMFERQLK----AGEVADNAAAKPLITTL-------LPKMIARINDWFEEVK- 88
Query: 244 AIAKEQERCRMAKHKVAYAPYFDQLPADMMAVITMHKLMGLLMTGGEHGRARVVQAACII 303
+ K A+ + ++ + +A IT+ + L T ++ + V +A I
Sbjct: 89 --------AKRGKRPTAFQ-FLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA--I 136
Query: 304 GDAIEQEVRIHKFLXXXXXXXXXXXXXXXXXXXSNTVTTEQEKLRKKVTDLIKKQKLPAV 363
G AIE E R + + +E+L K+V + KK + V
Sbjct: 137 GRAIEDEARFGRI---------------RDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVV 181
Query: 364 R-----RIVKGQDDFKPWGQDARAKVGSRVIELLTQTAYIQSPADQLA------DAPPDI 412
+ + G + + W ++ VG R IE+L ++ + S Q A ++
Sbjct: 182 EADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIEL 241
Query: 413 FPAFTHALRTVSKETKGGSKKYGVIECNPLVLKGLERTARHMVIPYMPMLVPPVKWTGYD 472
P + A+ T + G S P+ + P +VPP WTG
Sbjct: 242 APEYAEAIATRAGALAGIS---------PM---------------FQPCVVPPKPWTGIT 277
Query: 473 KGAHFF---LPSYVMRTHGAKQQRDTVKRTPKKQLEPVFEALDTLGNTKWRVNNRVLSVL 529
G ++ P ++RTH K + R + V++A++ NT W++N +VL+V
Sbjct: 278 GGGYWANGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVA 333
Query: 530 DRI--WS-CGGRLADLVDRNDVPL-PEKPETEDEAQLRKWQWKVRNVKKENRERHSQRCD 585
+ I W C ++R ++P+ PE + EA L W+ V ++++ R S+R
Sbjct: 334 NVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEA-LTAWKRAAAAVYRKDKARKSRRIS 392
Query: 586 IELKLSVARKMKDEEGFYYPHNVDFRGRAYPMHPYLNHLGSDLCRGILEFAEGRTLGKSG 645
+E L A K + + ++P+N+D+RGR Y + + N G+D+ +G+L A+G+ +GK G
Sbjct: 393 LEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKGLLTLAKGKPIGKEG 451
Query: 646 LHWLKIHLANLYAGGVDKLSHEGRLAFTENHLDDIFDSADKPLEGRRWWLKAEDPFQCLA 705
+WLKIH AN GVDK+ R+ F E + ++I A PLE WW + + PF LA
Sbjct: 452 YYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLE-NTWWAEQDSPFCFLA 508
Query: 706 VCINLTEALRSSSPETFISHIPVHQDGSCNGLQHYAALGRDTLGAAAVNLVAREKPADVY 765
C ++ +P+ DGSC+G+QH++A+ RD +G AVNL+ E D+Y
Sbjct: 509 FCFEYAGVQHHGL--SYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIY 566
Query: 766 SGIAARVLVIIQRDA----QRDPAVFPD---------------ALRAKLLLSQVDRKLVK 806
+A +V I+Q DA + D AL + L V R + K
Sbjct: 567 GIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTK 626
Query: 807 QTVMTSVYGVTYIGARDQIKRRLKERGAPMEEAELFG----ASCYAAKVTLTALGEMFQA 862
++VMT YG G R Q+ + + +F A+ Y AK+ ++ A
Sbjct: 627 RSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVA 686
Query: 863 ARGIMSWLGECAKIIASENQ------------PVRWTTPLGLPVVQPYRKLGRHTVKTSL 910
A M+WL AK++A+E + V W TP G PV Q Y+K ++T L
Sbjct: 687 AVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKK----PIQTRL 742
Query: 911 QILTLQR----------ETEKVMVKRQRTAFPPNFVHSLDGSHMMMTAV-ACRKAGL-TF 958
++ L + + ++ +Q + PNFVHS DGSH+ T V A K G+ +F
Sbjct: 743 NLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESF 802
Query: 959 AGVHDSYWTHACDVDEMNRILREKFVELYE-MPIFENLLDSFQKSFPKLVF---PPLPER 1014
A +HDS+ T D + + +RE V+ YE + + D F + P LP +
Sbjct: 803 ALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAK 862
Query: 1015 GDFDLREVLGSPYFF 1029
G+ +LR++L S + F
Sbjct: 863 GNLNLRDILESDFAF 877
>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 = 284 bits (727), Expect = 1e-76, Method: Compositional matrix adjust.
Identities = 247/915 (26%), Positives = 408/915 (44%), Gaps = 147/915 (16%)
Query: 184 MGSGKYRMLKMRQVKIETEAWEKAANEYRELLMDMCEQKLAPNLPYMKSLFLGWFEPLRD 243
MG ++R + RQ+K A E A N + L+ LP M + WFE ++
Sbjct: 52 MGEARFRKMFERQLK----AGEVADNAAAKPLITTL-------LPKMIARINDWFEEVK- 99
Query: 244 AIAKEQERCRMAKHKVAYAPYFDQLPADMMAVITMHKLMGLLMTGGEHGRARVVQAACII 303
+ K A+ + ++ + +A IT+ + L T ++ + V +A I
Sbjct: 100 --------AKRGKRPTAFQ-FLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA--I 147
Query: 304 GDAIEQEVRIHKFLXXXXXXXXXXXXXXXXXXXSNTVTTEQEKLRKKVTDLIKKQKLPAV 363
G AIE E R + + +E+L K+V + KK + V
Sbjct: 148 GRAIEDEARFGRI---------------RDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVV 192
Query: 364 R-----RIVKGQDDFKPWGQDARAKVGSRVIELLTQTAYIQSPADQLA------DAPPDI 412
+ + G + + W ++ VG R IE+L ++ + S Q A ++
Sbjct: 193 EADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIEL 252
Query: 413 FPAFTHALRTVSKETKGGSKKYGVIECNPLVLKGLERTARHMVIPYMPMLVPPVKWTGYD 472
P + A+ T + G S + + P +VPP WTG
Sbjct: 253 APEYAEAIATRAGALAGIS------------------------LMFQPCVVPPKPWTGIT 288
Query: 473 KGAHFF---LPSYVMRTHGAKQQRDTVKRTPKKQLEPVFEALDTLGNTKWRVNNRVLSVL 529
G ++ P ++RTH K + R + V++A++ NT W++N +VL+V
Sbjct: 289 GGGYWANGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVA 344
Query: 530 DRI--WS-CGGRLADLVDRNDVPL-PEKPETEDEAQLRKWQWKVRNVKKENRERHSQRCD 585
+ I W C ++R ++P+ PE + EA L W+ V ++++ R S+R
Sbjct: 345 NVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEA-LTAWKRAAAAVYRKDKARKSRRIS 403
Query: 586 IELKLSVARKMKDEEGFYYPHNVDFRGRAYPMHPYLNHLGSDLCRGILEFAEGRTLGKSG 645
+E L A K + + ++P+N+D+RGR Y + + N G+D+ +G+L A+G+ +GK G
Sbjct: 404 LEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKGLLTLAKGKPIGKEG 462
Query: 646 LHWLKIHLANLYAGGVDKLSHEGRLAFTENHLDDIFDSADKPLEGRRWWLKAEDPFQCLA 705
+WLKIH AN GVDK+ R+ F E + ++I A PLE WW + + PF LA
Sbjct: 463 YYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLENT-WWAEQDSPFCFLA 519
Query: 706 VCINLTEALRSSSPETFISHIPVHQDGSCNGLQHYAALGRDTLGAAAVNLVAREKPADVY 765
C ++ +P+ DGSC+G+QH++A+ RD +G AVNL+ E D+Y
Sbjct: 520 FCFEYAGVQHHGL--SYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIY 577
Query: 766 SGIAARVLVIIQRDA----QRDPAVFPD---------------ALRAKLLLSQVDRKLVK 806
+A +V I+Q DA + D AL + L V R + K
Sbjct: 578 GIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTK 637
Query: 807 QTVMTSVYGVTYIGARDQIKRRLKERGAPMEEAELFG----ASCYAAKVTLTALGEMFQA 862
++VMT YG G R Q+ + + +F A+ Y AK+ ++ A
Sbjct: 638 RSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVA 697
Query: 863 ARGIMSWLGECAKIIASENQ------------PVRWTTPLGLPVVQPYRKLGRHTVKTSL 910
A M+WL AK++A+E + V W TP G PV Q Y+K ++T L
Sbjct: 698 AVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKK----PIQTRL 753
Query: 911 QILTLQR----------ETEKVMVKRQRTAFPPNFVHSLDGSHMMMTAV-ACRKAGL-TF 958
++ L + + ++ +Q + PNFVHS DGSH+ T V A K G+ +F
Sbjct: 754 NLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESF 813
Query: 959 AGVHDSYWTHACDVDEMNRILREKFVELYE-MPIFENLLDSFQKSFPKLVF---PPLPER 1014
A +HDS+ T D + + +RE V+ YE + + D F + P LP +
Sbjct: 814 ALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAK 873
Query: 1015 GDFDLREVLGSPYFF 1029
G+ +LR++L S + F
Sbjct: 874 GNLNLRDILESDFAF 888
>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 = 284 bits (726), Expect = 2e-76, Method: Compositional matrix adjust.
Identities = 248/915 (27%), Positives = 409/915 (44%), Gaps = 147/915 (16%)
Query: 184 MGSGKYRMLKMRQVKIETEAWEKAANEYRELLMDMCEQKLAPNLPYMKSLFLGWFEPLRD 243
MG ++R + RQ+K A E A N + L+ LP M + WFE ++
Sbjct: 46 MGEARFRKMFERQLK----AGEVADNAAAKPLITTL-------LPKMIARINDWFEEVK- 93
Query: 244 AIAKEQERCRMAKHKVAYAPYFDQLPADMMAVITMHKLMGLLMTGGEHGRARVVQAACII 303
+ K A+ + ++ + +A IT+ + L T ++ + V +A I
Sbjct: 94 --------AKRGKRPTAFQ-FLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA--I 141
Query: 304 GDAIEQEVRIHKFLXXXXXXXXXXXXXXXXXXXSNTVTTEQEKLRKKVTDLIKKQKLPAV 363
G AIE E R + + +E+L K+V + KK + V
Sbjct: 142 GRAIEDEARFGRI---------------RDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVV 186
Query: 364 R-----RIVKGQDDFKPWGQDARAKVGSRVIELLTQTAYIQSPADQLA------DAPPDI 412
+ + G + + W ++ VG R IE+L ++ + S Q A ++
Sbjct: 187 EADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIEL 246
Query: 413 FPAFTHALRTVSKETKGGSKKYGVIECNPLVLKGLERTARHMVIPYMPMLVPPVKWTGYD 472
P + A+ T + G S P+ + P +VPP WTG
Sbjct: 247 APEYAEAIATRAGALAGIS---------PM---------------FQPCVVPPKPWTGIT 282
Query: 473 KGAHFF---LPSYVMRTHGAKQQRDTVKRTPKKQLEPVFEALDTLGNTKWRVNNRVLSVL 529
G ++ P ++RTH K + R + V++A++ NT W++N +VL+V
Sbjct: 283 GGGYWANGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVA 338
Query: 530 DRI--WS-CGGRLADLVDRNDVPL-PEKPETEDEAQLRKWQWKVRNVKKENRERHSQRCD 585
+ I W C ++R ++P+ PE + EA L W+ V ++++ R S+R
Sbjct: 339 NVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEA-LTAWKRAAAAVYRKDKARKSRRIS 397
Query: 586 IELKLSVARKMKDEEGFYYPHNVDFRGRAYPMHPYLNHLGSDLCRGILEFAEGRTLGKSG 645
+E L A K + + ++P+N+D+RGR Y + + N G+D+ +G+L A+G+ +GK G
Sbjct: 398 LEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKGLLTLAKGKPIGKEG 456
Query: 646 LHWLKIHLANLYAGGVDKLSHEGRLAFTENHLDDIFDSADKPLEGRRWWLKAEDPFQCLA 705
+WLKIH AN GVDK+ R+ F E + ++I A PLE WW + + PF LA
Sbjct: 457 YYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLENT-WWAEQDSPFCFLA 513
Query: 706 VCINLTEALRSSSPETFISHIPVHQDGSCNGLQHYAALGRDTLGAAAVNLVAREKPADVY 765
C ++ +P+ DGSC+G+QH++A+ RD +G AVNL+ E D+Y
Sbjct: 514 FCFEYAGVQHHGL--SYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIY 571
Query: 766 SGIAARVLVIIQRDA----QRDPAVFPD---------------ALRAKLLLSQVDRKLVK 806
+A +V I+Q DA + D AL + L V R + K
Sbjct: 572 GIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTK 631
Query: 807 QTVMTSVYGVTYIGARDQIKRRLKERGAPMEEAELFG----ASCYAAKVTLTALGEMFQA 862
++VMT YG G R Q+ + + +F A+ Y AK+ ++ A
Sbjct: 632 RSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVA 691
Query: 863 ARGIMSWLGECAKIIASENQ------------PVRWTTPLGLPVVQPYRKLGRHTVKTSL 910
A M+WL AK++A+E + V W TP G PV Q Y+K ++T L
Sbjct: 692 AVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKK----PIQTRL 747
Query: 911 QILTLQR----------ETEKVMVKRQRTAFPPNFVHSLDGSHMMMTAV-ACRKAGL-TF 958
++ L + + ++ +Q + PNFVHS DGSH+ T V A K G+ +F
Sbjct: 748 NLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESF 807
Query: 959 AGVHDSYWTHACDVDEMNRILREKFVELYE-MPIFENLLDSFQKSFPKLVF---PPLPER 1014
A +HDS+ T D + + +RE V+ YE + + D F + P LP +
Sbjct: 808 ALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAK 867
Query: 1015 GDFDLREVLGSPYFF 1029
G+ +LR++L S + F
Sbjct: 868 GNLNLRDILESDFAF 882
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 282 bits (722), Expect = 6e-76, Method: Compositional matrix adjust.
Identities = 248/916 (27%), Positives = 409/916 (44%), Gaps = 149/916 (16%)
Query: 184 MGSGKYRMLKMRQVKIETEAWEKAANEYRELLMDMCEQKLAPNLPYMKSLFLGWFEPLRD 243
MG ++R + RQ+K A E A N + L+ LP M + WFE ++
Sbjct: 46 MGEARFRKMFERQLK----AGEVADNAAAKPLITTL-------LPKMIARINDWFEEVK- 93
Query: 244 AIAKEQERCRMAKHKVAYAPYFDQLPADMMAVITMHKLMGLLMTGGEHGRARVVQAACII 303
+ K A+ + ++ + +A IT+ + L T ++ + V +A I
Sbjct: 94 --------AKRGKRPTAFQ-FLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA--I 141
Query: 304 GDAIEQEVRIHKFLXXXXXXXXXXXXXXXXXXXSNTVTTEQEKLRKKVTDLIKKQKLPAV 363
G AIE E R + +E+L K+V + KK + V
Sbjct: 142 GRAIEDEARFGRIRDLEAKHFKKNV---------------EEQLNKRVGHVYKKAFMQVV 186
Query: 364 R-----RIVKGQDDFKPWGQDARAKVGSRVIELLTQTAYIQSPADQLA------DAPPDI 412
+ + G + + W ++ VG R IE+L ++ + S Q A ++
Sbjct: 187 EADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIEL 246
Query: 413 FPAFTHALRTVSKETKGGSKKYGVIECNPLVLKGLERTARHMVIPYMPMLVPPVKWTGYD 472
P + A+ T + G S P+ + P +VPP WTG
Sbjct: 247 APEYAEAIATRAGALAGIS---------PM---------------FQPCVVPPKPWTGIT 282
Query: 473 KGAHFF---LPSYVMRTHGAKQQRDTVKRTPKKQLEPVFEALDTLGNTKWRVNNRVLSVL 529
G ++ P ++RTH K + R + V++A++ NT W++N +VL+V
Sbjct: 283 GGGYWANGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVA 338
Query: 530 DRI--WSCGGRLADL--VDRNDVPL-PEKPETEDEAQLRKWQWKVRNVKKENRERHSQRC 584
+ I W + D+ ++R ++P+ PE + EA L W+ V ++++ R S+R
Sbjct: 339 NVITKWK-HSPVEDIPAIEREELPMKPEDIDMNPEA-LTAWKRAAAAVYRKDKARKSRRI 396
Query: 585 DIELKLSVARKMKDEEGFYYPHNVDFRGRAYPMHPYLNHLGSDLCRGILEFAEGRTLGKS 644
+E L A K + + ++P+N+D+RGR Y + + N G+D+ +G+L A+G+ +GK
Sbjct: 397 SLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMF-NPQGNDMTKGLLTLAKGKPIGKE 455
Query: 645 GLHWLKIHLANLYAGGVDKLSHEGRLAFTENHLDDIFDSADKPLEGRRWWLKAEDPFQCL 704
G +WLKIH AN GVDK+ R+ F E + ++I A PLE WW + + PF L
Sbjct: 456 GYYWLKIHGAN--CAGVDKVPFPERIKFIEENHENIMACAKSPLENT-WWAEQDSPFCFL 512
Query: 705 AVCINLTEALRSSSPETFISHIPVHQDGSCNGLQHYAALGRDTLGAAAVNLVAREKPADV 764
A C ++ +P+ DGSC+G+QH++A+ RD +G AVNL+ E D+
Sbjct: 513 AFCFEYAGVQHHGL--SYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDI 570
Query: 765 YSGIAARVLVIIQRDA----QRDPAVFPD---------------ALRAKLLLSQVDRKLV 805
Y +A +V I+Q DA + D AL + L V R +
Sbjct: 571 YGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVT 630
Query: 806 KQTVMTSVYGVTYIGARDQIKRRLKERGAPMEEAELFG----ASCYAAKVTLTALGEMFQ 861
K++VMT YG G R Q+ + + +F A+ Y AK+ ++
Sbjct: 631 KRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVV 690
Query: 862 AARGIMSWLGECAKIIASE------------NQPVRWTTPLGLPVVQPYRKLGRHTVKTS 909
AA M+WL AK++A+E V W TP G PV Q Y+K ++T
Sbjct: 691 AAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRSAVHWVTPDGFPVWQEYKK----PIQTR 746
Query: 910 LQILTLQR----------ETEKVMVKRQRTAFPPNFVHSLDGSHMMMTAV-ACRKAGL-T 957
L ++ L + + ++ +Q + PNFVHS DGSH+ T V A K G+ +
Sbjct: 747 LNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIES 806
Query: 958 FAGVHDSYWTHACDVDEMNRILREKFVELYEMP-IFENLLDSFQKSFPKLVF---PPLPE 1013
FA +HDS+ T D + + +RE V+ YE + + D F + P LP
Sbjct: 807 FALIHDSFGTIPADAANLFKAVRETMVDTYESSDVLADFYDQFADQLHESQLDKMPALPA 866
Query: 1014 RGDFDLREVLGSPYFF 1029
+G+ +LR++L S + F
Sbjct: 867 KGNLNLRDILESDFAF 882
>pdb|3H5O|A Chain A, The Crystal Structure Of Transcription Regulator Gntr From
Chromobacterium Violaceum
pdb|3H5O|B Chain B, The Crystal Structure Of Transcription Regulator Gntr From
Chromobacterium Violaceum
Length = 339
Score = 30.8 bits (68), Expect = 4.5, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 882 QPVRWTTPLGLPVVQPYRKLGRHTVKTSLQIL 913
QP W TP V P R +G H K LQ++
Sbjct: 278 QPAAWCTPPLTTVATPRRDIGVHAAKALLQLI 309
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
0.322 0.136 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,741,250
Number of Sequences: 62578
Number of extensions: 1177804
Number of successful extensions: 2471
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2411
Number of HSP's gapped (non-prelim): 11
length of query: 1030
length of database: 14,973,337
effective HSP length: 109
effective length of query: 921
effective length of database: 8,152,335
effective search space: 7508300535
effective search space used: 7508300535
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)