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= 001982
(986 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 = 439 bits (1129), Expect = e-123, Method: Compositional matrix adjust.
Identities = 269/791 (34%), Positives = 417/791 (52%), Gaps = 82/791 (10%)
Query: 249 PHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKN 308
P + LL +V +++ + L G + +A + Q R+ ++ +N
Sbjct: 373 PFLCLLDEREVVRMLLQVLQALPAQGESFTTLARELSARTFSRHVVQRQRVSGQVQALQN 432
Query: 309 YKRKKIIADTEEVLSKEKELLRKRVNSLIKSKRVMEAQKLLKNEETKPWGRDTQAKLGSR 368
+ RK + + E L R+ +L + + E +PW Q +LG
Sbjct: 433 HYRKYLCLLASDAEVPEPCLPRQYWEALGAPEALRE----------QPWPLPVQMELGKL 482
Query: 369 LVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKTILKHPGQ-KTTKRYGVVECDPLVLE 427
L E+L++ + ++ +P R +L H + ++ G+++ P ++
Sbjct: 483 LAEMLVQATQMPCSLD---------KPHRSSRLVPVLYHVYSFRNVQQIGILKPHPAYVQ 533
Query: 428 GLDRSAKHMLI---PYVPMLVPPKKWKGYNKGGYLFLPSYVMRT-HGSRKQQEALKSVTG 483
L+++A+ L VPML PP W + G +L P+ +MRT G+ + QE L++
Sbjct: 534 LLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLSPTKLMRTVEGATQHQELLETCPP 593
Query: 484 NCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVSGGNIAGLVDRNDVLIPEKP---LSED 540
+ +AL LG+ WRVN +VL ++ ++ + G V P+ P L
Sbjct: 594 TALHGALDALTQLGNCAWRVNGRVLDLVLQLFQAKGCPQLGVPAPPSEAPQPPEAHLPHS 653
Query: 541 MTEVQK--WKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYP 598
+K + + +K+ +E HS R + +LS+A+ ++D F+ PHN+DFRGR YP
Sbjct: 654 AAPARKAELRRELAHCQKVAREMHSLRAEALYRLSLAQHLRDRV-FWLPHNMDFRGRTYP 712
Query: 599 MHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLKIHLANL--------------FSE--- 641
PH NHL SDV R +LEFA+GRPLG GL WLKIHL NL F+E
Sbjct: 713 CPPHFNHLGSDVARALLEFAQGRPLGPHGLDWLKIHLVNLTGLKKREPLRKRLAFAEEVM 772
Query: 642 --------NPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIHQDGSCNGL 693
P+ G +WW+ AE+P+Q LA C+ ++ A+++S P + +SHLP+HQDGSCNGL
Sbjct: 773 DDILDSADQPLTGRKWWMGAEEPWQTLACCMEVANAVRASDPAAYVSHLPVHQDGSCNGL 832
Query: 694 QHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILI 753
QHYAALGR+++ AA+VNL + P DVYS +A +V ++D+ + +A++L
Sbjct: 833 QHYAALGRDSVGAASVNLEPSDVPQDVYSGVAAQVEVFRRQDAQRG------MRVAQVLE 886
Query: 754 DQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFA--AACYAAKVTLTA 811
+ RK+VKQTVMT VYGVT G R QI++RL E ++D Q F A+ Y + +
Sbjct: 887 GFITRKVVKQTVMTVVYGVTRYGGRLQIEKRLRE---LSDFPQEFVWEASHYLVRQVFKS 943
Query: 812 LGEIFEAARSIMGWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNER-HLIRTSLQVLA 870
L E+F R+I WL + A++I+ V W TPLG+PV+QPY + + I +Q +
Sbjct: 944 LQEMFSGTRAIQHWLTESARLISHMGSVVEWVTPLGVPVIQPYRLDSKVKQIGGGIQSIT 1003
Query: 871 LQREGNLV---EIRKQRTAFPPNFVHSLDGSHMMMTAVACRDAGLHFAGVHDSFWTHACD 927
G++ RKQ+ FPPNF+HSLD SHMM+TA+ C GL F VHD +WTHA D
Sbjct: 1004 YTHNGDISRKPNTRKQKNGFPPNFIHSLDSSHMMLTALHCYRKGLTFVSVHDCYWTHAAD 1063
Query: 928 VDEMNQILRKKFVELYNMPMLENL------------LESFQTSYPTLSFPPLPERGNFDL 975
V MNQ+ R++FV L++ P+L++L + + S + +P+ G FDL
Sbjct: 1064 VSVMNQVCREQFVRLHSEPILQDLSRFLVKRFCSEPQKILEASQLKETLQAVPKPGAFDL 1123
Query: 976 EEVLESPYFFN 986
E+V S YFF+
Sbjct: 1124 EQVKRSTYFFS 1134
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 248 bits (634), Expect = 8e-66, Method: Compositional matrix adjust.
Identities = 248/906 (27%), Positives = 394/906 (43%), Gaps = 153/906 (16%)
Query: 178 LRRRQVKQETEAWERMVDEYKELEAKMIEKRL--------APNLPHIKGLFLGWFGPLSE 229
L R Q+ E E++E ++ KM E++L A P I L +++
Sbjct: 32 LAREQLALEHESYEMGEARFR----KMFERQLKAGEVADNAAAKPLITTLLPKMIARIND 87
Query: 230 AIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHI 289
E E K +R K+ A ++ + + VA I + + + + ++ VQ V +A I
Sbjct: 88 WFE-EVKAKRGKRPTAF--QFLQEIKPEAVAYITIKTTLACLTSA-DNTTVQAVASA--I 141
Query: 290 GMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNSLIKSK--RVMEA-- 345
G AIE E R + + +K + +E L KRV + K +V+EA
Sbjct: 142 GRAIEDEARFGRIRDLEAKHFKKNV-----------EEQLNKRVGHVYKKAFMQVVEADM 190
Query: 346 --QKLLKNEETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKT 403
+ LL E W ++ +G R +E+LIE+ + HR
Sbjct: 191 LSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGM----------------VSLHRQNA 234
Query: 404 ILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHM--LIP-YVPMLVPPKKWKGYNKGGYLF 460
+ +T +E P E + A + + P + P +VPPK W G GGY
Sbjct: 235 GVVGQDSET------IELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWA 288
Query: 461 ---LPSYVMRTHGSRKQQEALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESI--W 515
P ++RTH + AL M +V++A++ +T W++NK+VL+V I W
Sbjct: 289 NGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKW 344
Query: 516 V-SGGNIAGLVDRNDVLIPEKPLSEDMT--EVQKWKWSVRKAKKINQERHSQRCDTELKL 572
S ++R + +P KP DM + WK + + ++ R S+R E L
Sbjct: 345 KHSPVEDIPAIEREE--LPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFML 402
Query: 573 SVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWLK 632
A + + + ++P+N+D+RGR Y + N +D+ +G+L A+G+P+GK G WLK
Sbjct: 403 EQANKFANHKAIWFPYNMDWRGRVYAV-SMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLK 461
Query: 633 IHLAN--------------LFSENPIN---------GSRWWLTAEDPFQCLAACINLSEA 669
IH AN EN N + WW + PF LA C +
Sbjct: 462 IHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYA-- 519
Query: 670 LKSSSPHSVISH---LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAV 726
H +S+ LP+ DGSC+G+QH++A+ R+ + AVNL+ E D+Y +A
Sbjct: 520 ---GVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAK 576
Query: 727 RVHEIMKRDSNKDPSKH-------------------PQALLAKILIDQVDRKLVKQTVMT 767
+V+EI++ D+ +AL + L V R + K++VMT
Sbjct: 577 KVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMT 636
Query: 768 SVYGVTFVGAREQIKRRLEEKGHITDDRQLFA----AACYAAKVTLTALGEIFEAARSIM 823
YG G R+Q+ + + +F AA Y AK+ ++ AA M
Sbjct: 637 LAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAM 696
Query: 824 GWLGDCAKVIASE------------NQPVRWTTPLGLPVVQPYCK------NERHLIRTS 865
WL AK++A+E V W TP G PV Q Y K N L +
Sbjct: 697 NWLKSAAKLLAAEVKDKKTGEILRKRSAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFR 756
Query: 866 LQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACRDAGLH-FAGVHDSFWT 923
LQ + + ++ KQ + PNFVHS DGSH+ T V A G+ FA +HDSF T
Sbjct: 757 LQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGT 816
Query: 924 HACDVDEMNQILRKKFVELY-NMPMLENLLESF--QTSYPTLS-FPPLPERGNFDLEEVL 979
D + + +R+ V+ Y + +L + + F Q L P LP +GN +L ++L
Sbjct: 817 IPADAANLFKAVRETMVDTYESSDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDIL 876
Query: 980 ESPYFF 985
ES + F
Sbjct: 877 ESDFAF 882
>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 = 247 bits (631), Expect = 2e-65, Method: Compositional matrix adjust.
Identities = 250/910 (27%), Positives = 395/910 (43%), Gaps = 161/910 (17%)
Query: 178 LRRRQVKQETEAWERMVDEYKELEAKMIEKRL--------APNLPHIKGLFLGWFGPLSE 229
L R Q+ E E++E ++ KM E++L A P I L +++
Sbjct: 38 LAREQLALEHESYEMGEARFR----KMFERQLKAGEVADNAAAKPLITTLLPKMIARIND 93
Query: 230 AIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHI 289
E E K +R K+ A ++ + + VA I + + + + ++ VQ V +A I
Sbjct: 94 WFE-EVKAKRGKRPTAF--QFLQEIKPEAVAYITIKTTLACLTSA-DNTTVQAVASA--I 147
Query: 290 GMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNSLIKSK--RVMEA-- 345
G AIE E R + + +K + +E L KRV + K +V+EA
Sbjct: 148 GRAIEDEARFGRIRDLEAKHFKKNV-----------EEQLNKRVGHVYKKAFMQVVEADM 196
Query: 346 --QKLLKNEETKPWGRDTQAKLGSRLVELLIE-TAYVQ-HPVNPA----DYSPPDVRPAF 397
+ LL E W ++ +G R +E+LIE T V H N D ++ P +
Sbjct: 197 LSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEY 256
Query: 398 RHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHMLIPYVPMLVPPKKWKGYNKGG 457
T R G + L+ + P +VPPK W G GG
Sbjct: 257 AEAIAT-----------RAGALAGISLMFQ--------------PCVVPPKPWTGITGGG 291
Query: 458 YLF---LPSYVMRTHGSRKQQEALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESI 514
Y P ++RTH + AL M +V++A++ +T W++NK+VL+V I
Sbjct: 292 YWANGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVI 347
Query: 515 --W--VSGGNIAGLVDRNDVLIPEKPLSEDMT--EVQKWKWSVRKAKKINQERHSQRCDT 568
W +I ++R + +P KP DM + WK + + ++ R S+R
Sbjct: 348 TKWKHCPVEDIPA-IEREE--LPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISL 404
Query: 569 ELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGL 628
E L A + + + ++P+N+D+RGR Y + N +D+ +G+L A+G+P+GK G
Sbjct: 405 EFMLEQANKFANHKAIWFPYNMDWRGRVYAV-SMFNPQGNDMTKGLLTLAKGKPIGKEGY 463
Query: 629 RWLKIHLAN--------------LFSENPIN---------GSRWWLTAEDPFQCLAACIN 665
WLKIH AN EN N + WW + PF LA C
Sbjct: 464 YWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFE 523
Query: 666 LSEALKSSSPHSVISH---LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYS 722
+ H +S+ LP+ DGSC+G+QH++A+ R+ + AVNL+ E D+Y
Sbjct: 524 YA-----GVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYG 578
Query: 723 EIAVRVHEIMKRDSNKDPSKH-------------------PQALLAKILIDQVDRKLVKQ 763
+A +V+EI++ D+ +AL + L V R + K+
Sbjct: 579 IVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKR 638
Query: 764 TVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFA----AACYAAKVTLTALGEIFEAA 819
+VMT YG G R+Q+ + + +F AA Y AK+ ++ AA
Sbjct: 639 SVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAA 698
Query: 820 RSIMGWLGDCAKVIASENQ------------PVRWTTPLGLPVVQPYCK------NERHL 861
M WL AK++A+E + V W TP G PV Q Y K N L
Sbjct: 699 VEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFL 758
Query: 862 IRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACRDAGLH-FAGVHD 919
+ LQ + + ++ KQ + PNFVHS DGSH+ T V A G+ FA +HD
Sbjct: 759 GQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHD 818
Query: 920 SFWTHACDVDEMNQILRKKFVELY-NMPMLENLLESF--QTSYPTLS-FPPLPERGNFDL 975
SF T D + + +R+ V+ Y + +L + + F Q L P LP +GN +L
Sbjct: 819 SFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNL 878
Query: 976 EEVLESPYFF 985
++LES + F
Sbjct: 879 RDILESDFAF 888
>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 = 247 bits (631), Expect = 2e-65, Method: Compositional matrix adjust.
Identities = 248/907 (27%), Positives = 396/907 (43%), Gaps = 155/907 (17%)
Query: 178 LRRRQVKQETEAWERMVDEYKELEAKMIEKRL--------APNLPHIKGLFLGWFGPLSE 229
L R Q+ E E++E ++ KM E++L A P I L +++
Sbjct: 27 LAREQLALEHESYEMGEARFR----KMFERQLKAGEVADNAAAKPLITTLLPKMIARIND 82
Query: 230 AIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHI 289
E E K +R K+ A ++ + + VA I + + + + ++ VQ V +A I
Sbjct: 83 WFE-EVKAKRGKRPTAF--QFLQEIKPEAVAYITIKTTLACLTSA-DNTTVQAVASA--I 136
Query: 290 GMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNSLIKSK--RVMEA-- 345
G AIE E R + + +K + +E L KRV + K +V+EA
Sbjct: 137 GRAIEDEARFGRIRDLEAKHFKKNV-----------EEQLNKRVGHVYKKAFMQVVEADM 185
Query: 346 --QKLLKNEETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKT 403
+ LL E W ++ +G R +E+LIE+ + HR
Sbjct: 186 LSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGM----------------VSLHRQNA 229
Query: 404 ILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHM--LIP-YVPMLVPPKKWKGYNKGGYLF 460
+ +T +E P E + A + + P + P +VPPK W G GGY
Sbjct: 230 GVVGQDSET------IELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWA 283
Query: 461 ---LPSYVMRTHGSRKQQEALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESI--W 515
P ++RTH + AL M +V++A++ +T W++NK+VL+V I W
Sbjct: 284 NGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKW 339
Query: 516 --VSGGNIAGLVDRNDVLIPEKPLSEDMT--EVQKWKWSVRKAKKINQERHSQRCDTELK 571
+I ++R + +P KP DM + WK + + ++ R S+R E
Sbjct: 340 KHCPVEDIPA-IEREE--LPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFM 396
Query: 572 LSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWL 631
L A + + + ++P+N+D+RGR Y + N +D+ +G+L A+G+P+GK G WL
Sbjct: 397 LEQANKFANHKAIWFPYNMDWRGRVYAV-SMFNPQGNDMTKGLLTLAKGKPIGKEGYYWL 455
Query: 632 KIHLAN--------------LFSENPIN---------GSRWWLTAEDPFQCLAACINLSE 668
KIH AN EN N + WW + PF LA C +
Sbjct: 456 KIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYA- 514
Query: 669 ALKSSSPHSVISH---LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIA 725
H +S+ LP+ DGSC+G+QH++A+ R+ + AVNL+ E D+Y +A
Sbjct: 515 ----GVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVA 570
Query: 726 VRVHEIMKRDSNKDPSKH-------------------PQALLAKILIDQVDRKLVKQTVM 766
+V+EI++ D+ +AL + L V R + K++VM
Sbjct: 571 KKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVM 630
Query: 767 TSVYGVTFVGAREQIKRRLEEKGHITDDRQLFA----AACYAAKVTLTALGEIFEAARSI 822
T YG G R+Q+ + + +F AA Y AK+ ++ AA
Sbjct: 631 TLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEA 690
Query: 823 MGWLGDCAKVIASENQ------------PVRWTTPLGLPVVQPYCK------NERHLIRT 864
M WL AK++A+E + V W TP G PV Q Y K N L +
Sbjct: 691 MNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQF 750
Query: 865 SLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACRDAGLH-FAGVHDSFW 922
LQ + + ++ KQ + PNFVHS DGSH+ T V A G+ FA +HDSF
Sbjct: 751 RLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFG 810
Query: 923 THACDVDEMNQILRKKFVELY-NMPMLENLLESF--QTSYPTLS-FPPLPERGNFDLEEV 978
T D + + +R+ V+ Y + +L + + F Q L P LP +GN +L ++
Sbjct: 811 TIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDI 870
Query: 979 LESPYFF 985
LES + F
Sbjct: 871 LESDFAF 877
>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 = 246 bits (629), Expect = 3e-65, Method: Compositional matrix adjust.
Identities = 248/907 (27%), Positives = 396/907 (43%), Gaps = 155/907 (17%)
Query: 178 LRRRQVKQETEAWERMVDEYKELEAKMIEKRL--------APNLPHIKGLFLGWFGPLSE 229
L R Q+ E E++E ++ KM E++L A P I L +++
Sbjct: 32 LAREQLALEHESYEMGEARFR----KMFERQLKAGEVADNAAAKPLITTLLPKMIARIND 87
Query: 230 AIEREQKMQRTKKQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHI 289
E E K +R K+ A ++ + + VA I + + + + ++ VQ V +A I
Sbjct: 88 WFE-EVKAKRGKRPTAF--QFLQEIKPEAVAYITIKTTLACLTSA-DNTTVQAVASA--I 141
Query: 290 GMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKEKELLRKRVNSLIKSK--RVMEA-- 345
G AIE E R + + +K + +E L KRV + K +V+EA
Sbjct: 142 GRAIEDEARFGRIRDLEAKHFKKNV-----------EEQLNKRVGHVYKKAFMQVVEADM 190
Query: 346 --QKLLKNEETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPADYSPPDVRPAFRHRFKT 403
+ LL E W ++ +G R +E+LIE+ + HR
Sbjct: 191 LSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGM----------------VSLHRQNA 234
Query: 404 ILKHPGQKTTKRYGVVECDPLVLEGLDRSAKHM--LIP-YVPMLVPPKKWKGYNKGGYLF 460
+ +T +E P E + A + + P + P +VPPK W G GGY
Sbjct: 235 GVVGQDSET------IELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWA 288
Query: 461 ---LPSYVMRTHGSRKQQEALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESI--W 515
P ++RTH + AL M +V++A++ +T W++NK+VL+V I W
Sbjct: 289 NGRRPLALVRTHSKK----ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKW 344
Query: 516 --VSGGNIAGLVDRNDVLIPEKPLSEDMT--EVQKWKWSVRKAKKINQERHSQRCDTELK 571
+I ++R + +P KP DM + WK + + ++ R S+R E
Sbjct: 345 KHCPVEDIPA-IEREE--LPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFM 401
Query: 572 LSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLRWL 631
L A + + + ++P+N+D+RGR Y + N +D+ +G+L A+G+P+GK G WL
Sbjct: 402 LEQANKFANHKAIWFPYNMDWRGRVYAV-SMFNPQGNDMTKGLLTLAKGKPIGKEGYYWL 460
Query: 632 KIHLAN--------------LFSENPIN---------GSRWWLTAEDPFQCLAACINLSE 668
KIH AN EN N + WW + PF LA C +
Sbjct: 461 KIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYA- 519
Query: 669 ALKSSSPHSVISH---LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIA 725
H +S+ LP+ DGSC+G+QH++A+ R+ + AVNL+ E D+Y +A
Sbjct: 520 ----GVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVA 575
Query: 726 VRVHEIMKRDSNKDPSKH-------------------PQALLAKILIDQVDRKLVKQTVM 766
+V+EI++ D+ +AL + L V R + K++VM
Sbjct: 576 KKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVM 635
Query: 767 TSVYGVTFVGAREQIKRRLEEKGHITDDRQLFA----AACYAAKVTLTALGEIFEAARSI 822
T YG G R+Q+ + + +F AA Y AK+ ++ AA
Sbjct: 636 TLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEA 695
Query: 823 MGWLGDCAKVIASENQ------------PVRWTTPLGLPVVQPYCK------NERHLIRT 864
M WL AK++A+E + V W TP G PV Q Y K N L +
Sbjct: 696 MNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQF 755
Query: 865 SLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMTAV-ACRDAGLH-FAGVHDSFW 922
LQ + + ++ KQ + PNFVHS DGSH+ T V A G+ FA +HDSF
Sbjct: 756 RLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFG 815
Query: 923 THACDVDEMNQILRKKFVELY-NMPMLENLLESF--QTSYPTLS-FPPLPERGNFDLEEV 978
T D + + +R+ V+ Y + +L + + F Q L P LP +GN +L ++
Sbjct: 816 TIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDI 875
Query: 979 LESPYFF 985
LES + F
Sbjct: 876 LESDFAF 882
>pdb|1L2L|A Chain A, Crystal Structure Of Adp-Dependent Glucokinase From A
Pyrococcus Horikoshii
Length = 457
Score = 31.2 bits (69), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 45/92 (48%), Gaps = 24/92 (26%)
Query: 693 LQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKIL 752
L+H+ ++G N +E A+V V GEK E+ +R +KDP+ P A++ +L
Sbjct: 286 LKHFYSVGLNEVELASVVSVMGEK-------------ELAERIISKDPAD-PIAVIEGLL 331
Query: 753 IDQVDRKLVKQTVMTSV----YGVTFVGAREQ 780
KL+K+T + + YG RE+
Sbjct: 332 ------KLIKETGVKRIHFHTYGYYLALTREK 357
>pdb|1JYE|A Chain A, Structure Of A Dimeric Lac Repressor With C-Terminal
Deletion And K84l Substitution
Length = 349
Score = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 625 KSGLRWLKIHLANLFSENPING--SRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHL 682
+SG+ K + NL ++ ++G + L +D AAC N+ S + I+ +
Sbjct: 101 RSGVEACKTAVHNLLAQR-VSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSI 159
Query: 683 PI-HQDGSCNGLQHYAALG 700
H+DG+ G++H ALG
Sbjct: 160 IFSHEDGTRLGVEHLVALG 178
>pdb|1LBI|A Chain A, Lac Repressor
pdb|1LBI|B Chain B, Lac Repressor
pdb|1LBI|C Chain C, Lac Repressor
pdb|1LBI|D Chain D, Lac Repressor
pdb|1LBH|A Chain A, Intact Lactose Operon Repressor With Gratuitous Inducer
Iptg
pdb|1LBH|B Chain B, Intact Lactose Operon Repressor With Gratuitous Inducer
Iptg
pdb|1LBH|C Chain C, Intact Lactose Operon Repressor With Gratuitous Inducer
Iptg
pdb|1LBH|D Chain D, Intact Lactose Operon Repressor With Gratuitous Inducer
Iptg
pdb|1LBG|A Chain A, Lactose Operon Repressor Bound To 21-Base Pair Symmetric
Operator Dna, Alpha Carbons Only
pdb|1LBG|B Chain B, Lactose Operon Repressor Bound To 21-Base Pair Symmetric
Operator Dna, Alpha Carbons Only
pdb|1LBG|C Chain C, Lactose Operon Repressor Bound To 21-Base Pair Symmetric
Operator Dna, Alpha Carbons Only
pdb|1LBG|D Chain D, Lactose Operon Repressor Bound To 21-Base Pair Symmetric
Operator Dna, Alpha Carbons Only
Length = 360
Score = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 625 KSGLRWLKIHLANLFSENPING--SRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHL 682
+SG+ K + NL ++ ++G + L +D AAC N+ S + I+ +
Sbjct: 101 RSGVEACKTAVHNLLAQR-VSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSI 159
Query: 683 PI-HQDGSCNGLQHYAALG 700
H+DG+ G++H ALG
Sbjct: 160 IFSHEDGTRLGVEHLVALG 178
>pdb|1EFA|A Chain A, Crystal Structure Of The Lac Repressor Dimer Bound To
Operator And The Anti-Inducer Onpf
pdb|1EFA|B Chain B, Crystal Structure Of The Lac Repressor Dimer Bound To
Operator And The Anti-Inducer Onpf
pdb|1EFA|C Chain C, Crystal Structure Of The Lac Repressor Dimer Bound To
Operator And The Anti-Inducer Onpf
pdb|1JWL|A Chain A, Structure Of The Dimeric Lac RepressorOPERATOR O1ONPF
Complex
pdb|1JWL|B Chain B, Structure Of The Dimeric Lac RepressorOPERATOR O1ONPF
Complex
pdb|1JWL|C Chain C, Structure Of The Dimeric Lac RepressorOPERATOR O1ONPF
Complex
Length = 333
Score = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 625 KSGLRWLKIHLANLFSENPING--SRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHL 682
+SG+ K + NL ++ ++G + L +D AAC N+ S + I+ +
Sbjct: 101 RSGVEACKTAVHNLLAQR-VSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSI 159
Query: 683 PI-HQDGSCNGLQHYAALG 700
H+DG+ G++H ALG
Sbjct: 160 IFSHEDGTRLGVEHLVALG 178
>pdb|1JYF|A Chain A, Structure Of The Dimeric Lac Repressor With An 11-Residue
C-Terminal Deletion
Length = 349
Score = 30.4 bits (67), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 625 KSGLRWLKIHLANLFSENPING--SRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHL 682
+SG+ K + NL ++ ++G + L +D AAC N+ S + I+ +
Sbjct: 101 RSGVEACKTAVHNLLAQR-VSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSI 159
Query: 683 PI-HQDGSCNGLQHYAALG 700
H+DG+ G++H ALG
Sbjct: 160 IFSHEDGTRLGVEHLVALG 178
>pdb|4ESU|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1 Mutant
S2776m
Length = 210
Score = 30.4 bits (67), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 14/102 (13%)
Query: 505 KQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLSEDMTEVQKW------------KWSVR 552
K +++ W+ G N+ + + +L P K SE E+ +W +W++
Sbjct: 35 KWAFDKIQNNWMYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIE 94
Query: 553 KAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRG 594
KA++ +ER ++ K+S + D Y P D G
Sbjct: 95 KAREGEEERTEKKKTR--KISQTAQTYDPREGYNPQPPDLSG 134
>pdb|3EDC|A Chain A, Crystal Structure Of A 1.6-Hexanediol Bound Tetrameric
Form Of Escherichia Coli Lac-Repressor Refined To 2.1
Resolution
pdb|3EDC|B Chain B, Crystal Structure Of A 1.6-Hexanediol Bound Tetrameric
Form Of Escherichia Coli Lac-Repressor Refined To 2.1
Resolution
pdb|3EDC|C Chain C, Crystal Structure Of A 1.6-Hexanediol Bound Tetrameric
Form Of Escherichia Coli Lac-Repressor Refined To 2.1
Resolution
pdb|3EDC|D Chain D, Crystal Structure Of A 1.6-Hexanediol Bound Tetrameric
Form Of Escherichia Coli Lac-Repressor Refined To 2.1
Resolution
Length = 360
Score = 30.0 bits (66), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 625 KSGLRWLKIHLANLFSENPING--SRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHL 682
+SG+ K + NL ++ ++G + L +D AAC N+ S + I+ +
Sbjct: 101 RSGVEACKAAVHNLLAQR-VSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSI 159
Query: 683 PI-HQDGSCNGLQHYAALG 700
H+DG+ G++H ALG
Sbjct: 160 IFSHEDGTRLGVEHLVALG 178
>pdb|2PE5|A Chain A, Crystal Structure Of The Lac Repressor Bound To Onpg In
Repressed State
pdb|2PE5|B Chain B, Crystal Structure Of The Lac Repressor Bound To Onpg In
Repressed State
pdb|2PE5|C Chain C, Crystal Structure Of The Lac Repressor Bound To Onpg In
Repressed State
Length = 330
Score = 30.0 bits (66), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 625 KSGLRWLKIHLANLFSENPING--SRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHL 682
+SG+ K + NL ++ ++G + L +D AAC N+ S + I+ +
Sbjct: 100 RSGVEACKAAVHNLLAQR-VSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSI 158
Query: 683 PI-HQDGSCNGLQHYAALG 700
H+DG+ G++H ALG
Sbjct: 159 IFSHEDGTRLGVEHLVALG 177
>pdb|4ETT|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1 Mutant
E2764k
Length = 210
Score = 29.6 bits (65), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 14/102 (13%)
Query: 505 KQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLSEDMTEVQKW------------KWSVR 552
K +++ W G N+ + + +L P K SE E+ +W +W++
Sbjct: 35 KWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIE 94
Query: 553 KAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRG 594
KA++ +ER ++ K+S + D Y P D G
Sbjct: 95 KAREGEEERTEKKKTR--KISQTAQTYDPREGYNPQPPDLSG 134
>pdb|4ETU|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1 Mutant
R2939s
Length = 210
Score = 29.3 bits (64), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 14/102 (13%)
Query: 505 KQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLSEDMTEVQKW------------KWSVR 552
K +++ W G N+ + + +L P K SE E+ +W +W++
Sbjct: 35 KWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIE 94
Query: 553 KAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRG 594
KA++ +ER ++ K+S + D Y P D G
Sbjct: 95 KAREGEEERTEKKKTR--KISQTAQTYDPREGYNPQPPDLSG 134
>pdb|4ERT|A Chain A, Crystal Structure Of Rabbit Ryanodine Receptor 1
(2734-2940)
Length = 210
Score = 29.3 bits (64), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 14/102 (13%)
Query: 505 KQVLSVLESIWVSGGNIAGLVDRNDVLIPEKPLSEDMTEVQKW------------KWSVR 552
K +++ W G N+ + + +L P K SE E+ +W +W++
Sbjct: 35 KWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIE 94
Query: 553 KAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRG 594
KA++ +ER ++ K+S + D Y P D G
Sbjct: 95 KAREGEEERTEKKKTR--KISQTAQTYDPREGYNPQPPDLSG 134
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
0.320 0.134 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,672,300
Number of Sequences: 62578
Number of extensions: 1111476
Number of successful extensions: 2720
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 2666
Number of HSP's gapped (non-prelim): 30
length of query: 986
length of database: 14,973,337
effective HSP length: 108
effective length of query: 878
effective length of database: 8,214,913
effective search space: 7212693614
effective search space used: 7212693614
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)