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= psy13848
(409 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 135 bits (340), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 69/132 (52%), Positives = 91/132 (68%), Gaps = 4/132 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
+I++ W+ LQ H A + ++E G+P + + R L QRLKGK+GRFRGNLSGKRVDF
Sbjct: 261 IIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDF 320
Query: 60 TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG---LLR 116
+SRTVISPDPN+ I +VG+PE +AK LT PER+ N E L+Q V+NGPDK PG ++R
Sbjct: 321 SSRTVISPDPNISIDEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIR 380
Query: 117 AKERLLSEGYSK 128
R + Y K
Sbjct: 381 PDGRRIDLRYVK 392
Score = 88.6 bits (218), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 42/112 (37%), Positives = 68/112 (60%)
Query: 128 KCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMAL 187
+ + I+ ++G L+ PG + EE+LE IL L +R AG + L P N VMA
Sbjct: 671 EVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMAR 730
Query: 188 SGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNV 239
+G++GS +NI+QM A +GQQ++ G+R+ G+ R+LPHF + P ++G +
Sbjct: 731 TGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFI 782
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 134 bits (338), Expect = 7e-32, Method: Compositional matrix adjust.
Identities = 68/132 (51%), Positives = 91/132 (68%), Gaps = 4/132 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
+I++ W+ LQ H A + ++E G+P + + R L QRLKGK+GRFRGNLSGKRVDF
Sbjct: 261 IIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDF 320
Query: 60 TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG---LLR 116
+SRTVISPDPN+ I +VG+PE +A+ LT PER+ N E L+Q V+NGPDK PG ++R
Sbjct: 321 SSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIR 380
Query: 117 AKERLLSEGYSK 128
R + Y K
Sbjct: 381 PDGRRIDLRYVK 392
Score = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 42/112 (37%), Positives = 68/112 (60%)
Query: 128 KCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMAL 187
+ + I+ ++G L+ PG + EE+LE IL L +R AG + L P N VMA
Sbjct: 671 EVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMAR 730
Query: 188 SGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNV 239
+G++GS +NI+QM A +GQQ++ G+R+ G+ R+LPHF + P ++G +
Sbjct: 731 TGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFI 782
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 64/137 (46%), Positives = 90/137 (65%), Gaps = 4/137 (2%)
Query: 2 IQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDFT 60
I+E LQ H A +++++ +G P +Q + + + RLKGK+GR RGNL GKRVDF+
Sbjct: 289 IEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFS 348
Query: 61 SRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG---LLRA 117
+RTVIS DPNL++ QVG+P+ +AK LTYPE V N + L QLV NGP++HPG ++R
Sbjct: 349 ARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRD 408
Query: 118 KERLLSEGYSKCEGYIR 134
+ YSK G I+
Sbjct: 409 SGDRIDLRYSKRAGDIQ 425
Score = 91.7 bits (226), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 53/154 (34%), Positives = 82/154 (53%), Gaps = 7/154 (4%)
Query: 92 VHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEE 151
+H+ + + +GP +R ++E K + ++ L + G + E
Sbjct: 658 LHNGFSTGIGDTIADGP-----TMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRE 712
Query: 152 TLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAING 211
+ E +++ L+ RD AG+ L N M ++GSKGSFINI+QM ACVGQQ++ G
Sbjct: 713 SFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEG 772
Query: 212 KRVPNGFDNRSLPHFDKFSKDPASKGNVK--FLR 243
KR+ GF +R+LPHF K P SKG V+ +LR
Sbjct: 773 KRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLR 806
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 64/137 (46%), Positives = 90/137 (65%), Gaps = 4/137 (2%)
Query: 2 IQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDFT 60
I+E LQ H A +++++ +G P +Q + + + RLKGK+GR RGNL GKRVDF+
Sbjct: 289 IEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFS 348
Query: 61 SRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG---LLRA 117
+RTVIS DPNL++ QVG+P+ +AK LTYPE V N + L QLV NGP++HPG ++R
Sbjct: 349 ARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRD 408
Query: 118 KERLLSEGYSKCEGYIR 134
+ YSK G I+
Sbjct: 409 SGDRIDLRYSKRAGDIQ 425
Score = 91.7 bits (226), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 53/154 (34%), Positives = 82/154 (53%), Gaps = 7/154 (4%)
Query: 92 VHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEE 151
+H+ + + +GP +R ++E K + ++ L + G + E
Sbjct: 658 LHNGFSTGIGDTIADGP-----TMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRE 712
Query: 152 TLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAING 211
+ E +++ L+ RD AG+ L N M ++GSKGSFINI+QM ACVGQQ++ G
Sbjct: 713 SFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEG 772
Query: 212 KRVPNGFDNRSLPHFDKFSKDPASKGNVK--FLR 243
KR+ GF +R+LPHF K P SKG V+ +LR
Sbjct: 773 KRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLR 806
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 120 bits (301), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 64/137 (46%), Positives = 90/137 (65%), Gaps = 4/137 (2%)
Query: 2 IQEDWEWLQLHCALFINSETSGIPLNMQPKSK-SRGLIQRLKGKQGRFRGNLSGKRVDFT 60
I+E LQ H A +++++ +G P +Q + + + RLKGK+GR RGNL GKRVDF+
Sbjct: 289 IEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFS 348
Query: 61 SRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG---LLRA 117
+RTVIS DPNL++ QVG+P+ +AK LTYPE V N + L QLV NGP++HPG ++R
Sbjct: 349 ARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRD 408
Query: 118 KERLLSEGYSKCEGYIR 134
+ YSK G I+
Sbjct: 409 SGDRIDLRYSKRAGDIQ 425
Score = 91.7 bits (226), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 53/154 (34%), Positives = 82/154 (53%), Gaps = 7/154 (4%)
Query: 92 VHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEE 151
+H+ + + +GP +R ++E K + ++ L + G + E
Sbjct: 658 LHNGFSTGIGDTIADGP-----TMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRE 712
Query: 152 TLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAING 211
+ E +++ L+ RD AG+ L N M ++GSKGSFINI+QM ACVGQQ++ G
Sbjct: 713 SFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEG 772
Query: 212 KRVPNGFDNRSLPHFDKFSKDPASKGNVK--FLR 243
KR+ GF +R+LPHF K P SKG V+ +LR
Sbjct: 773 KRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLR 806
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 116 bits (290), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 55/114 (48%), Positives = 79/114 (69%), Gaps = 1/114 (0%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
++ E + LQ H A ++++E +G P +Q + + + RLKGK+GR RGNL GKRVDF
Sbjct: 294 IVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDF 353
Query: 60 TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
++RTVI+ DPNL + ++G+P +AK LTYPE V N L++LV NGPD+HPG
Sbjct: 354 SARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPG 407
Score = 101 bits (252), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 54/131 (41%), Positives = 78/131 (59%), Gaps = 2/131 (1%)
Query: 115 LRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQ 174
++ R + E + I+ + RL+ +PG + E+ EA + + L+ RD+AG++
Sbjct: 682 MKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAGRSAEH 741
Query: 175 ELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSKDPA 234
L SN M +GSKGSFINISQM ACVGQQ + GKR+P GF R+LPHF K P
Sbjct: 742 SLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPE 801
Query: 235 SKGNVK--FLR 243
S+G ++ +LR
Sbjct: 802 SRGFIENSYLR 812
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 36/91 (39%), Positives = 52/91 (57%), Gaps = 3/91 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS--RGLIQRLKGKQGRFRGNLSGKRVD 58
+I+ + LQ I++ G P+ P S+ R L L GKQGRFR NL GKRVD
Sbjct: 306 IIRNEKRMLQEAVDAVIDNGRRGSPVT-NPGSERPLRSLTDILSGKQGRFRQNLLGKRVD 364
Query: 59 FTSRTVISPDPNLQIYQVGIPEHVAKILTYP 89
++ R+VI P L+++Q G+P+ +A L P
Sbjct: 365 YSGRSVIVVGPQLKLHQCGLPKRMALELFKP 395
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1265
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 36/91 (39%), Positives = 52/91 (57%), Gaps = 3/91 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS--RGLIQRLKGKQGRFRGNLSGKRVD 58
+I+ + LQ I++ G P+ P S+ R L L GKQGRFR NL GKRVD
Sbjct: 306 IIRNEKRMLQEAVDAVIDNGRRGSPVT-NPGSERPLRSLTDILSGKQGRFRQNLLGKRVD 364
Query: 59 FTSRTVISPDPNLQIYQVGIPEHVAKILTYP 89
++ R+VI P L+++Q G+P+ +A L P
Sbjct: 365 YSGRSVIVVGPQLKLHQCGLPKRMALELFKP 395
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 36/91 (39%), Positives = 52/91 (57%), Gaps = 3/91 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS--RGLIQRLKGKQGRFRGNLSGKRVD 58
+I+ + LQ I++ G P+ P S+ R L L GKQGRFR NL GKRVD
Sbjct: 275 IIRNEKRMLQEAVDAVIDNGRRGSPVT-NPGSERPLRSLTDILSGKQGRFRQNLLGKRVD 333
Query: 59 FTSRTVISPDPNLQIYQVGIPEHVAKILTYP 89
++ R+VI P L+++Q G+P+ +A L P
Sbjct: 334 YSGRSVIVVGPQLKLHQCGLPKRMALELFKP 364
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 36/91 (39%), Positives = 52/91 (57%), Gaps = 3/91 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS--RGLIQRLKGKQGRFRGNLSGKRVD 58
+I+ + LQ I++ G P+ P S+ R L L GKQGRFR NL GKRVD
Sbjct: 566 IIRNEKRMLQEAVDAVIDNGRRGSPVT-NPGSERPLRSLTDILSGKQGRFRQNLLGKRVD 624
Query: 59 FTSRTVISPDPNLQIYQVGIPEHVAKILTYP 89
++ R+VI P L+++Q G+P+ +A L P
Sbjct: 625 YSGRSVIVVGPQLKLHQCGLPKRMALELFKP 655
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 58.5 bits (140), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 51/89 (57%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFT 60
+++ + LQ +++ G + K + L +KGKQGRFR NL GKRVD++
Sbjct: 291 IVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYS 350
Query: 61 SRTVISPDPNLQIYQVGIPEHVAKILTYP 89
R+VI+ P L+++Q G+P+ +A L P
Sbjct: 351 GRSVITVGPYLRLHQCGLPKKMALELFKP 379
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 58.5 bits (140), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 51/89 (57%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVDFT 60
+++ + LQ +++ G + K + L +KGKQGRFR NL GKRVD++
Sbjct: 291 IVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYS 350
Query: 61 SRTVISPDPNLQIYQVGIPEHVAKILTYP 89
R+VI+ P L+++Q G+P+ +A L P
Sbjct: 351 GRSVITVGPYLRLHQCGLPKKMALELFKP 379
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 58.2 bits (139), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 51/91 (56%), Gaps = 3/91 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS--RGLIQRLKGKQGRFRGNLSGKRVD 58
+I+ + LQ +++ G P+ P S R L L GKQGRFR NL GKRVD
Sbjct: 566 IIRNEKRMLQEAVDALLDNGRRGAPVT-NPGSDRPLRSLTDILSGKQGRFRQNLLGKRVD 624
Query: 59 FTSRTVISPDPNLQIYQVGIPEHVAKILTYP 89
++ R+VI P L+++Q G+P+ +A L P
Sbjct: 625 YSGRSVIVVGPQLKLHQCGLPKRMALELFKP 655
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 58.2 bits (139), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 51/91 (56%), Gaps = 3/91 (3%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS--RGLIQRLKGKQGRFRGNLSGKRVD 58
+I+ + LQ +++ G P+ P S R L L GKQGRFR NL GKRVD
Sbjct: 566 IIRNEKRMLQEAVDALLDNGRRGAPVT-NPGSDRPLRSLTDILSGKQGRFRQNLLGKRVD 624
Query: 59 FTSRTVISPDPNLQIYQVGIPEHVAKILTYP 89
++ R+VI P L+++Q G+P+ +A L P
Sbjct: 625 YSGRSVIVVGPQLKLHQCGLPKRMALELFKP 655
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNL 52
+I++ W+ LQ H +IN+E G+P + + L QRLKGK+GRFRGNL
Sbjct: 328 IIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNL 380
>pdb|1EWP|A Chain A, Cruzain Bound To Mor-Leu-Hpq
pdb|1F29|A Chain A, Crystal Structure Analysis Of Cruzain Bound To A Vinyl
Sulfone Derived Inhibitor (I)
pdb|1F29|B Chain B, Crystal Structure Analysis Of Cruzain Bound To A Vinyl
Sulfone Derived Inhibitor (I)
pdb|1F29|C Chain C, Crystal Structure Analysis Of Cruzain Bound To A Vinyl
Sulfone Derived Inhibitor (I)
pdb|1F2A|A Chain A, Crystal Structure Analysis Of Cruzain Bound To A Vinyl
Sulfone Derived Inhibitor (Ii)
pdb|1F2B|A Chain A, Crystal Structure Analysis Of Cruzain Bound To Vinyl
Sulfone Derived Inhibitor (Iii)
pdb|1F2C|A Chain A, Crystal Structure Analysis Of Cryzain Bound To Vinyl
Sulfone Derived Inhibitor (Iv)
pdb|1ME3|A Chain A, High Resolution Crystal Structure Analysis Of Cruzain Non-
Covalently Bound To A Hydroxymethyl Ketone Inhibitor
(Ii)
pdb|1ME4|A Chain A, High Resolution Crystal Structure Analysis Of Cruzain
Non-Covalently Bound To A Hydroxymethyl Ketone Inhibitor
(I)
pdb|1EWL|A Chain A, Crystal Structure Of Cruzain Bound To Wrr-99
pdb|1EWM|A Chain A, The Cysteine Protease Cruzain Bound To Wrr-112
pdb|1EWO|A Chain A, The Cysteine Protease Cruzain Bound To Wrr-204
pdb|1U9Q|X Chain X, Crystal Structure Of Cruzain Bound To An Alpha-Ketoester
pdb|2AIM|A Chain A, Cruzain Inhibited With
Benzoyl-Arginine-Alanine-Fluoromethylketone
pdb|2OZ2|A Chain A, Crystal Structure Analysis Of Cruzain Bound To Vinyl
Sulfone Derived Inhibitor (K11777)
pdb|2OZ2|C Chain C, Crystal Structure Analysis Of Cruzain Bound To Vinyl
Sulfone Derived Inhibitor (K11777)
pdb|3I06|A Chain A, Crystal Structure Of Cruzain Covalently Bound To A Purine
Nitrile
pdb|3KKU|A Chain A, Cruzain In Complex With A Non-Covalent Ligand
pdb|3LXS|A Chain A, Crystal Structure Analysis Of Cruzain Bound To Vinyl
Sulfone Derived Inhibitor (Wrr483)
pdb|3LXS|C Chain C, Crystal Structure Analysis Of Cruzain Bound To Vinyl
Sulfone Derived Inhibitor (Wrr483)
Length = 215
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 26/125 (20%), Positives = 56/125 (44%), Gaps = 6/125 (4%)
Query: 138 SGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINI 197
SG + P ++ T+ A I + + +D A A + NGP+ +A+ S
Sbjct: 93 SGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAV---NGPVAVAVDASSWMTYTG 149
Query: 198 SQMIACVGQQAINGKRVPNGFDNRSLPHF---DKFSKDPASKGNVKFLRYGNRLKIASEL 254
M +CV +Q +G + D+ ++P++ + ++ +G ++ + N+ + E
Sbjct: 150 GVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEA 209
Query: 255 KSAYL 259
SA +
Sbjct: 210 SSAVV 214
>pdb|3IUT|A Chain A, The Crystal Structure Of Cruzain In Complex With A
Tetrafluorophenoxymethyl Ketone Inhibitor
Length = 221
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 26/125 (20%), Positives = 55/125 (44%), Gaps = 6/125 (4%)
Query: 138 SGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINI 197
SG + P ++ T+ A I + + +D A A + NGP+ +A+ S
Sbjct: 93 SGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAV---NGPVAVAVDASSWMTYTG 149
Query: 198 SQMIACVGQQAINGKRVPNGFDNRSLPHF---DKFSKDPASKGNVKFLRYGNRLKIASEL 254
M +CV +Q +G + D ++P++ + ++ +G ++ + N+ + E
Sbjct: 150 GVMTSCVSEQLDHGVLLVGYNDGAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEA 209
Query: 255 KSAYL 259
SA +
Sbjct: 210 SSAVV 214
>pdb|3HD3|A Chain A, High Resolution Crystal Structure Of Cruzain Bound To The
Vinyl Sulfone Inhibitor Smdc-256047
pdb|3HD3|B Chain B, High Resolution Crystal Structure Of Cruzain Bound To The
Vinyl Sulfone Inhibitor Smdc-256047
Length = 215
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 26/125 (20%), Positives = 55/125 (44%), Gaps = 6/125 (4%)
Query: 138 SGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINI 197
SG + P ++ T+ A I + + +D A A + NGP+ +A+ S
Sbjct: 93 SGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAV---NGPVAVAVDASSWMTYTG 149
Query: 198 SQMIACVGQQAINGKRVPNGFDNRSLPHF---DKFSKDPASKGNVKFLRYGNRLKIASEL 254
M +CV +Q +G + D ++P++ + ++ +G ++ + N+ + E
Sbjct: 150 GVMTSCVSEQLDHGVLLVGYNDGAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEA 209
Query: 255 KSAYL 259
SA +
Sbjct: 210 SSAVV 214
>pdb|3CWB|B Chain B, Chicken Cytochrome Bc1 Complex Inhibited By An Iodinated
Analogue Of The Polyketide Crocacin-d
pdb|3CWB|O Chain O, Chicken Cytochrome Bc1 Complex Inhibited By An Iodinated
Analogue Of The Polyketide Crocacin-d
pdb|3H1H|B Chain B, Cytochrome Bc1 Complex From Chicken
pdb|3H1H|O Chain O, Cytochrome Bc1 Complex From Chicken
pdb|3H1I|B Chain B, Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex
From Chicken
pdb|3H1I|O Chain O, Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex
From Chicken
pdb|3H1J|B Chain B, Stigmatellin-Bound Cytochrome Bc1 Complex From Chicken
pdb|3H1J|O Chain O, Stigmatellin-Bound Cytochrome Bc1 Complex From Chicken
pdb|3H1K|B Chain B, Chicken Cytochrome Bc1 Complex With Zn++ And An Iodinated
Derivative Of Kresoxim-Methyl Bound
pdb|3H1K|O Chain O, Chicken Cytochrome Bc1 Complex With Zn++ And An Iodinated
Derivative Of Kresoxim-Methyl Bound
pdb|3H1L|B Chain B, Chicken Cytochrome Bc1 Complex With Ascochlorin Bound At
Qo And Qi Sites
pdb|3H1L|O Chain O, Chicken Cytochrome Bc1 Complex With Ascochlorin Bound At
Qo And Qi Sites
pdb|3L70|B Chain B, Cytochrome Bc1 Complex From Chicken With Trifloxystrobin
Bound
pdb|3L70|O Chain O, Cytochrome Bc1 Complex From Chicken With Trifloxystrobin
Bound
pdb|3L71|B Chain B, Cytochrome Bc1 Complex From Chicken With Azoxystrobin
Bound
pdb|3L71|O Chain O, Cytochrome Bc1 Complex From Chicken With Azoxystrobin
Bound
pdb|3L72|B Chain B, Chicken Cytochrome Bc1 Complex With Kresoxym-I-Dimethyl
Bound
pdb|3L72|O Chain O, Chicken Cytochrome Bc1 Complex With Kresoxym-I-Dimethyl
Bound
pdb|3L73|B Chain B, Cytochrome Bc1 Complex From Chicken With Triazolone
Inhibitor
pdb|3L73|O Chain O, Cytochrome Bc1 Complex From Chicken With Triazolone
Inhibitor
pdb|3L74|B Chain B, Cytochrome Bc1 Complex From Chicken With Famoxadone Bound
pdb|3L74|O Chain O, Cytochrome Bc1 Complex From Chicken With Famoxadone Bound
pdb|3L75|B Chain B, Cytochrome Bc1 Complex From Chicken With Fenamidone Bound
pdb|3L75|O Chain O, Cytochrome Bc1 Complex From Chicken With Fenamidone Bound
pdb|3TGU|B Chain B, Cytochrome Bc1 Complex From Chicken With Pfvs-Designed Moa
Inhibitor Bound
pdb|3TGU|O Chain O, Cytochrome Bc1 Complex From Chicken With Pfvs-Designed Moa
Inhibitor Bound
Length = 441
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 203 CVGQQAINGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKSAYLVWR 262
C G + + ++PNG SL +F PAS+ V F++ G+R + + L +A+L+ R
Sbjct: 20 CPGAEDLEITKLPNGLIIASLENF-----SPASRIGV-FIKAGSRYETTANLGTAHLL-R 72
Query: 263 VAGSISARG 271
+A ++ +G
Sbjct: 73 LASPLTTKG 81
>pdb|1AIM|A Chain A, Cruzain Inhibited By
Benzoyl-Tyrosine-Alanine-Fluoromethylketone
Length = 215
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/125 (20%), Positives = 55/125 (44%), Gaps = 6/125 (4%)
Query: 138 SGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKGSFINI 197
SG + P ++ T+ A I + + +D A A + NGP+ +A+ S
Sbjct: 93 SGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAV---NGPVAVAVDASSWMTYTG 149
Query: 198 SQMIACVGQQAINGKRVPNGFDNRSLPHF---DKFSKDPASKGNVKFLRYGNRLKIASEL 254
M +CV + +G + D+ ++P++ + ++ +G ++ + N+ + E
Sbjct: 150 GVMTSCVSEALDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEA 209
Query: 255 KSAYL 259
SA +
Sbjct: 210 SSAVV 214
>pdb|3G5U|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G5U|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
Length = 1284
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 31/139 (22%), Positives = 63/139 (45%), Gaps = 14/139 (10%)
Query: 64 VISPDPNLQIYQVGIPEHVA-----KILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAK 118
++S +P L + I E++A ++++Y E V A + ++ Q + + PDK+ + K
Sbjct: 1111 IVSQEPIL--FDCSIAENIAYGDNSRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDK 1168
Query: 119 ERLLSEGYSKCEGYIRAM--ESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQEL 176
LS G + RA+ + L SA +T +++E ++ + G+ C+
Sbjct: 1169 GTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTESEKVVQE-ALDKAREGRTCIVIA 1227
Query: 177 H----PSNGPLVMALSGSK 191
H N L++ + K
Sbjct: 1228 HRLSTIQNADLIVVIQNGK 1246
>pdb|3G60|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G60|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G61|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G61|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
Length = 1284
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 31/139 (22%), Positives = 63/139 (45%), Gaps = 14/139 (10%)
Query: 64 VISPDPNLQIYQVGIPEHVA-----KILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAK 118
++S +P L + I E++A ++++Y E V A + ++ Q + + PDK+ + K
Sbjct: 1111 IVSQEPIL--FDCSIAENIAYGDNSRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDK 1168
Query: 119 ERLLSEGYSKCEGYIRAM--ESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQEL 176
LS G + RA+ + L SA +T +++E ++ + G+ C+
Sbjct: 1169 GTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTESEKVVQE-ALDKAREGRTCIVIA 1227
Query: 177 H----PSNGPLVMALSGSK 191
H N L++ + K
Sbjct: 1228 HRLSTIQNADLIVVIQNGK 1246
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
0.318 0.134 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,945,124
Number of Sequences: 62578
Number of extensions: 478519
Number of successful extensions: 874
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 835
Number of HSP's gapped (non-prelim): 40
length of query: 409
length of database: 14,973,337
effective HSP length: 101
effective length of query: 308
effective length of database: 8,652,959
effective search space: 2665111372
effective search space used: 2665111372
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)