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= 037323
(475 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BGH|A Chain A, Crystal Structure Of Vinorine Synthase
pdb|2BGH|B Chain B, Crystal Structure Of Vinorine Synthase
Length = 421
Score = 189 bits (481), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 140/422 (33%), Positives = 204/422 (48%), Gaps = 33/422 (7%)
Query: 39 ISTEVIKPSSPTPKHLRTYKLSLLDQLFSKIYVPLVFFYSANCKHQYF-SKKSDLLKQSL 97
+S E+I PSSPTP+ L+ YK+S LDQL ++P + FY ++ S LKQSL
Sbjct: 8 VSEELILPSSPTPQSLKCYKISHLDQLLLTCHIPFILFYPNPLDSNLDPAQTSQHLKQSL 67
Query: 98 AKTLTHYYPFAGRLIDSFSVDCSDHGAAFIEANVGCDISKFLQP-PDMEXXXXXXXXXXX 156
+K LTH+YP AGR+ + SVDC+D G F+EA V +S+ +Q ++E
Sbjct: 68 SKVLTHFYPLAGRINVNSSVDCNDSGVPFVEARVQAQLSQAIQNVVELEKLDQYLPSAAY 127
Query: 157 X-XXXDVSERELLAVQVNLFSGGEMAIGVCFSHGVADGSAIFNFMKTWGEITRGXXXXXX 215
+V+E LAV+++ F G AIGV SH +AD ++ F+ W RG
Sbjct: 128 PGGKIEVNEDVPLAVKISFFECGGTAIGVNLSHKIADVLSLATFLNAWTATCRGETEIVL 187
Query: 216 XXXXXXXXXXXTSLFPPV-NFPKPYQIVTSPQSSGNIVFKRLLFDSKKIAALKEKVNKEI 274
FPPV N P P + N+V KR +FD +KI AL+ + +
Sbjct: 188 PNFDLAARH-----FPPVDNTPSPELV-----PDENVVMKRFVFDKEKIGALRAQAS--- 234
Query: 275 GKFNELQATRFGVVSALIWGAFIAIARERKRAIDNKLYSHAIYYTMNLRNKLNPPMIPQC 334
E +R +V A IW I + R + A + + A+ NLR+++NPP+
Sbjct: 235 SASEEKNFSRVQLVVAYIWKHVIDVTRAKYGAKNKFVVVQAV----NLRSRMNPPLPHYA 290
Query: 335 MGNIYRL----VRAEWSLAKDDAIEETSLLREVIKAKRMGREVMHNNEYLGFIKDMKETW 390
MGNI L V AEW D I LR ++ E HN+E L + + E
Sbjct: 291 MGNIATLLFAAVDAEWDKDFPDLI---GPLRTSLEKT----EDDHNHELLKGMTCLYEL- 342
Query: 391 EDSRSFGLTSVVGLPCYEVDFGWGKPVWFSVGPLLLIDLAILTSTSDGEGIEALMVMFKE 450
E TS L Y++DFGWGKP+ + A+L T G+G+EA + M ++
Sbjct: 343 EPQELLSFTSWCRLGFYDLDFGWGKPLSACTTTFPKRNAALLMDTRSGDGVEAWLPMAED 402
Query: 451 DM 452
+M
Sbjct: 403 EM 404
>pdb|4G22|A Chain A, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 1)
pdb|4G22|B Chain B, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 1)
Length = 439
Score = 105 bits (263), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 103/446 (23%), Positives = 187/446 (41%), Gaps = 45/446 (10%)
Query: 36 VQIISTEVIKPSSPTPKHLRTYKLSLLDQLFSKIYVPLVFFYSANCKHQYFSKKSDLLKQ 95
+++ + +++P+ TP R S +D + + P V+FY +F K +LK
Sbjct: 8 IEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFFDAK--VLKD 63
Query: 96 SLAKTLTHYYPFAGRLI----DSFSVDCSDHGAAFIEANVGCDISKFLQ-PPDMEXXXXX 150
+L++ L +YP AGRL ++C+ G F+EA + F P +E
Sbjct: 64 ALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTLELRRLI 123
Query: 151 XXXXXXXXXXDVSERELLAVQVNLFSGGEMAIGVCFSHGVADGSAIFNFMKTWGEITRGX 210
+S LL +QV F G +++GV H ADG + +F+ +W ++ RG
Sbjct: 124 PAVDYSQ---GISSYALLVLQVTYFKXGGVSLGVGMRHHAADGFSGLHFINSWSDMARGL 180
Query: 211 XXXX---XXXXXXXXXXXXTSLFPPVNFPKPYQIVTSPQSSGN--------IVFKRLLFD 259
F + + P + SPQ++ + +FK
Sbjct: 181 DVTLPPFIDRTLLRARDPPQPQFQHIEYQPPPALAVSPQTAASDSVPETAVSIFK---LT 237
Query: 260 SKKIAALKEKVNKEIGKFNELQATRFGVVSALIWGAFIAIARERKRAIDNKLYSHAIYYT 319
++I+ALK K +KE G N + + + +++ +W + R +D +Y
Sbjct: 238 REQISALKAK-SKEDG--NTISYSSYEMLAGHVW---RCACKARGLEVDQ---GTKLYIA 288
Query: 320 MNLRNKLNPPMIPQCMGNIYRLVRAEWSLAKDDAIEETSLLREVIK--AKRMGREVMHNN 377
+ R +L P + P GN+ ++A D + I RM + + +
Sbjct: 289 TDGRARLRPSLPPGYFGNVI-FTATPIAIAGDLEFKPVWYAASKIHDALARMDNDYLRSA 347
Query: 378 -EYLGFIKDMKETWEDSRSF-----GLTSVVGLPCYEVDFGWGKPVWFSVGPLLLIDLA- 430
+YL D+K + +F G+TS V LP ++ DFGWG+P++ G + L+
Sbjct: 348 LDYLELQPDLKALVRGAHTFKXPNLGITSWVRLPIHDADFGWGRPIFMGPGGIAYEGLSF 407
Query: 431 ILTSTSDGEGIEALMVMFKEDMDKFE 456
IL S ++ + + + E M F+
Sbjct: 408 ILPSPTNDGSMSVAISLQGEHMKLFQ 433
>pdb|4G2M|A Chain A, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 2)
Length = 439
Score = 105 bits (262), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 103/446 (23%), Positives = 187/446 (41%), Gaps = 45/446 (10%)
Query: 36 VQIISTEVIKPSSPTPKHLRTYKLSLLDQLFSKIYVPLVFFYSANCKHQYFSKKSDLLKQ 95
+++ + +++P+ TP R S +D + + P V+FY +F K +LK
Sbjct: 8 IEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFFDAK--VLKD 63
Query: 96 SLAKTLTHYYPFAGRLI----DSFSVDCSDHGAAFIEANVGCDISKFLQ-PPDMEXXXXX 150
+L++ L +YP AGRL ++C+ G F+EA + F P +E
Sbjct: 64 ALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTLELRRLI 123
Query: 151 XXXXXXXXXXDVSERELLAVQVNLFSGGEMAIGVCFSHGVADGSAIFNFMKTWGEITRGX 210
+S LL +QV F G +++GV H ADG + +F+ +W ++ RG
Sbjct: 124 PAVDYSQ---GISSYALLVLQVTYFKCGGVSLGVGMRHHAADGFSGLHFINSWSDMARGL 180
Query: 211 XXXXX---XXXXXXXXXXXTSLFPPVNFPKPYQIVTSPQSSGN--------IVFKRLLFD 259
F + + P + SPQ++ + +FK
Sbjct: 181 DVTLPPFIDRTLLRARDPPQPQFQHIEYQPPPALAVSPQTAASDSVPETAVSIFK---LT 237
Query: 260 SKKIAALKEKVNKEIGKFNELQATRFGVVSALIWGAFIAIARERKRAIDNKLYSHAIYYT 319
++I+ALK K +KE G N + + + +++ +W + R +D +Y
Sbjct: 238 REQISALKAK-SKEDG--NTISYSSYEMLAGHVWRC---ACKARGLEVDQ---GTKLYIA 288
Query: 320 MNLRNKLNPPMIPQCMGNIYRLVRAEWSLAKDDAIEETSLLREVIKAK--RMGREVMHNN 377
+ R +L P + P GN+ ++A D + I RM + + +
Sbjct: 289 TDGRARLRPSLPPGYFGNVI-FTATPIAIAGDLEFKPVWYAASKIHDALARMDNDYLRSA 347
Query: 378 -EYLGFIKDMKETWEDSRSF-----GLTSVVGLPCYEVDFGWGKPVWFSVGPLLLIDLA- 430
+YL D+K + +F G+TS V LP ++ DFGWG+P++ G + L+
Sbjct: 348 LDYLELQPDLKALVRGAHTFKXPNLGITSWVRLPIHDADFGWGRPIFMGPGGIAYEGLSF 407
Query: 431 ILTSTSDGEGIEALMVMFKEDMDKFE 456
IL S ++ + + + E M F+
Sbjct: 408 ILPSPTNDGSMSVAISLQGEHMKLFQ 433
>pdb|4G0B|A Chain A, Structure Of Native Hct From Coffea Canephora
pdb|4G0B|B Chain B, Structure Of Native Hct From Coffea Canephora
Length = 436
Score = 103 bits (258), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 103/446 (23%), Positives = 187/446 (41%), Gaps = 45/446 (10%)
Query: 36 VQIISTEVIKPSSPTPKHLRTYKLSLLDQLFSKIYVPLVFFYSANCKHQYFSKKSDLLKQ 95
+++ + +++P+ TP R S +D + + P V+FY +F K +LK
Sbjct: 5 IEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFFDAK--VLKD 60
Query: 96 SLAKTLTHYYPFAGRLI----DSFSVDCSDHGAAFIEANVGCDISKFLQ-PPDMEXXXXX 150
+L++ L +YP AGRL ++C+ G F+EA + F P +E
Sbjct: 61 ALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTLELRRLI 120
Query: 151 XXXXXXXXXXDVSERELLAVQVNLFSGGEMAIGVCFSHGVADGSAIFNFMKTWGEITRGX 210
+S LL +QV F G +++GV H ADG + +F+ +W ++ RG
Sbjct: 121 PAVDYSQ---GISSYALLVLQVTYFKCGGVSLGVGMRHHAADGFSGLHFINSWSDMARGL 177
Query: 211 XXXXX---XXXXXXXXXXXTSLFPPVNFPKPYQIVTSPQSSGN--------IVFKRLLFD 259
F + + P + SPQ++ + +FK
Sbjct: 178 DVTLPPFIDRTLLRARDPPQPQFQHIEYQPPPALKVSPQTAKSDSVPETAVSIFK---LT 234
Query: 260 SKKIAALKEKVNKEIGKFNELQATRFGVVSALIWGAFIAIARERKRAIDNKLYSHAIYYT 319
++I+ALK K +KE G N + + + +++ +W + R +D +Y
Sbjct: 235 REQISALKAK-SKEDG--NTISYSSYEMLAGHVWRC---ACKARGLEVDQ---GTKLYIA 285
Query: 320 MNLRNKLNPPMIPQCMGNIYRLVRAEWSLAKDDAIEETSLLREVIK--AKRMGREVMHNN 377
+ R +L P + P GN+ ++A D + I RM + + +
Sbjct: 286 TDGRARLRPSLPPGYFGNVI-FTATPIAIAGDLEFKPVWYAASKIHDALARMDNDYLRSA 344
Query: 378 -EYLGFIKDMKETWEDSRSF-----GLTSVVGLPCYEVDFGWGKPVWFSVGPLLLIDLA- 430
+YL D+K + +F G+TS V LP ++ DFGWG+P++ G + L+
Sbjct: 345 LDYLELQPDLKALVRGAHTFKCPNLGITSWVRLPIHDADFGWGRPIFMGPGGIAYEGLSF 404
Query: 431 ILTSTSDGEGIEALMVMFKEDMDKFE 456
IL S ++ + + + E M F+
Sbjct: 405 ILPSPTNDGSMSVAISLQGEHMKLFQ 430
>pdb|2E1T|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat
Complexed With Malonyl-coa
pdb|2E1T|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat
Complexed With Malonyl-coa
pdb|2E1U|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat
pdb|2E1U|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat
Length = 454
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 93/381 (24%), Positives = 148/381 (38%), Gaps = 61/381 (16%)
Query: 74 VFFYSANCKHQYFSKKS-DLLKQSLAKTLTHYYPFAGRLI---------DSFSVDCSDHG 123
+FFY F++ +K SL+ TL H+YPF G+L+ + V+
Sbjct: 45 LFFYELPITRSQFTETVVPNIKHSLSITLKHFYPFVGKLVVYPAPTKKPEICYVEGDSVA 104
Query: 124 AAFIEANVGCDISKFLQPPDMEX-XXXXXXXXXXXXXXDVSERELLAVQVNLFSGGEMAI 182
F E N+ + P + + D + L +VQV LF +AI
Sbjct: 105 VTFAECNLDLNELTGNHPRNCDKFYDLVPILGESTRLSDCIKIPLFSVQVTLFPNQGIAI 164
Query: 183 GVCFSHGVADGSAIFNFMKTWGEITR-GXXXXXXXXXXXXXXXXXTSLFPPVN------- 234
G+ H + D S F F+K W I R G +P ++
Sbjct: 165 GITNHHCLGDASTRFCFLKAWTSIARSGNNDESFLANGTRPLYDRIIKYPMLDEAYLKRA 224
Query: 235 ----FPKPY--QIVTSPQSSGNIVFKRLLFDSKKIAALKEKVNKEIGKFNELQATRFGVV 288
F + Y Q + P F + I LK++V ++ + + F V
Sbjct: 225 KVESFNEDYVTQSLAGPSDKLRATF---ILTRAVINQLKDRVLAQLPTLEYVSS--FTVA 279
Query: 289 SALIWGAFIAIARERKRAIDNKLYSHAIYYTMNLRNKLNPPMIPQCMGNIYRLVRAEWSL 348
A IW IA+ R + +L+ + ++ R ++ PP+ GN +
Sbjct: 280 CAYIWSC---IAKSRNDKL--QLFG----FPIDRRARMKPPIPTAYFGN---------CV 321
Query: 349 AKDDAIEETSLL---REVIKAKRMGREVMHNN--EYL-GFIKDMKETWEDSRSFGL---- 398
AI +T+LL I A ++ E +H +Y G +KD E++ D S G+
Sbjct: 322 GGCAAIAKTNLLIGKEGFITAAKLIGENLHKTLTDYKDGVLKDDMESFNDLVSEGMPTTM 381
Query: 399 TSVVGLP---CYEVDFGWGKP 416
T V G P Y++DFGWGKP
Sbjct: 382 TWVSGTPKLRFYDMDFGWGKP 402
>pdb|2E1V|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat, Seleno-
Methionine Derivative
pdb|2E1V|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat, Seleno-
Methionine Derivative
Length = 454
Score = 65.1 bits (157), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 93/381 (24%), Positives = 145/381 (38%), Gaps = 61/381 (16%)
Query: 74 VFFYSANCKHQYFSKKS-DLLKQSLAKTLTHYYPFAGRLI---------DSFSVDCSDHG 123
+FFY F++ +K SL+ TL H+YPF G+L+ + V+
Sbjct: 45 LFFYELPITRSQFTETVVPNIKHSLSITLKHFYPFVGKLVVYPAPTKKPEICYVEGDSVA 104
Query: 124 AAFIEANVGCDISKFLQPPDMEX-XXXXXXXXXXXXXXDVSERELLAVQVNLFSGGEMAI 182
F E N+ + P + + D + L +VQV LF +AI
Sbjct: 105 VTFAECNLDLNELTGNHPRNCDKFYDLVPILGESTRLSDCIKIPLFSVQVTLFPNQGIAI 164
Query: 183 GVCFSHGVADGSAIFNFMKTWGEITR-GXXXXXXXXXXXXXXXXXTSLFPPVN------- 234
G+ H + D S F F+K W I R G +P ++
Sbjct: 165 GITNHHCLGDASTRFCFLKAWTSIARSGNNDESFLANGTRPLYDRIIKYPXLDEAYLKRA 224
Query: 235 ----FPKPY--QIVTSPQSSGNIVFKRLLFDSKKIAALKEKVNKEIGKFNELQATRFGVV 288
F + Y Q + P F + I LK++V ++ + + F V
Sbjct: 225 KVESFNEDYVTQSLAGPSDKLRATF---ILTRAVINQLKDRVLAQLPTLEYVSS--FTVA 279
Query: 289 SALIWGAFIAIARERKRAIDNKLYSHAIYYTMNLRNKLNPPMIPQCMGNIYRLVRAEWSL 348
A IW IA+ R + +L+ + ++ R + PP+ GN +
Sbjct: 280 CAYIWS---CIAKSRNDKL--QLFG----FPIDRRARXKPPIPTAYFGN---------CV 321
Query: 349 AKDDAIEETSLL---REVIKAKRMGREVMHN--NEYL-GFIKDMKETWEDSRSFG----L 398
AI +T+LL I A ++ E +H +Y G +KD E++ D S G
Sbjct: 322 GGCAAIAKTNLLIGKEGFITAAKLIGENLHKTLTDYKDGVLKDDXESFNDLVSEGXPTTX 381
Query: 399 TSVVGLP---CYEVDFGWGKP 416
T V G P Y+ DFGWGKP
Sbjct: 382 TWVSGTPKLRFYDXDFGWGKP 402
>pdb|2XR7|A Chain A, Crystal Structure Of Nicotiana Tabacum Malonyltransferase
(Ntmat1) Complexed With Malonyl-Coa
Length = 453
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 62/272 (22%), Positives = 96/272 (35%), Gaps = 37/272 (13%)
Query: 167 LLAVQVNLFSGGEMAIGVCFSHGVADGSAIFNFMKTWGEITRGXXXXXXXXXXXXXXXXX 226
+LA+QV LF ++IG H DG+ I F++ W + +
Sbjct: 144 VLAIQVTLFPNHGISIGFTNHHVAGDGATIVKFVRAWALLNKFGGDEQFLANEFIPFYDR 203
Query: 227 TSLFPP-------VNFPKPYQ-------IVTSPQS-SGNIVFKRLLFDSKKIAALKEKVN 271
+ + P N K Y+ +VT P G + R I LK V
Sbjct: 204 SVIKDPNGVGXSIWNEXKKYKHXXKXSDVVTPPDKVRGTFIITR-----HDIGKLKNLVL 258
Query: 272 KEIGKFNELQATRFGVVSALIWGAFIAIARERKRAIDN---KLYSHAIYYTMNLRNKLNP 328
K + T F V A +W I ID + + A + R + NP
Sbjct: 259 TRRPKLTHV--TSFTVTCAYVWTCIIKSEAATGEEIDENGXEFFGCA----ADCRAQFNP 312
Query: 329 PMIPQCMGNI---YRLVRAEWSLAKDDAIE-ETSLLREVIKAKRMGREVMHNNEYLGFIK 384
P+ P GN Y + LA + L+ E I+ + E + + + K
Sbjct: 313 PLPPSYFGNALVGYVARTRQVDLAGKEGFTIAVELIGEAIRKRXKDEEWILSGSWF---K 369
Query: 385 DMKETWEDSRSFGLTSVVGLPCYEVDFGWGKP 416
+ + + RS + L Y DFGWG+P
Sbjct: 370 EYDKV-DAKRSLSVAGSPKLDLYAADFGWGRP 400
>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 443
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 12/81 (14%)
Query: 259 DSKKIAALKEKVNKEIGKFNELQATRFGVVSALI---------WGAFIAIARERKRAIDN 309
D+ + L E++ K + K +E +A + LI GAF + RER R I+N
Sbjct: 363 DAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIEN 422
Query: 310 KLYSHAIYY---TMNLRNKLN 327
K Y+ T LR+ L+
Sbjct: 423 KALRKLKYHESRTRKLRDFLD 443
>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
Length = 423
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 12/81 (14%)
Query: 259 DSKKIAALKEKVNKEIGKFNELQATRFGVVSALI---------WGAFIAIARERKRAIDN 309
D+ + L E++ K + K +E +A + LI GAF + RER R I+N
Sbjct: 343 DAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIEN 402
Query: 310 KLYSHAIYY---TMNLRNKLN 327
K Y+ T LR+ L+
Sbjct: 403 KALRKLKYHESRTRKLRDFLD 423
>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
Length = 423
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 12/81 (14%)
Query: 259 DSKKIAALKEKVNKEIGKFNELQATRFGVVSALI---------WGAFIAIARERKRAIDN 309
D+ + L E++ K + K +E +A + LI GAF + RER R I+N
Sbjct: 343 DAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIEN 402
Query: 310 KLYSHAIYY---TMNLRNKLN 327
K Y+ T LR+ L+
Sbjct: 403 KALRKLKYHESRTRKLRDFLD 423
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 104 YYPFAGRLIDSFSVDCSDHGAAFIEANVGCDISKFLQPPDM 144
+ PF G ++D V CS HG + ++K L P D+
Sbjct: 79 FKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDL 119
>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|G Chain G, Rna Polymerase Ii-Tfiis Complex
pdb|1WCM|G Chain G, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|G Chain G, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|G Chain G, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|G Chain G, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|G Chain G, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|1Y14|B Chain B, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|D Chain D, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|2B63|G Chain G, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2JA5|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|S Chain S, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|G Chain G, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|G Chain G, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|G Chain G, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|G Chain G, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|G Chain G, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|H Chain H, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|G Chain G, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|S Chain S, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|G Chain G, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|G Chain G, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|G Chain G, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|G Chain G, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|G Chain G, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|G Chain G, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|G Chain G, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3J0K|G Chain G, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|G Chain G, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|G Chain G, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|G Chain G, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|G Chain G, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 171
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 104 YYPFAGRLIDSFSVDCSDHGAAFIEANVGCDISKFLQPPDM 144
+ PF G ++D V CS HG + ++K L P D+
Sbjct: 79 FKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDL 119
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
0.321 0.136 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,306,448
Number of Sequences: 62578
Number of extensions: 453926
Number of successful extensions: 1233
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1209
Number of HSP's gapped (non-prelim): 16
length of query: 475
length of database: 14,973,337
effective HSP length: 102
effective length of query: 373
effective length of database: 8,590,381
effective search space: 3204212113
effective search space used: 3204212113
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: 53 (25.0 bits)