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= 009567
(532 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
Length = 332
Score = 179 bits (454), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 106/320 (33%), Positives = 188/320 (58%), Gaps = 23/320 (7%)
Query: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 273
+DP+R +L LLT +EE +L ++++ I+ E + L + RE + AK
Sbjct: 2 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 274 AIGLS------------CRDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 318
+G + ++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S
Sbjct: 59 ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 319 HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 378
DL+QEG+ GL+++VEKF+ + +F++YA WW+RQ I +AI +RTIR+P ++ ++
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETIN 178
Query: 379 KVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMPLSMQQPVWADQDTTF 436
K+ R QE P E++A +G +++E + I + P+S++ P+ ++D+ +
Sbjct: 179 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFY 238
Query: 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 496
+ D + P + + L+ + + L+ L+ +E +++LR G+ DG+ +L EVG
Sbjct: 239 GDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAY 298
Query: 497 FGLSKERVRQLESRALYRLK 516
FG+++ER+RQ+E++AL +LK
Sbjct: 299 FGVTRERIRQIENKALRKLK 318
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 179 bits (454), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 84/242 (34%), Positives = 155/242 (64%), Gaps = 4/242 (1%)
Query: 279 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 334
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 335 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 394
KF+ + G +F++YA WW+RQ I ++I +RTIR+P ++ ++K+ R +QE
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 395 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 454
P E+LA R+ + +K+ +++ I + P+SM+ P+ D+D+ + DT +E+P S
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 514
+ +R ++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 515 LK 516
L+
Sbjct: 598 LR 599
>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 613
Score = 179 bits (453), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 84/242 (34%), Positives = 155/242 (64%), Gaps = 4/242 (1%)
Query: 279 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 334
+D+ + G + ++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 335 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 394
KF+ + G +F++YA WW+RQ I ++I +RTIR+P ++ ++K+ R +QE
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 395 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 454
P E+LA R+ + +K+ +++ I + P+SM+ P+ D+D+ + DT +E+P S
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 514
+ +R ++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 515 LK 516
L+
Sbjct: 598 LR 599
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 175 bits (443), Expect = 6e-44, Method: Compositional matrix adjust.
Identities = 106/335 (31%), Positives = 188/335 (56%), Gaps = 38/335 (11%)
Query: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 273
+DP+R +L LLT +EE +L ++++ I+ E + L + RE + AK
Sbjct: 93 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 149
Query: 274 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 303
+G + ++LK LH G ++R+ LI ANLRL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 304 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363
VV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA WW+RQ I +AI
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI--TVEKLERLIFITRMP 421
+RTIR+P ++ ++K+ R QE P E++A +G +++E + I + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 422 LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFG 481
+S++ P+ ++D+ + + D + P + + L+ + + L+ L+ +E +++LR G
Sbjct: 330 VSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKG 389
Query: 482 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 390 LIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 424
>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 = 172 bits (435), Expect = 5e-43, Method: Compositional matrix adjust.
Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 406
WW+RQ I +AI +RTIR+P ++ ++K+ R QE P E++A +G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 407 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
+++E + I + P+S++ P+ ++D+ + + D + P + + L+ + + L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409
>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 = 172 bits (435), Expect = 5e-43, Method: Compositional matrix adjust.
Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 406
WW+RQ I +AI +RTIR+P ++ ++K+ R QE P E++A +G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 407 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
+++E + I + P+S++ P+ ++D+ + + D + P + + L+ + + L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409
>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 = 171 bits (434), Expect = 6e-43, Method: Compositional matrix adjust.
Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 406
WW+RQ I +AI +RTIR+P ++ ++K+ R QE P E++A +G
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 407 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
+++E + I + P+S++ P+ ++D+ + + D + P + + L+ + + L+
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 379
Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 380 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 429
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
Length = 241
Score = 116 bits (291), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
Query: 280 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 336
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF
Sbjct: 92 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 151
Query: 337 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 396
+ + +F++YA WW+RQ I +AI +RTIR+P ++ ++K+ R QE P
Sbjct: 152 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 211
Query: 397 KEDLARRVGIT--VEKLERLIFITRMPLSM 424
E++A +G +++E + I + P+S+
Sbjct: 212 YEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tacaat)
pdb|3UGP|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tataat)
pdb|4GOR|A Chain A, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
pdb|4GOR|B Chain B, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
Length = 245
Score = 116 bits (291), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 78/243 (32%), Positives = 130/243 (53%), Gaps = 38/243 (15%)
Query: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 273
+DP+R +L LLT +EE +L ++++ I+ E + L + RE + AK
Sbjct: 6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 62
Query: 274 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 303
+G + ++LK LH G ++R+ LI ANLRL
Sbjct: 63 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 304 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363
VV +AK+Y GRG+S DL+QEG+ GL+++VEKF+ + +F++YA WW+RQ I +AI
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMP 421
+RTIR+P ++ ++K+ R QE P E++A +G +++E + I + P
Sbjct: 183 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 242
Query: 422 LSM 424
+S+
Sbjct: 243 VSL 245
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
Length = 179
Score = 97.8 bits (242), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 280 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 336
++LK LH G ++R+ LI ANLRLVV +AK+Y GRG+S DL+QEG+ GL+++VEKF
Sbjct: 91 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 337 KPQAGCRFASYAYWWVRQTIRKAIFQHSR 365
+ + G F++YA WW+RQ I +AI +R
Sbjct: 151 EYKRGFAFSTYATWWIRQAINRAIADQAR 179
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 87.8 bits (216), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 58/74 (78%)
Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
++++++ ANLRLV+ +AK+Y RG+ DL+QEG++GLMK+V+KF+ + G +F++YA WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 352 VRQTIRKAIFQHSR 365
+RQ I ++I +R
Sbjct: 326 IRQAITRSIADQAR 339
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 61/229 (26%), Positives = 117/229 (51%), Gaps = 18/229 (7%)
Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
+R+++I N+RLV V +++ RG DL Q G +GL+KSV+KF +F++YA
Sbjct: 29 ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
+ I++ + T+++ ++ + +K+ +AK + +P ++A +GI+ E +
Sbjct: 89 IIGEIQR-FLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 412 ERLIFITRMPLSMQQPVW---ADQDTTFQEIT-ADTGVEIPDISVQKQLMRQHVRNLLTL 467
R+P S+ + V+ D T +I AD I+++K +
Sbjct: 148 VLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASWFDKIALKKAIEE--------- 198
Query: 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
L+ +ER IV LR+ K ++ SEV + G+S+ ++ +LE + L +K
Sbjct: 199 LDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513
+ LMR+ + +L L+P+E ++R+R+G+ DGKPK+L EVG F +++ER+RQ+E +AL
Sbjct: 5 RMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR 64
Query: 514 RLKQ 517
+L+
Sbjct: 65 KLRH 68
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 51/73 (69%)
Query: 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
M++ + ++L L +E ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 517 QSLGGKASYGYAD 529
K + D
Sbjct: 61 HPSRSKRLKDFMD 73
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 65.1 bits (157), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
M++ + ++L L +E ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 517 Q 517
Sbjct: 61 H 61
>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
Length = 239
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 65/253 (25%), Positives = 120/253 (47%), Gaps = 41/253 (16%)
Query: 287 HSGNSSREKLINANLRLVVHVA---KQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 343
+S RE+LI L LV +A K++ + + DL+ G +GL+K+V+ + R
Sbjct: 8 YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67
Query: 344 FASYAYWWVRQTIRKAIFQHSRTI------------RLPENIYTLLSKVLEAKRLYIQEG 391
A +++ I+ AI+ + R++ R+ E + L K+
Sbjct: 68 ----AEAYIKLRIKGAIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKL----------- 112
Query: 392 NHSPDKEDLARRVGITVEKLERLIFITRMP--LSMQQPVWADQDTTFQE-ITADTGVEIP 448
P E++A+ +GI+ E+L + + LS+++ V+ D + E I + T VE
Sbjct: 113 GREPTDEEVAKELGISTEELFKTLDKINFSYILSLEE-VFRDFARDYSELIPSSTNVE-- 169
Query: 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 508
V K+ + + V+ ++ L +E+ +++L F E+ K EV I S RV QL+
Sbjct: 170 -EEVIKRELTEKVKEAVSKLPEREKLVIQLIF-YEELPAK---EVAKILETSVSRVSQLK 224
Query: 509 SRALYRLKQSLGG 521
++AL RL++ L
Sbjct: 225 AKALERLREMLSN 237
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 292
R+++ KL+ + GREPT E AK +G+S +L L N S
Sbjct: 100 RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFS 142
>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
Sigma-Region4 Of Thermus Aquaticus Bound To Dna
Length = 73
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 40/52 (76%)
Query: 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
L+ L+ +E +++LR G+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 8 LSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment, Region 4
pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
Length = 73
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 40/52 (76%)
Query: 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
L+ L+ +E ++++R G+ DG+ +L EVG FG+++ER+RQ+E++AL +LK
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510
S + +R ++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++
Sbjct: 2 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 61
Query: 511 ALYRLKQ 517
AL +L+
Sbjct: 62 ALRKLRH 68
>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|OO Chain o, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
Length = 99
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510
S + +R ++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++
Sbjct: 3 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62
Query: 511 ALYRLKQ 517
AL +L+
Sbjct: 63 ALRKLRH 69
>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
pdb|3N97|D Chain D, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
Length = 72
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 40/53 (75%)
Query: 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
L+ L+ +E ++++R G+ DG+ +L EVG FG+++ER+RQ+E++AL +L+
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRH 60
>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
Length = 68
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 38/55 (69%)
Query: 463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
++L L +E ++R+RFGI+ +L EVG F +++ER+RQ+E++AL +L+
Sbjct: 1 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH 55
>pdb|3MZY|A Chain A, The Crystal Structure Of The Rna Polymerase Sigma-H Factor
F Fusobacterium Nucleatum To 2.5a
Length = 164
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 315 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ----TIRKA 359
G DL+QEG +GL+K++ KF + F+S+A+ +R+ IRKA
Sbjct: 1 GAEKEDLVQEGILGLLKAI-KFYDETKSSFSSFAFLCIRREXISAIRKA 48
>pdb|3IKM|A Chain A, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|D Chain D, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
Length = 1172
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 236 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKA 274
D+ F L+AQ Q L LE LQ+Q +P WA+
Sbjct: 67 DQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEG 105
>pdb|3HV0|A Chain A, Tryptophanyl-Trna Synthetase From Cryptosporidium Parvum
pdb|3HV0|B Chain B, Tryptophanyl-Trna Synthetase From Cryptosporidium Parvum
Length = 393
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 17/94 (18%)
Query: 173 FSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKL 232
F P ++ ++ + K +T ET+N ++K ++ GFD PE +
Sbjct: 106 FKVPLVIQLTDDEKFIFKSNLTLEETHNYAYENMKDIIACGFD-----------PELTFI 154
Query: 233 LTADEEFELIAQIQ-DLIRLEKE--KSKLQSQFG 263
T E IA++ D++R+EK+ S+++S FG
Sbjct: 155 FT---NLEYIAELYPDILRIEKKISCSQIKSIFG 185
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
0.317 0.133 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,908,846
Number of Sequences: 62578
Number of extensions: 530251
Number of successful extensions: 1771
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1719
Number of HSP's gapped (non-prelim): 45
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)