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= psy15215
(1432 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 555 bits (1429), Expect = e-158, Method: Compositional matrix adjust.
Identities = 292/610 (47%), Positives = 397/610 (65%), Gaps = 8/610 (1%)
Query: 827 ENLRKKFKILIKLGKERGYLTFSEINDFLPXXXXXXXXXXXXXKTFRYMDISVSEHVLDT 886
+N + + K+L+ GKE+GYLT++E+ND LP + M I V E D
Sbjct: 3 QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62
Query: 887 ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
+ LML+ T+D+D EA LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63 DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122
Query: 947 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSXXXXXXXXXX 1006
IE+G+ + +++ P I +L +++ E ++ +++ G +D N
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182
Query: 1007 XXXXXXXXXXXXADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
+ + + + + KF+ + + R + +G +
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242
Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
+ + +S R K + L +++R +++V E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302
Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
I +F NE + W + + ++ L + QKL ++ + L + ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362
Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
R+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422
Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482
Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
+A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED + P D+A S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542
Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
D+L LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602
Query: 1419 RYYKLKIFLE 1428
R L+ FL+
Sbjct: 603 RSEVLRSFLD 612
Score = 540 bits (1392), Expect = e-153, Method: Compositional matrix adjust.
Identities = 285/597 (47%), Positives = 388/597 (64%), Gaps = 8/597 (1%)
Query: 37 ENLRKKFKILIKLGKERGYLTFSEINDFLPXXXXXXXXXXXXXKTFRYMDISVSEHVLDT 96
+N + + K+L+ GKE+GYLT++E+ND LP + M I V E D
Sbjct: 3 QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62
Query: 97 ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
+ LML+ T+D+D EA LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63 DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122
Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSXXXXXXXXXX 216
IE+G+ + +++ P I +L +++ E ++ +++ G +D N
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182
Query: 217 XXXXXXXXXXXXADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
+ + + + + KF+ + + R + +G +
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242
Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
+ + +S R K + L +++R +++V E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302
Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
I +F NE + W + + ++ L + QKL ++ + L + ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362
Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
R+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422
Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482
Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
+A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED + P D+A S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542
Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
D+L LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 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 = 554 bits (1428), Expect = e-157, Method: Compositional matrix adjust.
Identities = 292/610 (47%), Positives = 397/610 (65%), Gaps = 8/610 (1%)
Query: 827 ENLRKKFKILIKLGKERGYLTFSEINDFLPXXXXXXXXXXXXXKTFRYMDISVSEHVLDT 886
+N + + K+L+ GKE+GYLT++E+ND LP + M I V E D
Sbjct: 3 QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62
Query: 887 ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
+ LML+ T+D+D EA LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63 DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122
Query: 947 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSXXXXXXXXXX 1006
IE+G+ + +++ P I +L D++ E ++ +++ G +D N
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182
Query: 1007 XXXXXXXXXXXXADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
+ + + + + KF+ + + R + +G +
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242
Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
+ + +S R K + L +++R +++V E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302
Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
I +F NE + W + + ++ L + QKL ++ + L + ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362
Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
R+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422
Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482
Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
+A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED + P D+A S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542
Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602
Query: 1419 RYYKLKIFLE 1428
R L+ FL+
Sbjct: 603 RSEVLRSFLD 612
Score = 540 bits (1391), Expect = e-153, Method: Compositional matrix adjust.
Identities = 285/597 (47%), Positives = 388/597 (64%), Gaps = 8/597 (1%)
Query: 37 ENLRKKFKILIKLGKERGYLTFSEINDFLPXXXXXXXXXXXXXKTFRYMDISVSEHVLDT 96
+N + + K+L+ GKE+GYLT++E+ND LP + M I V E D
Sbjct: 3 QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62
Query: 97 ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
+ LML+ T+D+D EA LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63 DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122
Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSXXXXXXXXXX 216
IE+G+ + +++ P I +L D++ E ++ +++ G +D N
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182
Query: 217 XXXXXXXXXXXXADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
+ + + + + KF+ + + R + +G +
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242
Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
+ + +S R K + L +++R +++V E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302
Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
I +F NE + W + + ++ L + QKL ++ + L + ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362
Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
R+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422
Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482
Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
+A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED + P D+A S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542
Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 599
>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 = 288 bits (738), Expect = 1e-77, Method: Compositional matrix adjust.
Identities = 149/250 (59%), Positives = 191/250 (76%), Gaps = 5/250 (2%)
Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
IA E +A A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +
Sbjct: 85 IAREGEA--ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF 142
Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
KFSTYATWWIRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA
Sbjct: 143 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAE 202
Query: 1302 KM--EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
M +++ + +KIA+EPVS+E+P+GD++DS GDFI DEN+ +P +AA + +
Sbjct: 203 AMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEE 262
Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPS 1418
++ L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE KALRKL+ H S
Sbjct: 263 LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHES 322
Query: 1419 RYYKLKIFLE 1428
R KL+ FLE
Sbjct: 323 RTRKLRDFLE 332
Score = 279 bits (714), Expect = 6e-75, Method: Compositional matrix adjust.
Identities = 141/236 (59%), Positives = 182/236 (77%), Gaps = 4/236 (1%)
Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
IA E +A A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +
Sbjct: 85 IAREGEA--ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF 142
Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
KFSTYATWWIRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA
Sbjct: 143 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAE 202
Query: 512 KM--EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
M +++ + +KIA+EPVS+E+P+GD++DS GDFI DEN+ +P +AA + +
Sbjct: 203 AMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEE 262
Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
++ L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 263 LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 318
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 28/35 (80%)
Query: 128 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
T DP++ Y+ E+G V LLT + EI++A+++EEG++
Sbjct: 1 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGME 35
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 28/35 (80%)
Query: 918 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
T DP++ Y+ E+G V LLT + EI++A+++EEG++
Sbjct: 1 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGME 35
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 287 bits (735), Expect = 3e-77, Method: Compositional matrix adjust.
Identities = 149/250 (59%), Positives = 191/250 (76%), Gaps = 5/250 (2%)
Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
IA E +A A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +
Sbjct: 191 IAREGEA--ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF 248
Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
KFSTYATWWIRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA
Sbjct: 249 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAE 308
Query: 1302 KM--EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
M +++ + +KIA+EPVS+E+P+GD++DS GDFI DEN+ +P +AA + +
Sbjct: 309 AMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEE 368
Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPS 1418
++ L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE KALRKL+ H S
Sbjct: 369 LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHES 428
Query: 1419 RYYKLKIFLE 1428
R KL+ FLE
Sbjct: 429 RTRKLRDFLE 438
Score = 278 bits (711), Expect = 1e-74, Method: Compositional matrix adjust.
Identities = 141/236 (59%), Positives = 182/236 (77%), Gaps = 4/236 (1%)
Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
IA E +A A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +
Sbjct: 191 IAREGEA--ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF 248
Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
KFSTYATWWIRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA
Sbjct: 249 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAE 308
Query: 512 KM--EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
M +++ + +KIA+EPVS+E+P+GD++DS GDFI DEN+ +P +AA + +
Sbjct: 309 AMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEE 368
Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
++ L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 369 LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 424
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 28/35 (80%)
Query: 128 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
T DP++ Y+ E+G V LLT + EI++A+++EEG++
Sbjct: 92 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGME 126
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 28/35 (80%)
Query: 918 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
T DP++ Y+ E+G V LLT + EI++A+++EEG++
Sbjct: 92 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGME 126
>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 = 287 bits (734), Expect = 4e-77, Method: Compositional matrix adjust.
Identities = 154/286 (53%), Positives = 205/286 (71%), Gaps = 7/286 (2%)
Query: 1147 CRNIPSIKE-LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 1205
R+IP +KE L K + +I L L +++ + + A++ + EANLRLV+S
Sbjct: 141 VRHIPGLKETLDPKTVE---EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS 197
Query: 1206 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 1265
IAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQART
Sbjct: 198 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 257
Query: 1266 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSM 1323
IRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+
Sbjct: 258 IRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 317
Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
E+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 318 ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID 377
Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPSRYYKLKIFLE 1428
+HTLEEVG F VTRERIRQIE KALRKL+ H SR KL+ FL+
Sbjct: 378 GREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 423
Score = 279 bits (714), Expect = 7e-75, Method: Compositional matrix adjust.
Identities = 147/272 (54%), Positives = 196/272 (72%), Gaps = 6/272 (2%)
Query: 357 CRNIPSIKE-LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 415
R+IP +KE L K + +I L L +++ + + A++ + EANLRLV+S
Sbjct: 141 VRHIPGLKETLDPKTVE---EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS 197
Query: 416 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 475
IAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQART
Sbjct: 198 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 257
Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSM 533
IRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+
Sbjct: 258 IRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 317
Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
E+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 318 ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID 377
Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
+HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 378 GREHTLEEVGAFFGVTRERIRQIENKALRKLK 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 = 287 bits (734), Expect = 4e-77, Method: Compositional matrix adjust.
Identities = 154/286 (53%), Positives = 205/286 (71%), Gaps = 7/286 (2%)
Query: 1147 CRNIPSIKE-LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 1205
R+IP +KE L K + +I L L +++ + + A++ + EANLRLV+S
Sbjct: 141 VRHIPGLKETLDPKTVE---EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS 197
Query: 1206 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 1265
IAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQART
Sbjct: 198 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 257
Query: 1266 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSM 1323
IRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+
Sbjct: 258 IRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 317
Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
E+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 318 ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID 377
Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPSRYYKLKIFLE 1428
+HTLEEVG F VTRERIRQIE KALRKL+ H SR KL+ FL+
Sbjct: 378 GREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 423
Score = 279 bits (714), Expect = 7e-75, Method: Compositional matrix adjust.
Identities = 147/272 (54%), Positives = 196/272 (72%), Gaps = 6/272 (2%)
Query: 357 CRNIPSIKE-LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 415
R+IP +KE L K + +I L L +++ + + A++ + EANLRLV+S
Sbjct: 141 VRHIPGLKETLDPKTVE---EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS 197
Query: 416 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 475
IAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQART
Sbjct: 198 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 257
Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSM 533
IRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+
Sbjct: 258 IRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 317
Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
E+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 318 ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID 377
Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
+HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 378 GREHTLEEVGAFFGVTRERIRQIENKALRKLK 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 = 286 bits (733), Expect = 4e-77, Method: Compositional matrix adjust.
Identities = 154/286 (53%), Positives = 205/286 (71%), Gaps = 7/286 (2%)
Query: 1147 CRNIPSIKE-LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 1205
R+IP +KE L K + +I L L +++ + + A++ + EANLRLV+S
Sbjct: 161 VRHIPGLKETLDPKTVE---EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS 217
Query: 1206 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 1265
IAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQART
Sbjct: 218 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 277
Query: 1266 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSM 1323
IRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+
Sbjct: 278 IRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 337
Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
E+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 338 ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID 397
Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPSRYYKLKIFLE 1428
+HTLEEVG F VTRERIRQIE KALRKL+ H SR KL+ FL+
Sbjct: 398 GREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 443
Score = 279 bits (714), Expect = 7e-75, Method: Compositional matrix adjust.
Identities = 147/272 (54%), Positives = 196/272 (72%), Gaps = 6/272 (2%)
Query: 357 CRNIPSIKE-LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 415
R+IP +KE L K + +I L L +++ + + A++ + EANLRLV+S
Sbjct: 161 VRHIPGLKETLDPKTVE---EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS 217
Query: 416 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 475
IAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQART
Sbjct: 218 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 277
Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSM 533
IRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+
Sbjct: 278 IRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 337
Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
E+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 338 ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLID 397
Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
+HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 398 GREHTLEEVGAFFGVTRERIRQIENKALRKLK 429
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 223 bits (569), Expect = 5e-58, Method: Compositional matrix adjust.
Identities = 127/342 (37%), Positives = 190/342 (55%), Gaps = 22/342 (6%)
Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSX 207
+GEI+IAKRIE+G+ + +++ P I +L +++ E ++ +++ G +D N
Sbjct: 5 EGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEED 64
Query: 208 XXXXXXXXXXXXXXXXXXXXXADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRK 259
+ + + + + KF+ + + R
Sbjct: 65 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRD 124
Query: 260 AFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQ 312
+ +G ++H E+L + R K + L +++R +++V E+
Sbjct: 125 TIKAKG-------RSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERL 177
Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 372
I+++ V +C MP+ +FI +F NE + W + + ++ L + QKL
Sbjct: 178 IMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQ 237
Query: 373 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 432
++ + L + ++DINR+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 238 IEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297
Query: 433 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 474
EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR
Sbjct: 298 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 339
Score = 223 bits (569), Expect = 5e-58, Method: Compositional matrix adjust.
Identities = 127/342 (37%), Positives = 190/342 (55%), Gaps = 22/342 (6%)
Query: 938 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSX 997
+GEI+IAKRIE+G+ + +++ P I +L +++ E ++ +++ G +D N
Sbjct: 5 EGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEED 64
Query: 998 XXXXXXXXXXXXXXXXXXXXXADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRK 1049
+ + + + + KF+ + + R
Sbjct: 65 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRD 124
Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
+ +G ++H E+L + R K + L +++R +++V E+
Sbjct: 125 TIKAKG-------RSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERL 177
Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
I+++ V +C MP+ +FI +F NE + W + + ++ L + QKL
Sbjct: 178 IMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQ 237
Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
++ + L + ++DINR+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 238 IEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297
Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 1264
EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR
Sbjct: 298 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 339
>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 = 185 bits (469), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 89/135 (65%), Positives = 110/135 (81%), Gaps = 2/135 (1%)
Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWW
Sbjct: 107 ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWW 166
Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEE 518
IRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA M +
Sbjct: 167 IRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAK 226
Query: 519 KIRKIMKIAKEPVSM 533
++ + +KIA+EPVS+
Sbjct: 227 RVEETLKIAQEPVSL 241
Score = 185 bits (469), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 89/135 (65%), Positives = 110/135 (81%), Gaps = 2/135 (1%)
Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWW
Sbjct: 107 ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWW 166
Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEE 1308
IRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA M +
Sbjct: 167 IRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAK 226
Query: 1309 KIRKIMKIAKEPVSM 1323
++ + +KIA+EPVS+
Sbjct: 227 RVEETLKIAQEPVSL 241
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 27/34 (79%)
Query: 128 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
T DP++ Y+ E+G V LLT + EI++A+++EEG+
Sbjct: 1 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGM 34
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 27/34 (79%)
Query: 918 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
T DP++ Y+ E+G V LLT + EI++A+++EEG+
Sbjct: 1 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGM 34
>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 = 184 bits (468), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 89/135 (65%), Positives = 110/135 (81%), Gaps = 2/135 (1%)
Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWW
Sbjct: 111 ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWW 170
Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEE 518
IRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA M +
Sbjct: 171 IRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAK 230
Query: 519 KIRKIMKIAKEPVSM 533
++ + +KIA+EPVS+
Sbjct: 231 RVEETLKIAQEPVSL 245
Score = 184 bits (468), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 89/135 (65%), Positives = 110/135 (81%), Gaps = 2/135 (1%)
Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWW
Sbjct: 111 ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWW 170
Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEE 1308
IRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA M +
Sbjct: 171 IRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAK 230
Query: 1309 KIRKIMKIAKEPVSM 1323
++ + +KIA+EPVS+
Sbjct: 231 RVEETLKIAQEPVSL 245
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 27/34 (79%)
Query: 128 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
T DP++ Y+ E+G V LLT + EI++A+++EEG+
Sbjct: 5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGM 38
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 27/34 (79%)
Query: 918 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
T DP++ Y+ E+G V LLT + EI++A+++EEG+
Sbjct: 5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGM 38
>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 = 122 bits (307), Expect = 1e-27, Method: Composition-based stats.
Identities = 57/78 (73%), Positives = 68/78 (87%)
Query: 397 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456
+ A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+RG+ FSTY
Sbjct: 102 EGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTY 161
Query: 457 ATWWIRQAITRSIADQAR 474
ATWWIRQAI R+IADQAR
Sbjct: 162 ATWWIRQAINRAIADQAR 179
Score = 122 bits (307), Expect = 1e-27, Method: Composition-based stats.
Identities = 57/78 (73%), Positives = 68/78 (87%)
Query: 1187 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246
+ A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+RG+ FSTY
Sbjct: 102 EGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTY 161
Query: 1247 ATWWIRQAITRSIADQAR 1264
ATWWIRQAI R+IADQAR
Sbjct: 162 ATWWIRQAINRAIADQAR 179
Score = 30.4 bits (67), Expect = 6.9, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 130 DPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
DP++ Y+ E+G V L + E+ A ++EEG++
Sbjct: 2 DPVRQYLHEIGEVLELDKWAELGAAAKVEEGME 34
Score = 30.4 bits (67), Expect = 6.9, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 920 DPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
DP++ Y+ E+G V L + E+ A ++EEG++
Sbjct: 2 DPVRQYLHEIGEVLELDKWAELGAAAKVEEGME 34
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 117 bits (294), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 56/80 (70%), Positives = 67/80 (83%)
Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
D+A S+R+ D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEA
Sbjct: 1 DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 60
Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
KALRKLRHPSR L+ FL+
Sbjct: 61 KALRKLRHPSRSEVLRSFLD 80
Score = 103 bits (256), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 49/67 (73%), Positives = 58/67 (86%)
Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
D+A S+R+ D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEA
Sbjct: 1 DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 60
Query: 619 KALRKLR 625
KALRKLR
Sbjct: 61 KALRKLR 67
>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 = 114 bits (285), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 54/76 (71%), Positives = 64/76 (84%)
Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
D+A S+R+ D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEA
Sbjct: 2 DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 61
Query: 1409 KALRKLRHPSRYYKLK 1424
KALRKLRHPSR L+
Sbjct: 62 KALRKLRHPSRSEVLR 77
Score = 103 bits (258), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 49/67 (73%), Positives = 58/67 (86%)
Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
D+A S+R+ D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEA
Sbjct: 2 DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 61
Query: 619 KALRKLR 625
KALRKLR
Sbjct: 62 KALRKLR 68
>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 = 108 bits (270), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 52/67 (77%), Positives = 60/67 (89%)
Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 1 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60
Query: 1422 KLKIFLE 1428
L+ FL+
Sbjct: 61 VLRSFLD 67
Score = 94.4 bits (233), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 45/54 (83%), Positives = 51/54 (94%)
Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 1 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 54
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 93.6 bits (231), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 46/73 (63%), Positives = 58/73 (79%)
Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
M+ ++D+L++LT RE VLR+RFG++ TLEEVGK F VTRERIRQIEAKALRKLR
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 1416 HPSRYYKLKIFLE 1428
HPSR +LK F++
Sbjct: 61 HPSRSKRLKDFMD 73
Score = 77.8 bits (190), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 39/60 (65%), Positives = 48/60 (80%)
Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
M+ ++D+L++LT RE VLR+RFG++ TLEEVGK F VTRERIRQIEAKALRKLR
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 88.6 bits (218), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 45/77 (58%), Positives = 56/77 (72%)
Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
A+ MR ++ +L +L+PRE+ VLRMR+G+ TLEEVG+ F+VTRERIRQIE KA
Sbjct: 3 AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62
Query: 1411 LRKLRHPSRYYKLKIFL 1427
LRKLRHPSR LK L
Sbjct: 63 LRKLRHPSRSKYLKSLL 79
Score = 76.6 bits (187), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 38/65 (58%), Positives = 49/65 (75%)
Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
A+ MR ++ +L +L+PRE+ VLRMR+G+ TLEEVG+ F+VTRERIRQIE KA
Sbjct: 3 AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62
Query: 621 LRKLR 625
LRKLR
Sbjct: 63 LRKLR 67
>pdb|3B39|A Chain A, Structure Of The Dnag Primase Catalytic Domain Bound To
Ssdna
pdb|3B39|B Chain B, Structure Of The Dnag Primase Catalytic Domain Bound To
Ssdna
Length = 322
Score = 87.4 bits (215), Expect = 5e-17, Method: Composition-based stats.
Identities = 48/145 (33%), Positives = 71/145 (48%), Gaps = 25/145 (17%)
Query: 692 GISGFLLTTPDPVH----ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQF 747
G G +L P + ET +FHK +LYGL+EA+ + +L+ EGYMDV+ L+Q+
Sbjct: 110 GFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQY 169
Query: 748 GF---------------------FANSSYTCFDGDQXXXXXXXXXLEVCLLYATDDKIIK 786
G N+ C+DGD+ LE L Y TD + ++
Sbjct: 170 GINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWCALETALPYMTDGRQLR 229
Query: 787 FLFLPDKYDPDSYIRKFGYKIFSKK 811
F+FLPD DPD+ +RK G + F +
Sbjct: 230 FMFLPDGEDPDTLVRKEGKEAFEAR 254
>pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core
pdb|1DDE|A Chain A, Structure Of The Dnag Catalytic Core
Length = 338
Score = 87.4 bits (215), Expect = 5e-17, Method: Composition-based stats.
Identities = 48/145 (33%), Positives = 71/145 (48%), Gaps = 25/145 (17%)
Query: 692 GISGFLLTTPDPVH----ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQF 747
G G +L P + ET +FHK +LYGL+EA+ + +L+ EGYMDV+ L+Q+
Sbjct: 122 GFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQY 181
Query: 748 GF---------------------FANSSYTCFDGDQXXXXXXXXXLEVCLLYATDDKIIK 786
G N+ C+DGD+ LE L Y TD + ++
Sbjct: 182 GINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLR 241
Query: 787 FLFLPDKYDPDSYIRKFGYKIFSKK 811
F+FLPD DPD+ +RK G + F +
Sbjct: 242 FMFLPDGEDPDTLVRKEGKEAFEAR 266
>pdb|1EQN|A Chain A, E.Coli Primase Catalytic Core
pdb|1EQN|B Chain B, E.Coli Primase Catalytic Core
pdb|1EQN|C Chain C, E.Coli Primase Catalytic Core
pdb|1EQN|D Chain D, E.Coli Primase Catalytic Core
pdb|1EQN|E Chain E, E.Coli Primase Catalytic Core
Length = 321
Score = 84.3 bits (207), Expect = 4e-16, Method: Composition-based stats.
Identities = 47/145 (32%), Positives = 69/145 (47%), Gaps = 25/145 (17%)
Query: 692 GISGFLLTTPDPVH----ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQF 747
G G +L P + ET +FHK +LYGL+EA+ + +L+ EGY DV+ L+Q+
Sbjct: 109 GFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYXDVVALAQY 168
Query: 748 GF---------------------FANSSYTCFDGDQXXXXXXXXXLEVCLLYATDDKIIK 786
G N+ C+DGD+ LE L Y TD + ++
Sbjct: 169 GINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYXTDGRQLR 228
Query: 787 FLFLPDKYDPDSYIRKFGYKIFSKK 811
F FLPD DPD+ +RK G + F +
Sbjct: 229 FXFLPDGEDPDTLVRKEGKEAFEAR 253
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 82.4 bits (202), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 68/248 (27%), Positives = 128/248 (51%), Gaps = 15/248 (6%)
Query: 380 PLND--LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
P+ D ++++ R+ G+ +AR E+ E N+RLV S+ +++ +RG + DL Q G IG
Sbjct: 9 PIKDQEMKELIRRSQEGDQEARD---EIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIG 65
Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
L+K+VDKF+ KFSTYA I I R + D T+++ + E NKI + ++
Sbjct: 66 LLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELS 124
Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
+ G P + IA + + E + + + P S+ V +++ GD I + +A
Sbjct: 125 KTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYEND----GDPITLLDQIAD 180
Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
+D A + + +K + L RE ++ +R+ D T EV + +++ ++ ++E
Sbjct: 181 ADEA-SWFDKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLE 235
Query: 618 AKALRKLR 625
K L+ ++
Sbjct: 236 KKILQHIK 243
Score = 82.4 bits (202), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 68/248 (27%), Positives = 128/248 (51%), Gaps = 15/248 (6%)
Query: 1170 PLND--LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
P+ D ++++ R+ G+ +AR E+ E N+RLV S+ +++ +RG + DL Q G IG
Sbjct: 9 PIKDQEMKELIRRSQEGDQEARD---EIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIG 65
Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
L+K+VDKF+ KFSTYA I I R + D T+++ + E NKI + ++
Sbjct: 66 LLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELS 124
Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
+ G P + IA + + E + + + P S+ V +++ GD I + +A
Sbjct: 125 KTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYEND----GDPITLLDQIAD 180
Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
+D A + + +K + L RE ++ +R+ D T EV + +++ ++ ++E
Sbjct: 181 ADEA-SWFDKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLE 235
Query: 1408 AKALRKLR 1415
K L+ ++
Sbjct: 236 KKILQHIK 243
>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 = 82.0 bits (201), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 43/65 (66%), Positives = 50/65 (76%)
Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
L+ L+ RE+ VL+MR G+ +HTLEEVG F VTRERIRQIE KALRKLRHPSR KL
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKL 67
Query: 1424 KIFLE 1428
+ FLE
Sbjct: 68 RDFLE 72
Score = 64.3 bits (155), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 34/52 (65%), Positives = 40/52 (76%)
Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
L+ L+ RE+ VL+MR G+ +HTLEEVG F VTRERIRQIE KALRKLR
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLR 59
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 79.7 bits (195), Expect = 1e-14, Method: Composition-based stats.
Identities = 41/62 (66%), Positives = 50/62 (80%)
Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
M+ ++D+L++LT RE VLR+RFG++ TLEEVGK F VTRERIRQIEAKALRKLR
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 1416 HP 1417
HP
Sbjct: 61 HP 62
Score = 74.3 bits (181), Expect = 5e-13, Method: Composition-based stats.
Identities = 39/60 (65%), Positives = 48/60 (80%)
Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
M+ ++D+L++LT RE VLR+RFG++ TLEEVGK F VTRERIRQIEAKALRKLR
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
>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 = 72.4 bits (176), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 41/66 (62%), Positives = 49/66 (74%), Gaps = 1/66 (1%)
Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPSRYYK 1422
L+ L+ RE+ VL+MR G+ +HTLEEVG F VTRERIRQIE KALRKL+ H SR K
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRK 67
Query: 1423 LKIFLE 1428
L+ FLE
Sbjct: 68 LRDFLE 73
Score = 63.2 bits (152), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/52 (63%), Positives = 40/52 (76%)
Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
L+ L+ RE+ VL+MR G+ +HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>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 = 71.2 bits (173), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 40/66 (60%), Positives = 49/66 (74%), Gaps = 1/66 (1%)
Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPSRYYK 1422
L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE KALRKL+ H SR K
Sbjct: 8 LSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRK 67
Query: 1423 LKIFLE 1428
L+ FLE
Sbjct: 68 LRDFLE 73
Score = 61.6 bits (148), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/52 (61%), Positives = 40/52 (76%)
Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 8 LSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59
>pdb|2AU3|A Chain A, Crystal Structure Of The Aquifex Aeolicus Primase (Zinc
Binding And Rna Polymerase Domains)
Length = 407
Score = 53.5 bits (127), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 34/166 (20%)
Query: 698 LTTPDPVHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF-------- 749
+ +PD + +F K L+GL+EAK I + G+ ++ EGY D++ L G
Sbjct: 217 INSPD----SRVFKKGENLFGLYEAKEYIKEEGFAILVEGYFDLLRLFSEGIRNVVAPLG 272
Query: 750 -------------FANSSYTCFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDP 796
F Y +DGD + + L + + ++LP+ YDP
Sbjct: 273 TALTQNQANLLSKFTKKVYILYDGDDAGRKAMKSAIPLLLSAGVE---VYPVYLPEGYDP 329
Query: 797 DSYIRKFGYK-----IFSKKNAFSFDIKSNSREEIENLRKKFKILI 837
D +I++FG + I S F IK+ +RE +E ++F+ +
Sbjct: 330 DEFIKEFGKEELRRLINSSGELFETLIKT-ARENLEEKTREFRYYL 374
>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 = 2e-06, Method: Compositional matrix adjust.
Identities = 61/234 (26%), Positives = 109/234 (46%), Gaps = 27/234 (11%)
Query: 410 LRLVISIA---KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI- 465
L LV +IA KK+ + DLI G IGL+KAVD + Y I+ AI
Sbjct: 22 LPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIY 81
Query: 466 --TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523
RS+ +R +R E +I + ++ ++ G EP +A ++ + E++ K
Sbjct: 82 DYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKT 135
Query: 524 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS-----DAALNASMRSVVKDILNSLT 578
+ + ++ + +E DF D + L PS + + + VK+ ++ L
Sbjct: 136 L----DKINFSYILSLEE--VFRDFARDYSELIPSSTNVEEEVIKRELTEKVKEAVSKLP 189
Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWL 632
RE V+++ F E+ + +EV K + + R+ Q++AKAL +LR + + L
Sbjct: 190 EREKLVIQLIFYEELPA----KEVAKILETSVSRVSQLKAKALERLREMLSNPL 239
Score = 52.0 bits (123), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 60/228 (26%), Positives = 106/228 (46%), Gaps = 27/228 (11%)
Query: 1200 LRLVISIA---KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI- 1255
L LV +IA KK+ + DLI G IGL+KAVD + Y I+ AI
Sbjct: 22 LPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIY 81
Query: 1256 --TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
RS+ +R +R E +I + ++ ++ G EP +A ++ + E++ K
Sbjct: 82 DYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKT 135
Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS-----DAALNASMRSVVKDILNSLT 1368
+ + ++ + +E DF D + L PS + + + VK+ ++ L
Sbjct: 136 L----DKINFSYILSLEE--VFRDFARDYSELIPSSTNVEEEVIKRELTEKVKEAVSKLP 189
Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
RE V+++ F E+ + +EV K + + R+ Q++AKAL +LR
Sbjct: 190 EREKLVIQLIFYEELPA----KEVAKILETSVSRVSQLKAKALERLRE 233
>pdb|4E2K|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
pdb|4EDG|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Atp And Manganese
pdb|4EDK|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Gtp And Manganese
pdb|4EDR|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Utp And Manganese
pdb|4EDT|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ppgpp And Manganese
pdb|4EDV|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Pppgpp And Manganese
pdb|4EE1|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ctp And Manganese
Length = 329
Score = 42.7 bits (99), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 39/143 (27%), Positives = 57/143 (39%), Gaps = 28/143 (19%)
Query: 692 GISGFLLTTPDPVH----ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQF 747
G SG T +P + ETP+F K LY L +A+ +I K +++ EG+MDVI
Sbjct: 111 GYSGRTYTGQEPKYLNSPETPIFQKRKLLYNLDKARKSIRKLDEIVLLEGFMDVIKSDTA 170
Query: 748 GF---------------------FANSSYTCFDGDQXXXXXXXXXLEVCLLYATDDKIIK 786
G ++ FDGD + L + +I+
Sbjct: 171 GLKNVVATMGTQLSDEHITFIRKLTSNITLMFDGDFAGSEATLKTGQHLLQQGLNVFVIQ 230
Query: 787 FLFLPDKYDPDSYIRKFGYKIFS 809
LP DPD YI K+G F+
Sbjct: 231 ---LPSGMDPDEYIGKYGNDAFT 250
>pdb|4FQX|D Chain D, Crystal Structure Of Hla-Dm Bound To Hla-Dr1
pdb|4GBX|D Chain D, Crystal Structure Of An Immune Complex At Ph 6.5
Length = 199
Score = 31.2 bits (69), Expect = 4.5, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
+EN +APS+ + S+ +V+ LN +++ + R+R G++ + HT G D TR
Sbjct: 39 EENKMAPSEFGVLNSLANVLSQHLNQ---KDTLMQRLRNGLQNCATHTQPFWGSLTDRTR 95
Query: 1401 ERIRQIEAKALRKLRHP 1417
Q+ R P
Sbjct: 96 PPSVQVAKTTPFNTREP 112
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 0.135 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,956,444
Number of Sequences: 62578
Number of extensions: 1417425
Number of successful extensions: 4940
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 4822
Number of HSP's gapped (non-prelim): 94
length of query: 1432
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1321
effective length of database: 8,027,179
effective search space: 10603903459
effective search space used: 10603903459
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)