RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15215
(1432 letters)
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I,
activator, RNA polymeras holoenzyme, sigma70, open
complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli
k-12}
Length = 613
Score = 692 bits (1787), Expect = 0.0
Identities = 301/610 (49%), Positives = 411/610 (67%), Gaps = 8/610 (1%)
Query: 827 ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
+N + + K+L+ GKE+GYLT++E+ND LPEDI+D + IE II+ 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 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--------IDKNFSSNN 998
IE+G+ + +++ P I +L +++ E ++ +++ G + +
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182
Query: 999 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
+ +++E E D + + + 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 = 674 bits (1741), Expect = 0.0
Identities = 294/597 (49%), Positives = 402/597 (67%), Gaps = 8/597 (1%)
Query: 37 ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
+N + + K+L+ GKE+GYLT++E+ND LPEDI+D + IE II+ 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 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--------IDKNFSSNN 208
IE+G+ + +++ P I +L +++ E ++ +++ G + +
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182
Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
+ +++E E D + + + 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
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1
a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F*
2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
Length = 423
Score = 492 bits (1267), Expect = e-161
Identities = 158/345 (45%), Positives = 217/345 (62%), Gaps = 3/345 (0%)
Query: 1087 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 1146
D +R ++++ Q+ LE V + +EI D ++ L
Sbjct: 79 DPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGS 138
Query: 1147 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 1206
R + +I L L +++ + + A++ + EANLRLV+SI
Sbjct: 139 ARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSI 198
Query: 1207 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 1266
AKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQARTI
Sbjct: 199 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTI 258
Query: 1267 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSME 1324
RIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+E
Sbjct: 259 RIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE 318
Query: 1325 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMS 1384
+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 319 TPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDG 378
Query: 1385 SDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPSRYYKLKIFLE 1428
+HTLEEVG F VTRERIRQIE KALRKL+ H SR KL+ FL+
Sbjct: 379 REHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 423
Score = 477 bits (1230), Expect = e-156
Identities = 151/332 (45%), Positives = 208/332 (62%), Gaps = 2/332 (0%)
Query: 297 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 356
D +R ++++ Q+ LE V + +EI D ++ L
Sbjct: 79 DPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGS 138
Query: 357 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 416
R + +I L L +++ + + A++ + EANLRLV+SI
Sbjct: 139 ARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSI 198
Query: 417 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 476
AKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQARTI
Sbjct: 199 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTI 258
Query: 477 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSME 534
RIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EPVS+E
Sbjct: 259 RIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE 318
Query: 535 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMS 594
+P+GD++DS GDFI DE++ +P DAA + + ++ L+ L+ RE+ VL++R G+
Sbjct: 319 TPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDG 378
Query: 595 SDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626
+HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 379 REHTLEEVGAFFGVTRERIRQIENKALRKLKY 410
Score = 97.3 bits (242), Expect = 3e-21
Identities = 31/181 (17%), Positives = 65/181 (35%), Gaps = 4/181 (2%)
Query: 50 GKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDD 109
+R E + + E + + D+ + L+ + L L D
Sbjct: 3 KSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLALEDDLLDLPEEGEGLD 62
Query: 110 VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAIS 169
+EE E + T DP++ Y+ E+G V LLT + E+E+A+++EEG++ +
Sbjct: 63 LEEEEED----LPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSE 118
Query: 170 SCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSA 229
I ++ I + + + + K+ +E +
Sbjct: 119 ITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAR 178
Query: 230 D 230
+
Sbjct: 179 E 179
Score = 97.3 bits (242), Expect = 3e-21
Identities = 31/181 (17%), Positives = 65/181 (35%), Gaps = 4/181 (2%)
Query: 840 GKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDD 899
+R E + + E + + D+ + L+ + L L D
Sbjct: 3 KSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLALEDDLLDLPEEGEGLD 62
Query: 900 VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAIS 959
+EE E + T DP++ Y+ E+G V LLT + E+E+A+++EEG++ +
Sbjct: 63 LEEEEED----LPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSE 118
Query: 960 SCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSA 1019
I ++ I + + + + K+ +E +
Sbjct: 119 ITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAR 178
Query: 1020 D 1020
+
Sbjct: 179 E 179
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA
complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Length = 438
Score = 486 bits (1253), Expect = e-159
Identities = 165/440 (37%), Positives = 241/440 (54%), Gaps = 6/440 (1%)
Query: 992 KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 1051
K S + K + +E + +L + + E + + +
Sbjct: 2 KKSKSKKKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPL 61
Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
+ EG + + E + S D +R ++++ Q+ LE ++
Sbjct: 62 DLEGPLEADLLPEEGLLEEEEEELSLPKVSTS---DPVRQYLHEIGQVPLLTLEEEIDLA 118
Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
+ +E + ++ L R ++ ++ L
Sbjct: 119 RKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKL 178
Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
L ++ + + A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++A
Sbjct: 179 KSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRA 238
Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
V+KFEY+R +KFSTYATWWIRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G
Sbjct: 239 VEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELG 298
Query: 1292 SEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
EP IA M +++ + +KIA+EPVS+E+P+GD++DS GDFI DEN+ +P +
Sbjct: 299 REPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVE 358
Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
AA + + ++ L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE K
Sbjct: 359 AAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENK 418
Query: 1410 ALRKLR-HPSRYYKLKIFLE 1428
ALRKL+ H SR KL+ FLE
Sbjct: 419 ALRKLKYHESRTRKLRDFLE 438
Score = 473 bits (1218), Expect = e-154
Identities = 157/427 (36%), Positives = 232/427 (54%), Gaps = 5/427 (1%)
Query: 202 KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 261
K S + K + +E + +L + + E + + +
Sbjct: 2 KKSKSKKKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPL 61
Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
+ EG + + E + S D +R ++++ Q+ LE ++
Sbjct: 62 DLEGPLEADLLPEEGLLEEEEEELSLPKVSTS---DPVRQYLHEIGQVPLLTLEEEIDLA 118
Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
+ +E + ++ L R ++ ++ L
Sbjct: 119 RKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKL 178
Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
L ++ + + A++ + EANLRLV+SIAKKYT RGL FLDLIQEGN GL++A
Sbjct: 179 KSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRA 238
Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
V+KFEY+R +KFSTYATWWIRQAI R+IADQARTIRIPVHM+ETINK+SR +RQ+ QE G
Sbjct: 239 VEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELG 298
Query: 502 SEPDPSVIAIKM--EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
EP IA M +++ + +KIA+EPVS+E+P+GD++DS GDFI DEN+ +P +
Sbjct: 299 REPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVE 358
Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
AA + + ++ L+ L+ RE+ VL++R G+ +HTLEEVG F VTRERIRQIE K
Sbjct: 359 AAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENK 418
Query: 620 ALRKLRP 626
ALRKL+
Sbjct: 419 ALRKLKY 425
Score = 73.1 bits (179), Expect = 2e-13
Identities = 30/202 (14%), Positives = 70/202 (34%), Gaps = 15/202 (7%)
Query: 29 KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 88
K ++ + +++ K L + ++ + PE + +E +
Sbjct: 8 KKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPLDLEGPL 67
Query: 89 VSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 148
++ + + E E + T DP++ Y+ E+G V LLT +
Sbjct: 68 EADLLPE---------------EGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLE 112
Query: 149 GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 208
EI++A+++EEG++ + + I +I +I + +
Sbjct: 113 EEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE 172
Query: 209 RVIKGNKNNNEEKILIESSSAD 230
V K+ +E + +
Sbjct: 173 EVDGKLKSLPKELKRYLHIARE 194
Score = 73.1 bits (179), Expect = 2e-13
Identities = 30/202 (14%), Positives = 70/202 (34%), Gaps = 15/202 (7%)
Query: 819 KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
K ++ + +++ K L + ++ + PE + +E +
Sbjct: 8 KKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPLDLEGPL 67
Query: 879 VSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
++ + + E E + T DP++ Y+ E+G V LLT +
Sbjct: 68 EADLLPE---------------EGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLE 112
Query: 939 GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 998
EI++A+++EEG++ + + I +I +I + +
Sbjct: 113 EEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE 172
Query: 999 RVIKGNKNNNEEKILIESSSAD 1020
V K+ +E + +
Sbjct: 173 EVDGKLKSLPKELKRYLHIARE 194
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma
factor, transcription regulation; 2.60A {Escherichia
coli} SCOP: a.177.1.1
Length = 339
Score = 368 bits (945), Expect = e-116
Identities = 128/336 (38%), Positives = 194/336 (57%), Gaps = 8/336 (2%)
Query: 147 RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS 206
+GEI+IAKRIE+G+ + +++ P I +L +++ E ++ +++ G +D N
Sbjct: 4 MEGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEE 63
Query: 207 N--------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
+ + +++E E D + + + KF+ + + R
Sbjct: 64 DLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTR 123
Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
+ +G + + + +S R K + L +++R +++V E+ I+++ V
Sbjct: 124 DTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCV 183
Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
+C MP+ +FI +F NE + W + + ++ L + QKL ++ +
Sbjct: 184 EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETG 243
Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
L + ++DINR+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 244 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 303
Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 474
MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR
Sbjct: 304 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 339
Score = 368 bits (945), Expect = e-116
Identities = 128/336 (38%), Positives = 194/336 (57%), Gaps = 8/336 (2%)
Query: 937 RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS 996
+GEI+IAKRIE+G+ + +++ P I +L +++ E ++ +++ G +D N
Sbjct: 4 MEGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEE 63
Query: 997 N--------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
+ + +++E E D + + + KF+ + + R
Sbjct: 64 DLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTR 123
Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
+ +G + + + +S R K + L +++R +++V E+ I+++ V
Sbjct: 124 DTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCV 183
Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
+C MP+ +FI +F NE + W + + ++ L + QKL ++ +
Sbjct: 184 EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETG 243
Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
L + ++DINR+M GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 244 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 303
Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 1264
MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR
Sbjct: 304 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 339
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding;
HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP:
a.4.13.2
Length = 243
Score = 314 bits (808), Expect = 1e-98
Identities = 65/256 (25%), Positives = 127/256 (49%), Gaps = 17/256 (6%)
Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
++Q + +++++ R+ G+ +AR E+ E N+RLV S+ +++ +RG + DL
Sbjct: 3 HMQGQSPIKDQEMKELIRRSQEGDQEARD---EIIEKNMRLVWSVVQRFLNRGYEADDLF 59
Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
Q G IGL+K+VDKF+ KFSTYA I I R + D T+++ + E NKI +
Sbjct: 60 QIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRK 118
Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS--HLGDFI 549
++ + G P + IA + + E + + + P S+ V +++ L D I
Sbjct: 119 AKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQI 178
Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
D + + D + +K + L RE ++ +R+ + T EV + ++
Sbjct: 179 ADADEASWFD-------KIALKKAIEELDERERLIVYLRYYKDQ----TQSEVASRLGIS 227
Query: 610 RERIRQIEAKALRKLR 625
+ ++ ++E K L+ ++
Sbjct: 228 QVQMSRLEKKILQHIK 243
Score = 314 bits (808), Expect = 1e-98
Identities = 65/256 (25%), Positives = 127/256 (49%), Gaps = 17/256 (6%)
Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
++Q + +++++ R+ G+ +AR E+ E N+RLV S+ +++ +RG + DL
Sbjct: 3 HMQGQSPIKDQEMKELIRRSQEGDQEARD---EIIEKNMRLVWSVVQRFLNRGYEADDLF 59
Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
Q G IGL+K+VDKF+ KFSTYA I I R + D T+++ + E NKI +
Sbjct: 60 QIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRK 118
Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS--HLGDFI 1339
++ + G P + IA + + E + + + P S+ V +++ L D I
Sbjct: 119 AKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQI 178
Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
D + + D + +K + L RE ++ +R+ + T EV + ++
Sbjct: 179 ADADEASWFD-------KIALKKAIEELDERERLIVYLRYYKDQ----TQSEVASRLGIS 227
Query: 1400 RERIRQIEAKALRKLR 1415
+ ++ ++E K L+ ++
Sbjct: 228 QVQMSRLEKKILQHIK 243
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial
promoter opening, G-quartet, quadruplex, DNA binding;
2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A*
3les_A*
Length = 245
Score = 302 bits (774), Expect = 6e-94
Identities = 96/243 (39%), Positives = 143/243 (58%), Gaps = 10/243 (4%)
Query: 297 DTLRNQINQVTQIE----KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDY 352
D +R ++++ Q+ ++ +++ K K+ ++ + + +
Sbjct: 7 DPVRQYLHEIGQVPLLTLEEEIDLA-RKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 65
Query: 353 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 412
+ ++ ++ L L ++ + + A++ + EANLRL
Sbjct: 66 TARI---QKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 413 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472
V+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQ
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEP 530
ARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EP
Sbjct: 183 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 242
Query: 531 VSM 533
VS+
Sbjct: 243 VSL 245
Score = 302 bits (774), Expect = 6e-94
Identities = 96/243 (39%), Positives = 143/243 (58%), Gaps = 10/243 (4%)
Query: 1087 DTLRNQINQVTQIE----KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDY 1142
D +R ++++ Q+ ++ +++ K K+ ++ + + +
Sbjct: 7 DPVRQYLHEIGQVPLLTLEEEIDLA-RKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 65
Query: 1143 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 1202
+ ++ ++ L L ++ + + A++ + EANLRL
Sbjct: 66 TARI---QKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 1203 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 1262
V+SIAKKYT RGL FLDLIQEGN GL++AV+KFEY+R +KFSTYATWWIRQAI R+IADQ
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 1263 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM--EMPEEKIRKIMKIAKEP 1320
ARTIRIPVHM+ETINK+SR +RQ+ QE G EP IA M +++ + +KIA+EP
Sbjct: 183 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 242
Query: 1321 VSM 1323
VS+
Sbjct: 243 VSL 245
Score = 61.4 bits (149), Expect = 3e-10
Identities = 22/105 (20%), Positives = 44/105 (41%)
Query: 126 GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI 185
T DP++ Y+ E+G V LLT + EI++A+++EEG++ + + I
Sbjct: 3 HMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAK 62
Query: 186 SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD 230
+I +I + + V K+ +E + +
Sbjct: 63 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIARE 107
Score = 61.4 bits (149), Expect = 3e-10
Identities = 22/105 (20%), Positives = 44/105 (41%)
Query: 916 GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI 975
T DP++ Y+ E+G V LLT + EI++A+++EEG++ + + I
Sbjct: 3 HMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAK 62
Query: 976 SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD 1020
+I +I + + V K+ +E + +
Sbjct: 63 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIARE 107
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A
{Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1
PDB: 1sc5_A
Length = 239
Score = 210 bits (537), Expect = 7e-62
Identities = 57/240 (23%), Positives = 104/240 (43%), Gaps = 17/240 (7%)
Query: 399 RKAKREMTEANLRLVISIA---KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
+ + E+ L LV +IA KK+ + DLI G IGL+KAVD +
Sbjct: 11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEA 70
Query: 456 YATWWIRQAITRSIADQARTI-RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
Y I+ A I D R++ + E +I + ++ ++ G EP +A ++
Sbjct: 71 YIKLRIKGA----IYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELG 126
Query: 515 MPEEKIRKIMKIAKEP--VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
+ E++ K + +S+E D + N + + + VK+
Sbjct: 127 ISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTN---VEEEVIKRELTEKVKE 183
Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWL 632
++ L RE V+++ F E+ +EV K + + R+ Q++AKAL +LR + + L
Sbjct: 184 AVSKLPEREKLVIQLIFYEEL----PAKEVAKILETSVSRVSQLKAKALERLREMLSNPL 239
Score = 208 bits (532), Expect = 3e-61
Identities = 56/233 (24%), Positives = 101/233 (43%), Gaps = 17/233 (7%)
Query: 1189 RKAKREMTEANLRLVISIA---KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
+ + E+ L LV +IA KK+ + DLI G IGL+KAVD +
Sbjct: 11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEA 70
Query: 1246 YATWWIRQAITRSIADQARTI-RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
Y I+ A I D R++ + E +I + ++ ++ G EP +A ++
Sbjct: 71 YIKLRIKGA----IYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELG 126
Query: 1305 MPEEKIRKIMKIAKEP--VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
+ E++ K + +S+E D + N + + + VK+
Sbjct: 127 ISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTN---VEEEVIKRELTEKVKE 183
Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
++ L RE V+++ F E+ +EV K + + R+ Q++AKAL +LR
Sbjct: 184 AVSKLPEREKLVIQLIFYEEL----PAKEVAKILETSVSRVSQLKAKALERLR 232
>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit
beta; winged-helix motif, transcription activation,
DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B
Length = 99
Score = 147 bits (372), Expect = 1e-41
Identities = 55/84 (65%), Positives = 65/84 (77%)
Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
D+A S+R+ D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEA
Sbjct: 2 DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 61
Query: 1409 KALRKLRHPSRYYKLKIFLEGKKN 1432
KALRKLRHPSR L+ G
Sbjct: 62 KALRKLRHPSRSEVLRSGSSGSGT 85
Score = 126 bits (318), Expect = 2e-34
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
>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA
polymerase, replication protein, transferase; HET: DNA;
1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A*
1eqn_A* 3b39_A*
Length = 338
Score = 152 bits (387), Expect = 1e-40
Identities = 51/126 (40%), Positives = 71/126 (56%), Gaps = 21/126 (16%)
Query: 706 ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------- 749
ET +FHK +LYGL+EA+ + +L+ EGYMDV+ L+Q+G
Sbjct: 140 ETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHI 199
Query: 750 -----FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFG 804
N+ C+DGD+AGR AA RALE L Y TD + ++F+FLPD DPD+ +RK G
Sbjct: 200 QLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEG 259
Query: 805 YKIFSK 810
+ F
Sbjct: 260 KEAFEA 265
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix,
transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2
Length = 87
Score = 141 bits (357), Expect = 8e-40
Identities = 45/84 (53%), Positives = 56/84 (66%)
Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
A+ MR ++ +L +L+PRE+ VLRMR+G+ TLEEVG+ F+VTRERIRQIE
Sbjct: 1 KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV 60
Query: 1409 KALRKLRHPSRYYKLKIFLEGKKN 1432
KALRKLRHPSR LK L
Sbjct: 61 KALRKLRHPSRSKYLKSLLSLMDE 84
Score = 121 bits (305), Expect = 8e-33
Identities = 38/67 (56%), Positives = 49/67 (73%)
Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
A+ MR ++ +L +L+PRE+ VLRMR+G+ TLEEVG+ F+VTRERIRQIE
Sbjct: 1 KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV 60
Query: 619 KALRKLR 625
KALRKLR
Sbjct: 61 KALRKLR 67
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication,
transf; HET: DNA; 2.00A {Aquifex aeolicus}
Length = 407
Score = 148 bits (376), Expect = 2e-38
Identities = 42/160 (26%), Positives = 71/160 (44%), Gaps = 29/160 (18%)
Query: 706 ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------- 749
++ +F K L+GL+EAK I + G+ ++ EGY D++ L G
Sbjct: 221 DSRVFKKGENLFGLYEAKEYIKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQNQA 280
Query: 750 -----FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFG 804
F Y +DGD AGR+A + A+ + L + + ++LP+ YDPD +I++FG
Sbjct: 281 NLLSKFTKKVYILYDGDDAGRKAMKSAIPLLL---SAGVEVYPVYLPEGYDPDEFIKEFG 337
Query: 805 YKIFSK-----KNAFSFDIKSNSREEIENLRKKFKILIKL 839
+ + F IK+ E R+ L +
Sbjct: 338 KEELRRLINSSGELFETLIKTARENLEEKTREFRYYLGFI 377
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma
70, sigma 70 domain 4, transcription, regulation,
helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2
Length = 68
Score = 133 bits (338), Expect = 2e-37
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 = 115 bits (289), Expect = 9e-31
Identities = 45/54 (83%), Positives = 51/54 (94%)
Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
D+L LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 1 DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 54
>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside
polyph protein-ligand complex, transferase; HET: DNA
ATP; 2.00A {Staphylococcus aureus} PDB: 4edk_A* 4edr_A*
4edt_A* 4edv_A* 4ee1_A*
Length = 329
Score = 139 bits (352), Expect = 4e-36
Identities = 36/126 (28%), Positives = 52/126 (41%), Gaps = 24/126 (19%)
Query: 706 ETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------- 749
ETP+F K LY L +A+ +I K +++ EG+MDVI G
Sbjct: 129 ETPIFQKRKLLYNLDKARKSIRKLDEIVLLEGFMDVIKSDTAGLKNVVATMGTQLSDEHI 188
Query: 750 -----FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFG 804
++ FDGD AG A + + L + + LP DPD YI K+G
Sbjct: 189 TFIRKLTSNITLMFDGDFAGSEATLKTGQHLL---QQGLNVFVIQLPSGMDPDEYIGKYG 245
Query: 805 YKIFSK 810
F+
Sbjct: 246 NDAFTT 251
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus
aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*
Length = 73
Score = 126 bits (318), Expect = 1e-34
Identities = 41/70 (58%), Positives = 51/70 (72%), Gaps = 1/70 (1%)
Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-HPS 1418
++ L+ L+ RE+ VL+MR G+ +HTLEEVG F VTRERIRQIE KALRKL+ H S
Sbjct: 4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHES 63
Query: 1419 RYYKLKIFLE 1428
R KL+ FLE
Sbjct: 64 RTRKLRDFLE 73
Score = 112 bits (282), Expect = 8e-30
Identities = 33/57 (57%), Positives = 42/57 (73%)
Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626
++ L+ L+ RE+ VL+MR G+ +HTLEEVG F VTRERIRQIE KALRKL+
Sbjct: 4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 60
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 92.6 bits (229), Expect = 5e-19
Identities = 108/706 (15%), Positives = 207/706 (29%), Gaps = 191/706 (27%)
Query: 138 EMGSVELLTRDGEIEIAKRIEEGL-KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 196
E G + +D I E+ + C + ++ + +SK EI D I
Sbjct: 10 ETGEHQYQYKD----ILSVFEDAFVDNF-----DC-KDVQDMPKSI--LSKEEI--DHI- 54
Query: 197 DGLIDKNFSSNNRVIKG---NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 253
++ K+ S + +K + +E E L N F
Sbjct: 55 --IMSKDAVSGTLRLFWTLLSKQEEMVQKFVE--------EVLRI----------NYKFL 94
Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSI--EKLCDTLRNQINQVTQIEK 311
++ + + YI+ + + N+ F ++ + LR + ++ +
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYND--NQVFAKYNVSRLQPYLKLRQALLELRPAKN 152
Query: 312 QILEIVVNKCGMP------------RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 359
+++ G+ + ++ + +I W+ NL C +
Sbjct: 153 ----VLI--DGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WL----------NLKNCNS 194
Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
++ E+ Q L I D + + + R RL+ S K
Sbjct: 195 PETVLEMLQ---KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR-------RLLKS--KP 242
Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYR-RGYKFSTYATWWIRQAITR--SIADQ---A 473
Y L L +Q + F + T TR + D A
Sbjct: 243 YE-NCLLVLLNVQNAKA-----WNAFNLSCK-----ILLT-------TRFKQVTDFLSAA 284
Query: 474 RTIRIPV-HMIETINKISRISRQILQETGSEPDPSVIAIKM-EMPEEKIRKIMKIAKEPV 531
T I + H T+ + +L + + ++P E + +
Sbjct: 285 TTTHISLDHHSMTLTP--DEVKSLLL--------KYLDCRPQDLPRE-VLTTNPRR---L 330
Query: 532 SMESPVGDDEDSHLGDFIEDE-NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
S+ + + I D + ++++ LN L P E + + R
Sbjct: 331 SI-----------IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379
Query: 591 IEMSSD-----HTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQRTH----QNEK 641
+ L + FDV + + + K L K + E E
Sbjct: 380 V-FPPSAHIPTILLSLI--WFDVIKSDVMVVVNK-LHKYSLVEKQPKESTISIPSIYLEL 435
Query: 642 IIACSSDSSNHNEHVTNNNFPPGFNIFHKLLRILQEYLESFLISFFLRNHGISGFLLTTP 701
+ ++ + H V + N P F+ + L +Y S + G L
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI-----------GHHLKNI 484
Query: 702 DPVHETPLFHKSNELY---GLFEAKNAIGKSGYVLITEGYM-DVIGLSQFGFFANSSYTC 757
+ LF ++ E K I G + + L Q F+ Y C
Sbjct: 485 EHPERMTLF---RMVFLDFRFLEQK--IRHDSTAWNASGSILNT--LQQLKFY--KPYIC 535
Query: 758 FDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 803
D D R L+ A I+ FL K + + K+
Sbjct: 536 -DNDPKYER---------LVNA----ILDFLP---KIEENLICSKY 564
Score = 88.4 bits (218), Expect = 1e-17
Identities = 107/809 (13%), Positives = 228/809 (28%), Gaps = 287/809 (35%)
Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
F+++ + D + + + I+ S S LR+ F +S EE+ ++F
Sbjct: 28 AFVDNFDCKDVQDMPKSILSKEEIDHIIMS-KDAVSGTLRL-FWTLLSKQ---EEMVQKF 82
Query: 607 DVTRERIRQIEAKALRKLRPLAHDWLEQRTHQNEKIIACSSDSSNHNEHVT---NNN--F 661
+E + LR + +L ++ S + + E N+N F
Sbjct: 83 ---------VE-EVLRI----NYKFLMSPIKTEQR--QPSMMTRMYIEQRDRLYNDNQVF 126
Query: 662 PPGFNIFHKLLRILQEYLESFLISFFLRN------HGISGFLLTTPDPVHETPLFHKSNE 715
+ L++ L LR G+ G
Sbjct: 127 AKYNVSRLQPYLKLRQALLE------LRPAKNVLIDGVLGS------------------- 161
Query: 716 LYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF------FANSSYTCFDGDQAGRRAAR 769
GK+ + + + + F N +
Sbjct: 162 -----------GKT--WVALDVCLSYKVQCKMDFKIFWLNLKNCN--------------- 193
Query: 770 RALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKNAFSFDIKSNSREEIENL 829
+ + +++ L +K Y+I + S D SN + I ++
Sbjct: 194 ----------SPETVLEML------------QKLLYQIDPNWTSRS-DHSSNIKLRIHSI 230
Query: 830 RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
+ + + L+K + Y N L ++ + F ++S + L
Sbjct: 231 QAELRRLLK---SKPY-----ENCLL---VLLNVQNAKAWNAF---NLSC-------KIL 269
Query: 890 MLSNITSD----DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
+ T D + AT +S T D E LL K
Sbjct: 270 L---TTRFKQVTDFLSAATTTHISLDHHSMTLTPD-------E--VKSLL--------LK 309
Query: 946 RIEEGLKDMIHAISSC-PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
++ +D+ + + P + +IA I D N+
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLS--IIAE-SIRDGLATWD---------NW---------- 347
Query: 1005 KNNNEEKI--LIESSSADLSTEQLEKLKYESL-IKFSNISFHFDKMRKAFEKEGYNSESY 1061
K+ N +K+ +IESS L + K+ ++ L + F
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKM-FDRLSV---------------FPP-------- 383
Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
+I +L + + + K + +VVNK L
Sbjct: 384 ---SAHIPTILLSLIWF-------------------DVIKSDVMVVVNKLHKYSL----- 416
Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN-LQTDIVLPLNDLRDINRK 1180
+ ++ I L L + + L + +++ +DL
Sbjct: 417 -----VEKQPKESTISI-PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLD 470
Query: 1181 M-----IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD--LIQEG-----NIGL 1228
I +K E E + + D +FL+ + + + +
Sbjct: 471 QYFYSHIGHHLK----NIEHPE----RMTLFRMVFLD--FRFLEQKIRHDSTAWNASGSI 520
Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ--I 1286
+ + + ++ + Y I + R + + + I + S+ +
Sbjct: 521 LNTLQQLKFYKPY-------------ICDNDPKYERLVNAILDFLPKIEENLICSKYTDL 567
Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMK 1315
L+ D ++ EE +++ +
Sbjct: 568 LRIALMAEDEAIF-------EEAHKQVQR 589
Score = 73.0 bits (178), Expect = 6e-13
Identities = 79/542 (14%), Positives = 160/542 (29%), Gaps = 150/542 (27%)
Query: 928 EMGSVELLTRDGEIEIAKRIEEGL-KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
E G + +D I E+ + C + ++ + +SK EI D I
Sbjct: 10 ETGEHQYQYKD----ILSVFEDAFVDNF-----DC-KDVQDMPKSI--LSKEEI--DHI- 54
Query: 987 DGLIDKNFSSNNRVIKG---NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
++ K+ S + +K + +E E L N F
Sbjct: 55 --IMSKDAVSGTLRLFWTLLSKQEEMVQKFVE--------EVLRI----------NYKFL 94
Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSI--EKLCDTLRNQINQVTQIEK 1101
++ + + YI+ + + N+ F ++ + LR + ++ +
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYND--NQVFAKYNVSRLQPYLKLRQALLELRPAKN 152
Query: 1102 QILEIVVNKCGMP------------RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
+++ G+ + ++ + +I W+ NL C +
Sbjct: 153 ----VLI--DGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WL----------NLKNCNS 194
Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
++ E+ Q L I D + + + R RL+ S K
Sbjct: 195 PETVLEMLQ---KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR-------RLLKS--KP 242
Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYR-RGYKFSTYATWWIRQAITR--SIADQ---A 1263
Y L L +Q + F + T TR + D A
Sbjct: 243 YE-NCLLVLLNVQNAKA-----WNAFNLSCK-----ILLT-------TRFKQVTDFLSAA 284
Query: 1264 RTIRIPV-HMIETINKISRISRQILQETGSEPDPSVIAIKM-EMPEEKIRKIMKIAKEPV 1321
T I + H T+ + +L + + ++P E + +
Sbjct: 285 TTTHISLDHHSMTLTP--DEVKSLLL--------KYLDCRPQDLPRE-VLTTNPRR---L 330
Query: 1322 SMESPVGDDEDSHLGDFIEDE-NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 1380
S+ + + I D + ++++ LN L P E + + R
Sbjct: 331 SI-----------IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379
Query: 1381 IEMSSD-----HTLEEVGKQFDVTRERIRQIEAKALRKL---RHP--SRYYKLKIFLEGK 1430
+ L + FDV + + + K + + P S I+LE K
Sbjct: 380 V-FPPSAHIPTILLSLI--WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELK 436
Query: 1431 KN 1432
Sbjct: 437 VK 438
Score = 69.9 bits (170), Expect = 5e-12
Identities = 87/632 (13%), Positives = 188/632 (29%), Gaps = 157/632 (24%)
Query: 874 YMDISVSEHVL---DTETLMLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMR 927
+MD EH D ++ + DV++ ++ LS + D I
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEID-----HIIMSKDA 60
Query: 928 EMGSVELLT--RDGEIEIAKR-IEEGLK-------DMIHAISSCPTTIMEILIAADKISK 977
G++ L + E+ ++ +EE L+ I P+ + + I
Sbjct: 61 VSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ----- 115
Query: 978 NEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKF 1037
D+ ++ N K N + + + + + L +L+
Sbjct: 116 ------------RDRLYNDNQVFAKYNVSRLQPYLKL--------RQALLELRPA----- 150
Query: 1038 SNISFHFDKMRKAFEK-----EGYNSESYIKAHNN----ISNEMLGIRFTAKSI----EK 1084
N+ + K + S + ++ L + +++ +K
Sbjct: 151 KNVLID--GV-LGSGKTWVALDVCLSYKVQCKMDFKIFWLN---LKNCNSPETVLEMLQK 204
Query: 1085 LCDTLR-NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH-DY 1142
L + N ++ L I + + RL K + + L V N +
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL 264
Query: 1143 N---LILCRNIP---SIKELQQKLINL-QTDIVLPLNDLRDINRKMIAGEMKARKAKREM 1195
+ L+ R + I+L + L ++++ + K + + + + RE+
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL--DCRPQDLPREV 322
Query: 1196 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF-------EYRRGYK----F- 1243
N R + IA+ D + + L ++ EYR+ + F
Sbjct: 323 LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP 382
Query: 1244 -------STYATWW-----------IRQAITRSIADQ---ARTIRIP---VHMIETINKI 1279
+ W + + S+ ++ TI IP + + +
Sbjct: 383 PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE 442
Query: 1280 SRISRQILQ--------ETGSEPDPSV-------IA---IKMEMPEEK--IRKIM----- 1314
+ R I+ ++ P + I +E PE R +
Sbjct: 443 YALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRF 502
Query: 1315 ---KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 1371
KI + + + L + + +D +V IL+ L E
Sbjct: 503 LEQKIRHDSTAWNASGSILNT--LQQLKFYKPYICDNDPKYER----LVNAILDFLPKIE 556
Query: 1372 SKVLR------MRFGIEMSSDHTLEEVGKQFD 1397
++ +R + + EE KQ
Sbjct: 557 ENLICSKYTDLLRIALMAEDEAIFEEAHKQVQ 588
Score = 57.2 bits (137), Expect = 4e-08
Identities = 76/479 (15%), Positives = 146/479 (30%), Gaps = 159/479 (33%)
Query: 6 KKTKIKNKKTKETLL-------KNAF-SFDIKSNSREEIENLRKKFKILIKLGKERGYLT 57
+ +K+K + LL A+ +F++ KIL+ T
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC-------------KILL--------TT 272
Query: 58 -FSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS--NITSDDDVEEAT 114
F ++ DFL H ++ T + + ++L+L + D E
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTL-------TPD--EVKSLLLKYLDCRPQDLPREVL 323
Query: 115 EA---ALSTV---DSDFGRTKDPIKMY-------MREMGSVELLTRDGEIEIAKRIEEGL 161
LS + D T D K + E S+ +L E K
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES-SLNVLEPA---EYRKM----F 375
Query: 162 KDMIHAI----SSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
+ ++ + PT ++ ++ + + +V+ L ++ K
Sbjct: 376 DRL--SVFPPSAHIPTILLSLIWFDVI----KSDVMVVVNKLHKY------SLV--EKQP 421
Query: 218 NEEKILIESSSADLSTEQLEKLK-YESLIKFSNI--SFHFDKMRKAFEKEGYNSESYIKA 274
E I I S +L + + + S++ NI +F D + + + Y S+I
Sbjct: 422 KESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL-DQY-FYSHIGH 479
Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
H K+IE E+ L F VF
Sbjct: 480 H-------------LKNIE--------------HPERMTL-------------FRMVF-- 497
Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
++ +++ KI+HD ++N L L+ + I
Sbjct: 498 --LDFRFLEQ--KIRHDSTAWNASG---------SILNT-------LQQLK-FYKPYIC- 535
Query: 395 EMKARKAKREMTEANLRLVISIAKK-YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
+ A L + I + + + DL++ I LM D+ + +K
Sbjct: 536 --DNDPKYERLVNAILDFLPKIEENLICSK---YTDLLR---IALMAE-DEAIFEEAHK 585
>2k6x_A Sigma-A, RNA polymerase sigma factor RPOD; DNA-binding,
transcription, transcription regulation; NMR {Thermotoga
maritima}
Length = 72
Score = 66.7 bits (163), Expect = 1e-13
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 36 IENLRKKFKILIKLGKERGYLTFSEINDFLPEDI--IDHEIIESIIKTFRYMDISVSEHV 93
+ + ++ K LI LGK++GY+T+ +I+ P D D +IE I + I++ E+
Sbjct: 4 MPQIERRIKKLISLGKKKGYITYEDIDKAFPPDFEGFDTNLIERIHEELEKHGINIVENE 63
Query: 94 LDTETLM 100
+ E +
Sbjct: 64 PEEEEIS 70
Score = 66.7 bits (163), Expect = 1e-13
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 826 IENLRKKFKILIKLGKERGYLTFSEINDFLPEDI--IDHEIIESIIKTFRYMDISVSEHV 883
+ + ++ K LI LGK++GY+T+ +I+ P D D +IE I + I++ E+
Sbjct: 4 MPQIERRIKKLISLGKKKGYITYEDIDKAFPPDFEGFDTNLIERIHEELEKHGINIVENE 63
Query: 884 LDTETLM 890
+ E +
Sbjct: 64 PEEEEIS 70
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 67.8 bits (165), Expect = 3e-11
Identities = 87/560 (15%), Positives = 153/560 (27%), Gaps = 210/560 (37%)
Query: 526 IAKEPVSMESPVGDDEDSH--------LGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
P E DDE + LG ++ + PS V+ L
Sbjct: 38 NKILPEPTEGFAADDEPTTPAELVGKFLG-YVSSL--VEPSKV---GQFDQVLNLCLTEF 91
Query: 578 TPRESKVLRMRFGIEMSSD-HTL-----EEVGKQFDVTRERIRQ-IEAKALRKLRPL--A 628
E+ L +D H L +E T+E I+ I A+ + K RP
Sbjct: 92 ---ENCYLE-------GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAK-RPFDKK 140
Query: 629 HD--WLEQRTHQNEKIIACSSDSSNHNEHVTNNNFPPGF----NI---FHKLLRILQEYL 679
+ N +++A F N F +L + Q Y
Sbjct: 141 SNSALFRAVGEGNAQLVAI-------------------FGGQGNTDDYFEELRDLYQTY- 180
Query: 680 ESFLISFFLRNHGISGFLLT-TPDPVHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGY 738
+ + L + +F + + E + Y+L
Sbjct: 181 HVLVGDLIKF---SAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237
Query: 739 MDVIGLSQFGFFANSSYTCFDGDQAGR-----RAARRALEVCL----------------- 776
+IG+ Q + T G R+ +
Sbjct: 238 CPLIGVIQLAHYVV---TA---KLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWES 291
Query: 777 LYATDDKIIKFLFL---------PDKYDPDSYIRKFGYKIFSKKNA-------FSFDIKS 820
+ + K I LF P+ P S + S +N S I +
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILED------SLENNEGVPSPMLS--ISN 343
Query: 821 NSREEIE---------------------NLRKKF-----------------KILIKLGKE 842
++E+++ N K K G +
Sbjct: 344 LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD 403
Query: 843 RGYLTFSE-----INDFLP-------------EDIIDHEIIESIIKTFRYMDISVSEHVL 884
+ + FSE N FLP D+I+ +++++ + +F DI + V
Sbjct: 404 QSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNV-SFNAKDIQI--PVY 460
Query: 885 DTET-----LMLSNITSD--DDV-------EEATEAALSTVDSDFGRTKDPIKMYMREMG 930
DT ++ +I+ D + E T+ + + DFG P G
Sbjct: 461 DTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHI-LDFG----P--------G 507
Query: 931 SVELLTRDGEIEIAKRIEEG 950
L + R ++G
Sbjct: 508 GASGLGV-----LTHRNKDG 522
Score = 60.4 bits (146), Expect = 4e-09
Identities = 93/609 (15%), Positives = 193/609 (31%), Gaps = 196/609 (32%)
Query: 248 SNISFHFDKMRKAFEKE-GYNSESYIKAHNNISN-EMLG--IRFTAKSIEKLCDTLRNQI 303
+ F ++++ F K +E + + E++G + + + +E
Sbjct: 24 TASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEP--------- 74
Query: 304 NQVTQIEKQILEIVVNKCGMPRLHFIKVF-PENEI-----NLNWVDNETKIQHDYNLILC 357
++V Q + Q+L + + F + N+I L +N+T + LI
Sbjct: 75 SKVGQFD-QVLNLCLT-------EFENCYLEGNDIHALAAKLL-QENDTTLVKTKELIKN 125
Query: 358 -------RNIPSIKELQQKLINL--------------QTDIVLPLNDLRDINR--KMIAG 394
P K+ L Q + +LRD+ + ++ G
Sbjct: 126 YITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVG 185
Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN-----------------IG 437
++ A+ R + K +T +GL L+ ++ + IG
Sbjct: 186 DLIKFSAETLSELI--RTTLDAEKVFT-QGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 438 LMKAVDKFEYRR-----GYKFSTYATWWIRQAITRS--------IADQARTIRIPVHMIE 484
+++ Y G+ ++ ++ A S IA + + E
Sbjct: 243 VIQLA---HYVVTAKLLGFTPGELRSY-LKGATGHSQGLVTAVAIA-ETDSW-------E 290
Query: 485 TINKISRISRQIL-------QET--GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 535
+ R + +L E + PS++ +E E P M S
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE----------GVPSPMLS 340
Query: 536 PVGDDEDSHLGDFIEDENMLAPSDAALNASM----RSVVKDILNSLT-PRESKVLRMRFG 590
+ + + D++ N P+ + S+ +++V ++ P +S L G
Sbjct: 341 -ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV------VSGPPQS--LY---G 388
Query: 591 IEMSSDHTLEEVGKQFDVTRERI--RQIEAKALRKLR------PLA---H-DWLEQRTHQ 638
+ + TL + + + RI + RKL+ P+A H L +
Sbjct: 389 L----NLTLRKAKAPSGLDQSRIPFSE------RKLKFSNRFLPVASPFHSHLLVPAS-- 436
Query: 639 NEKIIACSSDSSNHNEHVTNN--NFPPGFNIFH----KLLRILQEYLESFLISFFLRNHG 692
+ I D +N P ++ LR+L + ++
Sbjct: 437 -DLINK---DLVKNNVSFNAKDIQIP----VYDTFDGSDLRVLSGSISERIVD------- 481
Query: 693 ISGFLLTTPDPVH-----ETPLFH-------KSNELYGLFEAKNAIGKSGYVLITEGYMD 740
+ PV + H ++ L L +N G +G +I G +D
Sbjct: 482 ----CIIR-LPVKWETTTQFKATHILDFGPGGASGLGVLT-HRNKDG-TGVRVIVAGTLD 534
Query: 741 VIGLSQFGF 749
+ +GF
Sbjct: 535 INPDDDYGF 543
Score = 56.6 bits (136), Expect = 7e-08
Identities = 100/724 (13%), Positives = 199/724 (27%), Gaps = 282/724 (38%)
Query: 672 LRILQ-EY--LE-SFLIS---FF----LRNHGISGFLLTTPDPVHETPLFHKSNELYGLF 720
R L + LE L+ FF L+ F P+P T F +E
Sbjct: 6 TRPLTLSHGSLEHVLLVPTASFFIASQLQEQ----FNKILPEP---TEGFAADDEPTTPA 58
Query: 721 EAKNAIGKSGYVLITEGYMDVIGLSQF-GFFANSSYTCFDGDQAGRRAARRALEVCLLYA 779
E L + +F G+ ++ + + G+ + L +CL
Sbjct: 59 E-----------L----------VGKFLGYVSSL----VEPSKVGQF--DQVLNLCLTEF 91
Query: 780 TDDKIIKFLF----------LPDKYDPDSYIRKFGYKIFSKKNAFSFDIKSNSREEIENL 829
+ +L L + D+ + K I + A + ++ L
Sbjct: 92 ENC----YLEGNDIHALAAKLLQ--ENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL 145
Query: 830 RKKFKILIKLGKERGYLTF---SEINDFLPE--DIID--HEIIESIIKTFRYMDISVSEH 882
+ + G + F +D+ E D+ H ++ +IK +
Sbjct: 146 FRA----VGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRT 201
Query: 883 VLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
LD E + + ++ E E +T D D+ + PI S L+
Sbjct: 202 TLDAEKVFTQGL----NILEWLENPSNTPDKDYLLSI-PI--------SCPLI------- 241
Query: 943 IAKRIEEGLKDMIHAISSC------PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS 996
G+ + H + + P + L A S+ GL+ ++
Sbjct: 242 -------GVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ----------GLV----TA 280
Query: 997 NNRVIKGNKNNNEEKILIESSSA-----DLSTEQLEKLKY---ESLIKFSNISFHFDKMR 1048
+ I + + + + L + + N S +
Sbjct: 281 ---------------VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLP-PSIL 324
Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
+ + S ML I + + Q++ + +
Sbjct: 325 EDSLENNEGVPSP----------MLSIS----------NLTQ------EQVQDYVNK--T 356
Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
N H P + ++ I L+N ++V
Sbjct: 357 NS------HL----PAGK----------QV-------------EIS-----LVNGAKNLV 378
Query: 1169 L--PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR----GLQFLDLIQ 1222
+ P L +N + RKAK R +++R +FL
Sbjct: 379 VSGPPQSLYGLNLTL-------RKAKAPSGLDQSR------IPFSERKLKFSNRFL---- 421
Query: 1223 EGNIG-------LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
+ L+ A D + + +++ A+ I+IPV+
Sbjct: 422 --PVASPFHSHLLVPASDLIN---------------KDLVKNNVSFNAKDIQIPVYDTFD 464
Query: 1276 -INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
+ L+ ++ + I + PV E+ +H
Sbjct: 465 GSD---------LRVLSGSISERIV----DC----------IIRLPVKWETTTQFKA-TH 500
Query: 1335 LGDF 1338
+ DF
Sbjct: 501 ILDF 504
Score = 55.8 bits (134), Expect = 1e-07
Identities = 71/468 (15%), Positives = 154/468 (32%), Gaps = 146/468 (31%)
Query: 1038 SNISFHFDKMRKAFEKE-GYNSESYIKAHNNISN-EMLG--IRFTAKSIEKLCDTLRNQI 1093
+ F ++++ F K +E + + E++G + + + +E
Sbjct: 24 TASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEP--------- 74
Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVF-PENEI-----NLNWVDNETKIQHDYNLILC 1147
++V Q + Q+L + + F + N+I L +N+T + LI
Sbjct: 75 SKVGQFD-QVLNLCLT-------EFENCYLEGNDIHALAAKLL-QENDTTLVKTKELIKN 125
Query: 1148 -------RNIPSIKELQQKLINL--------------QTDIVLPLNDLRDINR--KMIAG 1184
P K+ L Q + +LRD+ + ++ G
Sbjct: 126 YITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVG 185
Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN-----------------IG 1227
++ A+ R + K +T +GL L+ ++ + IG
Sbjct: 186 DLIKFSAETLSELI--RTTLDAEKVFT-QGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 1228 LMKAVDKFEYRR-----GYKFSTYATWWIRQAITRS--------IADQARTIRIPVHMIE 1274
+++ Y G+ ++ ++ A S IA + + E
Sbjct: 243 VIQLA---HYVVTAKLLGFTPGELRSY-LKGATGHSQGLVTAVAIA-ETDSW-------E 290
Query: 1275 TINKISRISRQIL-------QET--GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 1325
+ R + +L E + PS++ +E E P M S
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE----------GVPSPMLS 340
Query: 1326 PVGDDEDSHLGDFIEDENMLAPSDAALNASM----RSVVKDILNSLT-PRESKVLRMRFG 1380
+ + + D++ N P+ + S+ +++V ++ P +S L G
Sbjct: 341 -ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV------VSGPPQS--LY---G 388
Query: 1381 IEMSSDHTLEEVGKQFDVTRERI--RQIEAKALRKLRHPSRYYKLKIF 1426
+ + TL + + + RI + RKL+ +R+ L +
Sbjct: 389 L----NLTLRKAKAPSGLDQSRIPFSE------RKLKFSNRF--LPVA 424
Score = 53.5 bits (128), Expect = 5e-07
Identities = 86/575 (14%), Positives = 167/575 (29%), Gaps = 204/575 (35%)
Query: 91 EHVLDTETLMLSNIT--SDD---DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
EHVL T + + + E TE D + P ++ + +G V L
Sbjct: 17 EHVLLVPTASFFIASQLQEQFNKILPEPTEG--FAADDE---PTTPAELVGKFLGYVSSL 71
Query: 146 TRDGEI----EIAKRI----EEGL---KDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
++ ++ E D IHA+ AA + +N+ + +
Sbjct: 72 VEPSKVGQFDQVLNLCLTEFENCYLEGND-IHAL------------AAKLLQENDTTLVK 118
Query: 195 IVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLST---------------EQLEKL 239
+ LI KN+ + + K + L + + E+L L
Sbjct: 119 TKE-LI-KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDL 176
Query: 240 --KYESLIK---------FSNISFHFDKMRKAFEKEGYN------------SESYIKAHN 276
Y L+ S + K F + G N + Y+
Sbjct: 177 YQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ-GLNILEWLENPSNTPDKDYL-LSI 234
Query: 277 NISNEMLGI------RFTAKSIEKLCDTLRNQINQVTQIEKQIL---------------E 315
IS ++G+ TAK + LR+ + T + ++
Sbjct: 235 PISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFV 294
Query: 316 IVVNKCGMPRLHFI-----KVFPENEI-----------------------NLNWVDNETK 347
V + L FI + +P + NL +
Sbjct: 295 SVRK--AITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY 352
Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVL--PLNDLRDINRKMIAGEMKARKAKREM 405
+ ++P+ K+++ L+N ++V+ P L +N + RKAK
Sbjct: 353 VNK-----TNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTL-------RKAKAPS 400
Query: 406 TEANLRLVISIAKKYTDR----GLQFLDLIQEGNIG-------LMKAVDKFEYRRGYKFS 454
R +++R +FL + L+ A D
Sbjct: 401 GLDQSR------IPFSERKLKFSNRFL------PVASPFHSHLLVPASDLIN-------- 440
Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIET-INKISRISRQILQETGSEPDPSVIAIKM 513
+ + +++ A+ I+IPV+ + L+ ++
Sbjct: 441 -------KDLVKNNVSFNAKDIQIPVYDTFDGSD---------LRVLSGSISERIV---- 480
Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
+ I + PV E+ +H+ DF
Sbjct: 481 DC----------IIRLPVKWETTTQFKA-THILDF 504
Score = 49.7 bits (118), Expect = 8e-06
Identities = 63/310 (20%), Positives = 106/310 (34%), Gaps = 103/310 (33%)
Query: 777 LYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKNAFSFDI-KSNSREEIENLRKKFKI 835
LY T + ++ ++ D + + +G+ I DI +N +
Sbjct: 1635 LYKTSK-AAQDVW--NRAD-NHFKDTYGFSIL--------DIVINNPVN----------L 1672
Query: 836 LIKLGKERG------Y--LTFSEIND-FLPEDIIDHEIIESIIK-TFRYMDISVSEHVLD 885
I G E+G Y + F I D L + I EI E TFR + +L
Sbjct: 1673 TIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS-----EKGLLS 1727
Query: 886 -TE-T---LMLSNITSDDDVEEAT--------------E-AALSTVDSDFGRTKDPIKMY 925
T+ T L L + +D++ E AAL+++ +D +
Sbjct: 1728 ATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASL-ADVMSIES----- 1781
Query: 926 MREMGSVELL-TRDGEI--EIAKRIEEGLKD--MIHAISSCPTTIMEIL------IAADK 974
VE++ R G R E G + MI AI+ P + ++
Sbjct: 1782 -----LVEVVFYR-GMTMQVAVPRDELGRSNYGMI-AIN--PGRVAASFSQEALQYVVER 1832
Query: 975 ISKNEIKIDEIVDGLIDKNFSSNNR--VIKGN-----------KNNNEEKILIESSSADL 1021
+ K + EIV N++ N+ V G+ +KI I L
Sbjct: 1833 VGKRTGWLVEIV------NYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSL 1886
Query: 1022 STEQLEKLKY 1031
S E++E +
Sbjct: 1887 SLEEVEGHLF 1896
Score = 47.4 bits (112), Expect = 4e-05
Identities = 59/276 (21%), Positives = 93/276 (33%), Gaps = 86/276 (31%)
Query: 20 LKNAFSFDIKSNSREEIENLRKKFKILIKLGKERG------Y--LTFSEIND-FLPEDII 70
K+ + F I NL F G E+G Y + F I D L + I
Sbjct: 1653 FKDTYGFSILDIVINNPVNLTIHF------GGEKGKRIRENYSAMIFETIVDGKLKTEKI 1706
Query: 71 DHEIIESIIK-TFRYMDISVSEHVLD-TE-T---LMLSNITSDDDVEEAT---------- 114
EI E TFR + +L T+ T L L + +D++
Sbjct: 1707 FKEINEHSTSYTFRS-----EKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG 1761
Query: 115 ----E-AALSTVDSDFGRTKDPIKMYMREMGSVELL-TRDGEI--EIAKRIEEGLKD--M 164
E AAL+++ +D + VE++ R G R E G + M
Sbjct: 1762 HSLGEYAALASL-ADVMSIES----------LVEVVFYR-GMTMQVAVPRDELGRSNYGM 1809
Query: 165 IHAISSCPTTIMEIL------IAADKISKNEIKIDEIVDGLIDKNFSSNNR--VIKGN-- 214
I AI+ P + +++ K + EIV N++ N+ V G+
Sbjct: 1810 I-AIN--PGRVAASFSQEALQYVVERVGKRTGWLVEIV------NYNVENQQYVAAGDLR 1860
Query: 215 ---------KNNNEEKILIESSSADLSTEQLEKLKY 241
+KI I LS E++E +
Sbjct: 1861 ALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHLF 1896
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics,
midwest center for structura genomics, protein structure
initiative; 2.50A {Fusobacterium nucleatum subsp}
Length = 164
Score = 50.6 bits (121), Expect = 3e-07
Identities = 31/207 (14%), Positives = 61/207 (29%), Gaps = 49/207 (23%)
Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
DL+QEG +GL+KA+ ++ + FS++A IR+ + I I K
Sbjct: 6 DLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREM-----------------ISAIRK 47
Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
+ +L E +E D++ H +
Sbjct: 48 ANTQKHMVLNEALKTNAI--------------------------LEDSAYFDDEGHNINN 81
Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
+ L + K N+ + E +VL ++ E+
Sbjct: 82 YKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI-----RGYSYREIATILSK 136
Query: 609 TRERIRQIEAKALRKLRPLAHDWLEQR 635
+ I + +K + +
Sbjct: 137 NLKSIDNTIQRIRKKSEEWIKEEENIK 163
Score = 50.6 bits (121), Expect = 4e-07
Identities = 31/197 (15%), Positives = 59/197 (29%), Gaps = 49/197 (24%)
Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
DL+QEG +GL+KA+ ++ + FS++A IR+ + I I K
Sbjct: 6 DLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREM-----------------ISAIRK 47
Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
+ +L E +E D++ H +
Sbjct: 48 ANTQKHMVLNEALKTNAI--------------------------LEDSAYFDDEGHNINN 81
Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
+ L + K N+ + E +VL ++ E+
Sbjct: 82 YKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI-----RGYSYREIATILSK 136
Query: 1399 TRERIRQIEAKALRKLR 1415
+ I + +K
Sbjct: 137 NLKSIDNTIQRIRKKSE 153
>1igt_B IGG2A intact antibody - MAB231; intact immunoglobulin V region C
region, immunoglobulin; HET: NAG FUL BMA MAN GAL FUC;
2.80A {Mus musculus} SCOP: b.1.1.1 b.1.1.2 b.1.1.2
b.1.1.2
Length = 444
Score = 34.9 bits (80), Expect = 0.21
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS Y +W+RQ
Sbjct: 26 GFTFSDYYMYWVRQT 40
Score = 34.9 bits (80), Expect = 0.21
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS Y +W+RQ
Sbjct: 26 GFTFSDYYMYWVRQT 40
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.4 bits (75), Expect = 0.23
Identities = 10/51 (19%), Positives = 20/51 (39%), Gaps = 24/51 (47%)
Query: 518 EK--IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
EK ++K+ + + + + DS AP+ A+ A+M
Sbjct: 18 EKQALKKL----QASLKLYAD-----DS------------APA-LAIKATM 46
Score = 33.4 bits (75), Expect = 0.23
Identities = 10/51 (19%), Positives = 20/51 (39%), Gaps = 24/51 (47%)
Query: 1308 EK--IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
EK ++K+ + + + + DS AP+ A+ A+M
Sbjct: 18 EKQALKKL----QASLKLYAD-----DS------------APA-LAIKATM 46
Score = 30.7 bits (68), Expect = 1.6
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 152 EIAKRIEEGLKDMIHAISSCP-----TTI 175
+ K+++ LK ++A S P T+
Sbjct: 21 AL-KKLQASLK--LYADDSAPALAIKATM 46
Score = 30.7 bits (68), Expect = 1.6
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 942 EIAKRIEEGLKDMIHAISSCP-----TTI 965
+ K+++ LK ++A S P T+
Sbjct: 21 AL-KKLQASLK--LYADDSAPALAIKATM 46
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding
anti-sigma factor, oxidative transcription regulation;
2.35A {Mycobacterium tuberculosis}
Length = 92
Score = 32.0 bits (73), Expect = 0.27
Identities = 12/79 (15%), Positives = 27/79 (34%), Gaps = 12/79 (15%)
Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT----RE 611
+ D A R ++ D L L+ V++ + + ++ + +
Sbjct: 17 STPDEVNAALDRLLIADALAQLSAEHRAVIQRSY-YR---GWSTAQIATDLGIAEGTVKS 72
Query: 612 RIRQIEAKALRKLRPLAHD 630
R+ A+R LR +
Sbjct: 73 RLH----YAVRALRLTLQE 87
Score = 31.6 bits (72), Expect = 0.30
Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 12/75 (16%)
Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT----RE 1401
+ D A R ++ D L L+ V++ + + ++ + +
Sbjct: 17 STPDEVNAALDRLLIADALAQLSAEHRAVIQRSY-YR---GWSTAQIATDLGIAEGTVKS 72
Query: 1402 RIRQIEAKALRKLRH 1416
R+ A+R LR
Sbjct: 73 RLH----YAVRALRL 83
>1iga_A IGA1; immunoglobulin; NMR {Homo sapiens} PDB: 2esg_A 2qtj_A 3chn_A
1r70_B 3cm9_A
Length = 475
Score = 34.5 bits (79), Expect = 0.27
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 450 GYKFSTYATWWIRQA 464
GY F++Y W+RQA
Sbjct: 27 GYSFTSYGLHWVRQA 41
Score = 34.5 bits (79), Expect = 0.27
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F++Y W+RQA
Sbjct: 27 GYSFTSYGLHWVRQA 41
>1hzh_H IGG, immunoglobulin heavy chain; antibody, immune system; HET: NAG
BMA MAN GAL FUC; 2.70A {Homo sapiens} SCOP: b.1.1.1
b.1.1.2 b.1.1.2 b.1.1.2 PDB: 2ig2_H 1mco_H*
Length = 457
Score = 34.5 bits (79), Expect = 0.29
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 450 GYKFSTYATWWIRQA 464
GY+FS + W+RQA
Sbjct: 26 GYRFSNFVIHWVRQA 40
Score = 34.5 bits (79), Expect = 0.29
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY+FS + W+RQA
Sbjct: 26 GYRFSNFVIHWVRQA 40
>2q1z_A RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc bindin
transcription factor; 2.40A {Rhodobacter sphaeroides}
PDB: 2z2s_A
Length = 184
Score = 33.3 bits (77), Expect = 0.31
Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 12/75 (16%)
Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT----RE 1401
+D + + + L + ++ F D T E+ + + +
Sbjct: 115 DQADVYEMQQENARLGRAIARLPEAQRALIERAF-FG---DLTHRELAAETGLPLGTIKS 170
Query: 1402 RIRQIEAKALRKLRH 1416
RIR AL +LR
Sbjct: 171 RIRL----ALDRLRQ 181
Score = 32.9 bits (76), Expect = 0.46
Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 12/74 (16%)
Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT----RE 611
+D + + + L + ++ F D T E+ + + +
Sbjct: 115 DQADVYEMQQENARLGRAIARLPEAQRALIERAF-FG---DLTHRELAAETGLPLGTIKS 170
Query: 612 RIRQIEAKALRKLR 625
RIR AL +LR
Sbjct: 171 RIRL----ALDRLR 180
>2fbj_H IGA-kappa J539 FAB (heavy chain); immunoglobulin; HET: NAG FUC;
1.95A {Mus musculus} SCOP: b.1.1.1 b.1.1.2 PDB: 1mcp_H
2mcp_H*
Length = 220
Score = 33.2 bits (77), Expect = 0.40
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS Y W+RQA
Sbjct: 26 GFDFSKYWMSWVRQA 40
Score = 33.2 bits (77), Expect = 0.40
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS Y W+RQA
Sbjct: 26 GFDFSKYWMSWVRQA 40
>1c5d_H Monoclonal antibody against the main immunogenic the human muscle
acetylcholine receptor...; immunoglobulin, immune
system; 2.40A {Rattus norvegicus} SCOP: b.1.1.1 b.1.1.2
PDB: 2arj_H 3b9k_H* 2gk0_H 2gjz_H 1fn4_B 3mj8_H 3mj9_H*
Length = 215
Score = 33.2 bits (77), Expect = 0.41
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
G+ +T W+RQ
Sbjct: 26 GFPLTTNGVSWVRQP 40
Score = 33.2 bits (77), Expect = 0.41
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ +T W+RQ
Sbjct: 26 GFPLTTNGVSWVRQP 40
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.8 bits (74), Expect = 0.45
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 7/46 (15%)
Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQRTHQNEKIIA 644
L+E+ V + R+ K L +W ++++ Q EK
Sbjct: 98 LQELDAASKVMEQEWREKAKKDL-------EEWNQRQSEQVEKNKI 136
>3m8o_H Immunoglobulin A1 heavy chain; immunoglobulin fold, immune system;
1.55A {Homo sapiens} PDB: 3qnx_B 3qny_B
Length = 221
Score = 32.9 bits (76), Expect = 0.51
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
G+ S W+RQA
Sbjct: 26 GFTLSGSNVHWVRQA 40
Score = 32.9 bits (76), Expect = 0.51
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ S W+RQA
Sbjct: 26 GFTLSGSNVHWVRQA 40
>2c6x_A Citrate synthase 1; tricarboxylic acid cycle, transferase,
allosteric enzyme, enzyme thermostability; HET: COZ CIT;
3.4A {Bacillus subtilis}
Length = 363
Score = 33.3 bits (77), Expect = 0.52
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 100 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGEIEI 153
ML +I + E + L + FG +TKDP +R+ + E+ D ++++
Sbjct: 222 MLEDIGEKEHAEAYLKEKLEKGERLMGFGHRVYKTKDPRAEALRQK-AEEVAGNDRDLDL 280
Query: 154 AKRIEE 159
A +E
Sbjct: 281 ALHVEA 286
Score = 33.3 bits (77), Expect = 0.52
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 890 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGEIEI 943
ML +I + E + L + FG +TKDP +R+ + E+ D ++++
Sbjct: 222 MLEDIGEKEHAEAYLKEKLEKGERLMGFGHRVYKTKDPRAEALRQK-AEEVAGNDRDLDL 280
Query: 944 AKRIEE 949
A +E
Sbjct: 281 ALHVEA 286
>1op3_H FAB 2G12, heavy chain; domain-swapped FAB 2G12, anti-carbohydrate
antibody, immune system; HET: MAN; 1.75A {Homo sapiens}
SCOP: b.1.1.1 b.1.1.2 PDB: 1om3_H* 1op5_H* 3oay_M*
1zlu_H* 1zlv_H* 1zlw_H* 2oqj_B 1zls_H* 3ob0_H* 3oau_H*
3oaz_H* 3ghe_H 3eyf_B 3eyo_B 3ghb_H 3c2a_H 1q1j_H
2fl5_H*
Length = 225
Score = 32.8 bits (76), Expect = 0.56
Identities = 3/15 (20%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
++ S + W+R+
Sbjct: 26 NFRISAHTMNWVRRV 40
Score = 32.8 bits (76), Expect = 0.56
Identities = 3/15 (20%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
++ S + W+R+
Sbjct: 26 NFRISAHTMNWVRRV 40
>3u2s_H PG9 heavy chain; greek KEY, immunoglobulin, immune recognition,
immune system; HET: PCA TYS BU3 NAG BMA MAN; 1.80A {Homo
sapiens} PDB: 3u4e_H* 3u36_H 3mug_B* 3lrs_H* 3mme_H*
2qsc_H*
Length = 248
Score = 32.9 bits (76), Expect = 0.57
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS W+RQA
Sbjct: 25 GFDFSRQGMHWVRQA 39
Score = 32.9 bits (76), Expect = 0.57
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS W+RQA
Sbjct: 25 GFDFSRQGMHWVRQA 39
>1pz5_B Heavy chain of FAB (SYA/J6); antibody-antigen structure,
peptide-carbohydrate mimicry, VA design, immune system;
1.80A {Mus musculus} SCOP: b.1.1.1 b.1.1.2 PDB: 1m7d_B*
1m71_B* 1m7i_B* 1r24_B 1uz6_F 1uz8_B* 1clz_H*
Length = 220
Score = 32.8 bits (76), Expect = 0.62
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS Y W+RQ+
Sbjct: 26 GFTFSNYWMEWVRQS 40
Score = 32.8 bits (76), Expect = 0.62
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS Y W+RQ+
Sbjct: 26 GFTFSNYWMEWVRQS 40
>1dee_B IGM RF 2A2; FAB-IBP complex 2.7A resolution binding outside the
antigen combining site superantigen FAB VH3 specificity;
2.70A {Homo sapiens} SCOP: b.1.1.1 b.1.1.2 PDB: 1hez_B
1adq_H
Length = 223
Score = 32.8 bits (76), Expect = 0.63
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS Y W+RQA
Sbjct: 26 GFTFSGYGMHWVRQA 40
Score = 32.8 bits (76), Expect = 0.63
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS Y W+RQA
Sbjct: 26 GFTFSGYGMHWVRQA 40
>3n9g_H FAB fragment of MAB CR4354, heavy chain; human neutralizing
antibody, immun anti-WEST NIle virus; 1.43A {Homo
sapiens} PDB: 3iyw_H 3qeh_A 3u0t_D 3c08_H 3lmj_H 3lqa_H*
3c09_H* 3pp4_H 3pp3_H 2jb5_H* 2jb6_B* 2eh7_H 2eh8_H
3jwd_H* 3jwo_H* 3t2n_H 3qot_H 3ma9_H 3nfs_H 3nfp_A ...
Length = 230
Score = 32.8 bits (76), Expect = 0.63
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
GY F+ Y W+RQA
Sbjct: 26 GYTFTHYYMHWVRQA 40
Score = 32.8 bits (76), Expect = 0.63
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F+ Y W+RQA
Sbjct: 26 GYTFTHYYMHWVRQA 40
>3liz_H 4C3 monoclonal antibody heavy chain; hydrolase-immune system
complex; HET: NAG BMA MAN; 1.80A {Mus musculus} PDB:
3rvv_D* 3rvu_D 3rvt_D* 3rvw_D* 3rvx_D 1lo4_H 1ub6_H
3r06_B 3r08_H
Length = 253
Score = 32.9 bits (76), Expect = 0.64
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS++A W RQ
Sbjct: 26 GFTFSSFAMSWGRQT 40
Score = 32.9 bits (76), Expect = 0.64
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS++A W RQ
Sbjct: 26 GFTFSSFAMSWGRQT 40
>3sob_H Antibody heavy chain, low-density lipoprotein receptor-related
protein; beta propeller, protein binding-immune system
complex; 1.90A {Homo sapiens} PDB: 1pkq_B
Length = 256
Score = 32.8 bits (76), Expect = 0.65
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G+ F+ W+RQA
Sbjct: 49 GFTFTNSYIHWVRQA 63
Score = 32.8 bits (76), Expect = 0.65
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ F+ W+RQA
Sbjct: 49 GFTFTNSYIHWVRQA 63
>3mlr_H Human monoclonal anti-HIV-1 GP120 V3 antibody 255 heavy chain;
human monoclonal antibody, FAB, third variable
antibody-antigen interaction; 1.80A {Homo sapiens} PDB:
3mls_H 3mlt_H 3mlu_H 3mlv_H
Length = 226
Score = 32.8 bits (76), Expect = 0.66
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
GY F W+RQ
Sbjct: 26 GYNFLDSWIGWVRQI 40
Score = 32.8 bits (76), Expect = 0.66
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F W+RQ
Sbjct: 26 GYNFLDSWIGWVRQI 40
>3u1s_H FAB PGT145 heavy chain; IGG, broadly neutralizing antibody, HIV-1
GP120, immune SYST; HET: TYS; 2.30A {Homo sapiens}
Length = 267
Score = 32.9 bits (76), Expect = 0.67
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G FS + W+RQA
Sbjct: 49 GNSFSNHDVHWVRQA 63
Score = 32.9 bits (76), Expect = 0.67
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G FS + W+RQA
Sbjct: 49 GNSFSNHDVHWVRQA 63
>1c1e_H Catalytic antibody 1E9 (heavy chain); diels-alder, immunoglobulin,
immune system; HET: ENH; 1.90A {Mus musculus} SCOP:
b.1.1.1 b.1.1.2 PDB: 1dbb_H* 1dba_H* 1dbj_H* 1dbk_H*
1dbm_H* 2dbl_H* 3ojd_B 1jgl_H* 1jhk_H 1ghf_H 1tet_H*
3e8u_H 1fj1_B 1cl7_H
Length = 219
Score = 32.4 bits (75), Expect = 0.69
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
GY F+ Y W++QA
Sbjct: 26 GYMFTNYGMNWVKQA 40
Score = 32.4 bits (75), Expect = 0.69
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F+ Y W++QA
Sbjct: 26 GYMFTNYGMNWVKQA 40
>2xqy_G A13-D6.3 monoclonal antibody, envelope glycoprotein H; immune
system-viral protein complex, envelope protein; HET:
NAG; 2.05A {Mus musculus}
Length = 261
Score = 32.9 bits (76), Expect = 0.69
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
GY F++Y W++Q
Sbjct: 32 GYSFTSYWMNWVKQR 46
Score = 32.9 bits (76), Expect = 0.69
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F++Y W++Q
Sbjct: 32 GYSFTSYWMNWVKQR 46
>3lh2_H FV 4E10 heavy chain; epitope-scaffold, immune system; 2.65A {Homo
sapiens} PDB: 3h3p_H 3lhp_H 2xtj_D
Length = 137
Score = 31.4 bits (72), Expect = 0.70
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 450 GYKFSTYATWWIRQA 464
G FSTYA W+RQA
Sbjct: 28 GGSFSTYALSWVRQA 42
Score = 31.4 bits (72), Expect = 0.70
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 1240 GYKFSTYATWWIRQA 1254
G FSTYA W+RQA
Sbjct: 28 GGSFSTYALSWVRQA 42
>1q9r_B S25-2 FAB (IGG1K) heavy chain; antigen-binding fragment,
anti-carbohydrate, anti-LPS, antibody, immunoglobulin,
KDO, complex, immune system; HET: KDA KDO; 1.45A {Mus
musculus} SCOP: b.1.1.1 b.1.1.2 PDB: 1q9l_B 1q9k_B*
1q9q_B* 1q9v_B* 2r1w_B* 2r1x_B* 2r1y_B* 2r2b_B* 2r2e_B*
2r2h_B* 3bpc_B* 3sy0_B* 3t4y_B* 3t65_B* 2r23_B* 1q9t_B*
3t77_B* 3okl_B* 3okk_B* 3okm_B ...
Length = 222
Score = 32.5 bits (75), Expect = 0.72
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G+ F+ Y W+RQ
Sbjct: 26 GFTFTDYYMSWVRQP 40
Score = 32.5 bits (75), Expect = 0.72
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ F+ Y W+RQ
Sbjct: 26 GFTFTDYYMSWVRQP 40
>3bn9_D E2 FAB heavy chain; antibody-protease complex, protein-protein
complex, enzyme- inhibitor complex, disease mutation,
glycoprotein, hydrolase; 2.17A {Homo sapiens} SCOP:
b.1.1.1 b.1.1.2 PDB: 3kr3_H 2xtj_E
Length = 257
Score = 32.5 bits (75), Expect = 0.72
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS+YA W+RQA
Sbjct: 26 GFTFSSYAMSWVRQA 40
Score = 32.5 bits (75), Expect = 0.72
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS+YA W+RQA
Sbjct: 26 GFTFSSYAMSWVRQA 40
>3iu4_H CHP3 FAB heavy chain; antibody, ganglioside, idiotype, immune
system; 1.75A {Mus musculus} PDB: 1ibg_H* 3iy6_B
Length = 263
Score = 32.6 bits (75), Expect = 0.76
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G+ S Y+ W+RQ
Sbjct: 26 GFSLSRYSVHWVRQP 40
Score = 32.6 bits (75), Expect = 0.76
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ S Y+ W+RQ
Sbjct: 26 GFSLSRYSVHWVRQP 40
>2ibp_A Citrate synthase; disulfide bond, homodimer, thermophilic, C
transferase; 1.60A {Pyrobaculum aerophilum}
Length = 409
Score = 32.9 bits (76), Expect = 0.82
Identities = 15/71 (21%), Positives = 24/71 (33%), Gaps = 12/71 (16%)
Query: 100 MLSNITSDDDVEEATEAALSTVD---SDFG----RTKDPIKMYMREMGSVELLTRDGE-- 150
I + +E EAA G + DP +E S + + + G+
Sbjct: 259 NYLEIGTPAKAKEIVEAATKPGGPKLMGVGHRVYKAYDPRAKIFKEF-SRDYVAKFGDPQ 317
Query: 151 --IEIAKRIEE 159
IA IE+
Sbjct: 318 NLFAIASAIEQ 328
Score = 32.9 bits (76), Expect = 0.82
Identities = 15/71 (21%), Positives = 24/71 (33%), Gaps = 12/71 (16%)
Query: 890 MLSNITSDDDVEEATEAALSTVD---SDFG----RTKDPIKMYMREMGSVELLTRDGE-- 940
I + +E EAA G + DP +E S + + + G+
Sbjct: 259 NYLEIGTPAKAKEIVEAATKPGGPKLMGVGHRVYKAYDPRAKIFKEF-SRDYVAKFGDPQ 317
Query: 941 --IEIAKRIEE 949
IA IE+
Sbjct: 318 NLFAIASAIEQ 328
>3u6r_H Antibody 1:7 (heavy chain); IG-like domain, neutralizing single
chain FV, immune system; 2.67A {Homo sapiens}
Length = 149
Score = 31.4 bits (72), Expect = 0.83
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G FS Y W+RQA
Sbjct: 29 GDTFSRYTIQWLRQA 43
Score = 31.4 bits (72), Expect = 0.83
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G FS Y W+RQA
Sbjct: 29 GDTFSRYTIQWLRQA 43
>1mju_H Immunoglobulin MS6-12; catalytic antibody, ester hydrolysis,
esterolytic, FAB, immune system; 1.22A {Mus musculus}
SCOP: b.1.1.1 b.1.1.2 PDB: 1mjj_B 1mie_H 1mj7_H* 1mj8_H
1mh5_B* 4aeh_H 2y5t_A 2vwe_E 2op4_H 2ntf_H 3loh_C 1e4x_H
2vl5_A 1e4x_I 1e4w_H 3opz_H 3oz9_H 1plg_H 1hi6_B 1cfn_B
...
Length = 227
Score = 32.1 bits (74), Expect = 0.85
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
GY F+ Y W++Q
Sbjct: 26 GYTFTNYWINWVKQR 40
Score = 32.1 bits (74), Expect = 0.85
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F+ Y W++Q
Sbjct: 26 GYTFTNYWINWVKQR 40
>3nl4_H Antigen binding fragment,immunoglobulin IGG - HEA; FAB, rabbit,
conformation-specific, amyloid, immune system; 1.54A
{Oryctolagus cuniculus}
Length = 215
Score = 32.1 bits (74), Expect = 0.90
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 450 GYKFSTYATWWIRQA 464
G+ +TY+ +W+RQA
Sbjct: 25 GFSLNTYSMFWVRQA 39
Score = 32.1 bits (74), Expect = 0.90
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ +TY+ +W+RQA
Sbjct: 25 GFSLNTYSMFWVRQA 39
>3fku_X Neutralizing antibody F10; influenza, hemagglutinin, SCFV, F
membrane, envelope protein, fusion protein, membrane,
trans virion; HET: NAG BMA; 3.20A {Homo sapiens}
Length = 280
Score = 32.3 bits (74), Expect = 0.93
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
FS++A W+RQA
Sbjct: 26 EVTFSSFAISWVRQA 40
Score = 32.3 bits (74), Expect = 0.93
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
FS++A W+RQA
Sbjct: 26 EVTFSSFAISWVRQA 40
>1dn0_B IGM-kappa cold agglutinin (heavy chain); FAB, antibody, human,
immune system; 2.28A {Homo sapiens} SCOP: b.1.1.1
b.1.1.2 PDB: 1qlr_B* 2j6e_H* 2agj_H* 2h32_H
Length = 232
Score = 32.1 bits (74), Expect = 0.96
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
G FS Y WIRQ
Sbjct: 26 GGSFSDYYWSWIRQP 40
Score = 32.1 bits (74), Expect = 0.96
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
G FS Y WIRQ
Sbjct: 26 GGSFSDYYWSWIRQP 40
>3g0o_A 3-hydroxyisobutyrate dehydrogenase; NAD(P), valine catabolism,
tartaric acid, target 11128H, NYSGXRC, PSI-2, structural
genomics; HET: TLA; 1.80A {Salmonella typhimurium}
Length = 303
Score = 32.5 bits (75), Expect = 0.97
Identities = 9/42 (21%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 642 IIACSSDSS----NHNEHVTNNNFPPGF--NIFHKLLRILQE 677
++ ++ +S N +HV + ++ P +IF K L ++ +
Sbjct: 213 VVTHAAGNSWMFENRMQHVVDGDYTPRSAVDIFVKDLGLVAD 254
>1i3u_A Antibody VHH LAMA domain; VHH fragment, immune system; HET: RR1;
1.95A {Lama glama} SCOP: b.1.1.1 PDB: 1i3v_A
Length = 127
Score = 30.9 bits (71), Expect = 1.0
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G TY W RQA
Sbjct: 26 GDSIGTYVIGWFRQA 40
Score = 30.9 bits (71), Expect = 1.0
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G TY W RQA
Sbjct: 26 GDSIGTYVIGWFRQA 40
>3d9a_H Heavy chain of hyhel10 antibody fragment (FAB); lysozyme, antigen,
allergen, antimic bacteriolytic enzyme, glycosidase,
hydrolase; 1.20A {Mus musculus} PDB: 3hfm_H 1gpo_H
3ks0_H* 1dqd_H 1ndm_B 1nak_H 1dqq_B 1dqm_H 1dqj_B 1nby_B
1nbz_B 1xgu_B 1ndg_B 1xgt_B 1xgp_B 1xgq_B 1xgr_B 1s5i_H
1f8t_H 1f90_H ...
Length = 210
Score = 32.1 bits (74), Expect = 1.0
Identities = 4/15 (26%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G ++ WIR+
Sbjct: 26 GDSITSDYWSWIRKF 40
Score = 32.1 bits (74), Expect = 1.0
Identities = 4/15 (26%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G ++ WIR+
Sbjct: 26 GDSITSDYWSWIRKF 40
>2d7t_H Anti polyhydroxybutyrate antibody FV, heavy chain; plastic, immune
system; 1.70A {Homo sapiens}
Length = 139
Score = 31.0 bits (71), Expect = 1.1
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
GY F+ W+RQA
Sbjct: 26 GYTFTGNYMHWVRQA 40
Score = 31.0 bits (71), Expect = 1.1
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F+ W+RQA
Sbjct: 26 GYTFTGNYMHWVRQA 40
>1za6_B IGG heavy chain; immunoglobulin fold, CH2-domain-deletion, immune
system; 2.80A {Homo sapiens} SCOP: b.1.1.1 b.1.1.2
b.1.1.2
Length = 344
Score = 32.1 bits (73), Expect = 1.1
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
GY F+ +A W++Q
Sbjct: 26 GYTFTDHAIHWVKQN 40
Score = 32.1 bits (73), Expect = 1.1
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F+ +A W++Q
Sbjct: 26 GYTFTDHAIHWVKQN 40
>1vgp_A 373AA long hypothetical citrate synthase; open form, transferase;
2.70A {Sulfolobus tokodaii}
Length = 373
Score = 32.5 bits (75), Expect = 1.1
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 10/70 (14%)
Query: 100 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDP----IKMYMREMGSVELLTRDG 149
M I S + V + LS FG +T DP +K Y + + E
Sbjct: 225 MFKEIGSPEKVNDYILNRLSNKQRIMGFGHRVYKTYDPRARILKQYAKLLAEKEGGEIYT 284
Query: 150 EIEIAKRIEE 159
+IA+++EE
Sbjct: 285 LYQIAEKVEE 294
Score = 32.5 bits (75), Expect = 1.1
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 10/70 (14%)
Query: 890 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDP----IKMYMREMGSVELLTRDG 939
M I S + V + LS FG +T DP +K Y + + E
Sbjct: 225 MFKEIGSPEKVNDYILNRLSNKQRIMGFGHRVYKTYDPRARILKQYAKLLAEKEGGEIYT 284
Query: 940 EIEIAKRIEE 949
+IA+++EE
Sbjct: 285 LYQIAEKVEE 294
>3gkz_A Anti-methamphetamine single chain FV; therapeutic antibody, MDMA,
IGG, immune system; HET: B40; 1.90A {Mus musculus} PDB:
3gm0_A* 1rvf_L 3ab0_C 2a0l_C 3iy5_A
Length = 257
Score = 31.9 bits (73), Expect = 1.2
Identities = 5/15 (33%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G ++ WIRQ
Sbjct: 34 GDSVTSGYWSWIRQF 48
Score = 31.9 bits (73), Expect = 1.2
Identities = 5/15 (33%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G ++ WIRQ
Sbjct: 34 GDSVTSGYWSWIRQF 48
>2p45_B Antibody CAB-RN05; seMet phasing, camelid single-domain antibody,
VHH, RNAse A, yeast surface display, hydrolase/immune
system complex; 1.10A {Camelus dromedarius} PDB: 2p46_B
2p47_B 2p48_B 2p44_B 2p49_B 2p42_B 2p43_B 1bzq_K 3qsk_B
2p4a_B 1op9_A 1sjx_A 3qxt_A* 3qxu_A 3eba_A
Length = 123
Score = 30.5 bits (70), Expect = 1.2
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
GY ++ W RQA
Sbjct: 28 GYAYTYIYMGWFRQA 42
Score = 30.5 bits (70), Expect = 1.2
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY ++ W RQA
Sbjct: 28 GYAYTYIYMGWFRQA 42
>1yc7_A Anti-VSG immunoglobulin heavy chain variable domain caban33;
antibody, camel antibody, immune system; 1.60A {Camelus
dromedarius} PDB: 1yc8_A 1yzz_A
Length = 124
Score = 30.5 bits (70), Expect = 1.2
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
G +S T W RQA
Sbjct: 26 GSTYSPCTTGWYRQA 40
Score = 30.5 bits (70), Expect = 1.2
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
G +S T W RQA
Sbjct: 26 GSTYSPCTTGWYRQA 40
>2l4h_A Calcium and integrin-binding protein 1; metal binding protei; NMR
{Homo sapiens} PDB: 2l4i_A 2lm5_A
Length = 214
Score = 31.8 bits (72), Expect = 1.2
Identities = 24/143 (16%), Positives = 51/143 (35%), Gaps = 15/143 (10%)
Query: 32 SREEIENLRKKFKILIKLGK------ERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYM 85
+++EI ++F L+ + R + F +I + E I + F
Sbjct: 46 TKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKA--NPFKERICRVF--- 100
Query: 86 DISVSEHVLDTE--TLMLSNITSDDDVEEATEAALSTVDSDF-GR-TKDPIKMYMREMGS 141
S ++ L E +LS + + + A D D G ++ + + +
Sbjct: 101 STSPAKDSLSFEDFLDLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTG 160
Query: 142 VELLTRDGEIEIAKRIEEGLKDM 164
TR E+ + I+ L++
Sbjct: 161 EGEDTRLSASEMKQLIDNILEES 183
Score = 31.8 bits (72), Expect = 1.2
Identities = 24/143 (16%), Positives = 51/143 (35%), Gaps = 15/143 (10%)
Query: 822 SREEIENLRKKFKILIKLGK------ERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYM 875
+++EI ++F L+ + R + F +I + E I + F
Sbjct: 46 TKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKA--NPFKERICRVF--- 100
Query: 876 DISVSEHVLDTE--TLMLSNITSDDDVEEATEAALSTVDSDF-GR-TKDPIKMYMREMGS 931
S ++ L E +LS + + + A D D G ++ + + +
Sbjct: 101 STSPAKDSLSFEDFLDLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTG 160
Query: 932 VELLTRDGEIEIAKRIEEGLKDM 954
TR E+ + I+ L++
Sbjct: 161 EGEDTRLSASEMKQLIDNILEES 183
>2ghw_B Anti-SARS SCFV antibody, 80R; S protein, neutralizing antibody,
virus/viral protein/antibiotic complex; 2.30A {Homo
sapiens} SCOP: b.1.1.1 b.1.1.1
Length = 247
Score = 31.9 bits (73), Expect = 1.2
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS+YA W+RQA
Sbjct: 28 GFAFSSYAMHWVRQA 42
Score = 31.9 bits (73), Expect = 1.2
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS+YA W+RQA
Sbjct: 28 GFAFSSYAMHWVRQA 42
>1iom_A Citrate synthase; open form, riken structural genomics/proteomics
in RSGI, structural genomics, lyase; 1.50A {Thermus
thermophilus} SCOP: a.103.1.1 PDB: 1ixe_A*
Length = 377
Score = 32.1 bits (74), Expect = 1.4
Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 100 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGE--- 150
M+ I + + E L+ + G + DP + ++ + + + G
Sbjct: 229 MIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGVLEKL-ARLVAEKHGHSKE 287
Query: 151 IEIAKRIEEGLKDM 164
+I K +EE +
Sbjct: 288 YQILKIVEEEAGKV 301
Score = 32.1 bits (74), Expect = 1.4
Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 890 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGE--- 940
M+ I + + E L+ + G + DP + ++ + + + G
Sbjct: 229 MIQEIGTPERAREWVREKLAKKERIMGMGHRVYKAFDPRAGVLEKL-ARLVAEKHGHSKE 287
Query: 941 IEIAKRIEEGLKDM 954
+I K +EE +
Sbjct: 288 YQILKIVEEEAGKV 301
>3k81_A Single strand antibody VHH domain; krepa6, single domain antibody,
immune system, RNA BIND protein; 3.40A {Lama glama}
Length = 127
Score = 30.5 bits (70), Expect = 1.4
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G F++ A W R+A
Sbjct: 26 GITFASEAWGWYRRA 40
Score = 30.5 bits (70), Expect = 1.4
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G F++ A W R+A
Sbjct: 26 GITFASEAWGWYRRA 40
>1vgm_A 378AA long hypothetical citrate synthase; open form, transferase;
2.00A {Sulfolobus tokodaii}
Length = 378
Score = 32.1 bits (74), Expect = 1.4
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 12/71 (16%)
Query: 100 MLSNITSDDDVEEATEAALSTVDSD---FG----RTKDPIKMYMREMGSVELLTRDGE-- 150
I S ++ ++ E + S FG +T DP + + + ++
Sbjct: 229 QFVEIGSVENADKWFEEKIIKGKSRLMGFGHRVYKTYDPRAKIFKTL-AKSFAEKNENVK 287
Query: 151 --IEIAKRIEE 159
EIA+RIE+
Sbjct: 288 KYYEIAERIEK 298
Score = 32.1 bits (74), Expect = 1.4
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 12/71 (16%)
Query: 890 MLSNITSDDDVEEATEAALSTVDSD---FG----RTKDPIKMYMREMGSVELLTRDGE-- 940
I S ++ ++ E + S FG +T DP + + + ++
Sbjct: 229 QFVEIGSVENADKWFEEKIIKGKSRLMGFGHRVYKTYDPRAKIFKTL-AKSFAEKNENVK 287
Query: 941 --IEIAKRIEE 949
EIA+RIE+
Sbjct: 288 KYYEIAERIEK 298
>3juy_B 3B3 single chain variant HIV-1 antibody; envelope protein GP120,
broadly neutralizing antibody, 3B3 single chain variable
fragment, immune system; 2.50A {Homo sapiens}
Length = 256
Score = 31.6 bits (72), Expect = 1.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 450 GYKFSTYATWWIRQA 464
GY+FS + W+RQA
Sbjct: 32 GYRFSHFTVHWVRQA 46
Score = 31.6 bits (72), Expect = 1.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY+FS + W+RQA
Sbjct: 32 GYRFSHFTVHWVRQA 46
>1sjv_A R9; camelids antibody, domain swapping, heavy chain antibody, AN;
1.94A {Lama glama} SCOP: b.1.1.1
Length = 114
Score = 30.1 bits (69), Expect = 1.5
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G FS W RQA
Sbjct: 26 GNTFSGGFMGWYRQA 40
Score = 30.1 bits (69), Expect = 1.5
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G FS W RQA
Sbjct: 26 GNTFSGGFMGWYRQA 40
>1ypz_F T-cell receptor gamma chain, beta-2-microglobulin; H2-T22 protein,
T cell receptor delta, immune system; HET: NAG MAN FUC;
3.40A {Mus musculus} SCOP: b.1.1.1 b.1.1.2
Length = 230
Score = 31.4 bits (72), Expect = 1.6
Identities = 4/15 (26%), Positives = 5/15 (33%)
Query: 450 GYKFSTYATWWIRQA 464
F + W RQ
Sbjct: 27 IESFRSVTIHWYRQK 41
Score = 31.4 bits (72), Expect = 1.6
Identities = 4/15 (26%), Positives = 5/15 (33%)
Query: 1240 GYKFSTYATWWIRQA 1254
F + W RQ
Sbjct: 27 IESFRSVTIHWYRQK 41
>2yc1_A Single chain antibody fragment 9004G; immune system-toxin complex,
scorpion toxin; 1.90A {Homo sapiens} PDB: 2ybr_A 1dql_H
3cfi_C
Length = 117
Score = 30.1 bits (69), Expect = 1.7
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G+ F YA W+RQ
Sbjct: 26 GFTFDNYAMHWLRQV 40
Score = 30.1 bits (69), Expect = 1.7
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ F YA W+RQ
Sbjct: 26 GFTFDNYAMHWLRQV 40
>1igy_B IGG1 intact antibody MAB61.1.3; intact immunoglobulin, V region, C
region, hinge region, immunoglobulin; HET: NAG FUL NDG
BMA MAN GAL FUC; 3.20A {Mus musculus} SCOP: b.1.1.1
b.1.1.2 b.1.1.2 b.1.1.2
Length = 434
Score = 31.8 bits (72), Expect = 1.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
GY F+TY WI+Q
Sbjct: 25 GYTFTTYTIHWIKQR 39
Score = 31.8 bits (72), Expect = 1.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY F+TY WI+Q
Sbjct: 25 GYTFTTYTIHWIKQR 39
>3c57_A Two component transcriptional regulatory protein; response
regulator, two-component regulatory system, DNA-BIN
protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A
1zlj_A
Length = 95
Score = 29.6 bits (67), Expect = 1.8
Identities = 7/36 (19%), Positives = 16/36 (44%)
Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
+ ++ S ++D L+ LT +E +L +
Sbjct: 3 SSHHHHHHSSGLVPRGSHMQDPLSGLTDQERTLLGL 38
Score = 29.6 bits (67), Expect = 1.8
Identities = 7/36 (19%), Positives = 16/36 (44%)
Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 1377
+ ++ S ++D L+ LT +E +L +
Sbjct: 3 SSHHHHHHSSGLVPRGSHMQDPLSGLTDQERTLLGL 38
>1rjc_A 1D2L19, camelid heavy chain antibody; beta sandwich, immunoglobulin
fold, protein-protein hetero C alpha-beta orthogonal
bundle, immune system-hydrolase compl; 1.40A {Camelus
dromedarius} SCOP: b.1.1.1 PDB: 1ri8_A 1xfp_A 1jtt_A
2x6m_A 1zmy_A 1f2x_K
Length = 137
Score = 30.5 bits (70), Expect = 1.9
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G S+ W RQA
Sbjct: 26 GATSSSNCMGWFRQA 40
Score = 30.5 bits (70), Expect = 1.9
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G S+ W RQA
Sbjct: 26 GATSSSNCMGWFRQA 40
>1kxv_C Camelid VHH domain CAB10; beta 8 alpha 8, beta barrel, hydrolase,
immune system; 1.60A {Camelus dromedarius} SCOP: b.1.1.1
Length = 121
Score = 30.1 bits (69), Expect = 1.9
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G TY W R+A
Sbjct: 26 GNTLCTYDMSWYRRA 40
Score = 30.1 bits (69), Expect = 1.9
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G TY W R+A
Sbjct: 26 GNTLCTYDMSWYRRA 40
>3k74_B Nanobody; immunoglobulin, antibiotic resista methotrexate
resistance, NADP, one-carbon metabolism, oxidoreductase,
trimethoprim resistance; 1.95A {Lama glama}
Length = 115
Score = 29.7 bits (68), Expect = 1.9
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 450 GYKFSTYATWWIRQA 464
G+ F+ Y +W+R+A
Sbjct: 24 GFTFNNYWMYWVRRA 38
Score = 29.7 bits (68), Expect = 1.9
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ F+ Y +W+R+A
Sbjct: 24 GFTFNNYWMYWVRRA 38
>1kxt_B Immunoglobulin VHH fragment; alpha 8 beta 8, beta barrel,
hydrolase, immune system; 2.00A {Camelus dromedarius}
SCOP: b.1.1.1
Length = 127
Score = 30.1 bits (69), Expect = 1.9
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
GY FS+Y W RQA
Sbjct: 26 GYTFSSYPMGWYRQA 40
Score = 30.1 bits (69), Expect = 1.9
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY FS+Y W RQA
Sbjct: 26 GYTFSSYPMGWYRQA 40
>3ljc_A ATP-dependent protease LA; LON N-domain, allosteric enzyme,
ATP-binding, DNA-binding, H nucleotide-binding, serine
protease, stress respo; 2.60A {Escherichia coli}
Length = 252
Score = 31.3 bits (72), Expect = 2.0
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ-ILEIV-VNKCGMPRL 326
E YIK + I E+L + +L DT+ + + +KQ +LE+ VN+ RL
Sbjct: 146 EGYIKLNKKIPPEVLTSLNSIDDPARLADTIAAHMP-LKLADKQSVLEMSDVNE----RL 200
Query: 327 HFIKVFPENEINLNWVDNETKIQ 349
++ E+EI+L V E +I+
Sbjct: 201 EYLMAMMESEIDLLQV--EKRIR 221
Score = 31.3 bits (72), Expect = 2.0
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ-ILEIV-VNKCGMPRL 1116
E YIK + I E+L + +L DT+ + + +KQ +LE+ VN+ RL
Sbjct: 146 EGYIKLNKKIPPEVLTSLNSIDDPARLADTIAAHMP-LKLADKQSVLEMSDVNE----RL 200
Query: 1117 HFIKVFPENEINLNWVDNETKIQ 1139
++ E+EI+L V E +I+
Sbjct: 201 EYLMAMMESEIDLLQV--EKRIR 221
>2xt1_B Camelid VHH 9; viral protein-immune system complex; 1.32A {Vicugna
pacos} PDB: 2xv6_B 2xxc_B 2xxm_B
Length = 121
Score = 30.2 bits (69), Expect = 2.0
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G F + W RQA
Sbjct: 28 GSFFMSNVMAWYRQA 42
Score = 30.2 bits (69), Expect = 2.0
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G F + W RQA
Sbjct: 28 GSFFMSNVMAWYRQA 42
>1zvh_A Immunoglobulin heavy chain antibody variable domain; beta sandwich,
immunoglobulin fold, protein-protein heterocomplex;
1.50A {Camelus dromedarius} SCOP: b.1.1.1 PDB: 3dwt_A
1g6v_K 1zv5_A 1kxq_E
Length = 134
Score = 30.1 bits (69), Expect = 2.0
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
GY S W RQA
Sbjct: 26 GYIASINYLGWFRQA 40
Score = 30.1 bits (69), Expect = 2.0
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY S W RQA
Sbjct: 26 GYIASINYLGWFRQA 40
>3ux9_B SCFV antibody; five helices, long loop connecting helix,
hydrophobic intera cytokine-immune system complex; 2.80A
{Homo sapiens}
Length = 256
Score = 31.1 bits (71), Expect = 2.1
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS+YA W+RQA
Sbjct: 160 GFTFSSYAMSWVRQA 174
Score = 31.1 bits (71), Expect = 2.1
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS+YA W+RQA
Sbjct: 160 GFTFSSYAMSWVRQA 174
>3tpk_A Immunoglobulin heavy chain antibody variable DOMA; immunoglobulin
heavy chain domains, VHH, complementarity DET regions,
CDR, oligomer-specific; 1.30A {Camelidae} PDB: 3ln9_A*
1zv5_A
Length = 136
Score = 30.2 bits (69), Expect = 2.2
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
GY FS W RQA
Sbjct: 30 GYTFSQEFVIWFRQA 44
Score = 30.2 bits (69), Expect = 2.2
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY FS W RQA
Sbjct: 30 GYTFSQEFVIWFRQA 44
>2wzp_D Camelid VHH5; baseplate, viral protein; 2.60A {Lama glama} PDB:
2bse_D
Length = 123
Score = 29.7 bits (68), Expect = 2.2
Identities = 4/15 (26%), Positives = 5/15 (33%)
Query: 450 GYKFSTYATWWIRQA 464
S + W RQ
Sbjct: 26 RRTGSNWCMGWFRQL 40
Score = 29.7 bits (68), Expect = 2.2
Identities = 4/15 (26%), Positives = 5/15 (33%)
Query: 1240 GYKFSTYATWWIRQA 1254
S + W RQ
Sbjct: 26 RRTGSNWCMGWFRQL 40
>1mqk_H Antibody 7E2 FV fragment, heavy chain; membrane protein, cytochrome
C oxidase, high- resolution structure, immune system;
1.28A {Mus musculus} SCOP: b.1.1.1 PDB: 1ar1_C 3ehb_C*
3hb3_C* 1qle_H* 2otu_B 2gsg_B 2otw_B 1qfw_I* 3ab0_B
1i8k_B 1i8i_B 1vhp_A 1bfv_H* 1cfv_H* 2bfv_H* 1dsf_H
Length = 127
Score = 30.1 bits (69), Expect = 2.2
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
G+ FS+Y W+RQ
Sbjct: 26 GFTFSSYTMSWVRQT 40
Score = 30.1 bits (69), Expect = 2.2
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ FS+Y W+RQ
Sbjct: 26 GFTFSSYTMSWVRQT 40
>3qyc_A VH domain of IGG molecule; immunoglobulin V domain fold, antibody,
immune system; 1.60A {Homo sapiens} PDB: 1ieh_A 1ohq_A
2uzi_H*
Length = 146
Score = 30.3 bits (69), Expect = 2.3
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G + S Y W+RQA
Sbjct: 28 GVRLSAYDMAWVRQA 42
Score = 30.3 bits (69), Expect = 2.3
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G + S Y W+RQA
Sbjct: 28 GVRLSAYDMAWVRQA 42
>3b9v_A Heavy chain variable domain; antibody engineering, phage display,
immune system; 1.80A {Homo sapiens} PDB: 1fvc_B 3p9w_B
1fgv_H 2vh5_H*
Length = 120
Score = 29.7 bits (68), Expect = 2.3
Identities = 4/15 (26%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
G+ W+R+A
Sbjct: 26 GFNIKDTYIGWVRRA 40
Score = 29.7 bits (68), Expect = 2.3
Identities = 4/15 (26%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ W+R+A
Sbjct: 26 GFNIKDTYIGWVRRA 40
>1zvy_A Immunoglobulin heavy chain antibody variable DOMA; beta sandwich,
immunoglobulin fold, protein protein heteroco alpha-beta
orthogonal bundle, hydrolase-immune system compl; 1.63A
{Camelus dromedarius} SCOP: b.1.1.1
Length = 136
Score = 30.1 bits (69), Expect = 2.3
Identities = 6/15 (40%), Positives = 6/15 (40%)
Query: 450 GYKFSTYATWWIRQA 464
G S W RQA
Sbjct: 26 GSTDSIEYMTWFRQA 40
Score = 30.1 bits (69), Expect = 2.3
Identities = 6/15 (40%), Positives = 6/15 (40%)
Query: 1240 GYKFSTYATWWIRQA 1254
G S W RQA
Sbjct: 26 GSTDSIEYMTWFRQA 40
>3k1k_C Enhancer; nanobody, antibody-complex, chromophore, luminescence,
photoprotein, luminescent protein/immune system complex;
HET: GYS; 2.15A {Lama pacos} PDB: 3miq_E* 3ogo_E*
Length = 123
Score = 29.8 bits (68), Expect = 2.4
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G+ + Y+ W RQA
Sbjct: 28 GFPVNRYSMRWYRQA 42
Score = 29.8 bits (68), Expect = 2.4
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ + Y+ W RQA
Sbjct: 28 GFPVNRYSMRWYRQA 42
>1jtp_A Single-domain antibody; immunoglobulin, heavy chain antibody, VHH,
interface, binding, antibody, hydrolase; 1.90A {Camelus
dromedarius} SCOP: b.1.1.1 PDB: 1jto_A 1mel_A 2x89_A
Length = 148
Score = 30.2 bits (69), Expect = 2.4
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 450 GYKFSTYATWWIRQA 464
GY Y W RQA
Sbjct: 26 GYTIGPYCMGWFRQA 40
Score = 30.2 bits (69), Expect = 2.4
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 1240 GYKFSTYATWWIRQA 1254
GY Y W RQA
Sbjct: 26 GYTIGPYCMGWFRQA 40
>2ehb_A Calcineurin B-like protein 4; protein complex, Ca(II) IONS bound
to SOS3 (EF-hands 1 and 4 FISL motif; 2.10A
{Arabidopsis thaliana} PDB: 1v1g_A 1v1f_A
Length = 207
Score = 30.9 bits (70), Expect = 2.5
Identities = 17/80 (21%), Positives = 25/80 (31%), Gaps = 8/80 (10%)
Query: 6 KKTKIKNKKTKETL--LKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
KK E L + F + EE+E L + FK L + G + E
Sbjct: 9 KKKNAMRPPGYEDPELLASVTPF-----TVEEVEALYELFKKLSSSIIDDGLIHKEEFQL 63
Query: 64 FLPEDIIDHE-IIESIIKTF 82
L + + I F
Sbjct: 64 ALFRNRNRRNLFADRIFDVF 83
Score = 30.1 bits (68), Expect = 3.8
Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 1/52 (1%)
Query: 822 SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHE-IIESIIKTF 872
+ EE+E L + FK L + G + E L + + I F
Sbjct: 32 TVEEVEALYELFKKLSSSIIDDGLIHKEEFQLALFRNRNRRNLFADRIFDVF 83
>3r0m_A Llama VHH A12; IG domain, immune system; 1.50A {Lama glama} PDB:
3rjq_B* 1g9e_A 1hcv_A 1shm_A 3qxw_A 3qxv_A
Length = 143
Score = 30.1 bits (69), Expect = 2.6
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
G S+Y W RQA
Sbjct: 26 GRISSSYDMGWFRQA 40
Score = 30.1 bits (69), Expect = 2.6
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
G S+Y W RQA
Sbjct: 26 GRISSSYDMGWFRQA 40
>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat,
response regulator helix-turn-HELX binding, 3-helix
bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A
Length = 90
Score = 29.1 bits (66), Expect = 2.7
Identities = 6/38 (15%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 552 ENMLAPSDAA--LNASMRSVVKDILNSLTPRESKVLRM 587
+ ++ + + + LTPRE +L+
Sbjct: 3 SSHHHHHHSSGLVPRGSHMSSQKEQDVLTPRECLILQE 40
Score = 29.1 bits (66), Expect = 2.7
Identities = 6/38 (15%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 1342 ENMLAPSDAA--LNASMRSVVKDILNSLTPRESKVLRM 1377
+ ++ + + + LTPRE +L+
Sbjct: 3 SSHHHHHHSSGLVPRGSHMSSQKEQDVLTPRECLILQE 40
>3g9a_B Minimizer; antibody complex, chromophore, luminescence,
photoprotein, fluorescent protein/immune system complex,
nanobody; HET: GYS; 1.61A {Lama pacos}
Length = 139
Score = 29.8 bits (68), Expect = 2.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 450 GYKFSTYATWWIRQA 464
G FS+Y+ W RQA
Sbjct: 28 GDTFSSYSMAWFRQA 42
Score = 29.8 bits (68), Expect = 2.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1240 GYKFSTYATWWIRQA 1254
G FS+Y+ W RQA
Sbjct: 28 GDTFSSYSMAWFRQA 42
>2x1q_A Gelsolin nanobody; contractIle protein; 1.06A {Lama glama} PDB:
2x1p_A 2xa3_A 3k7u_A 3sn6_N* 3stb_A 2x1o_A 3k80_A 1ol0_A
1u0q_A 1qd0_A* 3ezj_B 3p0g_B* 1mvf_A 1t2j_A
Length = 127
Score = 29.7 bits (68), Expect = 2.8
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 450 GYKFSTYATWWIRQA 464
G FS Y W RQA
Sbjct: 26 GRTFSNYRMGWFRQA 40
Score = 29.7 bits (68), Expect = 2.8
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 1240 GYKFSTYATWWIRQA 1254
G FS Y W RQA
Sbjct: 26 GRTFSNYRMGWFRQA 40
>3o8j_A 2-methylcitrate synthase; short chain fatty acids, propionate
metabolism, 2-methylcitr cycle, PRPC or 2-MCS, GLTA or
CS, 2-methy synthase; 2.41A {Salmonella enterica}
Length = 404
Score = 31.0 bits (71), Expect = 2.9
Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 10/69 (14%)
Query: 100 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGE--- 150
+ + D+ E + + FG DP ++ + + +L G
Sbjct: 260 IQQRYETPDEAEADIRKRVENKEVVIGFGHPVYTIADPRHQVIKRV-AKQLSEEGGSLKM 318
Query: 151 IEIAKRIEE 159
IA R+E
Sbjct: 319 YHIADRLET 327
Score = 31.0 bits (71), Expect = 2.9
Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 10/69 (14%)
Query: 890 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGE--- 940
+ + D+ E + + FG DP ++ + + +L G
Sbjct: 260 IQQRYETPDEAEADIRKRVENKEVVIGFGHPVYTIADPRHQVIKRV-AKQLSEEGGSLKM 318
Query: 941 IEIAKRIEE 949
IA R+E
Sbjct: 319 YHIADRLET 327
>3hwk_A Methylcitrate synthase; niaid, ssgcid, structural genomics, seattle
structural genomics center for infectious disease,
tubercluosis; 2.30A {Mycobacterium tuberculosis}
Length = 414
Score = 31.0 bits (71), Expect = 3.0
Identities = 11/69 (15%), Positives = 21/69 (30%), Gaps = 10/69 (14%)
Query: 100 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGE--- 150
+ I + E A L+ + FG R D M+ + T
Sbjct: 273 DMIEIGDPANAREWLRAKLARKEKIMGFGHRVYRHGDSRVPTMKRA-LERVGTVRDGQRW 331
Query: 151 IEIAKRIEE 159
++I + +
Sbjct: 332 LDIYQVLAA 340
Score = 31.0 bits (71), Expect = 3.0
Identities = 11/69 (15%), Positives = 21/69 (30%), Gaps = 10/69 (14%)
Query: 890 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGE--- 940
+ I + E A L+ + FG R D M+ + T
Sbjct: 273 DMIEIGDPANAREWLRAKLARKEKIMGFGHRVYRHGDSRVPTMKRA-LERVGTVRDGQRW 331
Query: 941 IEIAKRIEE 949
++I + +
Sbjct: 332 LDIYQVLAA 340
>1qok_A MFE-23 recombinant antibody fragment; immunoglobulin, single-chain
FV, anti-carcinoembryonic antigen; 2.4A {Mus musculus}
SCOP: b.1.1.1 b.1.1.1
Length = 282
Score = 30.8 bits (70), Expect = 3.2
Identities = 4/15 (26%), Positives = 6/15 (40%)
Query: 450 GYKFSTYATWWIRQA 464
G+ W+RQ
Sbjct: 52 GFNIKDSYMHWLRQG 66
Score = 30.8 bits (70), Expect = 3.2
Identities = 4/15 (26%), Positives = 6/15 (40%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ W+RQ
Sbjct: 52 GFNIKDSYMHWLRQG 66
>3auv_A SC-DSFV derived from the G6-FAB; SC-DSFV (disulfide-stabilized
SCFV), SCFV, monovalent antibo antibody engineering,
immune system; 2.40A {Homo sapiens} PDB: 2kh2_B 3iy0_L
Length = 276
Score = 30.7 bits (70), Expect = 3.2
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 450 GYKFSTYATWWIRQA 464
G+ S Y W+RQA
Sbjct: 160 GFTISDYWIHWVRQA 174
Score = 30.7 bits (70), Expect = 3.2
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 1240 GYKFSTYATWWIRQA 1254
G+ S Y W+RQA
Sbjct: 160 GFTISDYWIHWVRQA 174
>2p2w_A Citrate synthase; transferase, structural genomics, NPPSFA,
national project O structural and functional analyses;
HET: FLC; 1.90A {Thermotoga maritima}
Length = 367
Score = 30.6 bits (70), Expect = 3.9
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 100 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGEIEI 153
ML I S+D VEE + L FG +T DP ++++ + E I
Sbjct: 221 MLEEIGSEDRVEEFVQKCLKEKRKIMGFGHRVYKTYDPRAVFLKRVLQ-EHFPDSKLFRI 279
Query: 154 AKRIEE 159
A ++EE
Sbjct: 280 ASKLEE 285
Score = 30.6 bits (70), Expect = 3.9
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 890 MLSNITSDDDVEEATEAALSTVD--SDFG----RTKDPIKMYMREMGSVELLTRDGEIEI 943
ML I S+D VEE + L FG +T DP ++++ + E I
Sbjct: 221 MLEEIGSEDRVEEFVQKCLKEKRKIMGFGHRVYKTYDPRAVFLKRVLQ-EHFPDSKLFRI 279
Query: 944 AKRIEE 949
A ++EE
Sbjct: 280 ASKLEE 285
>2a19_B Interferon-induced, double-stranded RNA-activated kinase;
transferase, protein biosynthesis, protein synthesis
transferase complex; HET: TPO ANP; 2.50A {Homo sapiens}
PDB: 2a1a_B*
Length = 284
Score = 30.3 bits (69), Expect = 4.5
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 1392 VGKQFDVTRERIRQIEAKALRKLRHPS--RYY 1421
V K+ E+ + E KAL KL H + Y
Sbjct: 40 VIKRVKYNNEKAER-EVKALAKLDHVNIVHYN 70
>1dgu_A Calcium-saturated CIB; helical, EF-hands, blood clotting; NMR {Homo
sapiens} SCOP: a.39.1.5 PDB: 1dgv_A 1xo5_A 1y1a_A*
Length = 183
Score = 29.7 bits (67), Expect = 4.6
Identities = 20/143 (13%), Positives = 49/143 (34%), Gaps = 15/143 (10%)
Query: 32 SREEIENLRKKFKILIKLGK------ERGYLTFSEINDF--LPEDIIDHEIIESIIKTFR 83
+++EI ++F L+ + R + F +I L + I +
Sbjct: 15 TKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPA 74
Query: 84 YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGS 141
+S + + +LS + + + A + D D ++ + + +
Sbjct: 75 KDSLSFEDFL-----DLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTG 129
Query: 142 VELLTRDGEIEIAKRIEEGLKDM 164
TR E+ + I+ L++
Sbjct: 130 EGEDTRLSASEMKQLIDNILEES 152
Score = 29.7 bits (67), Expect = 4.6
Identities = 20/143 (13%), Positives = 49/143 (34%), Gaps = 15/143 (10%)
Query: 822 SREEIENLRKKFKILIKLGK------ERGYLTFSEINDF--LPEDIIDHEIIESIIKTFR 873
+++EI ++F L+ + R + F +I L + I +
Sbjct: 15 TKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPA 74
Query: 874 YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGS 931
+S + + +LS + + + A + D D ++ + + +
Sbjct: 75 KDSLSFEDFL-----DLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTG 129
Query: 932 VELLTRDGEIEIAKRIEEGLKDM 954
TR E+ + I+ L++
Sbjct: 130 EGEDTRLSASEMKQLIDNILEES 152
>2zfd_A Calcineurin B-like protein 2; calcium binding protein,
protein-protein complex, ATP-bindin kinase,
nucleotide-binding; 1.20A {Arabidopsis thaliana} SCOP:
a.39.1.5 PDB: 1uhn_A
Length = 226
Score = 29.4 bits (66), Expect = 8.1
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 32 SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIID-HEIIESIIKTF 82
S EIE L + FK + + G + E L + + + F
Sbjct: 43 SVSEIEALYELFKKISSAVIDDGLINKEEFQLALFKTNKKESLFADRVFDLF 94
Score = 29.4 bits (66), Expect = 8.1
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 822 SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIID-HEIIESIIKTF 872
S EIE L + FK + + G + E L + + + F
Sbjct: 43 SVSEIEALYELFKKISSAVIDDGLINKEEFQLALFKTNKKESLFADRVFDLF 94
>3m65_A ATP-dependent protease LA 1; coiled-coil, ATP-binding, hydrolase,
nucleotide-binding, Pro serine protease, stress
response; 2.60A {Bacillus subtilis}
Length = 209
Score = 29.0 bits (66), Expect = 8.6
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ-ILEIV-VNKCGMPRL 326
+ YIK IS E + ++ D + + + + +KQ ILE V RL
Sbjct: 137 DQYIKISKKISAETYAAVTDIEEPGRMADIVASHLP-LKLKDKQDILETADVKD----RL 191
Query: 327 HFIKVFPENEI 337
+ + F NE
Sbjct: 192 NKVIDFINNEK 202
Score = 29.0 bits (66), Expect = 8.6
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ-ILEIV-VNKCGMPRL 1116
+ YIK IS E + ++ D + + + + +KQ ILE V RL
Sbjct: 137 DQYIKISKKISAETYAAVTDIEEPGRMADIVASHLP-LKLKDKQDILETADVKD----RL 191
Query: 1117 HFIKVFPENEI 1127
+ + F NE
Sbjct: 192 NKVIDFINNEK 202
>3dd4_A KV channel-interacting protein 4; EF-hands protein, ION transport,
ionic channel, membrane, PO potassium channel, potassium
transport, transport; 3.00A {Mus musculus} PDB: 2e6w_A
Length = 229
Score = 29.1 bits (65), Expect = 9.9
Identities = 24/164 (14%), Positives = 53/164 (32%), Gaps = 14/164 (8%)
Query: 6 KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
+ ++++ LL+ F +++E++ L + FK G + +
Sbjct: 41 EMATVRHRPEALELLEAQSKF-----TKKELQILYRGFKNE----CPSGVVNEETFKEIY 91
Query: 66 PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA--LSTVDS 123
+ + F D + V + + +I V+E A L ++
Sbjct: 92 SQFFPQGDSTTYAHFLFNAFDTDHNGAVSFEDFIKGLSILLRGTVQEKLNWAFNLYDINK 151
Query: 124 DFGRTKD---PIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
D TK+ I + +M E + +E + M
Sbjct: 152 DGYITKEEMLDIMKAIYDMMGKCTYPVLKEDAPRQHVETFFQKM 195
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.135 0.372
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 21,917,054
Number of extensions: 1425628
Number of successful extensions: 4808
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4710
Number of HSP's successfully gapped: 294
Length of query: 1432
Length of database: 6,701,793
Length adjustment: 106
Effective length of query: 1326
Effective length of database: 3,742,167
Effective search space: 4962113442
Effective search space used: 4962113442
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (28.4 bits)