RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 001116
(1152 letters)
>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 = 72.4 bits (177), Expect = 9e-13
Identities = 91/595 (15%), Positives = 186/595 (31%), Gaps = 220/595 (36%)
Query: 447 QYILHLLDMDKLSATKRRILDYTKYEMLNTAFKTFGD--LGDDE------ELGPVDWPT- 497
Y+ L++ K+ ++LN F + L ++ +L + T
Sbjct: 66 GYVSSLVEPSKVGQFD---------QVLNLCLTEFENCYLEGNDIHALAAKL-LQENDTT 115
Query: 498 ---VKRYIRC---LNDLEGVPMHPHSAS------ETGDSLDPTNLRDIRIRLLNGVQ--- 542
K I+ + P S S G++ ++ + G Q
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNA---------QLVAIFGGQGNT 166
Query: 543 AAYWAMLDE------------GRITQTAANILMQSVDE----------GIDLASNELCDW 580
Y+ +E G + + +A L + + G+++ W
Sbjct: 167 DDYF---EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE-----W 218
Query: 581 RGLKDNVSFPNYYKFLQT---SMFPQKLITYFTVERLEFACSICAAFLRAHKIARQQLHD 637
L++ + P+ +L + S P LI ++ A + + +L
Sbjct: 219 --LENPSNTPDKD-YLLSIPIS-CP--LIGV-----IQLAHYV--VTAKLLGFTPGELRS 265
Query: 638 FI-GDSG-----IASVVIEESKVEGEDARKFLEDVRVNFPQVLHV---VKTR-QVTYSVL 687
++ G +G + +V I E+ E F + + + V + R Y
Sbjct: 266 YLKGATGHSQGLVTAVAIAETD-SWES---FFV----SVRKAITVLFFIGVRCYEAYPNT 317
Query: 688 NHLIDYIQNLEKVGLLEEKE---MLHLHDAVQSDLKRLLRNPPLVKFPKISDLISAHPLL 744
+ +++ + E ML + + Q ++ + + ++H
Sbjct: 318 SLPPSILEDSLENN---EGVPSPMLSISNLTQEQVQDYV------------NKTNSH--- 359
Query: 745 RELPPSVREPLELS---TKEIMKLSG--VTLY------REGSKPSGIWLISNGVVKWTSK 793
LP + +E+S + + +SG +LY R+ PSG+ +
Sbjct: 360 --LPAG--KQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGL-----------DQ 404
Query: 794 SIRNKHSL-HPVFTHGSNLGLYEVL-IGKPYMSDMVTDSVVLCFFIESDKILSILRSDPA 851
S R S F++ L + P+ S ++ + D I D
Sbjct: 405 S-RIPFSERKLKFSN-------RFLPVASPFHSHLLVPAS--------DLINK----DLV 444
Query: 852 VEDFLWQQSAIALSRILLPQIFEKLTMQDMRAL---IAERSKMTTCLRGEIIEIP----- 903
+ + I + P +++ D+R L I+ER + II +P
Sbjct: 445 KNNVSFNAKDIQI-----P-VYDTFDGSDLRVLSGSISER------IVDCIIRLPVKWET 492
Query: 904 ------YHCIGFLLEGFIKTHGLQEELITPPAALIPSQGNLSFRSAETSGVEAVS 952
H + F G GL G L+ R+ + +GV +
Sbjct: 493 TTQFKATHILDF---GPGGASGL---------------GVLTHRNKDGTGVRVIV 529
Score = 58.9 bits (142), Expect = 1e-08
Identities = 48/290 (16%), Positives = 95/290 (32%), Gaps = 91/290 (31%)
Query: 230 AQVSLGAVGMGL----AFGIASVLW----------LGFIFNDTVIEIALTLAVSYIAFFT 275
+Q GMG+ A +W GF ++++I + V+ F
Sbjct: 1626 SQ----EQGMGMDLYKTSKAAQDVWNRADNHFKDTYGF----SILDIVINNPVNLTIHFG 1677
Query: 276 AQEGADVSGVLTVMTLGMFYAA--VARTAFKGESQQSLHYFWEMVAYI----ANT--LIF 327
++G + + M FK ++ S Y + + T +
Sbjct: 1678 GEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALT 1737
Query: 328 ILS----GVVIAEGILGNDKIFQNHGNSWG-YLILLYIFVQVSRLFVVGTLYPVLRNFGY 382
++ + ++G++ D F H S G Y + L +
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGH--SLGEY----------AALASLA---------DV 1776
Query: 383 GLEWKEAIILVWSGLRGAVALSLSLSVKRSSGGSS---LITSETGTLFVFF--------- 430
+ + + +V+ RG +++ ++V R G S +I G + F
Sbjct: 1777 -MSIESLVEVVF--YRG---MTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVV 1830
Query: 431 ------TGGIVFLTLIVN--GSTTQYIL--HLLDMDKLSATKRRILDYTK 470
TG +V IVN QY+ L +D ++ +L++ K
Sbjct: 1831 ERVGKRTGWLVE---IVNYNVENQQYVAAGDLRALDTVT----NVLNFIK 1873
Score = 49.7 bits (118), Expect = 7e-06
Identities = 95/653 (14%), Positives = 178/653 (27%), Gaps = 257/653 (39%)
Query: 596 LQTSMF-PQKLITYFTVERL--EFACSI-------------------CAAFLR--AHKIA 631
L+ + P +F +L +F + FL + +
Sbjct: 16 LEHVLLVPTAS--FFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVE 73
Query: 632 RQQLHDFIGDSGIASVVIE-ESKV-EGED----ARKFLEDVRVNFPQVLHVVKTRQVTYS 685
++ F D + + E E+ EG D A K L++ + ++K +
Sbjct: 74 PSKVGQF--DQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKN---YIT 128
Query: 686 VLNHLIDYIQNLEKVGLLEEKEMLHLHDAVQSDLKRL----------------LRN---- 725
L AV +L LR+
Sbjct: 129 ARIMAKRPFDKKSNSALFR---------AVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT 179
Query: 726 -PPLVKFPKISDLI-SAHPLLRELPPSVREPLELSTK--EIMKLSGVTLYREGSKPSGIW 781
LV DLI + L EL + + ++ T+ I++ L + P +
Sbjct: 180 YHVLVG-----DLIKFSAETLSELIRTTLDAEKVFTQGLNILEW----LENPSNTPDKDY 230
Query: 782 LIS-------NGVVKWTS-KSIRNKHSLHP---------VFTHGSNLGLYEVLIGKPYMS 824
L+S GV++ P H L + V I +
Sbjct: 231 LLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGL-VTAVAIA---ET 286
Query: 825 DMVT-DSVVLCFFIESDKILSILRSDPAVEDFLW-----QQSAIALSRILLPQIFEKLTM 878
D + +S FF+ K +++L F + + A LP +
Sbjct: 287 D--SWES----FFVSVRKAITVL--------F-FIGVRCYE---AYPNTSLPP---SILE 325
Query: 879 QDMRALIAERSKMTTCLRGEIIEIPYHCIGFLLEGFIK---THGLQEELIT--------- 926
+ S M + E ++ ++ +H + +
Sbjct: 326 DSLENNEGVPSPMLSI-SNLTQE--------QVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 927 -----PPAALIPSQG-NLSFRSAE-TSGVE---------AVSFSHQGSCYLVETRARVII 970
PP +L G NL+ R A+ SG++ + FS++ +L
Sbjct: 377 LVVSGPPQSL---YGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNR---FLP-------- 422
Query: 971 FDIAA-FEADKAVVRRTSSLFSHSSDQPHKSLSREHGNLMSWPEHFYKARQQKQNSEETD 1029
+A+ F HS L+ A D
Sbjct: 423 --VASPF---------------HSH-------------LLV------PASDLI----NKD 442
Query: 1030 RKANSLSARAMQLSIFGNMVDVQRRSRSFATGT-QTMQSHSLSFPSIPSHLNRRLVSVRS 1088
N++S A + I V + T ++ S SI + ++ +
Sbjct: 443 LVKNNVSFNAKDIQI-----PV------YDTFDGSDLRVLS---GSISERIVDCIIRLP- 487
Query: 1089 EGATTVR-EKLEVSRSTGQIPAPPSQNAGANESHVIDYSSDDSGAEDELIVRI 1140
V+ E ++T H++D+ + L R
Sbjct: 488 -----VKWETTTQFKAT----------------HILDFGPGGASGLGVLTHRN 519
Score = 44.7 bits (105), Expect = 2e-04
Identities = 93/616 (15%), Positives = 181/616 (29%), Gaps = 239/616 (38%)
Query: 57 TRVPYTVALLIIGIALGSLEYG----TSH-----QL-------------GKIGDG----- 89
TR P T ++ GSLE+ T+ QL G D
Sbjct: 6 TR-PLT-------LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTP 57
Query: 90 IRLWAS--------IDP------DLLLAVFLPALLFESSF--AMEVHQIKRCLVQM--IL 131
L ++P D +L + L FE+ + ++H + L+Q
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE--FENCYLEGNDIHALAAKLLQENDTT 115
Query: 132 LAGPGVMISTFFLGAALKLTFPYDWSWKTSLLLGGLLSATDPVA-VVAL----------L 180
L +I + A + P+D S L + + A +VA+
Sbjct: 116 LVKTKELIKNYIT-ARIMAKRPFD-KKSNSALFR---AVGEGNAQLVAIFGGQGNTDDYF 170
Query: 181 KELGASKKLNTIIEGESLMNDGTAIVVYQLFFQMVLGKSFGWGAIIKFLAQVSLGAVGMG 240
+EL + L Y + ++ S + L+++ +
Sbjct: 171 EEL---RDLYQT---------------YHVLVGDLIKFSA------ETLSELIRTTLDAE 206
Query: 241 LAF--GIASVLWLGFIFNDTVIEIALTLAVSYIAFFTAQEGADVSGVLTVMTLGMFYAAV 298
F G+ + WL + + T Y+ +S L + Y
Sbjct: 207 KVFTQGLNILEWL----ENP----SNTPDKDYLLS------IPISCPLIGVIQLAHYVVT 252
Query: 299 ARTAFKGESQQSLHYFWEMVAYIANTLIF---ILSGVVIAEGILGNDKIFQNHGNSWGYL 355
A+ G + E+ +Y+ +++ V IAE +SW
Sbjct: 253 AKLL--GFTPG------ELRSYLKGATGHSQGLVTAVAIAET------------DSWES- 291
Query: 356 ILLYIFVQVSRLFVVGTLYPVLRNFGYGLEWKEAIILVWSGLRG-----AVALSLSL--- 407
F R + L + G+R +L S+
Sbjct: 292 -----FFVSVRKA---------------ITV-----LFFIGVRCYEAYPNTSLPPSILED 326
Query: 408 SVKRSSGGSSLITSETGTLFVFFTGGI------------VFLTLIVNGSTTQYI------ 449
S++ + G S + S + + V ++L VNG+ +
Sbjct: 327 SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISL-VNGA-KNLVVSGPPQ 384
Query: 450 -LHLLDMD--KLSA-----------TKRRILDYTKY---------EMLNTAFKTF-GDLG 485
L+ L++ K A ++R++ ++ +L A DL
Sbjct: 385 SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLV 444
Query: 486 DDEELGPVDWPTVKRYIRCLNDLEGVPMHPHSASETGDSLDPTNLR----DIRIRLLNGV 541
+ V + D+ +P++ + G ++LR I R+++ +
Sbjct: 445 KNN----VSFNA--------KDI-QIPVY---DTFDG-----SDLRVLSGSISERIVDCI 483
Query: 542 --QAAYWAMLDEGRIT 555
W + + T
Sbjct: 484 IRLPVKWETTTQFKAT 499
Score = 41.6 bits (97), Expect = 0.002
Identities = 42/242 (17%), Positives = 78/242 (32%), Gaps = 79/242 (32%)
Query: 956 QGS--------CYLVETRARVIIFDIAAFEADK-----------AVVRR-TSSLFSHSSD 995
QGS Y A+ + ++ AD +V +L H
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDV-WN----RADNHFKDTYGFSILDIVINNPVNLTIHFGG 1678
Query: 996 QPHKSLSREHGNLMSWPEHFYKARQQ-KQNSEETDRKANSLSAR---------------- 1038
+ K + RE+ + M + E + + ++ +E + + S + R
Sbjct: 1679 EKGKRI-RENYSAMIF-ETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL 1736
Query: 1039 -AMQLSIFGNMVDVQRRSR-------SFATGTQTMQSHSL-----------SFPSIPSHL 1079
M+ + F ++ +S+ +FA G HSL SI S +
Sbjct: 1737 TLMEKAAFEDL-----KSKGLIPADATFA-G------HSLGEYAALASLADVM-SIESLV 1783
Query: 1080 NRRLVSVRSEGATTVREKLEVSRSTGQIPA-PPSQNAGANESHVIDYSSDDSGAEDELIV 1138
+V R + E+ RS + A P + A + + Y + G +V
Sbjct: 1784 --EVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLV 1841
Query: 1139 RI 1140
I
Sbjct: 1842 EI 1843
Score = 39.6 bits (92), Expect = 0.007
Identities = 47/231 (20%), Positives = 79/231 (34%), Gaps = 63/231 (27%)
Query: 1 MESVSEGLLQLPYRTLEEEQKSGGG-------SSPSEGNPTDAVIFVGISLVL-GI-ACR 51
++ +E L +L TL+ E+ G +PS D ++ + IS L G+
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA 247
Query: 52 HLLRGTRVPYTVALLIIGIALGSLEYGTSHQLGKIGDGIRLWASIDPDLLLAVFLPALLF 111
H Y V ++G G L S+ G G L+ AV +
Sbjct: 248 H--------YVVTAKLLGFTPGEL---RSYLKGATGHS--------QGLVTAVAIAETDS 288
Query: 112 ESSFAMEVHQIKRCLVQMILLAGPGVMISTFFLGAALKLTFPYDWSWKTSLLLGGLLSAT 171
SF + V + L FF+G +P TSL L +
Sbjct: 289 WESFFVSVRKAITVL---------------FFIGVRCYEAYP-----NTSLPPSILEDSL 328
Query: 172 D-----P---VAVVAL-LKELGAS-KKLNTIIEGE-----SLMNDGTAIVV 207
+ P +++ L +++ K N+ + SL+N +VV
Sbjct: 329 ENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVV 379
Score = 34.3 bits (78), Expect = 0.30
Identities = 41/226 (18%), Positives = 69/226 (30%), Gaps = 87/226 (38%)
Query: 5 SEGLLQL-----P---------YRTLEEEQKSGGGSSPSEGN-PTDAVIFVGISLVLGIA 49
+GLL P + L+ + G P DA F G SL
Sbjct: 1722 EKGLLSATQFTQPALTLMEKAAFEDLKSK-----------GLIPADAT-FAGHSL----- 1764
Query: 50 CRHLLRGTRVPYTVALLIIGIALGSLEYGTSHQLGKIGDGIRLWASIDPDLLLAVFLPAL 109
G Y AL + + S+E + + VF +
Sbjct: 1765 ------GE---YA-ALASLADVM-SIE-----------SLVEV-----------VFYRGM 1791
Query: 110 LFESSFAMEVHQIKRCLVQMILLAGPGVMISTFFLGAALKLTFPYDWSWKTSLLL----- 164
+ A+ ++ R MI + PG + ++F A + +T L+
Sbjct: 1792 TMQV--AVPRDELGRSNYGMIAI-NPGRVAASFSQEALQYVV--ERVGKRTGWLVEIVNY 1846
Query: 165 ---------GGLLSATDPVAVVALLKELGASKKLNTIIEGESLMND 201
G L A D V +L + +K++ I +SL +
Sbjct: 1847 NVENQQYVAAGDLRALD--TVTNVLNFIKL-QKIDIIELQKSLSLE 1889
Score = 31.9 bits (72), Expect = 1.8
Identities = 23/142 (16%), Positives = 44/142 (30%), Gaps = 41/142 (28%)
Query: 166 GLLSATD---P------VAVVALLKELGASKKLNTIIEGESLMNDG--TAIVVYQLFFQM 214
GLLSAT P A LK G + G SL G A+
Sbjct: 1724 GLLSATQFTQPALTLMEKAAFEDLKSKGL-IPADATFAGHSL---GEYAALA-------- 1771
Query: 215 VLGKSFGWGAIIKFLAQ--------VSLGAVGMGLAFGIASVLWLGFIFNDTVIEIALTL 266
L ++++ + V +G +G+ ++ N +A +
Sbjct: 1772 SLADVMSIESLVEVVFYRGMTMQVAVPRDELGRS-NYGMIAI-------NPG--RVAASF 1821
Query: 267 AVSYIAFFTAQEGADVSGVLTV 288
+ + + + G ++ +
Sbjct: 1822 SQEALQYVVERVGKRTGWLVEI 1843
Score = 30.0 bits (67), Expect = 6.9
Identities = 36/213 (16%), Positives = 69/213 (32%), Gaps = 68/213 (31%)
Query: 441 VNGSTTQYILHLLDMDKLSATKRRILDYTKYEMLNTAFKTFGDLGDDEELGPVDWPTVKR 500
+N +T Y + LSAT+ +T+ + F DL + G +
Sbjct: 1710 INEHSTSYTFRS-EKGLLSATQ-----FTQPALTLMEKAAFEDL---KSKGLIPADAT-- 1758
Query: 501 YIRCLNDLEGVPMHPHS-------ASETGDSLDPTNLRDIRIRLLN--G--VQAAY---- 545
G HS AS D + + + + ++ G +Q A
Sbjct: 1759 -------FAG-----HSLGEYAALAS-LADVMS---IESL-VEVVFYRGMTMQVAVPRDE 1801
Query: 546 -----WAM--LDEGRITQTAANILMQSVDEGIDLASNELC----------------DWRG 582
+ M ++ GR+ + + +Q V E + + L D R
Sbjct: 1802 LGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRA 1861
Query: 583 LKDNVSFPNYYKFLQTSMFPQKLITYFTVERLE 615
L + N+ K + + +L ++E +E
Sbjct: 1862 LDTVTNVLNFIKLQKIDI--IELQKSLSLEEVE 1892
>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 = 69.9 bits (170), Expect = 4e-12
Identities = 96/650 (14%), Positives = 190/650 (29%), Gaps = 185/650 (28%)
Query: 304 KGESQQSLHYFWEMVAYIANTL-IFILSGVVIAEGILGNDKIF-----QNHGNSWGYLIL 357
K +L FW +++ + F+ E +L + F + +
Sbjct: 58 KDAVSGTLRLFWTLLSKQEEMVQKFV-------EEVLRINYKFLMSPIKTEQRQPSMMTR 110
Query: 358 LYIFVQVSRLFVVGTLYP-----------VLRNFGYGLEWKEAIILVWSGLRGAVALSLS 406
+YI Q RL+ ++ LR L + +++ G+ G+ ++
Sbjct: 111 MYIE-QRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID--GVLGSGKTWVA 167
Query: 407 LSVKRSSGGSSLITSETGTLFVFFTGGIVFLTLIVNGSTT------QYILHLLDMDKLSA 460
L V S + I +L L S Q +L+ +D + S
Sbjct: 168 LDVCLSYK-----------VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR 216
Query: 461 TKRRILDYTKYEMLNTAFKTFGDLGDDEELGPVDWPTVKRYIRCLNDLEGVPMHPHSASE 520
+ + + + L K Y CL L V ++
Sbjct: 217 SDHSSNIKLRIHSIQAELRRL--LKS------------KPYENCLLVLLNV-----QNAK 257
Query: 521 TGDSLDPTNLRDIRIRLLNGVQAAYWAMLDEGRITQTAANILMQSVDEGIDLASNELCDW 580
++ + + ++L + T+ S ++ +
Sbjct: 258 AWNAFN------LSCKIL--L------------TTRFKQVTDFLSAATTTHISLDHHSM- 296
Query: 581 RGLKDNVSFPNYYKFLQTSMFPQKLITYFTVERLE------FACSICAAFLRAHKIARQQ 634
L + K+L PQ L E SI A +R
Sbjct: 297 -TLTPDEVKSLLLKYLDCR--PQDL-------PREVLTTNPRRLSIIAESIRDGLATWDN 346
Query: 635 LHDFIGDSGIASVVIEES--KVEGEDARK-------FLEDVRVNFP-QVLHVV---KTRQ 681
D + +IE S +E + RK F + P +L ++ +
Sbjct: 347 WKHVNCDK--LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI--PTILLSLIWFDVIKS 402
Query: 682 VTYSVLNHLIDYIQNLEKVGLLEE--KEM-LHLHDAVQSDLKRLLRNPPLVKFPKISDLI 738
V+N L Y L+E+ KE + + + +LK K+ +
Sbjct: 403 DVMVVVNKLHKY-------SLVEKQPKESTISIPS-IYLELKV-----------KLENEY 443
Query: 739 SAHPLLRELPPSVREPLELSTKEIMK--------------LSGVTLYREGSKPSGIWLIS 784
+ H + + P + +++ L + + ++L
Sbjct: 444 ALHRSIVD---HYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL-- 498
Query: 785 NGVVKWTSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILS 844
+ ++ + IR H GS L + L K Y + ++D
Sbjct: 499 D--FRFLEQKIR--HDSTAWNASGSILNTLQQL--KFYKP----------YICDNDPKYE 542
Query: 845 ILRSDPAVEDFLWQQSAIAL----SRILLPQIFEKLTMQDMRALIAERSK 890
L + + DFL + + + +L +I L M + A+ E K
Sbjct: 543 RLVNA--ILDFLPKIEENLICSKYTDLL--RI--AL-MAEDEAIFEEAHK 585
Score = 49.1 bits (116), Expect = 9e-06
Identities = 69/446 (15%), Positives = 125/446 (28%), Gaps = 131/446 (29%)
Query: 660 RKFLEDVRVNFPQVLHVVKTRQVTYSVL-----NHLIDYIQNLEKV----GLLEEKEMLH 710
+ L F + + S+L +H+I + L K+
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQ--- 75
Query: 711 LHDAVQSDLKRLLRNPPLVKFPKISDLISAHPLLRELPP----SVREPLELSTKEIMKLS 766
+ VQ ++ +LR + + I + R+ L + K +
Sbjct: 76 -EEMVQKFVEEVLRI----NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130
Query: 767 GVTLYREGSKPSGIWLISNGVVKWTSKSIRNK-HSLHP---VFTHGSNLGLYEVLIGKPY 822
V+ R +P +R L P V G LG GK +
Sbjct: 131 -VS--RL--QPY--------------LKLRQALLELRPAKNVLIDGV-LG-----SGKTW 165
Query: 823 M-SDMVTDSVVLCFFIESDKILSILRSDPAVEDFLWQQSAIALSRI----LLPQIFEKLT 877
+ D+ V C KI F W + L + ++ +KL
Sbjct: 166 VALDVCLSYKVQCKM--DFKI------------F-W----LNLKNCNSPETVLEMLQKLL 206
Query: 878 MQDMRALIAERSKMTTCLRGEIIEIPYHCIGFLLEGFIKTHGLQEELITPPAALIPSQGN 937
Q + + I++ H I L +K+ + L L+
Sbjct: 207 YQIDPNWTSRSDHSSN------IKLRIHSIQAELRRLLKSKPYENCL------LV----- 249
Query: 938 LS-FRSAETSGVEAVSFSHQGSC-YLVETRARVIIFDIAAFEADKAVV---------RRT 986
L ++A+ A F+ C L+ TR + + ++A +
Sbjct: 250 LLNVQNAKA--WNA--FNLS--CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303
Query: 987 SSLFSHSSDQPHKSLSRE----------------HGNLMSWPEHFYKARQQKQNSEETDR 1030
SL D + L RE L +W +K + + +
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW--DNWKHVNCDKLTTIIES 361
Query: 1031 KANSLSARAMQ-----LSIFGNMVDV 1051
N L + LS+F +
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAHI 387
>2pqq_A Putative transcriptional regulator; APC7345, streptomyces
coelicolor structural genomics, PSI-2, protein structure
initiative; 2.00A {Streptomyces coelicolor A3}
Length = 149
Score = 50.0 bits (120), Expect = 4e-07
Identities = 27/135 (20%), Positives = 48/135 (35%), Gaps = 8/135 (5%)
Query: 734 ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSK 793
+ D++ +PL L L S E+ G TL+ EG +++++ G VK
Sbjct: 3 MDDVLRRNPLFAALDDEQSAELRASMSEVTLARGDTLFHEGDPGDRLYVVTEGKVKLHRT 62
Query: 794 SIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAVE 853
S + ++ V +G + P + + V + + L P V
Sbjct: 63 SPDGRENMLAVVGPSELIGELSLFDPGPRTATGTALTEVKLLALGHGDLQPWLNVRPEV- 121
Query: 854 DFLWQQSAIALSRIL 868
A AL R +
Sbjct: 122 -------ATALLRAV 129
>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP),
dimer, inactive(APO, unliganded allostery, DNA binding,
cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB:
3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*
Length = 227
Score = 50.7 bits (122), Expect = 6e-07
Identities = 26/159 (16%), Positives = 62/159 (38%), Gaps = 10/159 (6%)
Query: 734 ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSK 793
+ ++++ + + + PS L + + G T++ EG +++I +G VK +
Sbjct: 4 MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRR 63
Query: 794 SIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSD--MVTDSVVLCFFIESDKILSILRSDPA 851
+ + +L + G + P S +T+ + ++ D + S + P
Sbjct: 64 APDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAV--SMDRDALRSWIADRPE 121
Query: 852 VEDFLWQQSAIALSRIL--LPQIFEKLTMQDMRALIAER 888
+ +Q L+R L L D+ +A++
Sbjct: 122 ----ISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQ 156
>3gyd_A CNMP-BD protein, cyclic nucleotide-binding domain; nucleotide
binding protein, structural genomics; HET: MSE CMP;
1.79A {Methylobacillus flagellatus KT}
Length = 187
Score = 48.6 bits (116), Expect = 2e-06
Identities = 24/174 (13%), Positives = 50/174 (28%), Gaps = 4/174 (2%)
Query: 710 HLHDAVQSDLKRLLRNPPLVKFPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVT 769
+ DL L F +I ++++ L + L +
Sbjct: 15 LYFQGMYPDLVHLGGADK--YFEEILEIVNKIKLFGDFSNEEVRYLCSYMQCYAAPRDCQ 72
Query: 770 LYREGSKPSGIWLISNGVVKWTSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTD 829
L EG + LI G V G+ +G ++ G P + V
Sbjct: 73 LLTEGDPGDYLLLILTGEVNVIKDIPNKGIQTIAKVGAGAIIGEMSMIDGMPRSASCVAS 132
Query: 830 SVVLCFFIESDKILSILRSDPAVEDFLWQQSAIALSRIL--LPQIFEKLTMQDM 881
+ D + +L + P + + + + L+ T+ ++
Sbjct: 133 LPTDFAVLSRDALYQLLANMPKLGNKVLIRLLQLLTARFRESYDRILPKTLGEL 186
>3mdp_A Cyclic nucleotide-binding domain (CNMP-BD) protei; structural
genomics, joint center for structural genomics; HET:
MSE; 1.90A {Geobacter metallireducens}
Length = 142
Score = 47.7 bits (114), Expect = 2e-06
Identities = 22/134 (16%), Positives = 49/134 (36%), Gaps = 3/134 (2%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVK-WTSKS 794
+ + + L + + L ++E +G +++E SK + L+ G V+ + S
Sbjct: 6 ERLRVYRFFASLTDEQLKDIALISEEKSFPTGSVIFKENSKADNLMLLLEGGVELFYSNG 65
Query: 795 IRNKHSLHPV--FTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAV 852
+ V G+ G+ ++ Y S V I ++ + ++ A+
Sbjct: 66 GAGSAANSTVCSVVPGAIFGVSSLIKPYHYTSSARATKPVRVVDINGARLREMSENNQAL 125
Query: 853 EDFLWQQSAIALSR 866
L A A+
Sbjct: 126 GQVLMNNVAAAVLA 139
>2qcs_B CAMP-dependent protein kinase type I-alpha regula subunit,
CAMP-dependent protein kinase, alpha-catalytic SU;
cyclic adenosine monophosphate; HET: SEP TPO ANP TAM;
2.20A {Bos taurus} PDB: 1rl3_A* 1rgs_A* 1ne6_A* 1ne4_A*
Length = 291
Score = 47.7 bits (113), Expect = 1e-05
Identities = 19/138 (13%), Positives = 47/138 (34%), Gaps = 1/138 (0%)
Query: 716 QSDLKRLLRNPPLVKFPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGS 775
+ +R+L L K + +S +L L R + + + + G + +G
Sbjct: 137 RDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQKIVVQGE 196
Query: 776 KPSGIWLISNGVVKWTSKSIRNKHSLH-PVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLC 834
++I G + N+ + G +L+ +P + +V + C
Sbjct: 197 PGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPKAATVVARGPLKC 256
Query: 835 FFIESDKILSILRSDPAV 852
++ + +L +
Sbjct: 257 VKLDRPRFERVLGPCSDI 274
Score = 44.2 bits (104), Expect = 1e-04
Identities = 27/167 (16%), Positives = 64/167 (38%), Gaps = 12/167 (7%)
Query: 734 ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSK 793
++ I + L L + R + + + ++G T+ ++G + ++I G +
Sbjct: 37 LAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVY-- 94
Query: 794 SIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAVE 853
+ N+ G + G ++ G P + + + V + I+ D IL +
Sbjct: 95 -VNNEW--ATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRK 151
Query: 854 DFLWQQSAIALSRILLPQIFEKLTMQDMRALIAERSKMTTCLRGEII 900
++++ +S I E L + R +A+ + G+ I
Sbjct: 152 RKMYEEFLSKVS------ILESLDKWE-RLTVADALEPVQFEDGQKI 191
>4ev0_A Transcription regulator, CRP family; CAMP binding, winged
helix-turn-helix motif, DNA binding, transcription
activator; HET: CMP; 2.40A {Thermus thermophilus}
Length = 216
Score = 46.1 bits (110), Expect = 2e-05
Identities = 25/155 (16%), Positives = 57/155 (36%), Gaps = 10/155 (6%)
Query: 738 ISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSIRN 797
+ PL L P + + + G ++ +G ++L+++G V+ +
Sbjct: 1 MKGSPLFHGLAPEEVDLALSYFQRRLYPQGKPIFYQGDLGQALYLVASGKVRLFRTHLGG 60
Query: 798 KHSLHPVFTHGSNLGLYEVLIGKPYMSDMV--TDSVVLCFFIESDKILSILRSDPAVEDF 855
+ + G G +L + V D+ +L + + L+++R P
Sbjct: 61 QERTLALLGPGELFGEMSLLDEGERSASAVAVEDTELL--ALFREDYLALIRRLPL---- 114
Query: 856 LWQQSAIALSRIL--LPQIFEKLTMQDMRALIAER 888
+ A L+R L + L+ ++ R +A
Sbjct: 115 VAHNLAALLARRLREADLELDLLSFEEARNRVAYA 149
>2z69_A DNR protein; beta barrel, dimerization helix, transcription
regulator; 2.10A {Pseudomonas aeruginosa}
Length = 154
Score = 43.8 bits (104), Expect = 5e-05
Identities = 22/136 (16%), Positives = 45/136 (33%), Gaps = 13/136 (9%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
L+ +H L L P + L S+ + G ++R+G + + +G VK +
Sbjct: 12 QLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRLTP 71
Query: 796 RNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMV---TDSVVLCFFIESDKILSILRSDPAV 852
+ + V + + + P S + + L L+ + +
Sbjct: 72 EGQEKILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLF--RFSNKAYLRQLQDNTPL 129
Query: 853 EDFLWQQSAIALSRIL 868
A+AL L
Sbjct: 130 --------ALALLAKL 137
>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP
regulatory protein, structural genomi 2, protein
structure initiative; 2.20A {Ruegeria pomeroyi} PDB:
3h3z_A*
Length = 237
Score = 45.0 bits (107), Expect = 6e-05
Identities = 30/119 (25%), Positives = 47/119 (39%), Gaps = 4/119 (3%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
+ L+R LP + L G TL+ + K I ++ +G VK +
Sbjct: 11 AIARNSLLIRSLPEQHVDALLSQAVWRSYDRGETLFLQEEKAQAIHVVIDGWVKLFRMTP 70
Query: 796 RNKHSLHPVFTHGSNLGLYEVLIGKPYMSDM--VTDSVVLCFFIESDKILSILRSDPAV 852
++ VFT G + G L PY VT V+ I S +S++R DP +
Sbjct: 71 TGSEAVVSVFTRGESFGEAVALRNTPYPVSAEAVTPCEVM--HIPSPVFVSLMRRDPEI 127
>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural
genomics, joint center for structural genomics, JCSG;
HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}
Length = 231
Score = 44.6 bits (106), Expect = 7e-05
Identities = 20/119 (16%), Positives = 41/119 (34%), Gaps = 4/119 (3%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
D + PL + +P E + + ++ + L++ GVV+ + S+
Sbjct: 6 DDLKRSPLFQNVPEDAMREALKVVTERNFQPDELVVEQDAEGEALHLVTTGVVRVSRVSL 65
Query: 796 RNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMV--TDSVVLCFFIESDKILSILRSDPAV 852
+ + +G VL + + + T L + + ILR P V
Sbjct: 66 GGRERVLGDIYAPGVVGETAVLAHQERSASVRALTPVRTL--MLHREHFELILRRHPRV 122
>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic
nucleotide-binding domain, structural genomics, joint
for structural genomics; 2.55A {Eubacterium rectale atcc
33656}
Length = 220
Score = 43.8 bits (104), Expect = 1e-04
Identities = 18/157 (11%), Positives = 53/157 (33%), Gaps = 8/157 (5%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
+ PL +L + ++ + + G ++ +G+ L+ +G ++ S
Sbjct: 3 SFENYFPLWNDLNTAQKKLISDNLITQHVKKGTIIHNGNMDCTGLLLVKSGQLRTYILSD 62
Query: 796 RNKHSLHPVFTHGSNLGLYEVLI--GKPYMSDMV--TDSVVLCFFIESDKILSILRSDPA 851
+ L I + + D+ + I ++ I++
Sbjct: 63 EGREITLYRLFDMDMCLLSASCIMRSIQFEVTIEAEKDTDLW--IIPAEIYKGIMKDSAP 120
Query: 852 VEDFLWQQSAIALSRILLPQIFEKLTMQDMRALIAER 888
V ++ + A S ++ + E++ + + +A
Sbjct: 121 VANYTNELMATRFSDVM--WLIEQIMWKSLDKRVASF 155
>3shr_A CGMP-dependent protein kinase 1; cyclic nucleotide binding domains,
cyclic nucleotide protein transferase, PKG; HET: CMP;
2.50A {Bos taurus}
Length = 299
Score = 44.1 bits (104), Expect = 1e-04
Identities = 25/162 (15%), Positives = 59/162 (36%), Gaps = 1/162 (0%)
Query: 716 QSDLKRLLRNPPLVKFPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGS 775
+ + ++ L+K + + + + P + LP + L +E +G + R+G+
Sbjct: 137 RQCFQTIMMRTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGA 196
Query: 776 KPSGIWLISNGVVKWTSKSIRNKHSLH-PVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLC 834
+ ++IS G V T + N+ + G G + ++++ V C
Sbjct: 197 RGDTFFIISKGKVNVTREDSPNEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTC 256
Query: 835 FFIESDKILSILRSDPAVEDFLWQQSAIALSRILLPQIFEKL 876
I+ D ++ V + ++ + F L
Sbjct: 257 LVIDRDSFKHLIGGLDDVSNKAYEDAEAKAKYEAEAAFFANL 298
Score = 37.6 bits (87), Expect = 0.019
Identities = 27/181 (14%), Positives = 62/181 (34%), Gaps = 19/181 (10%)
Query: 727 PLVKFPK-------ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSG 779
KF K I + I + ++ L S + + + + +EG S
Sbjct: 23 AFRKFTKSERSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSL 82
Query: 780 IWLISNGVVKWTSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIES 839
++++ +G V+ + + G G +L + + T V + I+
Sbjct: 83 VYVMEDGKVE-----VTKEGVKLCTMGPGKVFGELAILYNCTRTATVKTLVNVKLWAIDR 137
Query: 840 DKILSILRSDPAVEDFLWQQSAIALSRILLPQIFEKLTMQDMRALIAERSKMTTCLRGEI 899
+I+ ++ + + L + F+ L + + +A+ + T GE
Sbjct: 138 QCFQTIMMRTGLIKHTEYME---FLKSV---PTFQSLPEEI-LSKLADVLEETHYENGEY 190
Query: 900 I 900
I
Sbjct: 191 I 191
>3tnp_B CAMP-dependent protein kinase type II-beta regula subunit; PKA RIIB
tetrameric holoenzyme, transferase; HET: SEP TPO; 2.30A
{Mus musculus} PDB: 3tnq_A* 1cx4_A* 2qvs_B*
Length = 416
Score = 44.0 bits (103), Expect = 2e-04
Identities = 21/143 (14%), Positives = 43/143 (30%), Gaps = 6/143 (4%)
Query: 716 QSDLKRLLRNPPLVKFPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGS 775
+ +R++ K I + P L+ L S R + + G + +G
Sbjct: 247 RVTFRRIIVKNNAKKRKMYESFIESLPFLKSLEVSERLKVVDVIGTKVYNDGEQIIAQGD 306
Query: 776 KPSGIWLISNGVVKWTSKSIRNKHSLHPVFTHGSNL------GLYEVLIGKPYMSDMVTD 829
+++ +G VK T K + G ++ KP +
Sbjct: 307 LADSFFIVESGEVKITMKRKGKSEVEENGAVEIARCFRGQYFGELALVTNKPRAASAHAI 366
Query: 830 SVVLCFFIESDKILSILRSDPAV 852
V C ++ +L +
Sbjct: 367 GTVKCLAMDVQAFERLLGPCMEI 389
Score = 38.6 bits (89), Expect = 0.011
Identities = 20/183 (10%), Positives = 55/183 (30%), Gaps = 15/183 (8%)
Query: 725 NPPLVKFPK-------ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKP 777
+ PK + + L + L P + + E + G + +G
Sbjct: 127 AESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVIDQGDDG 186
Query: 778 SGIWLISNGVVKWTSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFI 837
++I G K + + + + G ++ P + + S + +
Sbjct: 187 DNFYVIDRGTFDIYVKCDGVGRCVG-NYDNRGSFGELALMYNTPKAATITATSPGALWGL 245
Query: 838 ESDKILSILRSDPAVEDFLWQQSAIALSRILLPQIFEKLTMQDMRALIAERSKMTTCLRG 897
+ I+ + A + +++ + + + L + + + + G
Sbjct: 246 DRVTFRRIIVKNNAKKRKMYES---FIESL---PFLKSLEVSERLK-VVDVIGTKVYNDG 298
Query: 898 EII 900
E I
Sbjct: 299 EQI 301
>3of1_A CAMP-dependent protein kinase regulatory subunit; cyclic nucleotide
binding domain, evolution, PKA signaling, transfer; HET:
CMP; 2.21A {Saccharomyces cerevisiae}
Length = 246
Score = 42.9 bits (101), Expect = 3e-04
Identities = 25/137 (18%), Positives = 45/137 (32%), Gaps = 4/137 (2%)
Query: 716 QSDLKRLLRNPPLVKFPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGS 775
+ +++L K DL+ + P+L+ L R L + + G T+ REG
Sbjct: 105 RLTFRKILLGSSFKKRLMYDDLLKSMPVLKSLTTYDRAKLADALDTKIYQPGETIIREGD 164
Query: 776 KPSGIWLISNGVVKWTSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCF 835
+ +LI G V + K + L G +L P + +
Sbjct: 165 QGENFYLIEYGAVDVSKKGQGVINKLKD----HDYFGEVALLNDLPRQATVTATKRTKVA 220
Query: 836 FIESDKILSILRSDPAV 852
+ +L V
Sbjct: 221 TLGKSGFQRLLGPAVDV 237
Score = 39.4 bits (92), Expect = 0.004
Identities = 30/169 (17%), Positives = 58/169 (34%), Gaps = 16/169 (9%)
Query: 734 ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSK 793
+ I + L +L + + +E G T+ ++G + +++ G V +
Sbjct: 5 LEKSIRNNFLFNKLDSDSKRLVINCLEEKSVPKGATIIKQGDQGDYFYVVEKGTVDFYVN 64
Query: 794 SIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAVE 853
+S P GS+ G ++ P + +V S L + ++ R
Sbjct: 65 D-NKVNSSGP----GSSFGELALMYNSPRAATVVATSDCLLWALD--------RLTFRKI 111
Query: 854 DFLWQQSAIALSRILLPQ--IFEKLTMQDMRALIAERSKMTTCLRGEII 900
+ LL + + LT D RA +A+ GE I
Sbjct: 112 LLGSSFKKRLMYDDLLKSMPVLKSLTTYD-RAKLADALDTKIYQPGETI 159
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix,
homodimer, transcription regulator; 3.60A {Pseudomonas
aeruginosa}
Length = 227
Score = 41.9 bits (99), Expect = 5e-04
Identities = 24/155 (15%), Positives = 56/155 (36%), Gaps = 7/155 (4%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
L+ +H L L P + L S+ + G ++R+G + + +G VK +
Sbjct: 9 QLLQSHHLFEPLSPVQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLISGCVKIYRLTP 68
Query: 796 RNKHSLHPVFTHGSNLGLYEVLIGKP-YMSD--MVTDSVVLCFFIESDKILSILRSDPAV 852
+ + V + + + P Y++ V S + + L L+ + +
Sbjct: 69 EGQEKILEVTNERNTFAEAMMFMDTPNYVATAQAVVPSQLF--RFSNKAYLRQLQDNTPL 126
Query: 853 EDFLWQQSAIALSRILLPQIFEKLTMQDMRALIAE 887
L + + L + E L++++ +
Sbjct: 127 ALALLAKLSTRLHQ--RIDEIETLSLKNATHRVVR 159
>1o7f_A CAMP-dependent RAP1 guanine-nucleotide exchange factor; EPAC2,
CAMP-GEF2, campb binding doamin, regulation; 2.5A {Mus
musculus} SCOP: a.4.5.31 b.82.3.2 b.82.3.2
Length = 469
Score = 42.2 bits (98), Expect = 8e-04
Identities = 39/352 (11%), Positives = 92/352 (26%), Gaps = 20/352 (5%)
Query: 712 HDAVQSDLKRLLRNPPLVKFPK----ISDLISAHPLLRELPPSVREPLELSTKEIMKLSG 767
H ++ L PL + + I + + P++ + L G
Sbjct: 14 HSQSSAEWIACLDKRPLERSSEDVDIIFTRLKGVKAFEKFHPNLLRQICLCGYYENLEKG 73
Query: 768 VTLYREGSKPSGIWLISNGVVKWTSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMS-DM 826
+TL+R+G + + + G + + + T G E ++ +
Sbjct: 74 ITLFRQGDIGTNWYAVLAGSLDVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATI 133
Query: 827 VTDSVVLCFFIESDKILSILRSDPAVEDFL----WQQSAIALSRILLPQIFEKLTMQDMR 882
VT IE + ++ L + + +P + + +R
Sbjct: 134 VTRESSELLRIEQEDFKALWEKYRQYMAGLLAPPYGVMETGSNNDRIPDKENVPSEKILR 193
Query: 883 ALIAERSKMTTCLRGEIIEIPYHCIGFLLEGFIKTHGLQEELITPPAALIPSQGNLSFRS 942
A R + + I + YH + + EL+ +I + R
Sbjct: 194 AGKILRIAILSRAPHMIRDRKYH------LKTYRQCCVGTELVD---WMIQQTSCVHSR- 243
Query: 943 AETSGVEAVSFSHQGSCYLVETRARVIIFDIAAFEADKAVVRRTSSLFSHSSDQPHKSLS 1002
+ G V+ + D + +
Sbjct: 244 -TQAVGMWQVLLEDGVLNHVDQERHFQDKYLFYRFLDDEREDAPLPTEEEKKECDEELQD 302
Query: 1003 REHGNLMSWPEHFYKARQQKQNSEETDRKANSLSARAMQLSIFGNMVDVQRR 1054
P+ + +K + T + + + ++ +R
Sbjct: 303 TMLLLSQMGPDAHMRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKR 354
>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics,
porphyromona gingivalis, PSI, protein structure
initiative; 1.90A {Porphyromonas gingivalis} SCOP:
a.4.5.4 b.82.3.2
Length = 232
Score = 41.5 bits (98), Expect = 8e-04
Identities = 28/151 (18%), Positives = 59/151 (39%), Gaps = 10/151 (6%)
Query: 742 PLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSIRNKHSL 801
+ L RE L+ + T++ EG P+ ++ + G +K + + + +
Sbjct: 16 DVWSLLNEEERELLDKEIQPFPCKKASTVFSEGDIPNNLFYLYEGKIKILREGVYGRFHI 75
Query: 802 HPVFTHGSNLGLYEVLIGKPYMSD--MVTDSVVLCFFIESDKILSILRSDPAVEDFLWQQ 859
+ G G+ + S V +S VL I + I ++L+ + + +
Sbjct: 76 SRIVKPGQFFGMRPYFAEETCSSTAIAVENSKVL--AIPVEAIEALLKGNTS----FCRY 129
Query: 860 SAIALSRIL--LPQIFEKLTMQDMRALIAER 888
AL++ L + LT + +R +AE
Sbjct: 130 FLKALAKELGYAERRTVTLTQKHVRGRLAET 160
>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG,
PSI, protein structure initiative, joint center for S
genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2
Length = 213
Score = 41.1 bits (97), Expect = 8e-04
Identities = 20/153 (13%), Positives = 46/153 (30%), Gaps = 7/153 (4%)
Query: 738 ISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSIRN 797
+ + + + L K I+ G + + + ++ G +K S
Sbjct: 1 MGSDKIHHHHHHMDLKKLLPCGKVIVFRKGEIVKHQDDPIEDVLILLEGTLKTEHVSENG 60
Query: 798 KHSLHPVFTHGSNLGLYEVLIGKPYMSDMV---TDSVVLCFFIESDKILSILRSDPAVED 854
K + + +P V +S +L I + L +L D +
Sbjct: 61 KTLEIDEIKPVQIIASGFIFSSEPRFPVNVVAGENSKIL--SIPKEVFLDLLMKDRELLL 118
Query: 855 FLWQQSAIALSRILLPQIFEKLTMQDMRALIAE 887
F + + + + LT + +R +
Sbjct: 119 FFLKDVSEHFRV--VSEKLFFLTTKTLREKLMN 149
>4din_B CAMP-dependent protein kinase type I-beta regulat subunit,
CAMP-dependent protein kinase catalytic subunit A;
isoform diversity; HET: TPO SEP ATP; 3.70A {Homo
sapiens}
Length = 381
Score = 42.0 bits (98), Expect = 0.001
Identities = 19/138 (13%), Positives = 48/138 (34%), Gaps = 1/138 (0%)
Query: 716 QSDLKRLLRNPPLVKFPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGS 775
+ +R+L L K + +S +L L R + + + + G + +G
Sbjct: 228 RDSYRRILMGSTLRKRKMYEEFLSKVSILESLEKWERLTVADALEPVQFEDGEKIVVQGE 287
Query: 776 KPSGIWLISNGVVKWTSKSIRNKHSLH-PVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLC 834
++I+ G + N+ + G +L+ +P + +V + C
Sbjct: 288 PGDDFYIITEGTASVLQRRSPNEEYVEVGRLGPSDYFGEIALLLNRPRAATVVARGPLKC 347
Query: 835 FFIESDKILSILRSDPAV 852
++ + +L +
Sbjct: 348 VKLDRPRFERVLGPCSEI 365
>2ptm_A Hyperpolarization-activated (IH) channel; ION channel, cyclic
nucleotide binding domain, C-linker, CAM SPHCN1, HCN;
HET: CMP; 1.93A {Strongylocentrotus purpuratus}
Length = 198
Score = 39.6 bits (93), Expect = 0.002
Identities = 29/197 (14%), Positives = 75/197 (38%), Gaps = 15/197 (7%)
Query: 672 QVLHVVKTRQVTYSVLNHLIDYIQNLEKVGLLEEKEMLH-LHDAVQSDLKRLLRNPPLVK 730
QV ++ R++ + N ++DY + + + +E+ + + ++++ D+
Sbjct: 16 QVEEYMQYRKLPSHLRNKILDYYEYRYRGKMFDERHIFREVSESIRQDVANYNC------ 69
Query: 731 FPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKW 790
DL+++ P + + + + + +EG+ ++ I G+V
Sbjct: 70 ----RDLVASVPFFVGADSNFVTRVVTLLEFEVFQPADYVIQEGTFGDRMFFIQQGIVDI 125
Query: 791 TSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDP 850
SL GS G +L + ++ + ++ F + +L P
Sbjct: 126 IMSDGVIATSLSD----GSYFGEICLLTRERRVASVKCETYCTLFSLSVQHFNQVLDEFP 181
Query: 851 AVEDFLWQQSAIALSRI 867
A+ + + + L+RI
Sbjct: 182 AMRKTMEEIAVRRLTRI 198
>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding,
DNA-binding nucleotide-binding, transcription,
transcription regulation; HET: CMP; 1.66A {Escherichia
coli}
Length = 260
Score = 40.4 bits (95), Expect = 0.002
Identities = 27/161 (16%), Positives = 49/161 (30%), Gaps = 11/161 (6%)
Query: 733 KISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTS 792
K I + L + E S TL +G K ++ I G V
Sbjct: 43 KAMADIGSMVLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLI 102
Query: 793 KSIRNKHSLHPVFTHGSNLGLYEVLI-GKPYMSD--MVTDSVVLCFFIESDKILSILRSD 849
K K + G +G + G+ + T V I K +++ +
Sbjct: 103 KDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVA--EISYKKFRQLIQVN 160
Query: 850 PAVEDFLWQQSAIALSRIL--LPQIFEKLTMQDMRALIAER 888
P + + + ++R L + L + IA+
Sbjct: 161 PD----ILMRLSAQMARRLQVTSEKVGNLAFLLVTGRIAQT 197
>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural
genomics, joint center for structura genomics, JCSG;
2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4
b.82.3.2
Length = 232
Score = 39.9 bits (94), Expect = 0.003
Identities = 19/165 (11%), Positives = 48/165 (29%), Gaps = 21/165 (12%)
Query: 733 KISDLISAHPLLRELPPSVREPL-ELSTKEIMKLS-GVTLYREGSKPSGIWLISNGVVKW 790
+ D + PL + L + + +K G T+ + G+ + + + G +
Sbjct: 15 TMFDTLLQLPLFQGLCHEDFTSILDKVKLHFIKHKAGETIIKSGNPCTQLCFLLKGEISI 74
Query: 791 TSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMV---TDSVVLCFFIESDKILSILR 847
+ + N +++ + + + T+ + I +LS L
Sbjct: 75 VTNAKENIYTVIEQIEAPYLIEPQSLFGMNTNYASSYVAHTEVHTV--CISKAFVLSDLF 132
Query: 848 SDPAVEDFLWQQSAIALSRIL------LPQIFEKLTMQDMRALIA 886
+ I+ L D+++ I
Sbjct: 133 RYDIF--------RLNYMNIVSNRAQNLYSRLWDEPTLDLKSKII 169
>3bpz_A Potassium/sodium hyperpolarization-activated cyclic
nucleotide-gated channel 2; CNBD, C-linker, pacemaker,
HCN, HCN2, CAP, PKA, CAMP, ION channel; HET: CMP; 1.65A
{Mus musculus} PDB: 3ffq_A 1q3e_A* 1q43_A* 1q5o_A*
3u10_A* 2q0a_A* 3etq_A* 3u11_A* 3otf_A* 3u0z_A*
Length = 202
Score = 38.5 bits (90), Expect = 0.007
Identities = 32/197 (16%), Positives = 70/197 (35%), Gaps = 19/197 (9%)
Query: 672 QVLHVVKTRQVTYSVLNHLIDYIQNLEKVGLLEEKEMLH-LHDAVQSDLKRLLRNPPLVK 730
QV + ++ + DY ++ + + +E +L L+ ++ +
Sbjct: 17 QVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREKIVNFN------- 69
Query: 731 FPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKW 790
L+++ PL P+ + K + G + REG+ ++ I +GVV
Sbjct: 70 ---CRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSV 126
Query: 791 TSKSIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDP 850
+K + L GS G +L + + D+ + + D +L P
Sbjct: 127 LTKGNKEMK-LSD----GSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYP 181
Query: 851 AVEDFLWQQSAIALSRI 867
+ +A+ R+
Sbjct: 182 MMRRAF---ETVAIDRL 195
>1ft9_A Carbon monoxide oxidation system transcription regulator; heme
sensor, catabolite gene activator protein; HET: HEM;
2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1
Length = 222
Score = 36.9 bits (86), Expect = 0.020
Identities = 19/147 (12%), Positives = 47/147 (31%), Gaps = 10/147 (6%)
Query: 742 PLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSIRNKHSL 801
+ L E + + G + +G++++ +G ++ +
Sbjct: 6 NIANVLLSPDGETFFRGFRSKIHAKGSLVCTGEGDENGVFVVVDGRLR-VYLVGEEREIS 64
Query: 802 HPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAVEDFLWQQSA 861
T G ++ + + + V F + L++ P++ L
Sbjct: 65 LFYLTSGDMFCMHS-----GCLVEATERTEVR--FADIRTFEQKLQTCPSMAWGLIAILG 117
Query: 862 IALSRILLPQIFEKLTMQDMRALIAER 888
AL+ + + E L D++ IA
Sbjct: 118 RALTSCM--RTIEDLMFHDIKQRIAGF 142
>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 = 35.7 bits (81), Expect = 0.031
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 10/38 (26%)
Query: 81 HQLGKIGDGIRLWASIDPDLLLAVFLPALLFESSFAME 118
L K+ ++L+A D A PAL +++ ME
Sbjct: 20 QALKKLQASLKLYA---DD--SA---PALAIKAT--ME 47
Score = 35.3 bits (80), Expect = 0.037
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 760 KEIMKL-SGVTLYREGSKPSGIWLISNGVVK 789
+ + KL + + LY + S P+ L ++
Sbjct: 20 QALKKLQASLKLYADDSAPA---LAIKATME 47
>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat
transcription; HET: PR3; 2.3A {Listeria monocytogenes}
SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A
Length = 238
Score = 35.8 bits (83), Expect = 0.055
Identities = 14/123 (11%), Positives = 37/123 (30%), Gaps = 4/123 (3%)
Query: 767 GVTLYREGSKPSGIWLISNGVVKWTSKSIRNKHSLHPVFTHGSNLGLYEVLIGKP--YMS 824
++ + + +G+ K TS S + + + Y +
Sbjct: 26 KELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYN 85
Query: 825 DMVTDSVVLCFFIESDKILSILRSDPAVEDFLWQQSAIALSRILLPQIFEKLTMQDMRAL 884
V + I+ +++ +L + +++Q +S L F ++
Sbjct: 86 LEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSL--AKFNDFSINGKLGS 143
Query: 885 IAE 887
I
Sbjct: 144 ICS 146
>2l0e_A Sodium/hydrogen exchanger 1; transmembrane helix, membrane protein,
NHE1; NMR {Homo sapiens}
Length = 33
Score = 31.9 bits (72), Expect = 0.058
Identities = 14/29 (48%), Positives = 21/29 (72%)
Query: 159 KTSLLLGGLLSATDPVAVVALLKELGASK 187
K +LL G ++SA DPVAV+A+ +E+ K
Sbjct: 4 KDNLLFGSIISAVDPVAVLAVFEEIHKKK 32
>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery,
DNA binding cyclic A transcription regulator; HET: CMP;
1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A*
3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A*
1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A*
3rdi_A* 3rou_A* 3rpq_A* ...
Length = 210
Score = 35.3 bits (82), Expect = 0.073
Identities = 26/152 (17%), Positives = 47/152 (30%), Gaps = 11/152 (7%)
Query: 742 PLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSIRNKHSL 801
L + E S TL +G K ++ I G V K K +
Sbjct: 2 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMI 61
Query: 802 HPVFTHGSNLGLYEVLI-GKPYMSD--MVTDSVVLCFFIESDKILSILRSDPAVEDFLWQ 858
G +G + G+ + T V I K +++ +P +
Sbjct: 62 LSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVA--EISYKKFRQLIQVNPD----ILM 115
Query: 859 QSAIALSRIL--LPQIFEKLTMQDMRALIAER 888
+ + ++R L + L D+ IA+
Sbjct: 116 RLSAQMARRLQVTSEKVGNLAFLDVTGRIAQT 147
>1vp6_A CNBD, cyclic-nucleotide binding domain of mesorhizobium LOTI CNG
potassium channel; dimer helical bundle beta barrel core
with cyclic AMP bound; HET: CMP; 1.70A {Mesorhizobium
loti} SCOP: b.82.3.2 PDB: 3cl1_A* 2k0g_A* 2kxl_A 3clp_A*
1u12_A 3co2_A
Length = 138
Score = 33.8 bits (78), Expect = 0.11
Identities = 22/121 (18%), Positives = 48/121 (39%), Gaps = 7/121 (5%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
L++A PL ++L P+V + + + +G + R G ++ + G V + +
Sbjct: 11 QLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNP 70
Query: 796 RNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAVEDF 855
L P G+ G ++ G+P + + + V + S + S P + +
Sbjct: 71 V---ELGP----GAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEI 123
Query: 856 L 856
Sbjct: 124 F 124
>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA
transcription regulator, DNA binding protein; HET: HEM;
2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*
Length = 220
Score = 34.5 bits (80), Expect = 0.13
Identities = 23/152 (15%), Positives = 52/152 (34%), Gaps = 14/152 (9%)
Query: 738 ISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSIRN 797
++ LL L + +E LY ++ + ++L+ +G V+ + +
Sbjct: 6 LTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVR-VYLAYED 64
Query: 798 KHSLHPVFTHGSNLGLYEVLIGKPYMSDM--VTDSVVLCFFIESDKILSILRSDPAVEDF 855
K + G + + + + D+ +L + + +I+ PA
Sbjct: 65 KEFTLAILEAGD-------IFCTHTRAFIQAMEDTTIL--YTDIRNFQNIVVEFPAFSLN 115
Query: 856 LWQQSAIALSRILLPQIFEKLTMQDMRALIAE 887
+ + L I L +D R +AE
Sbjct: 116 MVKVLGDLLKN--SLTIINGLVFKDARLRLAE 145
>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity,
CRP, CLP, C-DI-GMP receptor, quorum SENS binding,
transcription; 2.30A {Xanthomonas campestris PV}
Length = 230
Score = 34.6 bits (80), Expect = 0.14
Identities = 18/161 (11%), Positives = 51/161 (31%), Gaps = 8/161 (4%)
Query: 734 ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSK 793
++ + L E + + ++R G ++ + +G V ++
Sbjct: 9 VTTTVRNATPSLTLDAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAE 68
Query: 794 SIRNKHSLHPVFTHGSNLGLYEVLI-GKPYMSD--MVTDSVVLCFFIESDKILSILRSDP 850
++ + F G +G + I T + I +++ + ++
Sbjct: 69 EDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELA--EISYERLQQLFQTSL 126
Query: 851 AVED-FLWQQSAIALSRIL--LPQIFEKLTMQDMRALIAER 888
+ + + + LS+ L + +L D+ I
Sbjct: 127 SPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRT 167
>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription,
transcription regulation; HET: BOG; 1.90A {Anabaena}
PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*
Length = 243
Score = 34.2 bits (79), Expect = 0.16
Identities = 15/123 (12%), Positives = 41/123 (33%), Gaps = 11/123 (8%)
Query: 734 ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSK 793
++ + + R++ P+ + + T++ G ++ + G VK +
Sbjct: 23 VTQDKALANVFRQMATGAFPPV---VETFER--NKTIFFPGDPAERVYFLLKGAVKLSRV 77
Query: 794 SIRNKHSLHPVFTHGSNLGLYEVLIGKPYMSDM----VTDSVVLCFFIESDKILSILRSD 849
+ + S G+ +L G T +L +++ L+ +
Sbjct: 78 YEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELL--SAPIEQVEQALKEN 135
Query: 850 PAV 852
P +
Sbjct: 136 PEL 138
>4ava_A Lysine acetyltransferase; allosteric regulation, domain coupling;
HET: ACO; 1.70A {Mycobacterium tuberculosis} PDB:
4avb_A* 4avc_A*
Length = 333
Score = 34.2 bits (78), Expect = 0.23
Identities = 18/125 (14%), Positives = 42/125 (33%), Gaps = 1/125 (0%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
+ ++ + + P L S + + +G L R+G LIS+G + +
Sbjct: 13 EDLAGMDVFQGCPAEGLVSLAASVQPLRAAAGQVLLRQGEPAVSFLLISSGSAEVS-HVG 71
Query: 796 RNKHSLHPVFTHGSNLGLYEVLIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAVEDF 855
+ ++ G +G +L P + + T + + +++ E
Sbjct: 72 DDGVAIIARALPGMIVGEIALLRDSPRSATVTTIEPLTGWTGGRGAFATMVHIPGVGERL 131
Query: 856 LWQQS 860
L
Sbjct: 132 LRTAR 136
>3ukn_A Novel protein similar to vertebrate potassium VOL channel,
subfamily H (EAG-related)...; KCNH, ELK, ERG, CNBD,
CNBHD, C-linker, ION channel; 2.20A {Danio rerio} PDB:
3ukt_B 3ukv_B
Length = 212
Score = 33.1 bits (76), Expect = 0.32
Identities = 27/203 (13%), Positives = 67/203 (33%), Gaps = 24/203 (11%)
Query: 672 QVLHVVKTRQVTYSVLNHLIDYIQNL--EKVGLLEEKEMLHLHDAVQSDLKRLLRNPPLV 729
+ ++ ++ ++ +++ Q G+ + + D +++D+ L N L+
Sbjct: 20 DLKDFIRVHRLPKALAQRMLECFQTTWSVNNGIDVSELLKDFPDELRADIAMHL-NKELL 78
Query: 730 KFPKISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVK 789
+ PL L L K G L R+G I+ + +G +
Sbjct: 79 Q----------LPLFESASRGCLRSLSLIIKTSFCAPGEFLIRQGDALQAIYFVCSGSM- 127
Query: 790 WTSKSIRNKHSLHPVFTHGSNLGLYEVLI----GKPYMSDMVTDSVVLCFFIESDKILSI 845
+ +++ L + G +G + +++ + +I + +
Sbjct: 128 ---EVLKDNTVLA-ILGKGDLIG--SDSLTKEQVIKTNANVKALTYCDLQYISLKGLREV 181
Query: 846 LRSDPAVEDFLWQQSAIALSRIL 868
LR P + L+ L
Sbjct: 182 LRLYPEYAQKFVSEIQHDLTYNL 204
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration;
HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP:
a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A*
3e5q_A 2h6b_A* 2h6c_A
Length = 250
Score = 32.3 bits (74), Expect = 0.64
Identities = 13/118 (11%), Positives = 31/118 (26%), Gaps = 5/118 (4%)
Query: 736 DLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVKWTSKSI 795
D A P G + G + + + + G +K
Sbjct: 9 DFCGAIIPDNFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFE 68
Query: 796 RNKHSLHPVFTHGSNLGLYEV-LIGKPYMSDMVTDSVVLCFFIESDKILSILRSDPAV 852
L S +G ++ G + + + + + ++ R+D +
Sbjct: 69 DGSEKLLYYAGGNSLIG--KLYPTGNNIYATAMEPTRTC--WFSEKSLRTVFRTDEDM 122
>2d93_A RAP guanine nucleotide exchange factor 6; CNMP_binding domain, PDZ
domain containing guanine nucleotide exchange factor 2,
PDZ-GEF2, RA-GEF-2; NMR {Homo sapiens}
Length = 134
Score = 31.6 bits (72), Expect = 0.65
Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 734 ISDLISAHPLLRELPPSVREPL-ELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVK 789
+ + + P + SVR L + E+++ +G + +G + ++I NG V+
Sbjct: 14 LLEFMHQLPAFANMTMSVRRELCSVMIFEVVEQAGAIILEDGQELDSWYVILNGTVE 70
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 32.6 bits (75), Expect = 0.90
Identities = 22/130 (16%), Positives = 46/130 (35%), Gaps = 29/130 (22%)
Query: 623 AFLRAHKIARQQLHDFIG---------DSGIASVVIEESKVEGEDARKFLED-VRVNFPQ 672
+ A AR+ H+F+ + A +E V+ R+ LE + P
Sbjct: 9 SLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPV 68
Query: 673 VLHVVKTRQVTYS-----VLNHLIDYIQNLEK---------VGLLEEKE-----MLHLHD 713
+ + R + VL + ++Q+ + V + E+E +L H+
Sbjct: 69 LPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHE 128
Query: 714 AVQSDLKRLL 723
+ D+ +
Sbjct: 129 VSRLDVVNFI 138
>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural
genomics, PSI-2, protein S initiative; HET: PG4 EPE;
1.82A {Clostridium difficile}
Length = 145
Score = 30.3 bits (69), Expect = 1.9
Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 11/62 (17%)
Query: 623 AFLRAHKIARQQLHDFIG-----------DSGIASVVIEESKVEGEDARKFLEDVRVNFP 671
A A + A+ H+ +G + GIA+ V+ + + D+
Sbjct: 15 AIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDMEGKGE 74
Query: 672 QV 673
++
Sbjct: 75 EI 76
>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics,
PSI2, MCSG, protein structure initiative; 1.60A
{Corynebacterium glutamicum}
Length = 146
Score = 29.2 bits (66), Expect = 4.1
Identities = 11/55 (20%), Positives = 24/55 (43%), Gaps = 11/55 (20%)
Query: 623 AFLRAHKIARQQLHDFIG-----------DSGIASVVIEESKVEGEDARKFLEDV 666
+ A + AR H++IG G+A+ +E + + R+ +E++
Sbjct: 14 VIVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISLDAVRQEVEEI 68
>1wgp_A Probable cyclic nucleotide-gated ION channel 6; cyclic nucleotide
monophosphate, CNMP, CNMP-binding, structural genomics;
NMR {Arabidopsis thaliana} SCOP: b.82.3.2
Length = 137
Score = 29.0 bits (65), Expect = 4.5
Identities = 10/56 (17%), Positives = 20/56 (35%)
Query: 734 ISDLISAHPLLRELPPSVREPLELSTKEIMKLSGVTLYREGSKPSGIWLISNGVVK 789
S + PL + + + + K + L REG + + I G ++
Sbjct: 4 GSSGVRRVPLFENMDERLLDAICERLKPCLFTEKSYLVREGDPVNEMLFIIRGRLE 59
>3gl3_A Putative thiol:disulfide interchange protein DSBE; oxidoreductase,
PSI-II, structural genomics, protein structure
initiative; 2.09A {Chlorobium tepidum tls}
Length = 152
Score = 29.2 bits (66), Expect = 4.7
Identities = 10/44 (22%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 633 QQLHDFIGDSG--IASVVIEESKVEGEDARKFLEDVRVNFPQVL 674
Q+ G + +V ++ DA KFL V F
Sbjct: 51 NQMQAKYKAKGFQVVAVNLDAKT---GDAMKFLAQVPAEFTVAF 91
>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC;
transcription, proteolysis; 1.50A {Bacillus subtilis}
PDB: 2y1r_A* 2k77_A
Length = 150
Score = 28.8 bits (65), Expect = 5.0
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 11/55 (20%)
Query: 623 AFLRAHKIARQQLHDFIG-----------DSGIASVVIEESKVEGEDARKFLEDV 666
A + A + H+ IG GIA+ ++ + E +K +E +
Sbjct: 13 VLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESL 67
>3ayf_A Nitric oxide reductase; oxidoreductase; HET: HEM BOG EPE LOP; 2.50A
{Geobacillus stearothermophilus} PDB: 3ayg_A*
Length = 800
Score = 30.0 bits (67), Expect = 5.6
Identities = 22/191 (11%), Positives = 57/191 (29%), Gaps = 11/191 (5%)
Query: 214 MVLGKSFGWGAIIKFLAQVSLGAVGMGLAFGIASVLWLGFIFNDTVIEIALTLAVSYIA- 272
+ + W + F+A + G + + W + + Y+
Sbjct: 359 AIFWIATAWLGMGIFIAPLVGGQEPKKQGLLVDLLFWALVVLVGGSMIGQWLGVNGYLGN 418
Query: 273 --FFTAQEGADVSG------VLTVMTLGMFYAAVARTAFKGESQQSLHYFWEMVAYIANT 324
F +G + ++ V+ + ++ V R +G ++S + + +
Sbjct: 419 EWFLLGHQGWEYIELGRIWQIILVVGMLLWLFIVFRGVKRGLKRESDKGGLIHLLFYSAI 478
Query: 325 LIFILSGVVIAEGILGNDKIFQNHGNSWGYLILLYIFVQVSRLFVVGTLYPVLRNFGYGL 384
+ N + W + + +V + V+G L LR
Sbjct: 479 AVPFFYIFAFFIQPDTNFTMAD-FWRWWIIHLWVEGIFEVFAVVVIGFLLVQLRLVTKKS 537
Query: 385 EWKEAIILVWS 395
+ A+ ++
Sbjct: 538 TVR-ALYFQFT 547
>4f8a_A Potassium voltage-gated channel subfamily H membe; probable
regulatory domain of potassium channel, membrane PR
transport protein; 2.20A {Mus musculus}
Length = 160
Score = 28.8 bits (65), Expect = 6.7
Identities = 12/89 (13%), Positives = 28/89 (31%), Gaps = 11/89 (12%)
Query: 701 GLLEEKEMLH-LHDAVQSDLKRLLRNPPLVKFPKISDLISAHPLLRELPPSVREPLELST 759
G +++L +++D+ L + HP R L +
Sbjct: 1 GSHMTEKVLQICPKDMRADICVHLN----------RKVFKEHPAFRLASDGCLRALAMEF 50
Query: 760 KEIMKLSGVTLYREGSKPSGIWLISNGVV 788
+ + G +Y G + + +G +
Sbjct: 51 QTVHCAPGDLIYHAGESVDSLCFVVSGSL 79
>3acz_A Methionine gamma-lyase; L-methionine; HET: LLP; 1.97A {Entamoeba
histolytica} PDB: 3aej_A* 3ael_A* 3aem_A* 3aen_A*
3aeo_A* 3aep_A*
Length = 389
Score = 29.4 bits (67), Expect = 7.1
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 7/41 (17%)
Query: 628 HKIARQQLHDFIGDSGIASVVIEESKVEGEDARKFLEDVRV 668
H IA++Q+ + ++ E A+K +E ++V
Sbjct: 293 HDIAKKQMTGY---GSTFLFEMKS----FEAAKKLMEHLKV 326
>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix,
two-stranded antiparallel coiled CO structural genomics,
PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB:
1xsx_A
Length = 95
Score = 27.5 bits (61), Expect = 7.5
Identities = 7/32 (21%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 678 KTRQVTYSVLNH--LIDYIQNLEKVGLLEEKE 707
KTR + + L++ YI+ L + ++ ++
Sbjct: 23 KTRIMYGANLSYALTGRYIKMLMDLEIIRQEG 54
>2f9s_A Thiol-disulfide oxidoreductase RESA; thioredoxin-like protein; HET:
MSE; 1.40A {Bacillus subtilis} SCOP: c.47.1.10 PDB:
1st9_A 1su9_A 2h1d_A 2h1b_A 2h1a_A 2h19_A 2h1g_A 3c71_A
3c73_A
Length = 151
Score = 28.4 bits (64), Expect = 7.7
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 5/44 (11%)
Query: 633 QQLHDFIGDSG--IASVVIEESKVEGEDARKFLEDVRVNFPQVL 674
+ G I +V + ESK F++ VNFP VL
Sbjct: 49 ANQYKHFKSQGVEIVAVNVGESK---IAVHNFMKSYGVNFPVVL 89
>1pff_A Methionine gamma-lyase; homocysteine; 2.50A {Trichomonas vaginalis}
SCOP: c.67.1.3
Length = 331
Score = 29.4 bits (67), Expect = 8.1
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 7/41 (17%)
Query: 628 HKIARQQLHDFIGDSGIASVVIEESKVEGEDARKFLEDVRV 668
H+IA++Q+ F + + ++ E A+K L++ V
Sbjct: 234 HEIAKKQMKMF---GSMIAFDVDG----LEKAKKVLDNCHV 267
>1gc0_A Methionine gamma-lyase; pyridoxal-5'-phosphate; HET: LLP; 1.70A
{Pseudomonas putida} SCOP: c.67.1.3 PDB: 1gc2_A* 1pg8_A*
1ukj_A* 2o7c_A*
Length = 398
Score = 29.0 bits (66), Expect = 8.7
Identities = 7/41 (17%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 628 HKIARQQLHDFIGDSGIASVVIEESKVEGEDARKFLEDVRV 668
+ +ARQQ+ G+ + ++ R+F+ +++
Sbjct: 300 YTLARQQMSQP---GGMIAFELKGGI---GAGRRFMNALQL 334
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
0.321 0.137 0.398
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 17,460,619
Number of extensions: 1097203
Number of successful extensions: 1931
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1907
Number of HSP's successfully gapped: 80
Length of query: 1152
Length of database: 6,701,793
Length adjustment: 104
Effective length of query: 1048
Effective length of database: 3,798,009
Effective search space: 3980313432
Effective search space used: 3980313432
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 63 (28.0 bits)