RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12113
(369 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 = 50.8 bits (121), Expect = 5e-07
Identities = 66/448 (14%), Positives = 128/448 (28%), Gaps = 166/448 (37%)
Query: 43 VSHAGAL-ISIFLPPALSIELTELYIRVFNPVKISKKQFKELTSEATICKLAQGESYAIE 101
+SH G+L + +P A ++L ++QF ++ E T E +A +
Sbjct: 11 LSH-GSLEHVLLVPTASFFIASQL-----------QEQFNKILPEPT-------EGFAAD 51
Query: 102 ERTSADERL---------SILLRGK-------LLLAVGFLISAFWAG--VHV-------- 135
+ + L S++ K L L + + + G +H
Sbjct: 52 DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE 111
Query: 136 -------------CFYDAFVW----------NMILAVVNVSHAGALISIF---------L 163
+ A + + + V +A L++IF
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQ-LVAIFGGQGNTDDYF 170
Query: 164 PPALSIELTELYIRVFNP-----VKISKKQFKELTSEATICKLAQGESYAIE------ER 212
EL +LY + ++ +K S + EL + + I
Sbjct: 171 E-----ELRDLY-QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSN 224
Query: 213 TSADERL-----SILLRGKMT------VTCNDTHLHYVCPFQFVDSPE------------ 249
T + L S L G + VT P + +
Sbjct: 225 TPDKDYLLSIPISCPLIG-VIQLAHYVVTAKLLGFT---PGELRSYLKGATGHSQGLVTA 280
Query: 250 -YMSCQNSSDELYQVSITAEEDCLYL------CWSRISLDRLLRH----------RPMLK 292
++ +S + + A ++ + SL + PML
Sbjct: 281 VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML- 339
Query: 293 SVFNSLIGKDITQKLYSLNELISTNAQNKDEPWRHKMNRSVSVDAVNTSSR----GQVRS 348
S+ ++TQ+ + + + N N P + V + VN + G +S
Sbjct: 340 SI------SNLTQE--QVQDYV--NKTNSHLP----AGKQVEISLVNGAKNLVVSGPPQS 385
Query: 349 -----SNWRSTHSSMKKNLSNI--SQSK 369
R + + S I S+ K
Sbjct: 386 LYGLNLTLRKAKAPSGLDQSRIPFSERK 413
Score = 39.6 bits (92), Expect = 0.002
Identities = 49/329 (14%), Positives = 96/329 (29%), Gaps = 115/329 (34%)
Query: 28 FYDAF-----VWNMILAVVNVSHAGALISIFL--PPALSI--------ELTELYIR-VFN 71
Y VWN ++ +++ I + P L+I + E Y +F
Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFE 1694
Query: 72 PVK----ISKKQFKELTSEATICKLAQGESYAIEERTSADERLS--------ILLRGKLL 119
+ ++K FKE+ +T SY S LS + L K
Sbjct: 1695 TIVDGKLKTEKIFKEINEHST--------SYTFR---SEKGLLSATQFTQPALTLMEKAA 1743
Query: 120 LAV----GFL-ISAFWAGVH----VCFYDAFVWNMILAVVNVSHAGALISIFLPPALSIE 170
G + A +AG H Y A LA S A + + + +
Sbjct: 1744 FEDLKSKGLIPADATFAG-HSLGE---YAA------LA----SLADVM---SIESLVEV- 1785
Query: 171 LTELYIRVFNPVKISKKQFKELTSEATICKLAQGE--SYAIEERTSADERLSI--LLRGK 226
++ R G A+ + + G+
Sbjct: 1786 ---VFYR--------------------------GMTMQVAVPRDELGRSNYGMIAINPGR 1816
Query: 227 MTVTCNDTHLHYVCPFQFVDSPEYMSCQ----NSSDELYQVSITAEE---DCLYLCWSRI 279
+ + + L YV + V + N ++ Q + D + + +
Sbjct: 1817 VAASFSQEALQYVV--ERVGKRTGWLVEIVNYNVENQ--QYVAAGDLRALDTV----TNV 1868
Query: 280 SLDRLLRHRPMLKSVFNSLIGKDITQKLY 308
L+ + + + + SL +++ L+
Sbjct: 1869 -LNFIKLQKIDIIELQKSLSLEEVEGHLF 1896
Score = 35.8 bits (82), Expect = 0.029
Identities = 37/229 (16%), Positives = 66/229 (28%), Gaps = 97/229 (42%)
Query: 7 KGLLLAVGFLISA------------------FWAGV--HVCFYDAFVWN----------- 35
+GL+ AV I+ F+ GV + + + +
Sbjct: 275 QGLVTAV--AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE 332
Query: 36 -----MILAVVNVSHAGALISI------FLPPALSIELTELYIRVFNPVKISKKQF---- 80
M L++ N++ + LP + I + N K
Sbjct: 333 GVPSPM-LSISNLTQE-QVQDYVNKTNSHLPAGKQV-----EISLVN----GAKNLVVSG 381
Query: 81 --KELTSEATICKLAQGESYAIEERTSADERLSILLRGKLLLAVGFL-ISA-FWAGVHVC 136
+ L + A+ S + R ER KL + FL +++ F H
Sbjct: 382 PPQSLYGLNLTLRKAKAPSGLDQSRIPFSER-------KLKFSNRFLPVASPF----H-- 428
Query: 137 FYDAFVWNMILAVVNVSH----AGALISIFLPPA-LSIELTELYIRVFN 180
SH A LI+ L +S ++ I V++
Sbjct: 429 ----------------SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYD 461
>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 = 34.5 bits (78), Expect = 0.019
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 16/44 (36%)
Query: 186 KKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTV 229
K+ K+L +A++ KL YA + SA L+I K T+
Sbjct: 19 KQALKKL--QASL-KL-----YADD---SAPA-LAI----KATM 46
Score = 32.6 bits (73), Expect = 0.093
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 12/36 (33%)
Query: 77 KKQFKELTSEATICKLAQGESYAIEERTSADERLSI 112
K+ K+L +A++ KL YA + SA L+I
Sbjct: 19 KQALKKL--QASL-KL-----YADD---SAPA-LAI 42
Score = 29.5 bits (65), Expect = 1.1
Identities = 5/17 (29%), Positives = 10/17 (58%), Gaps = 3/17 (17%)
Query: 50 ISIFLP---PALSIELT 63
+ ++ PAL+I+ T
Sbjct: 29 LKLYADDSAPALAIKAT 45
Score = 29.5 bits (65), Expect = 1.1
Identities = 5/17 (29%), Positives = 10/17 (58%), Gaps = 3/17 (17%)
Query: 159 ISIFLP---PALSIELT 172
+ ++ PAL+I+ T
Sbjct: 29 LKLYADDSAPALAIKAT 45
>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 = 35.3 bits (82), Expect = 0.021
Identities = 17/138 (12%), Positives = 44/138 (31%), Gaps = 17/138 (12%)
Query: 184 ISKKQFKELTSEAT--ICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----L 236
+ + F + + K GE+ + +L LL+G++++ N +
Sbjct: 29 LCHEDFTSILDKVKLHFIKHKAGETIIKSG--NPCTQLCFLLKGEISIVTNAKENIYTVI 86
Query: 237 HYVCPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPMLKSVFN 296
+ + + Y S A + +C S+ + L + N
Sbjct: 87 EQIEAPYLI--EPQSLF--GMNTNYASSYVAHTEVHTVCISKAFVLSDLFRYDIF--RLN 140
Query: 297 SLIGKDITQKLYSLNELI 314
+ ++ + +L +
Sbjct: 141 YM--NIVSNRAQNLYSRL 156
>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 = 36.0 bits (82), Expect = 0.024
Identities = 53/379 (13%), Positives = 112/379 (29%), Gaps = 125/379 (32%)
Query: 53 FLPPALSIE------LTELYI----RVFNPVKISKKQFKELTSEATICKLAQGESYAIEE 102
FL + E +T +YI R++N ++ K ++ KL Q A+ E
Sbjct: 93 FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN--VSRLQPYLKLRQ----ALLE 146
Query: 103 RTSADERLSILLRG-----KLLLAV------------GFLISAFWAGVHVCFYDAFVWNM 145
A ++L+ G K +A+ F I FW + C V M
Sbjct: 147 LRPAK---NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI--FWLNLKNCNSPETVLEM 201
Query: 146 I--LAVVNVSHAGALISIFLPPALSIELTELYIRVFNPVKISKKQFKE-------LTSEA 196
+ L + + L I + +R + K ++ + +
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL----LKSKPYENCLLVLLNVQNAK 257
Query: 197 TI------CKL---------------AQGESYAIEERTSA---DERLSILLRGKMTVTCN 232
CK+ A +++ + DE S+LL+ + C
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK---YLDCR 314
Query: 233 DTHL-HYVC---PF----------QFVDSPEY----------------MSCQNSSD--EL 260
L V P + + + ++ ++ ++
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM 374
Query: 261 YQ--------VSITAEEDCLYLCWSRISLDRLLRHRPMLKSVFN-SLIGKDITQKLYSLN 311
+ I L L W + ++ ++ + SL+ K + S+
Sbjct: 375 FDRLSVFPPSAHIP--TILLSLIWFDVIKSDVMV---VVNKLHKYSLVEKQPKESTISIP 429
Query: 312 EL-ISTNAQNKDEPWRHKM 329
+ + + ++E H+
Sbjct: 430 SIYLELKVKLENEYALHRS 448
Score = 35.2 bits (80), Expect = 0.037
Identities = 23/156 (14%), Positives = 48/156 (30%), Gaps = 27/156 (17%)
Query: 225 GKMTVTCNDTHLHYVCPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRIS-LDR 283
G+ D + F + C++ D + E D + + +S R
Sbjct: 12 GEHQYQYKDILSVFEDAFV-----DNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 284 L---LRHRPMLKSVFNSLIGKDITQKLYS-LNELISTNAQNKDEP------WRHKMNRSV 333
L L + + + + ++ + Y L I T + R ++
Sbjct: 67 LFWTLLSKQ--EEMVQKFVE-EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 334 SVDAVNTSSRGQVRSSNWRSTHSSMKKNLSNISQSK 369
V A SR Q + +++ L + +K
Sbjct: 124 QVFAKYNVSRLQ--------PYLKLRQALLELRPAK 151
Score = 33.7 bits (76), Expect = 0.098
Identities = 46/291 (15%), Positives = 86/291 (29%), Gaps = 70/291 (24%)
Query: 15 FLISAFWAGV--HVCFYDAFVWNMILAVVNVSHAGALISIF---LPPALSIELTELYIR- 68
+S + + +D W VN +I L PA E +++ R
Sbjct: 328 RRLSIIAESIRDGLATWDN--WKH----VNCDKLTTIIESSLNVLEPA---EYRKMFDRL 378
Query: 69 -VFNP-VKISKK-------QFKELTSEATICKLAQ---------GESYAI-----EERTS 105
VF P I + + KL + + +I E +
Sbjct: 379 SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVK 438
Query: 106 ADERLSILLRGKLLLAVGFLISAFWAGVHVCFYDAFVWNMILAVVNVSHAGALISIFLPP 165
+ + L ++ + + + D + ++ I H L
Sbjct: 439 LENEYA--LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI-----GHH--------LKN 483
Query: 166 ALSIELTELYIRVF-NPVKISKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLR 224
E L+ VF + F+ L E I +S A S L L
Sbjct: 484 IEHPERMTLFRMVFLD--------FRFL--EQKIRH----DSTAWNASGSILNTLQQLKF 529
Query: 225 GKMTVTCNDTHLH-YVCPF-QFVDSPEYMSCQNSSDELYQVSITAEEDCLY 273
K + ND V F+ E + +L ++++ AE++ ++
Sbjct: 530 YKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIF 580
>2z69_A DNR protein; beta barrel, dimerization helix, transcription
regulator; 2.10A {Pseudomonas aeruginosa}
Length = 154
Score = 32.7 bits (75), Expect = 0.086
Identities = 24/146 (16%), Positives = 48/146 (32%), Gaps = 31/146 (21%)
Query: 184 ISKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHY 238
+S Q +EL + + + L +G Y + A L+ G + + L
Sbjct: 23 LSPVQLQELLASSDLVNLDKGA-YVFRQGEPAH-AFYYLISGCVKIYRLTPEGQEKILEV 80
Query: 239 VCPFQ-------FVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
F+D+P Y+ + A +S + R L+ L
Sbjct: 81 TNERNTFAEAMMFMDTPNYV-----------ATAQAVVPSQLFRFSNKAYLRQLQDNTPL 129
Query: 292 KSVFNSL-IGKDITQKLYSLNELIST 316
+L + ++ +L+ + I T
Sbjct: 130 -----ALALLAKLSTRLHQRIDEIET 150
>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 = 32.8 bits (75), Expect = 0.10
Identities = 11/51 (21%), Positives = 21/51 (41%)
Query: 264 SITAEEDCLYLCWSRISLDRLLRHRPMLKSVFNSLIGKDITQKLYSLNELI 314
S A + SR +L +LL + P L + + + +T + + I
Sbjct: 128 SCVASLPTDFAVLSRDALYQLLANMPKLGNKVLIRLLQLLTARFRESYDRI 178
>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 = 32.2 bits (74), Expect = 0.17
Identities = 7/62 (11%), Positives = 25/62 (40%)
Query: 257 SDELYQVSITAEEDCLYLCWSRISLDRLLRHRPMLKSVFNSLIGKDITQKLYSLNELIST 316
++V+I AE+D +++ + + N L+ + ++ + +++
Sbjct: 87 RSIQFEVTIEAEKDTDLWIIPAEIYKGIMKDSAPVANYTNELMATRFSDVMWLIEQIMWK 146
Query: 317 NA 318
+
Sbjct: 147 SL 148
>3kv5_D JMJC domain-containing histone demethylation protein 1D;
epigenetics, histone CODE, jumonji lysine demethylase,
metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo
sapiens} PDB: 3kv6_A*
Length = 488
Score = 32.7 bits (73), Expect = 0.21
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 9/80 (11%)
Query: 21 WAGVHVCFYDAFVWNMILAVVNVSHAGALISIFLPPALSIELTELYIRVFNPVKISKKQF 80
+ H+ F VW + G I + P + E Y + V S+ F
Sbjct: 278 YTDFHIDFGGTSVWYHV-------LWGEKIFYLIKP--TDENLARYESWSSSVTQSEVFF 328
Query: 81 KELTSEATICKLAQGESYAI 100
+ + C + QG + +
Sbjct: 329 GDKVDKCYKCVVKQGHTLFV 348
Score = 32.7 bits (73), Expect = 0.21
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 9/80 (11%)
Query: 130 WAGVHVCFYDAFVWNMILAVVNVSHAGALISIFLPPALSIELTELYIRVFNPVKISKKQF 189
+ H+ F VW + G I + P + E Y + V S+ F
Sbjct: 278 YTDFHIDFGGTSVWYHV-------LWGEKIFYLIKP--TDENLARYESWSSSVTQSEVFF 328
Query: 190 KELTSEATICKLAQGESYAI 209
+ + C + QG + +
Sbjct: 329 GDKVDKCYKCVVKQGHTLFV 348
>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 = 31.8 bits (73), Expect = 0.26
Identities = 6/33 (18%), Positives = 10/33 (30%)
Query: 259 ELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
+ I A ED L + ++ P
Sbjct: 80 THTRAFIQAMEDTTILYTDIRNFQNIVVEFPAF 112
>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 = 31.4 bits (72), Expect = 0.27
Identities = 18/112 (16%), Positives = 35/112 (31%), Gaps = 11/112 (9%)
Query: 185 SKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHYV 239
+ + S I K I + A+ L +++G + V D L Y+
Sbjct: 8 TDPTLEWFLSHCHIHKYPSKS-TLIHQGEKAE-TLYYIVKGSVAVLIKDEEGKEMILSYL 65
Query: 240 CPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
F+ + E + A+ C S +L++ P +
Sbjct: 66 NQGDFIG---ELGLFEEGQE-RSAWVRAKTACEVAEISYKKFRQLIQVNPDI 113
>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 = 31.2 bits (71), Expect = 0.42
Identities = 18/112 (16%), Positives = 35/112 (31%), Gaps = 11/112 (9%)
Query: 185 SKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHYV 239
+ + S I K I + A+ L +++G + V D L Y+
Sbjct: 58 TDPTLEWFLSHCHIHKYPSKS-TLIHQGEKAE-TLYYIVKGSVAVLIKDEEGKEMILSYL 115
Query: 240 CPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
F+ + E + A+ C S +L++ P +
Sbjct: 116 NQGDFIG---ELGLFEEGQE-RSAWVRAKTACEVAEISYKKFRQLIQVNPDI 163
>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 = 31.1 bits (71), Expect = 0.51
Identities = 20/112 (17%), Positives = 33/112 (29%), Gaps = 12/112 (10%)
Query: 185 SKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHYV 239
LT + +G E D RL I++ GK+ + L +
Sbjct: 18 EPSAIAALTKQLQPVDFPRGH-TVFAEGEPGD-RLYIIISGKVKIGRRAPDGRENLLTIM 75
Query: 240 CPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
P E +S S T + + R +L + RP +
Sbjct: 76 GPSDMF--GE-LSI--FDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEI 122
>2pqq_A Putative transcriptional regulator; APC7345, streptomyces
coelicolor structural genomics, PSI-2, protein structure
initiative; 2.00A {Streptomyces coelicolor A3}
Length = 149
Score = 30.3 bits (69), Expect = 0.52
Identities = 26/145 (17%), Positives = 49/145 (33%), Gaps = 30/145 (20%)
Query: 184 ISKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHY 238
+ +Q EL + + LA+G+ E D RL ++ GK+ + L
Sbjct: 16 LDDEQSAELRASMSEVTLARGD-TLFHEGDPGD-RLYVVTEGKVKLHRTSPDGRENMLAV 73
Query: 239 VCPFQFV------DSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPMLK 292
V P + + D + TA + L L L RP +
Sbjct: 74 VGPSELIGELSLFD-----------PGPRTATGTALTEVKLLALGHGDLQPWLNVRPEV- 121
Query: 293 SVFNSL-IGKDITQKLYSLNELIST 316
+ + + + ++L N+ +S
Sbjct: 122 ----ATALLRAVARRLRKTNDAMSD 142
>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix,
transcription factor, CAMP-B proteins, CAMP receptor
protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP:
a.4.5.4 b.82.3.2
Length = 207
Score = 29.9 bits (68), Expect = 0.90
Identities = 15/114 (13%), Positives = 34/114 (29%), Gaps = 12/114 (10%)
Query: 185 SKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHYV 239
K +L + + I E L +++G +T+ D + Y+
Sbjct: 2 KLKHLDKLLAHCHRRRYTAKS--TIIYAGDRCETLFFIIKGSVTILIEDDDGREMIIGYL 59
Query: 240 CPFQFV--DSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
F + + S++ + A+ +C S L + +
Sbjct: 60 NSGDFFGELG---LFEKEGSEQERSAWVRAKVECEVAEISYAKFRELSQQDSEI 110
>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 = 29.9 bits (68), Expect = 0.93
Identities = 9/63 (14%), Positives = 22/63 (34%)
Query: 257 SDELYQVSITAEEDCLYLCWSRISLDRLLRHRPMLKSVFNSLIGKDITQKLYSLNELIST 316
++E + A E+ L +++ LL+ F + K++ L
Sbjct: 92 AEETCSSTAIAVENSKVLAIPVEAIEALLKGNTSFCRYFLKALAKELGYAERRTVTLTQK 151
Query: 317 NAQ 319
+ +
Sbjct: 152 HVR 154
>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 = 29.5 bits (67), Expect = 1.4
Identities = 8/56 (14%), Positives = 18/56 (32%), Gaps = 4/56 (7%)
Query: 259 ELYQVSITAEEDCLYLCWSRISLDRLLRHRPMLKSVFNSLIGKDITQKLYSLNELI 314
+ A E + ++ L+ P + +++G + L S I
Sbjct: 76 MHSGCLVEATERTEVRFADIRTFEQKLQTCPSMAWGLIAILG----RALTSCMRTI 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 = 29.5 bits (67), Expect = 1.6
Identities = 7/34 (20%), Positives = 12/34 (35%)
Query: 258 DELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
+ S+ A L R + +LR P +
Sbjct: 89 HQERSASVRALTPVRTLMLHREHFELILRRHPRV 122
>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 = 29.1 bits (66), Expect = 1.7
Identities = 19/136 (13%), Positives = 43/136 (31%), Gaps = 18/136 (13%)
Query: 185 SKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHYV 239
+ ++ S QG+ I + + L ++ GK+ + L +
Sbjct: 11 APEEVDLALSYFQRRLYPQGK--PIFYQGDLGQALYLVASGKVRLFRTHLGGQERTLALL 68
Query: 240 CPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPMLKSVFNSL- 298
P + + + S A ED L R L+R P++ +
Sbjct: 69 GPGELFGEMSLLD-----EGERSASAVAVEDTELLALFREDYLALIRRLPLV-----AHN 118
Query: 299 IGKDITQKLYSLNELI 314
+ + ++L + +
Sbjct: 119 LAALLARRLREADLEL 134
>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 = 29.2 bits (66), Expect = 1.7
Identities = 8/35 (22%), Positives = 12/35 (34%)
Query: 257 SDELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
+ Y VS A C + L+R P +
Sbjct: 93 RNTPYPVSAEAVTPCEVMHIPSPVFVSLMRRDPEI 127
>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone
modifications, jumonji demethylase, mental retardation,
metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo
sapiens}
Length = 447
Score = 29.5 bits (65), Expect = 1.8
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 9/80 (11%)
Query: 21 WAGVHVCFYDAFVWNMILAVVNVSHAGALISIFLPPALSIELTELYIRVFNPVKISKKQF 80
+ H+ F VW +L G I + P + L+ + ++ F
Sbjct: 243 YTDFHIDFGGTSVWYHVL-------KGEKIFYLIRP--TNANLTLFECWSSSSNQNEMFF 293
Query: 81 KELTSEATICKLAQGESYAI 100
+ + C + QG++ I
Sbjct: 294 GDQVDKCYKCSVKQGQTLFI 313
Score = 29.5 bits (65), Expect = 1.8
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 9/80 (11%)
Query: 130 WAGVHVCFYDAFVWNMILAVVNVSHAGALISIFLPPALSIELTELYIRVFNPVKISKKQF 189
+ H+ F VW +L G I + P + L+ + ++ F
Sbjct: 243 YTDFHIDFGGTSVWYHVL-------KGEKIFYLIRP--TNANLTLFECWSSSSNQNEMFF 293
Query: 190 KELTSEATICKLAQGESYAI 209
+ + C + QG++ I
Sbjct: 294 GDQVDKCYKCSVKQGQTLFI 313
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix,
homodimer, transcription regulator; 3.60A {Pseudomonas
aeruginosa}
Length = 227
Score = 28.8 bits (65), Expect = 2.2
Identities = 6/33 (18%), Positives = 10/33 (30%)
Query: 259 ELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
Y + A +S + R L+ L
Sbjct: 94 PNYVATAQAVVPSQLFRFSNKAYLRQLQDNTPL 126
>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 = 28.4 bits (64), Expect = 3.4
Identities = 17/112 (15%), Positives = 31/112 (27%), Gaps = 15/112 (13%)
Query: 185 SKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCNDTH-----LHYV 239
++ + T I A+G I + L+ GK+ + L+Y
Sbjct: 21 PIEKLRNYTQMGLIRDFAKGS-AVIMPGEEIT-SMIFLVEGKIKLDIIFEDGSEKLLYYA 78
Query: 240 CPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
+ + TA E +S SL + R +
Sbjct: 79 GGNSLIGKL--------YPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDM 122
>1ijt_A FGF4, fibroblast growth factor 4; B-trefoil fold, hormone/growth
factor complex; 1.80A {Homo sapiens} SCOP: b.42.1.1
Length = 128
Score = 27.0 bits (59), Expect = 5.4
Identities = 11/67 (16%), Positives = 16/67 (23%), Gaps = 14/67 (20%)
Query: 212 RTSADERLSILLRGKMTVTCNDTHLHYVCPFQFVDSPEYMSCQNSSDELYQVSITAEEDC 271
L L G++ DT + S E VSI
Sbjct: 11 NVGIGFHLQALPDGRIGGAHADTR--------------DSLLELSPVERGVVSIFGVASR 56
Query: 272 LYLCWSR 278
++ S
Sbjct: 57 FFVAMSS 63
>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 = 26.9 bits (60), Expect = 6.0
Identities = 19/139 (13%), Positives = 43/139 (30%), Gaps = 29/139 (20%)
Query: 185 SKKQFKELTSEATICKLAQGESYAIEERTSADERLSILLRGKMTVTCND--------THL 236
+ +Q K++ + G +E + AD L +LL G + + ++ + +
Sbjct: 18 TDEQLKDIALISEEKSFPTGS-VIFKENSKAD-NLMLLLEGGVELFYSNGGAGSAANSTV 75
Query: 237 HYVCPFQFV-------DSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRP 289
V P Y S A + + + L + +
Sbjct: 76 CSVVPGAIFGVSSLIKPYH------------YTSSARATKPVRVVDINGARLREMSENNQ 123
Query: 290 MLKSVFNSLIGKDITQKLY 308
L V + + + +L+
Sbjct: 124 ALGQVLMNNVAAAVLARLH 142
>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 = 27.7 bits (62), Expect = 6.1
Identities = 5/31 (16%), Positives = 9/31 (29%)
Query: 261 YQVSITAEEDCLYLCWSRISLDRLLRHRPML 291
A L +++ L+ P L
Sbjct: 108 RFYHAVAFTPVELLSAPIEQVEQALKENPEL 138
>3sv0_A Casein kinase I-like; typical kinase domain fold, cytosol,
transferase; 2.00A {Oryza sativa japonica group}
Length = 483
Score = 27.7 bits (61), Expect = 6.9
Identities = 17/131 (12%), Positives = 43/131 (32%), Gaps = 3/131 (2%)
Query: 234 THLHYVCPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYLCWSRISLDRLLRHRPMLKS 293
++ HY +F D P+Y + +L+ + D ++ W+ + + ++
Sbjct: 250 SYFHYCRSLRFDDKPDYSYLKRLFRDLFI-REGFQFDYVF-DWTILKYQQSQIASAPPRA 307
Query: 294 VFNSLIGKDITQKLYSLNELISTNAQNKDEPWRHKMNRSVSVDAVNTSSRGQVRSSNWRS 353
V + G N+ S + + W R + + + ++
Sbjct: 308 VGHG-AGPSGLAPPALQNDRQSGVDEGRTSGWSSMDRRRAPPPIASVGTLAKQKAPVGND 366
Query: 354 THSSMKKNLSN 364
S + +S
Sbjct: 367 ASFSKEPVISA 377
>2h7c_A Liver carboxylesterase 1; enzyme, cholesteryl esterase, hydrolase;
HET: NAG NDG SIA COA; 2.00A {Homo sapiens} SCOP:
c.69.1.1 PDB: 2dqy_A* 2dr0_A* 2dqz_A* 1mx1_A* 1mx5_A*
1mx9_A* 4ab1_A* 1ya4_A* 1yah_A* 1yaj_A* 1ya8_A* 2hrr_A*
2hrq_A* 3k9b_A* 1k4y_A*
Length = 542
Score = 27.8 bits (62), Expect = 7.3
Identities = 9/36 (25%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 239 VCPFQFVDSPEYMSCQNSSDELYQVSITAEEDCLYL 274
+C Q + + +S + ++ + + EDCLYL
Sbjct: 68 MCT-QDPKAGQLLS-ELFTNRKENIPLKLSEDCLYL 101
>3bix_A Neuroligin-1, neuroligin I; esterase domain, alpha-beta hydrolase,
cell adhesion, cell J glycoprotein, membrane,
postsynaptic cell membrane; HET: NAG; 1.80A {Rattus
norvegicus} PDB: 3biw_A* 3b3q_A* 3be8_A* 2wqz_A* 2xb6_A*
2vh8_A 3bl8_A*
Length = 574
Score = 27.4 bits (61), Expect = 9.2
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 5/46 (10%)
Query: 234 THLHYVCP-----FQFVDSPEYMSCQNSSDELYQVSITAEEDCLYL 274
T VCP + + + N+ D + EDCLYL
Sbjct: 69 TQFAPVCPQNIIDGRLPEVMLPVWFTNNLDVVSSYVQDQSEDCLYL 114
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
0.322 0.133 0.394
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,276,147
Number of extensions: 302336
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 479
Number of HSP's successfully gapped: 42
Length of query: 369
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 274
Effective length of database: 4,049,298
Effective search space: 1109507652
Effective search space used: 1109507652
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: 58 (26.0 bits)