RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4871
(494 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 = 42.0 bits (98), Expect = 5e-04
Identities = 84/478 (17%), Positives = 143/478 (29%), Gaps = 189/478 (39%)
Query: 3 FETTFGFSLIGS------CRRLGKFEGCKVRINSMIPPQTY--SRIMVSGTYTGRFGS-- 52
FE + L G+ + L + + V+ +I + Y +RIM + + S
Sbjct: 91 FENCY---LEGNDIHALAAKLLQENDTTLVKTKELI--KNYITARIMAKRPFDKKSNSAL 145
Query: 53 -EAHA-----CIAAFT-TGMSFAWSAPVLEEL--LSKESPIPMSPNEGSWVVAIIE-IGN 102
A +A F G + + EEL L + V +I+
Sbjct: 146 FRAVGEGNAQLVAIFGGQGNTDDY----FEELRDLYQTYH--------VLVGDLIKFSAE 193
Query: 103 YLSPI-----------PAGMLVNRIGRKW----------SLLMTGPITTASW-IIAMYSR 140
LS + G+ + +W L++ PI S +I +
Sbjct: 194 TLSELIRTTLDAEKVFTQGLNI----LEWLENPSNTPDKDYLLSIPI---SCPLIGVIQ- 245
Query: 141 SVLGLY-VMRTLQGFSMAAIYVISPMYLGEISETSIRGTIGTLFQISCHLGILYTYVLGS 199
L Y V L GF+ P GE+ ++G G G++ +
Sbjct: 246 --LAHYVVTAKLLGFT--------P---GELRS-YLKGATG------HSQGLVTAVAIAE 285
Query: 200 ELSYMNYLTYSLIIPIIFTVTFMFMPESPYFYAIKNQEGKAIESLKW--LR-NKTADQVQ 256
S+ ES F+ KAI L + +R +
Sbjct: 286 TDSW----------------------ES--FFVSVR---KAITVLFFIGVRCYEAYPNTS 318
Query: 257 SELQIIKQNTSKNVERTNFREFMGR-SNMKAFVFMAFLAVFRAFTG-----VQSIIAYAN 310
I+ +++ +N E G S M L++ + VQ + N
Sbjct: 319 LPPSIL-EDSLENNE--------GVPSPM--------LSI----SNLTQEQVQDYVNKTN 357
Query: 311 TIFASSETFLPSD---YISILFAIILLVSIFPSTYYIDRAGRRVLFLVSSAGCSLFSFIA 367
+ LP+ IS LV+ G + +VS SL+
Sbjct: 358 S-------HLPAGKQVEIS-------LVN-----------GAKN-LVVSGPPQSLYGLNL 391
Query: 368 GL-YYYVTIEL-QYEIPYTSWVPFLSISLLGVFFNLGFGPLFTPLLSEYFSSNMKAVS 423
L L Q IP++ F+ F P+ +P + S + S
Sbjct: 392 TLRKAKAPSGLDQSRIPFSERKLK---------FSNRFLPVASP----FHSHLLVPAS 436
Score = 33.9 bits (77), Expect = 0.15
Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 18/86 (20%)
Query: 3 FETTFGFSLIGSCRR--------LGKFEGCKVRINSMIPPQTYSRIMVSGTYTGRFGSEA 54
F+ T+GFS++ G +G ++R N YS ++ G+ +E
Sbjct: 1653 FKDTYGFSILDIVINNPVNLTIHFGGEKGKRIREN-------YSAMIFETIVDGKLKTEK 1705
Query: 55 HACIAAFTTGMSFAWSAPVLEELLSK 80
+ S+ + + + LLS
Sbjct: 1706 IFKEINEHS-TSYTFRSE--KGLLSA 1728
Score = 28.5 bits (63), Expect = 7.0
Identities = 19/114 (16%), Positives = 35/114 (30%), Gaps = 37/114 (32%)
Query: 1 MSFETTFGFSLIGSCRRLGKFEGCKVRINSMIPPQTYSRIMVSGTYTGRFGSEAHACIAA 60
MS E+ ++ R G + +P G + IA
Sbjct: 1777 MSIESLV--EVV--FYR-GMT------MQVAVPR-------------DELGRSNYGMIAI 1812
Query: 61 FTTGMSFAWSAPVLEELLSKESPIPMSPNEGSWVVAIIEIGNYLSP----IPAG 110
++ ++S L+ ++ + W+V EI NY + AG
Sbjct: 1813 NPGRVAASFSQEALQYVVERVG------KRTGWLV---EIVNYNVENQQYVAAG 1857
>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 = 37.9 bits (87), Expect = 0.009
Identities = 53/400 (13%), Positives = 109/400 (27%), Gaps = 143/400 (35%)
Query: 21 FE-GCKVRINSMIPPQTYSRIM--VSGTYTGRFGSEAHACIAAFTTGMSFAWSAPVLEEL 77
F CK+ + + + ++ +S T + H+ T + L
Sbjct: 262 FNLSCKILLTT-----RFKQVTDFLSAATTTHISLDHHS--MTLTPDEV--------KSL 306
Query: 78 LSK--ESPIPMSPNEGSWVVAIIEIGNYLSPIPAGMLVNRIGRKWSLLMTGPITTASW-- 133
L K + P E V+ +P ++ I + G T +W
Sbjct: 307 LLKYLDCRPQDLPRE---VLTT-------NP----RRLSIIAE---SIRDGLATWDNWKH 349
Query: 134 --------IIAMYSRSVLGLYVMRTLQGFSMAAIYV----ISPMYL----GEISETSIRG 177
II S +VL R + F +++ I + L ++ ++ +
Sbjct: 350 VNCDKLTTIIES-SLNVLEPAEYRKM--FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMV 406
Query: 178 TIGTLFQISC-----HLGILYTYVLGSEL----------------SYMNYLTY---SLII 213
+ L + S + + EL Y T+ LI
Sbjct: 407 VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
Query: 214 PIIFTVTFMFMPESPYFY-------AIKNQEGKAIE------SLKWLRNKTADQVQSELQ 260
P YFY + ++L K
Sbjct: 467 P----------YLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK---------- 506
Query: 261 IIKQNTSKNVERT---------NFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAYANT 311
I +T+ N + ++ ++ ++ + + + A +
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYKPYICDND-------------PKYE--RLVNAILDF 551
Query: 312 IFASSETFLPSDYISILFAIILLVSIFPSTYYIDRAGRRV 351
+ E + S Y +L I L+ + A ++V
Sbjct: 552 LPKIEENLICSKYTDLL-RIALM---AEDEAIFEEAHKQV 587
>2cfq_A Lactose permease; transport, transport mechanism, lactose/H+
symport, sugar transport, transmembrane, formylation;
2.95A {Escherichia coli} SCOP: f.38.1.2 PDB: 1pv7_A*
1pv6_A 2cfp_A 2v8n_A 2y5y_A*
Length = 417
Score = 37.2 bits (86), Expect = 0.012
Identities = 25/121 (20%), Positives = 53/121 (43%), Gaps = 5/121 (4%)
Query: 109 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 168
A +++NRIG K +LL+ G I + I + ++ S L + +++TL F + + V Y+
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT 338
Query: 169 EISETSIRGTIGTLF-----QISCHLGILYTYVLGSELSYMNYLTYSLIIPIIFTVTFMF 223
E TI + Q++ + + + + ++ + FT+ +F
Sbjct: 339 SQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVF 398
Query: 224 M 224
Sbjct: 399 T 399
>3o7q_A L-fucose-proton symporter; transporter, multi-PASS membrane protei
transport protein; HET: BNG; 3.14A {Escherichia coli}
PDB: 3o7p_A*
Length = 438
Score = 35.7 bits (82), Expect = 0.030
Identities = 39/334 (11%), Positives = 98/334 (29%), Gaps = 32/334 (9%)
Query: 86 MSPNEGSWVVAIIEIGNYLSPIPAGMLVNRIGRKWSL---LMTGPITTASWIIAMYSRSV 142
++ + + + G ++ PIPAG+L+ ++ K + L + A + A +
Sbjct: 58 LTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNY 117
Query: 143 LGLYVMRTLQGFSMAAIYVISPMYLGEISETSIRGTIGTLFQISCHLG-----ILYTYVL 197
V + + + + ++ + S L Q G + ++
Sbjct: 118 TLFLVGLFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLI 177
Query: 198 GSELSYMNYLTYSLIIPIIFTVTFMFMPES---PYFYAIKNQEGKAIESLKWLRNKTADQ 254
S + + + + P + + S PY + A+ +
Sbjct: 178 LSNVPHQSQDVLDKMSPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSD 237
Query: 255 VQSELQIIKQNTSKNVERTNFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAYANTIFA 314
S+ + + + + V F V +I YA
Sbjct: 238 NHSD-------AKQGSFSASLSRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEEIP 290
Query: 315 SSETFLPSDYISILFAIILLVSIFPSTYYIDRAGRRVLFLVSSAGCSLFSFIAGLYYYVT 374
++Y++ + + F T+ I R + + I+
Sbjct: 291 GMTAGFAANYLTG-TMVCFFIGRFTGTWLISRFAPHKVLAAYALIAMALCLIS------- 342
Query: 375 IELQYEIPYTSWVPFLSISLLGVFFNLGFGPLFT 408
V ++++L F ++ + +F+
Sbjct: 343 ------AFAGGHVGLIALTLCSAFMSIQYPTIFS 370
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 32.2 bits (74), Expect = 0.36
Identities = 12/55 (21%), Positives = 27/55 (49%)
Query: 109 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVIS 163
G + +R+GR+ +L+ I + ++A+ + S+ L +QG V++
Sbjct: 55 YGPISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIAASAMQGMGTGVGGVMA 109
>3rko_L NADH-quinone oxidoreductase subunit L; complex I, proton pump,
membrane protein, Na ubiquinone, cytoplasmic membrane;
HET: LFA CA7; 3.00A {Escherichia coli}
Length = 613
Score = 30.7 bits (70), Expect = 1.1
Identities = 16/99 (16%), Positives = 41/99 (41%), Gaps = 11/99 (11%)
Query: 41 MVSGTYTGRFGSEAHACIAAFTTGMSFAWSAPVLEELLSKESPIPMSPNEGSWVVAIIEI 100
++ GR+ A + + G++ +A + + + S +W + +
Sbjct: 16 VLLAFSRGRWSENVSAIVGVGSVGLAALVTAFIGVDFFANGEQ-TYSQPLWTW----MSV 70
Query: 101 GNYLSPIPAGMLVNRIGRKWSLLMTGPITTASWIIAMYS 139
G++ I ++++ + SL M +T ++I MY+
Sbjct: 71 GDF--NIGFNLVLDGL----SLTMLSVVTGVGFLIHMYA 103
>1pw4_A Glycerol-3-phosphate transporter; transmembrane, inner membrane,
major facilitator superfamily, secondary active membrane
transporter; 3.30A {Escherichia coli} SCOP: f.38.1.1
Length = 451
Score = 29.6 bits (67), Expect = 2.7
Identities = 28/209 (13%), Positives = 74/209 (35%), Gaps = 17/209 (8%)
Query: 66 SFAWSAPVLEELLSKESPIPMSPNEGSWVVAIIEIGNYLSPIPAGMLVNRIGRKW----S 121
+FA + P L E S + + ++ I I S G + +R +
Sbjct: 46 NFALAMPYLVEQ-------GFSRGDLGFALSGISIAYGFSKFIMGSVSDRSNPRVFLPAG 98
Query: 122 LLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLGEISETSIRGTIGT 181
L++ + + + S+ ++V+ L G+ + + RG I +
Sbjct: 99 LILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMGWPPCGRTMVHWWSQKERGGIVS 158
Query: 182 LFQISCHLG-ILYTYVLGSELSYMNYLTYSLIIP-----IIFTVTFMFMPESPYFYAIKN 235
++ + ++G + + +++ N +L +P ++ F M ++P +
Sbjct: 159 VWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYMPAFCAILVALFAFAMMRDTPQSCGLPP 218
Query: 236 QEGKAIESLKWLRNKTADQVQSELQIIKQ 264
E + K ++ ++ ++
Sbjct: 219 IEEYKNDYPDDYNEKAEQELTAKQIFMQY 247
>2ww9_A SEC sixty-one protein homolog; ribonucleoprotein, transmembrane,
phospho signal sequence, membrane, ribosome, transport;
8.60A {Saccharomyces cerevisiae} PDB: 2wwa_A
Length = 490
Score = 28.9 bits (64), Expect = 4.4
Identities = 37/257 (14%), Positives = 74/257 (28%), Gaps = 14/257 (5%)
Query: 45 TYTGRFGSEAHACIAAFTTGMSFAWSAPV--LEELLSKESPIPMSPNEGSWVVAIIEIGN 102
+ G FG + L E++ K S + I +
Sbjct: 136 IFAGYFGDDLSVVQIGLINFQLVGAGIFTTLLAEVIDKGFGF------SSGAMIINTVVI 189
Query: 103 YLSPIPAGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVI 162
+ + V++I + I + S+ + G A
Sbjct: 190 ATNLVADTFGVSQIKVGEDDQTEAQGALINLIQGLRSKHKT------FIGGIISAFNRDY 243
Query: 163 SPMYLGEISETSIRGTIGTLFQISCHLGILYTYVLGSELSYMNYLTYSLIIPIIFTVTFM 222
P I +I + L + L I T G+ Y L Y+ + ++F+ T +
Sbjct: 244 LPNLTTTIIVLAIAIIVCYLQSVRVELPIRSTRARGTNNVYPIKLLYTGCLSVLFSYTIL 303
Query: 223 FMPESPYFYAIKNQEGKAIESLKWLRNKTADQVQSELQIIKQNTSKNVERTNFREFMGRS 282
F F I+ + + + L + S T+F + + +
Sbjct: 304 FYIHIFAFVLIQLVAKNEPTHIICKIMGHYENANNLLAVPTFPLSLLAPPTSFFKGVTQQ 363
Query: 283 NMKAFVFMAFLAVFRAF 299
+ + AF+ V +
Sbjct: 364 PLTFITYSAFILVTGIW 380
>3ufx_B Succinyl-COA synthetase beta subunit; ATP-grAsp fold, ligase; HET:
GDP; 2.35A {Thermus aquaticus}
Length = 397
Score = 27.9 bits (63), Expect = 9.5
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 342 YY----IDRAGRRVLFLVSSAG 359
YY +DRA +RV+ ++S G
Sbjct: 100 YYAGLILDRAKKRVVLMLSKEG 121
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
0.325 0.138 0.411
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,388,807
Number of extensions: 438077
Number of successful extensions: 868
Number of sequences better than 10.0: 1
Number of HSP's gapped: 862
Number of HSP's successfully gapped: 29
Length of query: 494
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 397
Effective length of database: 3,993,456
Effective search space: 1585402032
Effective search space used: 1585402032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.7 bits)