RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4866
(537 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 = 51.2 bits (122), Expect = 8e-07
Identities = 83/463 (17%), Positives = 131/463 (28%), Gaps = 183/463 (39%)
Query: 41 NGQWNYTADFGSELRYLHTVLFLFSFLCVTACIAAFTTGMSFAWSAPVLEELLSKESPIP 100
GQ N T D+ ELR L+ + V I SA L EL+
Sbjct: 161 GGQGN-TDDYFEELRDLYQT----YHVLVGDLIKF---------SAETLSELIRTTLDAE 206
Query: 101 MSPNEG----SWVVAIIEIGNYLSPIPAGMLVNRIGRKWSLLMTGPITTASW-IIAMYSR 155
+G W+ S P L++ PI S +I +
Sbjct: 207 KVFTQGLNILEWL-------ENPSNTPDK----------DYLLSIPI---SCPLIGVIQ- 245
Query: 156 SVLGLY-VMRTLQGFSMAAIYVISPMYLGEISETSIRGTIGTLFQISCHLGILYTYVLGS 214
L Y V L GF+ P GE+ ++G G G++ +
Sbjct: 246 --LAHYVVTAKLLGFT--------P---GELRS-YLKGATG------HSQGLVTAVAIAE 285
Query: 215 ELSYMNYLTYSLIIPIIFTVTFMFMPESPYFYAIKNQEGKAIESLKW--LR-NKTADQVQ 271
S+ ES F+ KAI L + +R +
Sbjct: 286 TDSW----------------------ES--FFVSVR---KAITVLFFIGVRCYEAYPNTS 318
Query: 272 SELQIIKQNTSKNVERTNFREFMGR-SNMKAFVFMAFLAVFRAFTG-----VQSIIAYAN 325
I+ +++ +N E G S M L++ + VQ + N
Sbjct: 319 LPPSIL-EDSLENNE--------GVPSPM--------LSI----SNLTQEQVQDYVNKTN 357
Query: 326 TIFASSETFLPSD---YISILFAIILLVSIFPSTYYIDRAGRRVLFLVSSAGCSLFSFIA 382
+ LP+ IS LV+ G + +VS SL+
Sbjct: 358 S-------HLPAGKQVEIS-------LVN-----------GAKN-LVVSGPPQSLYGLNL 391
Query: 383 GL-YYYVTIEL-QYEIPYTSWVPFLSISLLGVFFNLGFGPLFTPLLSEYFSSNMKAVSCA 440
L L Q IP++ F+ F P+ +P + S + S
Sbjct: 392 TLRKAKAPSGLDQSRIPFSERKLK---------FSNRFLPVASP----FHSHLLVPASDL 438
Query: 441 VINILCTTLGLISYKLFFLMDKHIGMYSNFLFGGVSSLVCTVY 483
+ L + +N F + VY
Sbjct: 439 INKDL--------------------VKNNVSFNA-KDIQIPVY 460
>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 = 39.5 bits (91), Expect = 0.003
Identities = 66/463 (14%), Positives = 132/463 (28%), Gaps = 164/463 (35%)
Query: 7 YFHYKYCNSIDSVRAVEGVQGANNSMIPPNIQQNNGQWNY---TADFGSELR-------Y 56
+ + K CNS ++V +E +Q + P +++ N +ELR Y
Sbjct: 186 WLNLKNCNSPETV--LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243
Query: 57 LHTVLFL-----------FSFLC---VT---ACIAAFTTG----------MSFAWSAPVL 89
+ +L L F+ C +T + F + S + +
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303
Query: 90 EELLSK--ESPIPMSPNEGSWVVAIIEIGNYLSPIPAGMLVNRIGRKWSLLMTGPITTAS 147
+ LL K + P E V+ +P ++ I + G T +
Sbjct: 304 KSLLLKYLDCRPQDLPRE---VLTT-------NP----RRLSIIAE---SIRDGLATWDN 346
Query: 148 W----------IIAMYSRSVLGLYVMRTLQGFSMAAIYV----ISPMYL----GEISETS 189
W II S +VL R + F +++ I + L ++ ++
Sbjct: 347 WKHVNCDKLTTIIES-SLNVLEPAEYRKM--FDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 190 IRGTIGTLFQISC-----HLGILYTYVLGSEL----------------SYMNYLTY---S 225
+ + L + S + + EL Y T+
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDD 463
Query: 226 LIIPIIFTVTFMFMPESPYFY-------AIKNQEGKAIE------SLKWLRNKTADQVQS 272
LI P YFY + ++L K
Sbjct: 464 LIPP----------YLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK------- 506
Query: 273 ELQIIKQNTSKNVERT---------NFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAY 323
I +T+ N + ++ ++ ++ + + + A
Sbjct: 507 ---IRHDSTAWNASGSILNTLQQLKFYKPYICDND-------------PKYE--RLVNAI 548
Query: 324 ANTIFASSETFLPSDYISILFAIILLVSIFPSTYYIDRAGRRV 366
+ + E + S Y +L I L+ + A ++V
Sbjct: 549 LDFLPKIEENLICSKYTDLL-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 = 0.011
Identities = 25/121 (20%), Positives = 53/121 (43%), Gaps = 5/121 (4%)
Query: 124 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVISPMYLG 183
A +++NRIG K +LL+ G I + I + ++ S L + +++TL F + + V Y+
Sbjct: 279 APLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT 338
Query: 184 EISETSIRGTIGTLF-----QISCHLGILYTYVLGSELSYMNYLTYSLIIPIIFTVTFMF 238
E TI + Q++ + + + + ++ + FT+ +F
Sbjct: 339 SQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVF 398
Query: 239 M 239
Sbjct: 399 T 399
Score = 29.9 bits (67), Expect = 2.2
Identities = 51/406 (12%), Positives = 112/406 (27%), Gaps = 55/406 (13%)
Query: 101 MSPNEGSWVVAIIEIGNYLSPIPAGMLVNRIGRKWSLLMTGPITTA--------SWIIAM 152
+S ++ + A I + + L G+L +++G + LL + +
Sbjct: 40 ISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLL 99
Query: 153 YSRSVLGLYVMRTLQGFSMAAIYVISPMYLGEISETSIR--GTIGTLFQISCHLGILYTY 210
++G V GF A ++ ++S S G + LG
Sbjct: 100 QYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALGASIVG 159
Query: 211 VLGSELSYMNYLTYSLIIPIIFTVTFMFMPESPYFYAIKNQEGKAIESLKWLRNKTADQV 270
++ + + + S I+ + F ++P + N G +
Sbjct: 160 IMFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLK-------- 211
Query: 271 QSELQIIKQNTSKNVERTNFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAYANTIFAS 330
E + + Q + + FA+
Sbjct: 212 ------------------LALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFAT 253
Query: 331 SETFLPSDYISILFAIILL---VSIFPSTYYIDRAGRRVLFLVSSAGCSLFSFIAGLYYY 387
E + + + L +F + I+R G + L++ S+ +
Sbjct: 254 GE--QGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFA-- 309
Query: 388 VTIELQYEIPYTSWVPFLSISLLGVFFNLGFGPLFTPLLSEYFSSNMKAVSCAVINILCT 447
++ + +L ++ F A V
Sbjct: 310 ----------TSALEVVILKTLHMFEVPF-LLVGCFKYITSQFEVRFSATIYLVCFCFFK 358
Query: 448 TLGLISYKLFF-LMDKHIGMYSNFLFGGVSSLVCTVYLYYFLLETK 492
L +I + M + IG +L G+ +L T+ + L
Sbjct: 359 QLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPG 404
>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 = 36.1 bits (83), Expect = 0.028
Identities = 39/334 (11%), Positives = 98/334 (29%), Gaps = 32/334 (9%)
Query: 101 MSPNEGSWVVAIIEIGNYLSPIPAGMLVNRIGRKWSL---LMTGPITTASWIIAMYSRSV 157
++ + + + G ++ PIPAG+L+ ++ K + L + A + A +
Sbjct: 58 LTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNY 117
Query: 158 LGLYVMRTLQGFSMAAIYVISPMYLGEISETSIRGTIGTLFQISCHLG-----ILYTYVL 212
V + + + + ++ + S L Q G + ++
Sbjct: 118 TLFLVGLFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLI 177
Query: 213 GSELSYMNYLTYSLIIPIIFTVTFMFMPES---PYFYAIKNQEGKAIESLKWLRNKTADQ 269
S + + + + P + + S PY + A+ +
Sbjct: 178 LSNVPHQSQDVLDKMSPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSD 237
Query: 270 VQSELQIIKQNTSKNVERTNFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAYANTIFA 329
S+ + + + + V F V +I YA
Sbjct: 238 NHSD-------AKQGSFSASLSRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEEIP 290
Query: 330 SSETFLPSDYISILFAIILLVSIFPSTYYIDRAGRRVLFLVSSAGCSLFSFIAGLYYYVT 389
++Y++ + + F T+ I R + + I+
Sbjct: 291 GMTAGFAANYLTG-TMVCFFIGRFTGTWLISRFAPHKVLAAYALIAMALCLIS------- 342
Query: 390 IELQYEIPYTSWVPFLSISLLGVFFNLGFGPLFT 423
V ++++L F ++ + +F+
Sbjct: 343 ------AFAGGHVGLIALTLCSAFMSIQYPTIFS 370
>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 = 35.8 bits (83), Expect = 0.032
Identities = 55/458 (12%), Positives = 129/458 (28%), Gaps = 52/458 (11%)
Query: 47 TADFGSELRYLHTVLFLFSFLCVTACIAAFTTGMSFAWSAPVLEELLSKESPIPMSPNEG 106
A+ R L +FL F A + +FA + P L E S +
Sbjct: 15 AAEIDPTYRRLRWQIFLGIFFGYAA---YYLVRKNFALAMPYLVEQ-------GFSRGDL 64
Query: 107 SWVVAIIEIGNYLSPIPAGMLVNRIGRKW----SLLMTGPITTASWIIAMYSRSVLGLYV 162
+ ++ I I S G + +R + L++ + + + S+ ++V
Sbjct: 65 GFALSGISIAYGFSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFV 124
Query: 163 MRTLQGFSMAAIYVISPMYLGEISETSIRGTIGTLFQISCHLG-ILYTYVLGSELSYMNY 221
+ L G+ + + RG I +++ + ++G + + +++ N
Sbjct: 125 LLFLCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFND 184
Query: 222 LTYSLIIP-----IIFTVTFMFMPESPYFYAIKNQEGKAIESLKWLRNKTADQVQSELQI 276
+L +P ++ F M ++P +S + +
Sbjct: 185 WHAALYMPAFCAILVALFAFAMMRDTP-------------QSCGLPPIEEYKNDYPDDYN 231
Query: 277 IKQNTSKNVERTNFREFMGRSNMKAFVFMAFLAVFRAFTGVQSIIAYANTIFASSE--TF 334
K ++ + + + + I+ ++ T +
Sbjct: 232 EKAEQELTAKQIFMQYVLPNKLLWYIAIANVFVYLLRYG----ILDWSPTYLKEVKHFAL 287
Query: 335 LPSDYISILFAIILLVSIFPSTYYIDR--AGRRVLFLVSSAGCSLFSFIAGLYYYVTIEL 392
S + L+ + + D+ G R V + I
Sbjct: 288 DKSSWAYFLYEYAGIPGTLLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPAG--- 344
Query: 393 QYEIPYTSWVPFLSISLLGVFFNLGFGPLFTPLLSEYFSSNMKAVSCAVINILCTTLGLI 452
V + + ++G F G L E + + G +
Sbjct: 345 ------NPTVDMICMIVIG-FLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSV 397
Query: 453 SYKLFF-LMDKHIGMYSNFLFGGVSSLVCTVYLYYFLL 489
+ G F+ S++ + L ++
Sbjct: 398 AASAIVGYTVDFFGWDGGFMVMIGGSILAVILLIVVMI 435
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 32.6 bits (75), Expect = 0.33
Identities = 12/55 (21%), Positives = 27/55 (49%)
Query: 124 AGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQGFSMAAIYVIS 178
G + +R+GR+ +L+ I + ++A+ + S+ L +QG V++
Sbjct: 55 YGPISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIAASAMQGMGTGVGGVMA 109
Score = 28.4 bits (64), Expect = 7.4
Identities = 14/132 (10%), Positives = 34/132 (25%), Gaps = 11/132 (8%)
Query: 48 ADFGSELRYLHTVLFLFSFLCVTACIAAFTTGMSFAWSAPVLEELLSKESPIPMSPNEGS 107
+ + +L + A IAAF ++ +L +S S
Sbjct: 190 TSYKTLFGNSGFNCYLLMLIGGLAGIAAFEACSGV-----LMGAVLG------LSSMTVS 238
Query: 108 WVVAIIEIGNYLSPIPAGMLVNRIGRKWSLLMTGPITTASWIIAMYSRSVLGLYVMRTLQ 167
+ + + AG R + + + V+ ++ +
Sbjct: 239 ILFILPIPAAFFGAWFAGRPNKRFSTLMWQSVICCLLAGLLMWIPDWFGVMNVWTLLVPA 298
Query: 168 GFSMAAIYVISP 179
++ P
Sbjct: 299 ALFFFGAGMLFP 310
>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 = 9.6
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 357 YY----IDRAGRRVLFLVSSAG 374
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 0.414
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: 7,996,941
Number of extensions: 471333
Number of successful extensions: 1042
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1033
Number of HSP's successfully gapped: 28
Length of query: 537
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 439
Effective length of database: 3,965,535
Effective search space: 1740869865
Effective search space used: 1740869865
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: 60 (27.1 bits)