RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13786
(219 letters)
>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 = 33.5 bits (77), Expect = 0.049
Identities = 21/157 (13%), Positives = 57/157 (36%), Gaps = 8/157 (5%)
Query: 71 LPQMSYLTIDQASWFASISAITMPIGCLLSGPIIDKY--GRKSALMITNVPSLCGWLLMA 128
L ++ + +D++SW + G LL G + DK G + A + + + ++
Sbjct: 279 LKEVKHFALDKSSWAYFLYEYAGIPGTLLCGWMSDKVFRGNRGATGVFFMTLVTIATIVY 338
Query: 129 TKSDLINLYISRLLSGLSVGLATTPAAVYAAECITIHNTDLRGSLS----TWSTI--ALT 182
+ N + + + L P + + + G+ + + + ++
Sbjct: 339 WMNPAGNPTVDMICMIVIGFLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVA 398
Query: 183 SGILLSYLTGAFFWYTTVAYIGAFVSFLSLVLVAMII 219
+ ++ Y F W + ++L+ ++I
Sbjct: 399 ASAIVGYTVDFFGWDGGFMVMIGGSILAVILLIVVMI 435
>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 = 33.5 bits (76), Expect = 0.060
Identities = 33/173 (19%), Positives = 58/173 (33%), Gaps = 48/173 (27%)
Query: 5 EKLLGKTKKSYAHPVIATSSNAA-------DIIDI-------SNGEHT---------DTP 41
+ LL T + P + AA +I S GE+
Sbjct: 1723 KGLLSAT--QFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIE 1780
Query: 42 TLFRLIYL-GLIV--ILPGVAPGMS-FGFPAVALPQMSYLTIDQASWFASISAITMPIGC 97
+L +++ G+ + +P G S +G A+ +++ + Q + + + G
Sbjct: 1781 SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA-ASFSQEALQYVVERVGKRTGW 1839
Query: 98 LLSGPIIDKY----------GRKSAL-MITNVPSLCGWLLMATKSDLINLYIS 139
L+ I Y G AL +TNV + K D+I L S
Sbjct: 1840 LVE---IVNYNVENQQYVAAGDLRALDTVTNVLNFIK----LQKIDIIELQKS 1885
>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 = 32.6 bits (74), Expect = 0.078
Identities = 25/165 (15%), Positives = 56/165 (33%), Gaps = 12/165 (7%)
Query: 61 GMSFGFPAVALPQMSYLTIDQASWFASISAITMPIGCLLSGPIIDKYGRKSALM----IT 116
G F F + L +++++ + ++ + L G + DK G + L+
Sbjct: 24 GAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGM 83
Query: 117 NVPSLCGWLLMATKSDLINLYISRLLSGLSVGL---ATTPAAVYAAECITIHNTDLRGSL 173
V ++ + N+ + ++ G+ +G A PA E ++ + G
Sbjct: 84 LVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRA 143
Query: 174 STWSTI-----ALTSGILLSYLTGAFFWYTTVAYIGAFVSFLSLV 213
+ + A GI+ + FW + + V
Sbjct: 144 RMFGCVGWALGASIVGIMFTINNQFVFWLGSGCALILAVLLFFAK 188
Score = 32.6 bits (74), Expect = 0.089
Identities = 24/177 (13%), Positives = 55/177 (31%), Gaps = 4/177 (2%)
Query: 43 LFRLIYLGLIVILPGVAPGMSFGFPAVALPQMSYLTIDQASWFASISAITMPIGCLLSGP 102
F +Y+ + V F + ++ + +
Sbjct: 223 WFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQ-GTRVFGYVTTMGELLNASIMFFAPL 281
Query: 103 IIDKYGRKSALMITNVPSLCGWLLMATKSDLINLYISRLLSGLSVGLATTPAAVYAAECI 162
II++ G K+AL++ + + + + + I + L V Y
Sbjct: 282 IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQF 341
Query: 163 TIHNTDLRGSLSTWSTIALTSGILLSYLTGAFFWYTTVAYIGAFVSFLSLVLVAMII 219
+ + + L + I +S L G Y ++ + GA++ + L +I
Sbjct: 342 EVRFSATIYLVCFCFFKQL-AMIFMSVLAGNM--YESIGFQGAYLVLGLVALGFTLI 395
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 29.9 bits (68), Expect = 0.56
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 70 ALPQM-SYLTIDQASWFASISA--ITMPIGCLLSGPIIDKYGRKSALMITNVPSLCGWLL 126
A+ M L + + + + + A +T + L GPI D+ GR+ +++ + L+
Sbjct: 22 AIADMARDLNVREGAVQSVMGAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFMLATLV 81
Query: 127 MATKSDLINLYISRLLSGLSVG 148
T S L L + + G+ G
Sbjct: 82 AVTTSSLTVLIAASAMQGMGTG 103
>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 = 29.4 bits (65), Expect = 0.98
Identities = 25/141 (17%), Positives = 43/141 (30%), Gaps = 56/141 (39%)
Query: 32 ISNGEHTDTPTLFRLIYLGLIVILPGVAPGMSFGFPAVALPQMSYLTIDQASWFASISAI 91
+ N EH + TLFR+++L F F ++Q I
Sbjct: 481 LKNIEHPERMTLFRMVFL-------------DFRF------------LEQK-----IRHD 510
Query: 92 TMPIGCLLSGPIID------KYGRKSALMIT-NVPSLCGWLLMATKSDLI--------NL 136
+ SG I++ Y I N P + + ++ NL
Sbjct: 511 STAWNA--SGSILNTLQQLKFYKP----YICDNDPKYERLV-----NAILDFLPKIEENL 559
Query: 137 YISRLLSGLSVGLATTPAAVY 157
S+ L + L A++
Sbjct: 560 ICSKYTDLLRIALMAEDEAIF 580
>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 = 27.2 bits (60), Expect = 5.4
Identities = 11/81 (13%), Positives = 28/81 (34%)
Query: 57 GVAPGMSFGFPAVALPQMSYLTIDQASWFASISAITMPIGCLLSGPIIDKYGRKSALMIT 116
G A+ ++ +T A+ + + + + IG +I ++ L
Sbjct: 272 GAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISRFAPHKVLAAY 331
Query: 117 NVPSLCGWLLMATKSDLINLY 137
+ ++ L+ A + L
Sbjct: 332 ALIAMALCLISAFAGGHVGLI 352
>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase,
signaling protein,transfera cycle complex; HET: MES AGS;
2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B*
Length = 293
Score = 26.5 bits (57), Expect = 6.9
Identities = 17/90 (18%), Positives = 28/90 (31%), Gaps = 10/90 (11%)
Query: 134 INLYISRLLSGLSVGLATTPAAVYAAECITIHNTDLRGSLSTWSTIALTSGILLS-YLTG 192
I Y RL S+ ++Y + + D + T LT+ + + L
Sbjct: 77 IFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCD 136
Query: 193 AFFWYTTVAYIGAF---------VSFLSLV 213
+F A +G FL V
Sbjct: 137 SFSTNAHYAKVGGVRCHELNILENDFLKRV 166
>1wom_A RSBQ, sigma factor SIGB regulation protein RSBQ; alpha/beta
hydrolase, signaling protein; 2.50A {Bacillus subtilis}
PDB: 1wpr_A*
Length = 271
Score = 26.0 bits (58), Expect = 8.5
Identities = 5/27 (18%), Positives = 8/27 (29%)
Query: 149 LATTPAAVYAAECITIHNTDLRGSLST 175
+T + +D R LS
Sbjct: 182 FCSTDPVIARQFAKAAFFSDHREDLSK 208
>1vb3_A Threonine synthase; PLP-dependent enzyme, lyase; HET: KPA; 2.20A
{Escherichia coli} SCOP: c.79.1.1
Length = 428
Score = 26.4 bits (59), Expect = 9.0
Identities = 9/33 (27%), Positives = 12/33 (36%), Gaps = 8/33 (24%)
Query: 17 HPVIATSSNAADIIDISNGEHTDTPTLFRLIYL 49
AT SNA D+ +N R+ L
Sbjct: 291 KATQATLSNAMDVSQPNNWP--------RVEEL 315
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
0.323 0.136 0.405
Gapped
Lambda K H
0.267 0.0537 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,205,993
Number of extensions: 182045
Number of successful extensions: 306
Number of sequences better than 10.0: 1
Number of HSP's gapped: 303
Number of HSP's successfully gapped: 30
Length of query: 219
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 129
Effective length of database: 4,188,903
Effective search space: 540368487
Effective search space used: 540368487
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.4 bits)