RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6058
(235 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 = 47.3 bits (113), Expect = 1e-06
Identities = 22/130 (16%), Positives = 46/130 (35%), Gaps = 5/130 (3%)
Query: 10 VASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGL--SLAYVTA 67
+ S D+ R G I++ + V + + + F + CG + +
Sbjct: 81 IMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMGWPPC 140
Query: 68 VVSIAYWF-DKKRTLATSLGACGTGIGTFVYAPLTQYWIEE-YGWRGTILLLAG-TFLQM 124
++ +W+ K+R S+ C +G + L + W + + A L
Sbjct: 141 GRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYMPAFCAILVA 200
Query: 125 CICGALMKDP 134
A+M+D
Sbjct: 201 LFAFAMMRDT 210
>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 = 43.0 bits (101), Expect = 4e-05
Identities = 18/143 (12%), Positives = 43/143 (30%), Gaps = 10/143 (6%)
Query: 10 VASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAYVTAVV 69
A +++ G + +L G I + S+ +++ + + + + V
Sbjct: 278 FAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSAL--EVVILKTLHMFEVPFLLVGCFK 335
Query: 70 SIAYWFDKKR--TLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGTFLQMCIC 127
I F+ + T+ + + L E G++G L+L L +
Sbjct: 336 YITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLI 395
Query: 128 GALMKDPEWWIREQKRLQNPTPS 150
+ + L
Sbjct: 396 SV------FTLSGPGPLSLLRRQ 412
>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 = 40.2 bits (93), Expect = 4e-04
Identities = 28/209 (13%), Positives = 57/209 (27%), Gaps = 74/209 (35%)
Query: 75 FDKK-RTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRG-----TILLLAGTFL------ 122
F+ + L T+ + F+ A T + ++ LL +L
Sbjct: 262 FNLSCKILLTTRFK---QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL-KYLDCRPQD 317
Query: 123 ---QMC--------ICGALMKDP----EWWIREQKRLQNPTPSHSIATKSNRNSIAESAA 167
++ I ++D + W K + + I +S+
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNW----KHVNCDKLTTII-----ESSL---NV 365
Query: 168 VDPGLVAVEIKEIRR------VLMDGGNI-ESLL--------FTEEEEMTKRGHNSVL-- 210
++P E R+ V +I LL ++ + + H L
Sbjct: 366 LEP-------AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418
Query: 211 ---NLPTFFLYD---DVSGQHREEFGKLH 233
T + ++ E LH
Sbjct: 419 KQPKESTISIPSIYLELK-VKLENEYALH 446
Score = 28.7 bits (63), Expect = 1.9
Identities = 29/189 (15%), Positives = 45/189 (23%), Gaps = 82/189 (43%)
Query: 47 AQYIT-FGCIAGCGLS-LAYVTAVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYW 104
A+ + G + G G + +A V K +W
Sbjct: 150 AKNVLIDG-VLGSGKTWVA--LDVCL-----SYKVQCKMDFKI---------------FW 186
Query: 105 I---EEYGWRGTILLLAGTFLQMCICGALMKDPEWWIREQKRLQNPTPSHSIATKSNRNS 161
+ + +L Q+ DP W R HS K +S
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQI--------DPNWTSR---------SDHSSNIKLRIHS 229
Query: 162 IAESAAVDPGLVAVEIKEIRRVLMDGGNIESLLFTEEEEMTKRGHNSVLNLPTFFLYDDV 221
I E+RR+L LL VL +V
Sbjct: 230 IQA--------------ELRRLLKSKPYENCLL--------------VL--------LNV 253
Query: 222 -SGQHREEF 229
+ + F
Sbjct: 254 QNAKAWNAF 262
>4aps_A DI-OR tripeptide H+ symporter; transport protein, peptide
transport, major facilitator SUPE transporter, MFS;
3.30A {Streptococcus thermophilus}
Length = 491
Score = 32.4 bits (74), Expect = 0.10
Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 4/99 (4%)
Query: 16 DKY-GCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIA-GCGLSLAYVTAVVSIAY 73
D+ G R GG++ G ++ A + A + + I G G V+ +V Y
Sbjct: 79 DRIIGARPAVFWGGVLIMLGHIVLA-LPFGASALFGSIILIIIGTGFLKPNVSTLVGTLY 137
Query: 74 -WFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWR 111
D++R S+ G +G F+ + E G+
Sbjct: 138 DEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYH 176
>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 = 31.9 bits (72), Expect = 0.18
Identities = 42/218 (19%), Positives = 75/218 (34%), Gaps = 64/218 (29%)
Query: 34 GFVLSATVANSIEAQYITFGCIAGCGLSLAYVTAVVSIAYWFDKKRTLATSLGACGTGIG 93
GF + V N+ I FG G + Y A F+ G
Sbjct: 1658 GFSILDIVINNPVNLTIHFGGEKGKRIRENY------SAMIFETIVD--------GKLKT 1703
Query: 94 TFVYAPLTQYWIEEYGWRGTILLLAGT-FLQ---MCICGALMKDPEWWIREQKRLQNPTP 149
++ + ++ Y +R LL+ T F Q + A +D ++ + + P
Sbjct: 1704 EKIFKEINEH-STSYTFRSEKGLLSATQFTQPALTLMEKAAFED----LKSKGLI--PAD 1756
Query: 150 S----HSI------ATKSNRNSIAESAAVDPGLV---------AVEIKEIRR--VLM--- 185
+ HS+ A+ ++ SI + V+ +V AV E+ R M
Sbjct: 1757 ATFAGHSLGEYAALASLADVMSI--ESLVE--VVFYRGMTMQVAVPRDELGRSNYGMIAI 1812
Query: 186 DGGNIESLLFTEE------EEMTKRGHNSV----LNLP 213
+ G + + F++E E + KR V N+
Sbjct: 1813 NPGRV-AASFSQEALQYVVERVGKRTGWLVEIVNYNVE 1849
Score = 30.8 bits (69), Expect = 0.47
Identities = 17/93 (18%), Positives = 34/93 (36%), Gaps = 22/93 (23%)
Query: 138 IREQ--KRLQNPTPSHSIATKSNRNSIAESAA---------VDPG-------LVAVEIKE 179
++EQ K L P P+ A + AE V+P ++ + + E
Sbjct: 33 LQEQFNKIL--PEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE 90
Query: 180 IRRVLMDGGNIESLL--FTEEEEMTKRGHNSVL 210
++G +I +L +E + T ++
Sbjct: 91 FENCYLEGNDIHALAAKLLQENDTTLVKTKELI 123
Score = 27.3 bits (60), Expect = 5.4
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 9/31 (29%)
Query: 206 HNSV---LNLPT--FFLYDDVSGQHREEFGK 231
H S+ L +PT FF+ Q +E+F K
Sbjct: 13 HGSLEHVLLVPTASFFIAS----QLQEQFNK 39
>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 = 29.1 bits (65), Expect = 1.3
Identities = 18/129 (13%), Positives = 35/129 (27%), Gaps = 12/129 (9%)
Query: 5 LLLGPVASSFVDKYGCRWMTILGGIISGTG---FVLSATVANSIEAQYITFGCIAGCGLS 61
++ A + K + I G + G F +A + N ++ I GL
Sbjct: 75 FIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNY--TLFLVGLFIIAAGLG 132
Query: 62 L------AYVTAVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTIL 115
+VT + + + LA + + G I L +
Sbjct: 133 CLETAANPFVTVLGPESS-GHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDK 191
Query: 116 LLAGTFLQM 124
+
Sbjct: 192 MSPEQLSAY 200
>3nzq_A ADC, biosynthetic arginine decarboxylase; alpha-beta protein,
structural genomics, PSI-biology, protei structure
initiative; 3.10A {Escherichia coli}
Length = 666
Score = 27.6 bits (61), Expect = 4.6
Identities = 17/73 (23%), Positives = 24/73 (32%), Gaps = 14/73 (19%)
Query: 154 ATKSNRN-SIAESAA---VDPGLVAVEIKEIRRVLMDGGNIESLLF-----TEEE----- 199
K N++ + ES GL A E+ VL G S++ E
Sbjct: 125 PIKVNQHRRVIESLIHSGEPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYIRLAL 184
Query: 200 EMTKRGHNSVLNL 212
K GH L +
Sbjct: 185 IGEKMGHKVYLVI 197
>3hm8_A Hexokinase-3; glucose, glucose-6-phosphate, non-protein kinase,
structural genomics consortium, SGC, A enzyme,
ATP-binding, glycolysis; HET: GLC BG6; 2.80A {Homo
sapiens}
Length = 445
Score = 26.5 bits (58), Expect = 9.7
Identities = 11/68 (16%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 40 TVANSIEAQY----ITFGCIAGCGLSLAYVTAVVSIAYWFDKKRTLATSLGACGTGIGTF 95
TV + Y G I G G + Y+ + ++A + ++ G
Sbjct: 187 TVGTMMSCGYEDPRCEIGLIVGTGTNACYMEELRNVAGVPGDSGRMCINMEWGAFGDDGS 246
Query: 96 VYAPLTQY 103
+ T++
Sbjct: 247 LAMLSTRF 254
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 0.137 0.426
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: 3,696,130
Number of extensions: 221914
Number of successful extensions: 447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 21
Length of query: 235
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 144
Effective length of database: 4,160,982
Effective search space: 599181408
Effective search space used: 599181408
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: 56 (25.6 bits)