RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15908
(354 letters)
>3org_A CMCLC; transporter, transport protein; 3.50A {Cyanidioschyzon
merolae}
Length = 632
Score = 97.1 bits (242), Expect = 3e-22
Identities = 20/106 (18%), Positives = 41/106 (38%), Gaps = 9/106 (8%)
Query: 236 WVIFFLIGVLTACIGIFIDISIEFIAVFKYSTLKRYLDNSGNTGMLVPLAVWLGFNIVPV 295
L+GV A +D+++ + + + G +++ +
Sbjct: 11 VCFLTLLGVTAALFIFAVDLAVHGLEELRMKISR-------LAGRFAGYILYVVSGVALC 63
Query: 296 LIGSLLVVYVEPVALGSGIPQVKCYLNGI--KMPRLVRIKTLVVKT 339
L+ + + A GSG+PQ+K L+G KM + ++ L K
Sbjct: 64 LLSTFWCAVLSTEAEGSGLPQMKSILSGFYDKMRSALELRVLFAKA 109
>1ots_A Voltage-gated CLC-type chloride channel ERIC; CLC chloride channel,
FAB complex, membrane protein; 2.51A {Escherichia coli}
SCOP: f.20.1.1 PDB: 2fee_A 2h2p_A 2exw_A 1kpk_A 2exy_A
2htl_A 3ejy_A 2ht2_A 2fed_A 2fec_A 1otu_A 3ejz_A 2ht4_A
2htk_A 2ht3_A 1ott_A 2h2s_A 3det_A 2ez0_A 3nmo_A ...
Length = 465
Score = 59.7 bits (145), Expect = 5e-10
Identities = 23/123 (18%), Positives = 42/123 (34%), Gaps = 7/123 (5%)
Query: 216 LTQSETWKSYNFILYKDFARWVIFFLIGVLTACIGIFIDISIEFIAVFKYSTLKRYLDNS 275
L + + + A + ++G L + D + ++ + L DN
Sbjct: 16 LRRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNY 75
Query: 276 GNTGMLVPLAVWLGFNIVPVLIGSLLVVYVEPVALGSGIPQVKCYLNGIKMPRLVRIKTL 335
+ L + + G LV P A GSGIP+++ L + + L
Sbjct: 76 PLLLTVAFLCSAVLA-----MFGYFLVRKYAPEAGGSGIPEIEGALED--QRPVRWWRVL 128
Query: 336 VVK 338
VK
Sbjct: 129 PVK 131
>3nd0_A SLL0855 protein; CLC family CL-/H+ antiporter, CLC_EC1 homolog,
transport protein; 3.20A {Synechocystis} PDB: 3q17_A
Length = 466
Score = 55.9 bits (135), Expect = 7e-09
Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 7/103 (6%)
Query: 236 WVIFFLIGVLTACIGIFIDISIEFIAVFKYSTLKRYLDNSGNTGMLVPLAVWLGFNIVPV 295
V ++G++T +G ++ + ++ + ++ L V
Sbjct: 32 LVAAIVVGLITGVLGAGFKSAVNNMLQWRSQLAQILAPIPPLAWLVTALISGGM-----V 86
Query: 296 LIGSLLVVYVEPVALGSGIPQVKCYLNGIKMPRLVRIKTLVVK 338
+ L+ P GSGIPQ++ +L G LV + L +K
Sbjct: 87 ALSFWLMKRFAPDTSGSGIPQIEGHLEG--KLPLVWQRVLPIK 127
>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 = 48.7 bits (115), Expect = 2e-06
Identities = 45/333 (13%), Positives = 97/333 (29%), Gaps = 82/333 (24%)
Query: 6 KYLITSNEA------------ESSGEDDRPPLMQQDSET----------SILPRQSRSRR 43
K L+T+ S + L + ++ LPR+
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREV---- 322
Query: 44 RKCSVLPTVDTVIETTIKKGA--------------SNIISSKFESLDYDLMENYLTQSMT 89
+ P ++I +I+ G + II S L+ ++
Sbjct: 323 --LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF-DRLS 379
Query: 90 ---ESHKYLITSNE-----TESSGEDDRPPLMQQDSETSILPRQSRSRRRKCSVLPTVDT 141
S I + + D ++ + + S++ +Q + +P++
Sbjct: 380 VFPPSAH--IPTILLSLIWFDVIKSDVM-VVVNKLHKYSLVEKQPKEST---ISIPSIYL 433
Query: 142 VIETTIKKGKVTHIQI--KSKPIKTKPVPTCCENH--QFFFQ------MSCRQYN----F 187
++ ++ H I KT + Q+F+ + F
Sbjct: 434 ELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF 493
Query: 188 R---LAFAFPGASNIISSKFESLDYDLMENYLTQSETWKSY---NFILYKDFARWVIFFL 241
R L F F I + N L Q + +K Y N Y+ ++ FL
Sbjct: 494 RMVFLDFRFLEQK-IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552
Query: 242 IGVLTACI-GIFIDISIEFIAVFKYSTLKRYLD 273
+ I + D+ + + + + + +
Sbjct: 553 PKIEENLICSKYTDL-LRIALMAEDEAI--FEE 582
Score = 31.0 bits (69), Expect = 0.69
Identities = 35/201 (17%), Positives = 65/201 (32%), Gaps = 56/201 (27%)
Query: 173 NHQFFFQMSCRQYNFRLAFAFPGASNIIS---SKF-ESLDY----DLMENYLTQSETWKS 224
+H F+ QY ++ +I+S F ++ D D+ ++ L++ E
Sbjct: 4 HHHMDFETGEHQYQYK---------DILSVFEDAFVDNFDCKDVQDMPKSILSKEE---- 50
Query: 225 YNFILYKDFARWVIFFLIGVL----TACIGIFIDISIEFIAVFKYSTLK-RYLDNSGNTG 279
+ I+ A L L + F++ + F S +K S T
Sbjct: 51 IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR 110
Query: 280 MLV----PLAVWLGFNIVPVLIGSLLVVYVEPVALGSGIPQVKCYLNGIKMPRLVRIKTL 335
M + L +N V V ++P +++ L L K +
Sbjct: 111 MYIEQRDRL-----YNDNQVFA-KYNVSRLQPYL------KLRQALL-----ELRPAKNV 153
Query: 336 VV-------KTNRIAASRVCR 349
++ KT A VC
Sbjct: 154 LIDGVLGSGKT--WVALDVCL 172
>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 = 31.1 bits (70), Expect = 0.52
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 12/65 (18%)
Query: 237 VIFFLIGVLTACIGIFIDISIEFIAVFKYSTLKRYLDNSGNTGMLVPLAVWLGFNIVPVL 296
+FFL V I + ++ + L+ A + G+ I+P+
Sbjct: 33 SLFFLWAVANNLNDILLPQ------------FQQAFTLTNFQAGLIQSAFYFGYFIIPIP 80
Query: 297 IGSLL 301
G L+
Sbjct: 81 AGILM 85
>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 = 30.3 bits (67), Expect = 0.58
Identities = 8/22 (36%), Positives = 12/22 (54%), Gaps = 7/22 (31%)
Query: 266 STLKRYLDNSGNTGMLVP-LAV 286
++LK Y D+S P LA+
Sbjct: 27 ASLKLYADDSA------PALAI 42
>2pz4_A Protein GBS052; SPAB, GRAM-positive pilins, adhesions, IGG-like
domain, cell adhesion; 1.80A {Streptococcus agalactiae}
PDB: 3phs_A
Length = 239
Score = 29.8 bits (66), Expect = 1.0
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 140 DTVIETTIKKGKVTHIQIKSKPIKTKPVPT 169
TI+K K + I++K + T VP+
Sbjct: 209 QAETAVTIEKSKTVTVTIENKKVPTPKVPS 238
>2xw7_A Dihydrofolate reductase; oxidoreductase, NADPH; HET: PG4 NDP; 2.00A
{Mycobacterium smegmatis}
Length = 178
Score = 27.4 bits (61), Expect = 4.9
Identities = 5/28 (17%), Positives = 8/28 (28%), Gaps = 8/28 (28%)
Query: 296 LIGSLL--------VVYVEPVALGSGIP 315
+ + +V P LG G
Sbjct: 120 VAAQFVAADLIDEIIVSYAPCTLGVGSR 147
>3jtw_A Dihydrofolate reductase; YP_805003.1, structural GE joint center
for structural genomics, JCSG, protein structu
initiative; 1.90A {Pediococcus pentosaceus atcc 25745}
Length = 178
Score = 27.3 bits (61), Expect = 6.5
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 8/28 (28%)
Query: 296 LIGSLL--------VVYVEPVALGSGIP 315
+I L+ ++ P+ LGSGI
Sbjct: 121 IIDPLVQANLIDTYILTTVPIFLGSGIR 148
>3ky8_A Putative riboflavin biosynthesis protein; structural genomic center
for structural genomics, JCSG, protein structure INI
PSI-2; HET: MSE UNL; 2.12A {Shewanella loihica}
Length = 197
Score = 26.9 bits (60), Expect = 9.0
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 301 LVVYVEPVALGSGIP 315
+V+ P+ LG G+P
Sbjct: 150 MVITRFPILLGGGVP 164
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
0.320 0.134 0.395
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,061,507
Number of extensions: 285386
Number of successful extensions: 449
Number of sequences better than 10.0: 1
Number of HSP's gapped: 442
Number of HSP's successfully gapped: 13
Length of query: 354
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 259
Effective length of database: 4,049,298
Effective search space: 1048768182
Effective search space used: 1048768182
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 (21.8 bits)
S2: 58 (26.2 bits)