RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15907
(260 letters)
>3org_A CMCLC; transporter, transport protein; 3.50A {Cyanidioschyzon
merolae}
Length = 632
Score = 183 bits (466), Expect = 5e-54
Identities = 43/208 (20%), Positives = 81/208 (38%), Gaps = 17/208 (8%)
Query: 1 MPRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFK 60
M + ++ L K +G+I + GGL G EGP +H I+A + +
Sbjct: 96 MRSALELRVLFAKALGLICAIGGGLPVGWEGPNVHIACIIAHQFYRLGVFK--------E 147
Query: 61 YFREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFT 120
+ + ++ A G+A++FGAP+GGVL+S+E ASF+ W+ +
Sbjct: 148 LCTDRALRLQTLAAACAVGLASSFGAPLGGVLYSIETIASFYLVQAFWKGVLSALSGAIV 207
Query: 121 LNVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKL 180
++ + F + Y G G+ GAL+ +
Sbjct: 208 YELLYT--------TPLVEAFEGTNFDASDVSRTQTLLYAILGALMGVLGALFIRCVRSI 259
Query: 181 TVFRIRYMSARYVKVLEAVLVAMVSACV 208
R+R+ + +VA+ ++ +
Sbjct: 260 YELRMRHYPGTN-RYFLVGVVALFASAL 286
>3nd0_A SLL0855 protein; CLC family CL-/H+ antiporter, CLC_EC1 homolog,
transport protein; 3.20A {Synechocystis} PDB: 3q17_A
Length = 466
Score = 94.4 bits (235), Expect = 2e-22
Identities = 41/213 (19%), Positives = 82/213 (38%), Gaps = 25/213 (11%)
Query: 2 PRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKY 61
LV + L +K +G ++ G+ G EGP I G + FK
Sbjct: 116 LPLVWQRVLPIKLVGGFLSLGAGMLAGFEGPTIQMGGSIGQMTGG-----------WFK- 163
Query: 62 FREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTL 121
+R ++ GA AG+A AF AP+ GV EE + + +
Sbjct: 164 -ATQENQRILIAVGAGAGLATAFNAPLAGVALIGEEMHPRF--RSQTLAYHSLLFGCVMA 220
Query: 122 NVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKLT 181
++L G S +++ +F + L ++ ++ G+ G+ G +N K+
Sbjct: 221 TIILRMIRG------QSAIISLTEFKRV--PLDSLWMFIILGILFGVMGYTFNRGLFKVL 272
Query: 182 VF--RIRYMSARYVKVLEAVLVAMVSACVPIIM 212
+ R+ ++ ++ L ++ ++S +
Sbjct: 273 DWFDRLPPLATKWKGFLLGSIIGILSLFPLPLT 305
>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 = 90.1 bits (224), Expect = 8e-21
Identities = 47/213 (22%), Positives = 83/213 (38%), Gaps = 25/213 (11%)
Query: 2 PRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKY 61
+ + L VK G + T+ GG+ G+EGP + G + + IF+
Sbjct: 120 RPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLD-----------IFR- 167
Query: 62 FREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEE-GASFWNQSLTWRIFFGTIVTTFT 120
+ D + ++ GAAAG+AAAF AP+ G+LF +EE F T +
Sbjct: 168 LKGDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQF---RYTLISIKAVFIGVIM 224
Query: 121 LNVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKL 180
++ + L++ GK D L ++ Y+ G+ G+ G ++N +
Sbjct: 225 STIMYRIFNH------EVALIDVGKLSDA--PLNTLWLYLILGIIFGIFGPIFNKWVLGM 276
Query: 181 TVFRIRYMSARYVK-VLEAVLVAMVSACVPIIM 212
R K VL + + + +
Sbjct: 277 QDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVA 309
>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 = 43.9 bits (103), Expect = 4e-05
Identities = 36/218 (16%), Positives = 58/218 (26%), Gaps = 88/218 (40%)
Query: 27 GGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFK-YFREDHE-KRDFVSGG------AA- 77
G + IH+ +AA + Q T+ ++ K Y KR F A
Sbjct: 97 EGND---IHA---LAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVG 150
Query: 78 ---AGVAAAFG---------------------------APVGGVLFSL----EEGASFWN 103
A + A FG L L + +
Sbjct: 151 EGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT 210
Query: 104 QSL---TW---------RIFFGTIVTTFTLNVV--LSAYY------G-HPGELTN--SGL 140
Q L W + + +I + L V L+ Y G PGEL + G
Sbjct: 211 QGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGA 270
Query: 141 LNFGK----------------FYDLRYDLLEMFFYVGA 162
+ F+ + + F++G
Sbjct: 271 TGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV 308
>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 = 39.1 bits (90), Expect = 0.001
Identities = 30/184 (16%), Positives = 55/184 (29%), Gaps = 55/184 (29%)
Query: 102 WNQSLTWRIF-FG--TIVTTFTLNV---VLSAYYGHP------GELTNSGLLN-FGKFYD 148
N W F ++TT V + +A H LT + + K+ D
Sbjct: 254 QNAK-AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLD 312
Query: 149 LRYDLL--EMFFYVGAGVFGGLTGALYNSLNHKLTVFRIRYMSAR---YVKVLEAVLVAM 203
R L E+ LT N + IR A + V L +
Sbjct: 313 CRPQDLPREV-----------LTT---NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 204 VSACVPIIMIYSIDDCRPLGEDPTEHAVQMY--CG---DG---EYNTLAALWLQVPEKSV 255
+ + + ++ +P E+ +M+ L+ +W V + V
Sbjct: 359 IESSLNVL-------------EPAEYR-KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDV 404
Query: 256 RTML 259
++
Sbjct: 405 MVVV 408
>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET:
DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11
PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*
Length = 296
Score = 28.0 bits (63), Expect = 2.9
Identities = 14/61 (22%), Positives = 18/61 (29%), Gaps = 23/61 (37%)
Query: 39 IVAAGISQGKSTSFGTDFQIFKYFREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEG 98
+V +G GK ++F A A G VG L LEE
Sbjct: 39 MVTSGSGMGK-STFVRQQ--------------------ALQWGTAMGKKVG--LAMLEES 75
Query: 99 A 99
Sbjct: 76 V 76
>2plj_A Lysine/ornithine decarboxylase; type IV decarboxylase, beta/alpha
barrel, beta barrel, lyase; HET: P3T; 1.70A {Vibrio
vulnificus} PDB: 2plk_A*
Length = 419
Score = 28.0 bits (63), Expect = 3.6
Identities = 6/30 (20%), Positives = 19/30 (63%)
Query: 155 EMFFYVGAGVFGGLTGALYNSLNHKLTVFR 184
++++Y+ G++G +G +++ + LT +
Sbjct: 315 QIWYYLDDGIYGSFSGLMFDDARYPLTTIK 344
>3by9_A Sensor protein; histidine kinase sensor domain, phosphoprotein,
transferase, two-component regulatory system; 1.70A
{Vibrio cholerae}
Length = 260
Score = 27.5 bits (60), Expect = 4.7
Identities = 16/101 (15%), Positives = 29/101 (28%), Gaps = 6/101 (5%)
Query: 33 MIHSGAIVAAGISQGKSTSFGTDFQIFKYFRE---DHEKRDFVSGGAAAGVAAAFGAPV- 88
+ G +A+ + G +F YF + + F G + + PV
Sbjct: 78 IDRFGNTIASSNWNLDRSFIGRNFAWRPYFYLSIAGQKSQYFALGSTSGQRGYYYAYPVI 137
Query: 89 --GGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTLNVVLSA 127
+L + W+ V T VV +
Sbjct: 138 YAAEILGVIVVKMDLSAIEQGWQNKSSYFVATDDHQVVFMS 178
>2ivf_A Ethylbenzene dehydrogenase alpha-subunit; anaerobic hydrocarbon
degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO
reductase family; HET: MES MGD MD1 HEM; 1.88A
{Aromatoleum aromaticum}
Length = 976
Score = 26.6 bits (58), Expect = 9.3
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 69 RDFVSGGAAAGVAAAFGAPVGGVLFSLEEGAS 100
RDF+ AA ++ + + GV+ + A
Sbjct: 22 RDFLKRSGAAVLSLSLSSLATGVVPGFLKDAQ 53
>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette,
hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}
Length = 279
Score = 26.4 bits (59), Expect = 9.9
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 7/59 (11%)
Query: 78 AGVAAAFGAPVGGVLFSLEEGAS---FWNQSLTWRIFFGTIVTTFTLNVVLSAYYGHPG 133
+G FG G V +S E F + SL + G V ++VV+S + G
Sbjct: 75 SGTVNLFGKMPGKVGYSAETVRQHIGFVSHSLLEKFQEGERV----IDVVISGAFKSIG 129
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
0.324 0.141 0.425
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,171,902
Number of extensions: 260146
Number of successful extensions: 742
Number of sequences better than 10.0: 1
Number of HSP's gapped: 730
Number of HSP's successfully gapped: 34
Length of query: 260
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 168
Effective length of database: 4,133,061
Effective search space: 694354248
Effective search space used: 694354248
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 (21.5 bits)
S2: 56 (25.7 bits)