RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7965
(257 letters)
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 46.9 bits (112), Expect = 2e-06
Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 1 PFADKFGRKPVILAFCFPYILSWLLILFAQNIYMLFVARFIAGVGTG 47
P +D+ GR+PVIL ++L+ L+ + ++ +L A + G+GTG
Sbjct: 57 PISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIAASAMQGMGTG 103
>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 = 44.3 bits (104), Expect = 2e-05
Identities = 50/260 (19%), Positives = 75/260 (28%), Gaps = 84/260 (32%)
Query: 27 LFAQNIYMLFVARFIAGVGTGGLCAIIPMFIGEIAESSIRGALGSFFQMFLTLGVLYVYC 86
L + ++ +V+ + G + + L F +L
Sbjct: 60 LVGK--FLGYVSSLVEPSKVGQFDQV------------LNLCLTEFENCYLE-------- 97
Query: 87 LGLSTYTVIAIGCLTPIFLMKSGKPEKAEVSLRYYRGAQYDVATELAAIQKEIDAASEKK 146
G + + A L K + ++ Y A ++ D S
Sbjct: 98 -GNDIHALAA--KLLQE---NDTTLVKTKELIKNYITA-------RIMAKRPFDKKSN-- 142
Query: 147 ATFSDLFSSRANLRGLIVSLGLM-IF--QQFSGVNTVIF------YS------NDIFKSA 191
S LF RA G + L+ IF Q G F Y D+ K +
Sbjct: 143 ---SALF--RAVGEG---NAQLVAIFGGQ---GNTDDYFEELRDLYQTYHVLVGDLIKFS 191
Query: 192 GSTLDPSISAIIVGVVQC-----IVTGLSNSGS--DVS---SIAF-LPLISVIMF----I 236
TL I + I+ L N + D SI PLI VI +
Sbjct: 192 AETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVV 251
Query: 237 VMFSLGFGPIPWMMVGELFA 256
LGF P GEL +
Sbjct: 252 TAKLLGFTP------GELRS 265
Score = 34.3 bits (78), Expect = 0.044
Identities = 28/163 (17%), Positives = 46/163 (28%), Gaps = 46/163 (28%)
Query: 123 GAQ--------YDVATELAAIQKEIDAASEKKATFSDLFSSRANLRGLIVSLG------- 167
G+Q Y + + D + FS L N L + G
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRI 1684
Query: 168 -----LMIFQQFSGVNTVIFYSNDIFKSAGSTLDPSISAIIVGVVQCIVTGLSNSGSDVS 222
MIF+ + IFK ++ ++ + +S
Sbjct: 1685 RENYSAMIFETIVDGKLK---TEKIFKE----INEHSTSYT----------FRSEKGLLS 1727
Query: 223 SIAF----LPLISVIMFIVMFSLGFGPIPWMM----VGELFAA 257
+ F L L+ F + S G P +GE +AA
Sbjct: 1728 ATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGE-YAA 1769
Score = 30.8 bits (69), Expect = 0.50
Identities = 50/242 (20%), Positives = 77/242 (31%), Gaps = 69/242 (28%)
Query: 9 KPVILAFCFPYILSW--LLILFAQNIYMLFVARFIAGV---GTGGLCAIIPMFI------ 57
+ ++ A SW + + I +LF FI GV ++ P +
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAITVLF---FI-GVRCYEAYPNTSLPPSILEDSLEN 330
Query: 58 GEIAES---SIRGALGSFFQMFLTLGVLYVYCLGLSTYTVIAIGCL--TPIFLMKSGKPE 112
E S SI Q ++ L + I L L+ SG P+
Sbjct: 331 NEGVPSPMLSISNLTQEQVQDYVNK-----TNSHLPAGKQVEIS-LVNGAKNLVVSGPPQ 384
Query: 113 KAEVSLRYYRGAQYDVATELAAI-------QKEIDAASEKKATFSDLFSSRANLRGLIVS 165
SL Y + L Q I SE+K FS+ F L V+
Sbjct: 385 ----SL-------YGLNLTLRKAKAPSGLDQSRI-PFSERKLKFSNRF--------LPVA 424
Query: 166 L----GLM------IFQQFSGVNTVIFYSND----IFKSA-GSTLDPSISAIIVGVVQCI 210
L+ I + N V F + D ++ + GS L +I +V CI
Sbjct: 425 SPFHSHLLVPASDLINKDLVKNN-VSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCI 483
Query: 211 VT 212
+
Sbjct: 484 IR 485
Score = 29.2 bits (65), Expect = 1.5
Identities = 28/130 (21%), Positives = 42/130 (32%), Gaps = 39/130 (30%)
Query: 57 IGE------IAES-SIRGAL------GSFFQMFLTLGVLYVYCLGLSTYTVIAIGCLTPI 103
+GE +A+ SI + G Q+ + L G S Y +IAI P
Sbjct: 1764 LGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDEL-----GRSNYGMIAIN---PG 1815
Query: 104 FLMKSGKPEK-----AEVSLR---------Y-YRGAQYDVATELAAIQ---KEIDAASEK 145
+ S E V R Y QY A +L A+ ++ +
Sbjct: 1816 RVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQ 1875
Query: 146 KATFSDLFSS 155
K +L S
Sbjct: 1876 KIDIIELQKS 1885
Score = 27.7 bits (61), Expect = 5.1
Identities = 18/114 (15%), Positives = 37/114 (32%), Gaps = 29/114 (25%)
Query: 28 FAQNIYMLF---------VARFIAGVGTGGLCAIIPMFIG---------EIAESSIRGAL 69
+ ++F V R G G+ AI P + + E +
Sbjct: 1779 IESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVE-RVGKRT 1837
Query: 70 GSFFQM--FLTLGVLYVYCLGLSTYTVIAIGCLTPI--FL-MKSGKPEKAEVSL 118
G ++ + YV G + A+ +T + F+ ++ + + SL
Sbjct: 1838 GWLVEIVNYNVENQQYV-AAG----DLRALDTVTNVLNFIKLQKIDIIELQKSL 1886
Score = 26.9 bits (59), Expect = 8.4
Identities = 45/259 (17%), Positives = 77/259 (29%), Gaps = 91/259 (35%)
Query: 13 LAFC---FPYILSWLLILFAQNIYMLF----------VARFIAGVGTGGLCAIIPMFIGE 59
L P I +I A Y++ + ++ G TG ++
Sbjct: 231 LLSIPISCPLIG---VIQLAH--YVVTAKLLGFTPGELRSYLKGA-TGHSQGLVTAVA-- 282
Query: 60 IAESSIRGALGSFFQMFLT-LGVLYVYCLGLSTYTVIAIGCLTPIFLMKSGKPEKAE--- 115
IAE+ + SFF + VL+ +G+ Y L P L S + +
Sbjct: 283 IAET---DSWESFFVSVRKAITVLFF--IGVRCYEAYPNTSLPPSILEDSLENNEGVPSP 337
Query: 116 -VSLRYYRGAQYDVATELAAIQKEIDAASEKKATFSDLFSSRANLRGLIVSLGLMIFQQF 174
+S+ +Q ++ + L + + V + L
Sbjct: 338 MLSIS---NL------TQEQVQDYVNKTNSH------LPAGKQ------VEISL------ 370
Query: 175 SGVNT----VIFYSNDIFKSAGSTLDPSISAIIVGVVQCIVTGLSNSGSDVSSIAF---L 227
VN V+ +G P S + G+ + + SG D S I F
Sbjct: 371 --VNGAKNLVV---------SG----PPQS--LYGLNLTLRKAKAPSGLDQSRIPFSERK 413
Query: 228 PLISVIMFIVMFSLGFGPI 246
FS F P+
Sbjct: 414 L---------KFSNRFLPV 423
>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 = 34.2 bits (77), Expect = 0.016
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 8/33 (24%)
Query: 112 EKAEVSLRYYRGAQYDVATELAAIQKEIDAASE 144
+K + SL+ Y A D A LA I A E
Sbjct: 23 KKLQASLKLY--AD-DSAPALA-----IKATME 47
>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 = 33.7 bits (76), Expect = 0.069
Identities = 26/180 (14%), Positives = 48/180 (26%), Gaps = 43/180 (23%)
Query: 86 CLGLSTYTVIAIGCLTP--IFLMKSGKPEKAEVSLR-----YYRGAQYDVATE--LAAIQ 136
+ L + C IF + E L Y+ + + I+
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224
Query: 137 KEIDAASEKKATFSDLFSSRANLRGLIV-------------SLG---LM------IFQQF 174
I + + L S+ L+V +L L+ +
Sbjct: 225 LRIHSIQAEL---RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL 281
Query: 175 SGVNTVIFYSNDIFKSAGSTLDPSISAIIVGVVQCIVTGLSNSGSDVSSIAFLPL-ISVI 233
S T + S T D S +++ + C L + P +S+I
Sbjct: 282 SAATTTHISLDHH--SMTLTPDEVKS-LLLKYLDCRPQDLPREVLTTN-----PRRLSII 333
>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 = 31.4 bits (71), Expect = 0.28
Identities = 9/75 (12%), Positives = 21/75 (28%)
Query: 2 FADKFGRKPVILAFCFPYILSWLLILFAQNIYMLFVARFIAGVGTGGLCAIIPMFIGEIA 61
++ G K +L + + FA + + + + + L +I
Sbjct: 282 IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQF 341
Query: 62 ESSIRGALGSFFQMF 76
E + F
Sbjct: 342 EVRFSATIYLVCFCF 356
>3s1s_A Restriction endonuclease bpusi; PD--(D/E)XK catalytic motif,
gamma-N6M-adenosine methyltrans S-adenosyl-methionine
binding, hydrolase; HET: SAH; 2.35A {Bacillus pumilus}
Length = 878
Score = 28.0 bits (61), Expect = 3.4
Identities = 13/87 (14%), Positives = 26/87 (29%), Gaps = 11/87 (12%)
Query: 31 NIYMLFVARFIAGVGTGGLCAII----PMFIGEIAESSIRGALGSFFQMFLTLGVLYVYC 86
+ LF+ V G + + I + + R L F + +
Sbjct: 442 GVEALFLELVTELVQDGTVISAIMPKQYLTAQGNESKAFREFLVGNFGL---EHIFLYPR 498
Query: 87 LGLSTYTVIAIGCLTPIFLMKSGKPEK 113
GL + T +F+ + G +
Sbjct: 499 EGLFEEVIKD----TVVFVGRKGSSVE 521
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
0.329 0.143 0.425
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: 3,850,523
Number of extensions: 228333
Number of successful extensions: 593
Number of sequences better than 10.0: 1
Number of HSP's gapped: 589
Number of HSP's successfully gapped: 35
Length of query: 257
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 165
Effective length of database: 4,133,061
Effective search space: 681955065
Effective search space used: 681955065
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 56 (25.6 bits)