RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15226
(362 letters)
>3rko_A NADH-quinone oxidoreductase subunit A; complex I, proton pump,
membrane protein, Na ubiquinone, cytoplasmic membrane;
HET: LFA CA7; 3.00A {Escherichia coli}
Length = 147
Score = 64.7 bits (158), Expect = 6e-13
Identities = 17/44 (38%), Positives = 25/44 (56%)
Query: 307 REKTSPFECGFDPISKPRISYSLHFFSIALIFLIFDIEITLIFP 350
R K PFE G D + R+ S F+ +A+ F+IFD+E +F
Sbjct: 44 RSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFDVEALYLFA 87
>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 = 61.6 bits (149), Expect = 2e-10
Identities = 80/486 (16%), Positives = 129/486 (26%), Gaps = 207/486 (42%)
Query: 22 ALSILPVIFFIL------FSF-VPETPHFHAAKNNLKKT-EKSL-KWYRGNKKDVMEEMN 72
A S P L VP F A++ L++ K L + G D +E
Sbjct: 3 AYSTRP---LTLSHGSLEHVLLVPTASFFIASQ--LQEQFNKILPEPTEGFAAD--DEPT 55
Query: 73 SIMDKTQEDLKSK-TGYLELLTNKSNRRAFTLVMAASL--FQR--LGG------ITSMIT 121
+ +L K GY+ L S F V+ L F+ L G ++
Sbjct: 56 T-----PAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQ 110
Query: 122 YSSTLLPKLDNAYFGPDQCILVFMIIMFLSNFLQAPLMDILGRKPLSCFSAALGCLLTFS 181
+ T L K + N++ A + R ++AL
Sbjct: 111 ENDTTLVKTKE----------------LIKNYITA--RIMAKRPFDKKSNSAL--FRAVG 150
Query: 182 TGLFYLY-----QG-------ELPNFQ--YIPYITTLLYAAS---------------YYG 212
G L QG EL + Y + L+ ++ +
Sbjct: 151 EGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT 210
Query: 213 IGC-----------------LPNILVSELFPINVRCQ----------------------- 232
G L +I +S P+ Q
Sbjct: 211 QGLNILEWLENPSNTPDKDYLLSIPIS--CPLIGVIQLAHYVVTAKLLGFTPGELRSYLK 268
Query: 233 -ASSCAS---VALAFGSFIT-TKFHILITKSLGQHVIFFIYSSVHFCSVVFNYFYL---- 283
A+ + A+A + F + + K++ V+FFI V C + L
Sbjct: 269 GATGHSQGLVTAVAIAETDSWESFFVSVRKAI--TVLFFI--GVR-CYEAYPNTSLPPSI 323
Query: 284 --------------M--------ETKQKTLAE----------IQESIMNSHKQ------- 304
M E Q + + ++ S++N K
Sbjct: 324 LEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPP 383
Query: 305 ---------LRREKTSPFECGFD----PIS--KPRISYSLHFFSIALIFLIFDIEITLIF 349
LR+ K G D P S K + S FL + F
Sbjct: 384 QSLYGLNLTLRKAKAPS---GLDQSRIPFSERKLKFSNR---------FL----PVASPF 427
Query: 350 PSPLIK 355
S L+
Sbjct: 428 HSHLLV 433
Score = 31.2 bits (70), Expect = 0.60
Identities = 39/223 (17%), Positives = 64/223 (28%), Gaps = 92/223 (41%)
Query: 43 FHAAKNNLKKTEKSLKWYRGNKKDVMEEMNSIMDKTQEDLKSKTGYLELLTNKSNRRAFT 102
F + KTEK K ++ E S ++++ L S T FT
Sbjct: 1693 FETIVDGKLKTEKIFK-------EINEHSTSYTFRSEKGLLSAT-------------QFT 1732
Query: 103 ----LVMAASLFQRLGGITSMITYSSTLLPKLDNAYF-GPDQCILVFMIIMFLSNFLQAP 157
+M + F+ L S L+P +A F G S
Sbjct: 1733 QPALTLMEKAAFEDLK--------SKGLIP--ADATFAG-------------HS------ 1763
Query: 158 LMDILGRKPLSCFSAALGCL---LTFSTG---LFY---LYQGELPNFQYIPYITTLLYAA 208
LG ++ AL L ++ + +FY Q +P +
Sbjct: 1764 ----LGE-----YA-ALASLADVMSIESLVEVVFYRGMTMQVAVPRDE---------LGR 1804
Query: 209 SYYGI-GCLPNILVSELFPINVRCQASS---CASVALAFGSFI 247
S YG+ P + + Q + V G +
Sbjct: 1805 SNYGMIAINPGRVAASF------SQEALQYVVERVGKRTGWLV 1841
>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 = 56.0 bits (134), Expect = 1e-08
Identities = 51/265 (19%), Positives = 83/265 (31%), Gaps = 75/265 (28%)
Query: 5 LAILLIG-------------NHVSYNSLN--IALSI--L-PVIF---FILFSFVPETPHF 43
+ +I HV+ + L I S+ L P + F S P
Sbjct: 328 RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPP---- 383
Query: 44 HAAKNNLKKTEKSLK--WYRGNKKDVMEEMNSIMDKT--QEDLKSKT-----GYLELLTN 94
+ L W+ K DVM +N + + ++ K T YLEL
Sbjct: 384 -----SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVK 438
Query: 95 KSNRRAFTLVMAASLFQRLGGITSMITYSSTLLPKLDNAYF-----------GPDQCILV 143
N A + S+ I + P LD YF + + +
Sbjct: 439 LENEYA----LHRSIVDHY-NIPKTFDSDDLIPPYLDQ-YFYSHIGHHLKNIEHPERMTL 492
Query: 144 FMIIMFLS-NFLQAPLMDILGRKPLSCFSAALGCLLTFSTGLFYLYQGELPNFQYI---- 198
F ++ FL FL+ + R + ++A+ L T FY YI
Sbjct: 493 FRMV-FLDFRFLEQKI-----RHDSTAWNASGSILNTLQQLKFYK--------PYICDND 538
Query: 199 PYITTLLYAASYYGIGCLPNILVSE 223
P L+ A + N++ S+
Sbjct: 539 PKYERLVNAILDFLPKIEENLICSK 563
>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 = 38.4 bits (88), Expect = 0.001
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 47 KNNLKKTEKSLKWY 60
K LKK + SLK Y
Sbjct: 19 KQALKKLQASLKLY 32
>1gl2_A Endobrevin; membrane protein, membrane fusion protein complex,
coiled coil, transmembrane; 1.9A {Rattus norvegicus}
SCOP: h.1.15.1
Length = 65
Score = 29.4 bits (66), Expect = 0.31
Identities = 10/45 (22%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 68 MEEMNSIMDKTQEDLKSKTGYLELLTNKSNRRAFTLVMAASLFQR 112
+E + +IM + E + ++ L+ L NK+ L + F+
Sbjct: 18 VEGVKNIMTQNVERILARGENLDHLRNKTED----LEATSEHFKT 58
>1gcy_A Glucan 1,4-alpha-maltotetrahydrolase; beta-alpha-barrel, beta
sheet; 1.60A {Pseudomonas stutzeri} SCOP: b.71.1.1
c.1.8.1 PDB: 1jdc_A* 1jda_A* 1jdd_A* 1qi5_A* 1qi3_A*
1qi4_A* 2amg_A 1qpk_A*
Length = 527
Score = 31.2 bits (70), Expect = 0.55
Identities = 27/209 (12%), Positives = 58/209 (27%), Gaps = 23/209 (11%)
Query: 58 KWYRGNKKDVM---EEMNSIMDKTQEDLKSKTGYLELLTNKSNRRAFTLVMAASLFQRL- 113
W + + E + D ++ + +++ + S+R V +L +R+
Sbjct: 205 SWMTDSADNSFCVGELWKGPSEYPNWDWRNTASWQQIIKDWSDRAKCP-VFDFALKERMQ 263
Query: 114 -GGITSMITYSSTLLPKLDNAYFGPDQCILVFMIIMFLSN-----FLQAPLMDILGRKPL 167
G I + F+ N
Sbjct: 264 NGSIADWKHGLNGNPDPRWREVAVT-----------FVDNHDTGYSPGQNGGQHHWALQD 312
Query: 168 SCFSAALGCLLTFSTGLFYLYQGELPNFQYIPYITTLLYAASYYGIGCLPNILVSELFPI 227
A +LT S G +Y + ++ Y +I L+ G+ I +
Sbjct: 313 GLIRQAYAYILT-SPGTPVVYWDHMYDWGYGDFIRQLIQVRRAAGVRADSAISFHSGYSG 371
Query: 228 NVRCQASSCASVALAFGSFITTKFHILIT 256
V + S ++ +A S + +
Sbjct: 372 LVATVSGSQQTLVVALNSDLGNPGQVASG 400
>1n7s_A Vesicle-associated membrane protein 2; neuronal snare protein
complex, four helix bundle, transport protein; 1.45A
{Rattus norvegicus} SCOP: h.1.15.1 PDB: 1kil_A 3rk2_A
3rk3_A 3rl0_A 3fii_B 3g94_B
Length = 63
Score = 28.2 bits (63), Expect = 0.67
Identities = 11/68 (16%), Positives = 26/68 (38%), Gaps = 15/68 (22%)
Query: 45 AAKNNLKKTEKSLKWYRGNKKDVMEEMNSIMDKTQEDLKSKTGYLELLTNKSNRRAFTLV 104
+ L++T+ + +E+ IM + + + L L ++++ L
Sbjct: 1 GSNRRLQQTQAQV-----------DEVVDIMRVNVDKVLERDQKLSELDDRAD----ALQ 45
Query: 105 MAASLFQR 112
AS F+
Sbjct: 46 AGASQFET 53
>3bc9_A AMYB, alpha amylase, catalytic region; acarbose, thermostable,
halophilic, N domain, starch binding, hydrolase; HET:
G6D GLC ACI BGC ACR; 1.35A {Halothermothrix orenii} PDB:
3bcd_A* 3bcf_A
Length = 599
Score = 31.1 bits (70), Expect = 0.68
Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 10/80 (12%)
Query: 149 FLSN-----FLQAPLMDILGRKPLSCFSAALGCLLTFSTGLFYLYQGELPNFQYIPYITT 203
F+ N + + I RK A +LT + G+ +Y + ++ +
Sbjct: 442 FVDNHDTDRDEGSYTVSIYSRKYQ-----AYAYILTRAEGVPTVYWKDYYIWEMKEGLDK 496
Query: 204 LLYAASYYGIGCLPNILVSE 223
LL A YY G + ++
Sbjct: 497 LLTARRYYAYGPGYEVDNND 516
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 27.2 bits (61), Expect = 9.5
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 143 VFMIIMFLSNFLQAPLMDILGRKP-----LSCFS-AALGCLLTFSTGLFYL 187
+++ +S P+ D +GR+P +S F A L + T S +
Sbjct: 43 AYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIA 93
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
0.328 0.141 0.417
Gapped
Lambda K H
0.267 0.0681 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,207,861
Number of extensions: 296264
Number of successful extensions: 661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 659
Number of HSP's successfully gapped: 17
Length of query: 362
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 267
Effective length of database: 4,049,298
Effective search space: 1081162566
Effective search space used: 1081162566
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 (21.7 bits)
S2: 58 (26.2 bits)