RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 018715
(351 letters)
>2k3c_A TMIX peptide; membrane peptide, dodecylphosphocholine micelle,
NHE1, Na+/H+ transporter, metal transport; NMR
{Synthetic}
Length = 33
Score = 37.0 bits (85), Expect = 3e-04
Identities = 13/26 (50%), Positives = 21/26 (80%)
Query: 261 AYLSYMLAELFYLSGILTVFFCGIVM 286
+Y++Y+ AELF+LSGI+ + G+VM
Sbjct: 3 SYMAYLSAELFHLSGIMALIASGVVM 28
>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 = 40.8 bits (95), Expect = 6e-04
Identities = 56/349 (16%), Positives = 95/349 (27%), Gaps = 132/349 (37%)
Query: 14 SMLSSDHKSVVSMNLFV-ALLCACIVIGHLLEENRWMNESITALIIGLCTGIVILLTT-- 70
+L + ++V + + A I+ ++ S AL + G L+
Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKS---NS--ALFRAVGEGNAQLVAIFG 161
Query: 71 -NGTSSHVLMFSE--DLFFIYLLPPIIFNAGFQVKKKQFFRNFMTIMLFGAVGTLISFVI 127
G + F E DL+ Y ++ + + TL +
Sbjct: 162 GQGNTDDY--FEELRDLYQTY--HVLV---------GDLIKF--------SAETLSELIR 200
Query: 128 ISAGAVHFFKQMNIGTLKIGDYLAIGAIFAATDSVCTLQVLNQDETP----LLYSLVFGE 183
+ A F Q L I ++L N TP LL +
Sbjct: 201 TTLDAEKVFTQ----GLNILEWLE-----------------NPSNTPDKDYLLSIPI--- 236
Query: 184 GVVNDATSVVLFNAIQSFDLSHINLSIALKFVG----SFFYLFIASTMLGVIAGLLSAFI 239
S L IQ L+H + K +G +T G GL++A
Sbjct: 237 -------SCPLIGVIQ---LAHY--VVTAKLLGFTPGELRSYLKGAT--GHSQGLVTAVA 282
Query: 240 IKKLYMGRHSTDREVALMILMAYLSYMLAELFYLSGILTVFFCGIVMSHYTWHNVTESSR 299
I + E + + ++ + FF G V +
Sbjct: 283 I------AETDSWESFFVSVRKAITVL-------------FFIG-VRCY----------- 311
Query: 300 VTTKHAFATLSFVAEIFIFLYVGMDALDIEKWRVVRDSLPV-QAIPSCM 347
A+ S I + DSL + +PS M
Sbjct: 312 ----EAYPNTSLPPSI------------------LEDSLENNEGVPSPM 338
Score = 31.6 bits (71), Expect = 0.46
Identities = 61/371 (16%), Positives = 114/371 (30%), Gaps = 129/371 (34%)
Query: 67 LLTTNGTSSHVLMFSEDLFFIYLLPPIIFNAGFQVKKKQFFRNFMT-------------- 112
L ++G+ HVL+ FFI ++QF +
Sbjct: 9 LTLSHGSLEHVLLVPTASFFIA-----------SQLQEQFNKILPEPTEGFAADDEPTTP 57
Query: 113 IMLFGAVGTLISFVI--ISAGAVHFFKQMNIGTLKIG------DYLAIGAI--FAATDSV 162
L VG + +V + V F Q+ L + YL I AA
Sbjct: 58 AEL---VGKFLGYVSSLVEPSKVGQFDQV----LNLCLTEFENCYLEGNDIHALAAK--- 107
Query: 163 CTLQVLNQDETPLL--------Y---SLVFGEGVVNDATSVVLFNAIQSFDLSHINLSIA 211
+L +++T L+ Y ++ + S LF A+ + L +A
Sbjct: 108 ----LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS-ALFRAVGE---GNAQL-VA 158
Query: 212 LKFVG-----SFF---------YLFIASTMLGVIAGLLSAFI-----IKKLYMGRHSTDR 252
+ F G +F Y + ++ A LS I +K++ +
Sbjct: 159 I-FGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVF--TQGLN- 214
Query: 253 EVALMILMAYL---------SYMLAELFYLSGI-LTVFFCGIVMSH---YTWHNVTESSR 299
++ +L Y+L+ I + +V + +T + +
Sbjct: 215 ------ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLK 268
Query: 300 VTTKHAFATLSFVAEIFI--------FLYVGMDALDIEKWRVVR--DSLPVQAIPSCM-- 347
T H+ V + I F A+ + + VR ++ P ++P +
Sbjct: 269 GATGHSQGL---VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE 325
Query: 348 -------GTPS 351
G PS
Sbjct: 326 DSLENNEGVPS 336
Score = 27.7 bits (61), Expect = 7.0
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 19/85 (22%)
Query: 6 SNLMERSLSMLSSDHKSVVSMNL-FVALLCACIVI----GHLLEENRWMNESITALIIGL 60
S+L+ + +++ D +V N+ F A V G L R ++ SI+ I+
Sbjct: 429 SHLLVPASDLINKD---LVKNNVSFNAKDIQIPVYDTFDGSDL---RVLSGSISERIVDC 482
Query: 61 CTGIVIL-----LTTNGTSSHVLMF 80
I+ L TT ++H+L F
Sbjct: 483 ---IIRLPVKWETTTQFKATHILDF 504
>1y4e_A Sodium/hydrogen exchanger 1; NHE1 isoform, transmembrane,
membrane protein; HET: HSL; NMR {Homo sapiens}
Length = 27
Score = 31.4 bits (71), Expect = 0.027
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 79 MFSEDLFFIYLLPPIIFNAGF 99
D+FF++LLPPII +AG+
Sbjct: 1 FLQSDVFFLFLLPPIILDAGY 21
>2htg_A NHE-1, NHE1 isoform of Na+/H+ exchanger 1, solute; membrane
protein, transmembrane segment, helix-KINK-helix; NMR
{Synthetic}
Length = 28
Score = 28.4 bits (63), Expect = 0.28
Identities = 13/21 (61%), Positives = 18/21 (85%)
Query: 175 LLYSLVFGEGVVNDATSVVLF 195
LL+ LVFGE ++NDA +VVL+
Sbjct: 5 LLHILVFGESLLNDAVTVVLY 25
>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis;
HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB:
2ze5_A* 2ze7_A* 2ze8_A
Length = 253
Score = 29.0 bits (65), Expect = 1.8
Identities = 3/20 (15%), Positives = 9/20 (45%)
Query: 127 IISAGAVHFFKQMNIGTLKI 146
+++ V Q+ G+ +
Sbjct: 29 VVALDRVQCCPQIATGSGRP 48
>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2; 2.70A
{Staphylococcus epidermidis atcc 12228}
Length = 340
Score = 29.1 bits (66), Expect = 2.4
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 127 IISAGAVHFFKQMNIGTLKI 146
IIS ++ ++ M+IGT K+
Sbjct: 35 IISGDSMQVYQGMDIGTAKV 54
>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation,
ATP-binding, cytoplasm, mitochondrion,
nucleotide-binding, nucleus; 2.95A {Saccharomyces
cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*
Length = 409
Score = 28.8 bits (65), Expect = 2.7
Identities = 5/20 (25%), Positives = 12/20 (60%)
Query: 127 IISAGAVHFFKQMNIGTLKI 146
+I++ ++ +K + I T K
Sbjct: 30 VINSDSMQVYKDIPIITNKH 49
>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2, protein structure
initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A
Length = 322
Score = 28.6 bits (65), Expect = 2.9
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 127 IISAGAVHFFKQMNIGTLKI 146
+IS ++ ++ M+IGT KI
Sbjct: 31 VISGDSMQVYRGMDIGTAKI 50
>4e4f_A Mannonate dehydratase; magnesium binding, enzyme function
initiative, isomerase; 2.00A {Pectobacterium carotovorum
subsp}
Length = 426
Score = 27.6 bits (62), Expect = 6.6
Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 304 HAFATLSFVAEIFIFLYVGMDALDIEK-WRVVRDS 337
S++ + +G DA IE W+
Sbjct: 61 RELPVASYLNDHVCPQLIGRDAHQIEDIWQYFYKG 95
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC
micelle, snare, coiled coil, membrane fusion,
transmembrane; NMR {Rattus norvegicus}
Length = 119
Score = 26.3 bits (57), Expect = 8.9
Identities = 7/29 (24%), Positives = 19/29 (65%)
Query: 100 QVKKKQFFRNFMTIMLFGAVGTLISFVII 128
++K+K +++N +++ G + +I +II
Sbjct: 86 KLKRKYWWKNLKMMIILGVICAIILIIII 114
>3vcn_A Mannonate dehydratase; enolase, magnesium binding site, enzyme
function initiative, lyase; 1.45A {Caulobacter
crescentus} PDB: 4fi4_A 3thu_A
Length = 425
Score = 27.2 bits (61), Expect = 9.9
Identities = 8/30 (26%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 304 HAFATLSFVAEIFIFLYVGMDALDIEK-WR 332
+ +SF+ + + +G DA IE W+
Sbjct: 62 RELSVVSFLQDHMVPSLIGRDAHQIEDIWQ 91
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
0.330 0.141 0.413
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,182,804
Number of extensions: 309979
Number of successful extensions: 826
Number of sequences better than 10.0: 1
Number of HSP's gapped: 823
Number of HSP's successfully gapped: 36
Length of query: 351
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 257
Effective length of database: 4,077,219
Effective search space: 1047845283
Effective search space used: 1047845283
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 (21.9 bits)
S2: 58 (26.0 bits)