RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9896
(145 letters)
>1g7s_A Translation initiation factor IF2/EIF5B; translational GTPase; HET:
GDP; 2.00A {Methanothermobacterthermautotrophicus} SCOP:
b.43.3.1 b.43.3.1 c.20.1.1 c.37.1.8 PDB: 1g7r_A* 1g7t_A*
Length = 594
Score = 143 bits (363), Expect = 3e-41
Identities = 41/141 (29%), Positives = 77/141 (54%), Gaps = 3/141 (2%)
Query: 8 IQYCQTFLKKRLMFKNELQA--TVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGP 65
+ Q +L+++L + + A T+LEVK GLG TID ++ +G L + DT+ + +
Sbjct: 213 MGLAQQYLREQLKIEEDSPARGTILEVKEETGLGMTIDAVIYDGILRKDDTIAMMTSKDV 272
Query: 66 IVTQIRSLLMPQPMQELR-VKNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDE 124
I T+IRSLL P+P++E+R + + + ++ G+KI A ++ +AG LRV D ++
Sbjct: 273 ISTRIRSLLKPRPLEEMRESRKKFQKVDEVVAAAGIKIVAPGIDDVMAGSPLRVVTDPEK 332
Query: 125 IDDLCDEVARELKSALSTIKL 145
+ + ++K +
Sbjct: 333 VREEILSEIEDIKIDTDEAGV 353
>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 = 40.4 bits (94), Expect = 9e-05
Identities = 17/161 (10%), Positives = 41/161 (25%), Gaps = 57/161 (35%)
Query: 18 RLMFKNELQATVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQIRSLLMP- 76
++F+ + + K + + + + +L+ T TQ LM
Sbjct: 1690 AMIFETIVDGKLKTEKIFKEINEHSTSYT-----FRSEKGLLSATQ---FTQPALTLMEK 1741
Query: 77 ---QPMQE--LRVKNAYV------EY-------------------------------KKI 94
+ ++ L +A EY +
Sbjct: 1742 AAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDE 1801
Query: 95 KGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDLCDEVARE 135
G + A + + A Q+ + + + V +
Sbjct: 1802 LGRSNYGMIAINPGRVAASF------SQEALQYVVERVGKR 1836
Score = 28.5 bits (63), Expect = 1.0
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 26/67 (38%)
Query: 47 VNGTLY--EGDTVVLAGTDGPIVTQIRSLLMPQPMQELRVKNAYVEYKKIKGTQGVKIAA 104
VN Y E V AG +R+L + + + + K++ KI
Sbjct: 1844 VN---YNVENQQYVAAGD-------LRAL---DTVTNV------LNFIKLQ-----KIDI 1879
Query: 105 KDLEKTI 111
+L+K++
Sbjct: 1880 IELQKSL 1886
Score = 27.7 bits (61), Expect = 1.8
Identities = 6/47 (12%), Positives = 14/47 (29%), Gaps = 17/47 (36%)
Query: 76 PQPMQELRVKNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQ 122
P PM L + N + + ++ + N + +
Sbjct: 335 PSPM--LSISN---------------LTQEQVQDYVNKTNSHLPAGK 364
>1zo1_I IF2, translation initiation factor 2; E. coli, ribosome, initiation
of protein synthesis, cryo-eletron microscopy,
translation/RNA complex; 13.80A {Escherichia coli}
Length = 501
Score = 33.6 bits (78), Expect = 0.016
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 16/53 (30%)
Query: 25 LQATVLEVKAIP---GLGTTID-----------TILV-NGTLYEGDTVVLAGT 62
LQA VLE+KA+ G I+ T+LV GTL++GD +VL G
Sbjct: 163 LQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGD-IVLCGF 214
>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA,
ribosomal; 10.80A {Bos taurus}
Length = 537
Score = 30.6 bits (70), Expect = 0.14
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 16/53 (30%)
Query: 25 LQATVLEVKAIP---GLGTTID-----------TILV-NGTLYEGDTVVLAGT 62
A +LE+KA P GT I+ T ++ GTL +G +V AG
Sbjct: 164 ALAEMLELKADPTGAVEGTVIESFTDKGRGPVTTAIIQRGTLRKGSILV-AGK 215
>1dbg_A Chondroitinase B; beta helix, polysaccharide lyase, dematan
sulfate; HET: MAN RAM GCU MXY G4D BGC; 1.70A {Pedobacter
heparinus} SCOP: b.80.1.4 PDB: 1dbo_A* 1ofl_A* 1ofm_A*
Length = 506
Score = 30.4 bits (67), Expect = 0.21
Identities = 14/148 (9%), Positives = 40/148 (27%), Gaps = 27/148 (18%)
Query: 5 MREIQYCQTFLKKRLMFKNELQATVLEVKAIPGLGTTI------DTILVNGTLYEGDTVV 58
M+ + +L ++ N V + L + + + Y+ ++
Sbjct: 1 MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTYKDVQLI 60
Query: 59 LAG---TDGPIVTQIRSLLMPQPMQELRVKNAYVEYKKIKGTQGVKIAAKDLEKTIAGLN 115
++ + PI +K G V++ + L + G+
Sbjct: 61 VSNSGKSGLPIT----------------IKALNPGKVFFTGDAKVELRGEHL--ILEGIW 102
Query: 116 LRVAKDQDEIDDLCDEVARELKSALSTI 143
+ + + + + I
Sbjct: 103 FKDGNRAIQAWKSHGPGLVAIYGSYNRI 130
>1wqa_A Phospho-sugar mutase; alpha-beta protein, unphosphorylated form,
enzyme-metal COMP isomerase; 2.00A {Pyrococcus
horikoshii}
Length = 455
Score = 28.7 bits (65), Expect = 0.73
Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 19/85 (22%)
Query: 76 PQPMQELRVKN----AYVEYKKIKGTQGVKIAAKDLEKTIAGLN------------LRV- 118
Q + V+ + ++ +G + D K I +R+
Sbjct: 371 YQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVRASGTEPIIRIF 430
Query: 119 --AKDQDEIDDLCDEVARELKSALS 141
AK +++ + + L+ ALS
Sbjct: 431 SEAKSKEKAQEYLNLGIELLEKALS 455
>3tig_A TTL protein; ATP-grAsp, ligase, tubulin; 2.50A {Silurana} PDB:
3tii_A* 3tin_A*
Length = 380
Score = 26.5 bits (58), Expect = 4.1
Identities = 7/41 (17%), Positives = 12/41 (29%)
Query: 11 CQTFLKKRLMFKNELQATVLEVKAIPGLGTTIDTILVNGTL 51
M L+ ++EV P + L G +
Sbjct: 314 SFQLFGFDFMVDKNLKVWLIEVNGAPACAQKLYAELCKGIV 354
>3iwa_A FAD-dependent pyridine nucleotide-disulphide oxidoreductase;
structural genomics, PSI-2, protein structur initiative;
2.30A {Desulfovibrio vulgaris}
Length = 472
Score = 26.0 bits (58), Expect = 5.0
Identities = 6/30 (20%), Positives = 14/30 (46%)
Query: 31 EVKAIPGLGTTIDTILVNGTLYEGDTVVLA 60
+V + G + ++ + + D V+LA
Sbjct: 224 KVVRLEGENGKVARVITDKRTLDADLVILA 253
>2cdu_A NADPH oxidase; flavoenzyme, oxidoreductase; HET: FAD ADP; 1.8A
{Lactobacillus sanfranciscensis}
Length = 452
Score = 25.9 bits (58), Expect = 6.3
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 31 EVKAIPGLGTTIDTILVNGTLYEGDTVVLA 60
+V A + I T ++G + D +L
Sbjct: 213 KVAAFEEVDDEIITKTLDGKEIKSDIAILC 242
>2qcu_A Aerobic glycerol-3-phosphate dehydrogenase; glycerol-3-phoshate
dehydrogenase, oxidoreductase; HET: BOG FAD TAM; 1.75A
{Escherichia coli} PDB: 2r45_A* 2r46_A* 2r4e_A* 2r4j_A*
Length = 501
Score = 25.6 bits (57), Expect = 7.4
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 118 VAKDQDEIDDLCDEVARELKSALS 141
V ++ EI+ L + K LS
Sbjct: 282 VKIEESEINYLLNVYNTHFKKQLS 305
>3l6v_A GYRA, DNA gyrase subunit A; gyrase A C-terminal domain, GYRA
C-terminal domain, DNA wrapping, beta-strand-bearing
proline, ATP-binding; HET: DNA; 2.19A {Xanthomonas
campestris PV}
Length = 370
Score = 25.3 bits (56), Expect = 9.8
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 97 TQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDLCDE 131
TQGV + + + + R+ +E +D+ DE
Sbjct: 324 TQGVTLIRLSKGEKLQAV-ERLDASLEEPEDVVDE 357
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
0.317 0.134 0.362
Gapped
Lambda K H
0.267 0.0822 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,124,036
Number of extensions: 124823
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 442
Number of HSP's successfully gapped: 35
Length of query: 145
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 60
Effective length of database: 4,328,508
Effective search space: 259710480
Effective search space used: 259710480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (23.6 bits)