RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15783
(86 letters)
>2z1m_A GDP-D-mannose dehydratase; short-chain dehydrogenase/reductase,
lyase, structural genom NPPSFA; HET: NDP GDP; 2.00A
{Aquifex aeolicus} PDB: 2z95_A*
Length = 345
Score = 133 bits (337), Expect = 5e-40
Identities = 41/72 (56%), Positives = 52/72 (72%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
AMW+M+QQ P D+VIATGETH+VREFVE A G I W G G +E G +++TG V V
Sbjct: 230 AMWLMMQQPEPDDYVIATGETHTVREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIV 289
Query: 72 KVNENYFRPTEV 83
+V+E +FRP EV
Sbjct: 290 EVSEEFFRPAEV 301
>1t2a_A GDP-mannose 4,6 dehydratase; structural genomics consortium,
rossman-fold, short-chain dehydrogenase/reductase, SDR,
structural genomics,lyase; HET: NDP GDP; 1.84A {Homo
sapiens} SCOP: c.2.1.2
Length = 375
Score = 133 bits (338), Expect = 6e-40
Identities = 50/72 (69%), Positives = 60/72 (83%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
AMW+MLQ D P+DFVIATGE HSVREFVE +FL+IGKTIVWEG ++EVG+ K+TG V V
Sbjct: 259 AMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHV 318
Query: 72 KVNENYFRPTEV 83
V+ Y+RPTEV
Sbjct: 319 TVDLKYYRPTEV 330
>1db3_A GDP-mannose 4,6-dehydratase; NADP, GDP-fucose, lyase; 2.30A
{Escherichia coli} SCOP: c.2.1.2
Length = 372
Score = 125 bits (317), Expect = 7e-37
Identities = 37/82 (45%), Positives = 47/82 (57%), Gaps = 10/82 (12%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVG---------- 61
WMMLQQ+ P+DFVIATG +SVR+FVE A +G + +EGTG +E G
Sbjct: 235 MQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEEKGIVVSVTGHDA 294
Query: 62 KEKDTGIVRVKVNENYFRPTEV 83
G V + V+ YFRP EV
Sbjct: 295 PGVKPGDVIIAVDPRYFRPAEV 316
>1n7h_A GDP-D-mannose-4,6-dehydratase; rossmann fold, SDR, short-chain
dehydrogenase/reductase, LYA; HET: NDP GDP; 1.80A
{Arabidopsis thaliana} SCOP: c.2.1.2 PDB: 1n7g_A*
Length = 381
Score = 104 bits (261), Expect = 1e-28
Identities = 28/72 (38%), Positives = 43/72 (59%), Gaps = 17/72 (23%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
AMW+MLQQ+ P D+V+AT E H+V EF++ +F Y+G + W+ V
Sbjct: 264 AMWLMLQQEKPDDYVVATEEGHTVEEFLDVSFGYLG--LNWKD---------------YV 306
Query: 72 KVNENYFRPTEV 83
++++ YFRP EV
Sbjct: 307 EIDQRYFRPAEV 318
>1rpn_A GDP-mannose 4,6-dehydratase; short-chain dehydrogenase/reductase,
rossmann fold, lyase; HET: NDP GDP; 2.15A {Pseudomonas
aeruginosa} SCOP: c.2.1.2
Length = 335
Score = 102 bits (256), Expect = 3e-28
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 17/72 (23%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
AMW+MLQQD D+V+ATG T +VR+ + AF ++G + + +
Sbjct: 241 AMWLMLQQDKADDYVVATGVTTTVRDMCQIAFEHVG--LDYR---------------DFL 283
Query: 72 KVNENYFRPTEV 83
K++ +FRP EV
Sbjct: 284 KIDPAFFRPAEV 295
>2pk3_A GDP-6-deoxy-D-LYXO-4-hexulose reductase; SDR, short-chain
dehydrogenase/reductase, rossmann fold, oxidoreductase;
HET: A2R GDD; 1.82A {Aneurinibacillus thermoaerophilus}
Length = 321
Score = 90.3 bits (225), Expect = 8e-24
Identities = 11/73 (15%), Positives = 24/73 (32%), Gaps = 20/73 (27%)
Query: 12 AMWMMLQQDTPQD-FVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVR 70
A W++ Q D + + +G +++ ++ I
Sbjct: 232 AYWLLSQYGKTGDVYNVCSGIGTRIQDVLDLLLAMANVKI-------------------D 272
Query: 71 VKVNENYFRPTEV 83
++N RP+EV
Sbjct: 273 TELNPLQLRPSEV 285
>1sqr_A 50S ribosomal protein L35AE; PFR48, structure, autostructure,
northeast structural genomics consortium, beta-barrel;
NMR {Pyrococcus furiosus} SCOP: b.43.3.3 PDB: 2lp6_A
Length = 95
Score = 25.2 bits (55), Expect = 1.7
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 40 EAAFLYIGKTIVWEGTGKDEV-GKEKDT----GIVRVKVNEN 76
E A IG+ ++W+ + GK G VR + +
Sbjct: 33 EEASKLIGRLVLWKSPSGKILKGKIVRVHGTKGAVRARFEKG 74
>2pzm_A Putative nucleotide sugar epimerase/ dehydratase; rossman fold,
protein-NAD complex, protein-nucleotide comple binding
protein; HET: NAD UDP; 2.00A {Bordetella bronchiseptica}
PDB: 2pzl_A* 2pzk_A*
Length = 330
Score = 24.8 bits (55), Expect = 4.3
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 27 IATGETHSVREFVEAAFLYIGKTIVWE 53
++TGE HS++E + Y+G T+
Sbjct: 243 VSTGEGHSIKEVFDVVLDYVGATLAEP 269
>3ko8_A NAD-dependent epimerase/dehydratase; isomerase, UDP-galactose
4-epimerase; HET: NAD; 1.80A {Pyrobaculum calidifontis}
PDB: 3icp_A* 3aw9_A*
Length = 312
Score = 24.0 bits (53), Expect = 6.8
Identities = 2/24 (8%), Positives = 7/24 (29%)
Query: 27 IATGETHSVREFVEAAFLYIGKTI 50
+ + V + + +G
Sbjct: 232 VGNVDAVRVLDIAQIVAEVLGLRP 255
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
0.318 0.135 0.397
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,313,526
Number of extensions: 68210
Number of successful extensions: 107
Number of sequences better than 10.0: 1
Number of HSP's gapped: 102
Number of HSP's successfully gapped: 11
Length of query: 86
Length of database: 6,701,793
Length adjustment: 54
Effective length of query: 32
Effective length of database: 5,194,059
Effective search space: 166209888
Effective search space used: 166209888
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 (21.7 bits)
S2: 51 (23.3 bits)