RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1381
(102 letters)
>2wvv_A Alpha-L-fucosidase; alpha-L-fucose, hydrolase, glycoside hydrolase
family 29; 1.73A {Bacteroides thetaiotaomicron} PDB:
2xii_A* 2xib_A* 2wvv_B 2wvt_A* 2wvu_A* 2wvs_A*
Length = 450
Score = 112 bits (281), Expect = 6e-31
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 13 FMERNYKPGFTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYTLWPSKYAF 72
P + + FDA WA + G KYV +T+KHHEG+ LWPSKY
Sbjct: 55 LKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYT- 113
Query: 73 SWNSMDIGPKRDLV 86
+ + KRD++
Sbjct: 114 KYTVANTPYKRDIL 127
>2zxd_A Alpha-L-fucosidase, putative; TIM barrel, hydrolase; HET: ZXD;
2.15A {Thermotoga maritima} PDB: 2zwy_A* 2zx5_A* 2zx6_A*
2zx7_A* 2zwz_A* 2zx9_A* 2zxa_A* 2zxb_A* 2zx8_A* 1hl9_A*
1hl8_A* 1odu_A* 2wsp_A*
Length = 455
Score = 90.1 bits (223), Expect = 6e-23
Identities = 37/82 (45%), Positives = 51/82 (62%), Gaps = 1/82 (1%)
Query: 5 NPNSTVTKFMERNYKPGFTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYT 64
S ++ + Y F Y+ FA FTAE +D WAD+ +GAKYV+ T+KHH+G+
Sbjct: 74 IKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFC 133
Query: 65 LWPSKYAFSWNSMDIGPKRDLV 86
LW +KY +NS+ GPKRDLV
Sbjct: 134 LWGTKYT-DFNSVKRGPKRDLV 154
>3eyp_A Putative alpha-L-fucosidase; structural genomics, hydrolase,
lipoprotein, PSI-2, protein initiative; 1.90A
{Bacteroides thetaiotaomicron}
Length = 469
Score = 89.3 bits (221), Expect = 1e-22
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 2/72 (2%)
Query: 17 NYKPGFTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYTLWPSKYA--FSW 74
Y + F D W L ++G +LT+KH +G+ LWPSKY
Sbjct: 35 EYVNEGDGKASTAIFNPTALDCRQWMQTLKAAGIPAAILTAKHADGFCLWPSKYTDYSVK 94
Query: 75 NSMDIGPKRDLV 86
N+ K D+V
Sbjct: 95 NAAWKNGKGDVV 106
>3gza_A Putative alpha-L-fucosidase; NP_812709.1, structural genomic center
for structural genomics, JCSG; HET: MSE EPE; 1.60A
{Bacteroides thetaiotaomicron vpi-5482}
Length = 443
Score = 83.8 bits (207), Expect = 1e-20
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 2/80 (2%)
Query: 9 TVTKFMERNYKPGFTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYTLWPS 68
+ F + + W ++G K+ VLT+ H G+ LW S
Sbjct: 32 VFDGIRYGQGNNRINPIEDYNIFNPTELNTDQWVQAAKAAGCKFAVLTATHETGFGLWQS 91
Query: 69 KY-AFSWNSMD-IGPKRDLV 86
+ ++ K D+V
Sbjct: 92 DVNPYCLKAVKWRDGKGDIV 111
>3ues_A Alpha-1,3/4-fucosidase; TIM barrel, hydrolase-hydrolase inhibitor
complex; HET: DFU; 1.60A {Bifidobacterium longum subsp}
PDB: 3mo4_A* 3uet_A*
Length = 478
Score = 81.6 bits (201), Expect = 7e-20
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 21 GFTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYTLWPSKYAF--SWNSMD 78
G ++D F D + W D L + G V+LT KHH+G+ LWPS+ +S
Sbjct: 48 GLGHED-PALFNPRNVDVDQWMDALVAGGMAGVILTCKHHDGFCLWPSRLTRHTVASSPW 106
Query: 79 IGPKRDLV 86
K DLV
Sbjct: 107 REGKGDLV 114
>3pzs_A PM kinase, pyridoxamine kinase; structural genomics, center for
structural genomics of infec diseases, csgid,
transferase; HET: MSE; 1.89A {Yersinia pestis} PDB:
1td2_A* 1vi9_A*
Length = 289
Score = 30.5 bits (69), Expect = 0.064
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 37 DANHWADILASSGAKYVVLTSKHHEGY 63
A A L + G K V++ GY
Sbjct: 165 QAVQVARSLCARGPKVVLVKHLSRAGY 191
>3mbh_A Putative phosphomethylpyrimidine kinase; structural genomics, joint
center for structural genomics, J protein structure
initiative; HET: MSE PXL; 2.00A {Bacteroides
thetaiotaomicron} PDB: 3mbj_A*
Length = 291
Score = 30.3 bits (69), Expect = 0.080
Identities = 5/26 (19%), Positives = 12/26 (46%)
Query: 37 DANHWADILASSGAKYVVLTSKHHEG 62
+ + +L+ G + V++TS
Sbjct: 166 ELKEYLRLLSDKGPQVVIITSVPVHD 191
>3zs7_A Pyridoxal kinase; transferase, sleeping sickness; HET: ATP; 2.00A
{Trypanosoma brucei}
Length = 300
Score = 29.0 bits (65), Expect = 0.24
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 37 DANHWADILASSGAKYVVLTSKHHEG 62
A AD + G +V++ S +
Sbjct: 166 SAILAADWFHNCGVAHVIIKSFREQE 191
>2ddm_A Pyridoxine kinase; pyridoxal kinase, ribokinase, pyridoxal
5'-phosphate, vitamin B6, phosphorylation, transferase;
2.10A {Escherichia coli} PDB: 2ddo_A* 2ddw_A*
Length = 283
Score = 28.8 bits (65), Expect = 0.26
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 37 DANHWADILASSGAKYVVLTSKHHEG 62
A A L S K+VV+TS
Sbjct: 176 SAIAAAKSLLSDTLKWVVVTSASGNE 201
>2yxt_A Pyridoxal kinase; beta sheet with alpha helix, metal ION,
transferase; 2.00A {Homo sapiens} PDB: 2yxu_A* 3kbi_A*
3keu_A* 4en4_A* 4eoh_A* 2f7k_A 3fhy_A* 3fhx_A* 2ajp_A*
1lhp_A 1lhr_A* 1rft_A* 1rfu_A* 1rfv_A* 1ygj_A* 1ygk_A*
1yhj_A*
Length = 312
Score = 27.5 bits (61), Expect = 0.83
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 37 DANHWADILASSGAKYVVLTSKHHEG 62
+A D+L S G VV+TS
Sbjct: 167 EALRVMDMLHSMGPDTVVITSSDLPS 192
>2h78_A Hibadh, 3-hydroxyisobutyrate dehydrogenase; APC6014, pseudomonas
aeruginosa PA01, PSI-2, structural genomics; HET: PG4;
2.20A {Pseudomonas aeruginosa} PDB: 3cum_A 3obb_A*
3q3c_A*
Length = 302
Score = 26.8 bits (60), Expect = 1.1
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 6 PNSTVTKFMERNYKPGFTYQDFAKD 30
P R+Y GF Q AKD
Sbjct: 225 PGVMENAPASRDYSGGFMAQLMAKD 249
>1k1x_A 4-alpha-glucanotransferase; 2.40A {Thermococcus litoralis} SCOP:
a.8.3.2 b.30.5.8 c.6.2.2 PDB: 1k1w_A 1k1y_A*
Length = 659
Score = 26.5 bits (58), Expect = 1.5
Identities = 12/64 (18%), Positives = 22/64 (34%), Gaps = 8/64 (12%)
Query: 25 QDFAKDF--------TAEFFDANHWADILASSGAKYVVLTSKHHEGYTLWPSKYAFSWNS 76
+D+A+ E L +G +YVV+ H L + + + +
Sbjct: 106 KDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFMSAGLSKEELFWPYYT 165
Query: 77 MDIG 80
D G
Sbjct: 166 EDGG 169
>3oby_A Protein pelota homolog; SM fold, hydrolase; 2.90A {Archaeoglobus
fulgidus}
Length = 352
Score = 25.8 bits (56), Expect = 2.5
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 32 TAEFFDANHWADILASSGAKYVVLTSKHHEGYTL 65
E +D + + SG K V+++++ G L
Sbjct: 295 EREKWDVDGLLREVEESGGKVVIMSTEFEPGKRL 328
>3g0o_A 3-hydroxyisobutyrate dehydrogenase; NAD(P), valine catabolism,
tartaric acid, target 11128H, NYSGXRC, PSI-2, structural
genomics; HET: TLA; 1.80A {Salmonella typhimurium}
Length = 303
Score = 25.6 bits (57), Expect = 2.7
Identities = 8/27 (29%), Positives = 11/27 (40%), Gaps = 3/27 (11%)
Query: 4 ENPNSTVTKFMERNYKPGFTYQDFAKD 30
EN V ++ +Y P F KD
Sbjct: 225 ENRMQHV---VDGDYTPRSAVDIFVKD 248
>3gm8_A Glycoside hydrolase family 2, candidate beta-GLYC; structural
genomics, glycosidase, PSI-2, protein initiative; 2.40A
{Bacteroides vulgatus}
Length = 801
Score = 25.5 bits (56), Expect = 3.7
Identities = 4/23 (17%), Positives = 10/23 (43%)
Query: 22 FTYQDFAKDFTAEFFDANHWADI 44
F D K ++ ++ + W +
Sbjct: 15 FHLGDAGKGASSSSYNDSQWRIL 37
>2gf2_A Hibadh, 3-hydroxyisobutyrate dehydrogenase; structural genomics,
structural genomics consortium, SGC, oxidoreductase;
2.38A {Homo sapiens} PDB: 2i9p_A*
Length = 296
Score = 25.3 bits (56), Expect = 3.8
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 16 RNYKPGFTYQDFAKD 30
NY+ GF AKD
Sbjct: 232 NNYQGGFGTTLMAKD 246
>2z1a_A 5'-nucleotidase; metal-binding, nucleotide-binding, hydrolase,
structural genomics, NPPSFA; HET: THM; 1.75A {Thermus
thermophilus} SCOP: d.114.1.1 d.159.1.2
Length = 552
Score = 25.0 bits (55), Expect = 6.1
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 6/34 (17%)
Query: 34 EFFD----ANHWADILASSGAKYVVLTSKHHEGY 63
F D A L + G +V+ S H GY
Sbjct: 187 AFLDPYESAQKAVYELLAKGVNKIVVLS--HLGY 218
>3obw_A Protein pelota homolog; SM fold, hydrolase; 2.60A {Sulfolobus
solfataricus}
Length = 364
Score = 24.7 bits (53), Expect = 7.1
Identities = 3/44 (6%), Positives = 13/44 (29%)
Query: 22 FTYQDFAKDFTAEFFDANHWADILASSGAKYVVLTSKHHEGYTL 65
+D E + + + + +++ + + L
Sbjct: 306 LVIEDLLSSDEQERLTIERMLEDIENKRGEVILVPKESPIYFEL 349
>3cky_A 2-hydroxymethyl glutarate dehydrogenase; rossmann fold, two domain
enzyme, oxidoreductase; 2.30A {Eubacterium barkeri}
Length = 301
Score = 24.5 bits (54), Expect = 7.4
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 14 MERNYKPGFTYQDFAKD 30
M ++ GF KD
Sbjct: 228 MSGDFAGGFAMDLQHKD 244
>1vic_A 3-deoxy-manno-octulosonate cytidylyltransferase; structural
genomics; 1.80A {Haemophilus influenzae} SCOP:
c.68.1.13 PDB: 1vh3_A 3duv_A*
Length = 262
Score = 24.4 bits (54), Expect = 7.6
Identities = 9/20 (45%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 42 ADILASSGAKYVVLTSKHHE 61
AD+ S GA+ V +TS +H
Sbjct: 55 ADVAKSFGAE-VCMTSVNHN 73
>3tqd_A 3-deoxy-manno-octulosonate cytidylyltransferase; cell envelope;
1.80A {Coxiella burnetii}
Length = 256
Score = 24.4 bits (54), Expect = 7.6
Identities = 6/20 (30%), Positives = 9/20 (45%), Gaps = 1/20 (5%)
Query: 42 ADILASSGAKYVVLTSKHHE 61
+ GA V +TS H+
Sbjct: 62 RQVAEDFGAV-VCMTSSDHQ 80
>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 = 24.8 bits (53), Expect = 8.3
Identities = 8/34 (23%), Positives = 10/34 (29%), Gaps = 6/34 (17%)
Query: 1 MLSENPNSTVTKFME----RNYKPGFTYQDFAKD 30
L V KF+E NY F +
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINY--KFLMSPIKTE 101
>1vpd_A Tartronate semialdehyde reductase; structural genomics, MCSG,
protein structure initiative, PSI, midwest center for
structural genomics; HET: MSE TLA; 1.65A {Salmonella
typhimurium} SCOP: a.100.1.1 c.2.1.6
Length = 299
Score = 24.4 bits (54), Expect = 8.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 14 MERNYKPGFTYQDFAKD 30
M+RN+KPGF KD
Sbjct: 228 MDRNFKPGFRIDLHIKD 244
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 0.133 0.433
Gapped
Lambda K H
0.267 0.0638 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,686,232
Number of extensions: 84722
Number of successful extensions: 314
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 38
Length of query: 102
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 35
Effective length of database: 4,831,086
Effective search space: 169088010
Effective search space used: 169088010
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 (23.6 bits)