RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1878
(98 letters)
>1ktb_A Alpha-N-acetylgalactosaminidase; glycoprotein, (beta/alpha)8
barrel, hydrolase; HET: NAG; 1.90A {Gallus gallus} SCOP:
b.71.1.1 c.1.8.1 PDB: 1ktc_A* 3h55_A* 3h54_A* 3h53_A*
3igu_A*
Length = 405
Score = 64.5 bits (156), Expect = 7e-14
Identities = 35/55 (63%), Positives = 44/55 (80%)
Query: 35 PNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDPDMV 89
N+T + E CNLWRN+DDIQDSW S+ SI+D++ NQD + P AGPGHWNDPDM+
Sbjct: 184 VNYTLLGEICNLWRNYDDIQDSWDSVLSIVDWFFTNQDVLQPFAGPGHWNDPDML 238
>3a21_A Putative secreted alpha-galactosidase; beta-alpha-barrel, greek KEY
motif, beta-jellyroll, beta-TRE hydrolase; HET: GOL 1PG
EPE; 1.51A {Streptomyces avermitilis} PDB: 3a22_A*
3a23_A*
Length = 614
Score = 63.3 bits (153), Expect = 2e-13
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 4/62 (6%)
Query: 29 CQAYLIPNFTSIIEHCNLWRNFDDI--QDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDP 86
C + LWR DI + S+ S++ + +Q G++NDP
Sbjct: 180 CNWGYQNPWNWAAGQAPLWRTSTDIIYYGNQPSMTSLLSNF--DQTLHPTAQHTGYYNDP 237
Query: 87 DM 88
DM
Sbjct: 238 DM 239
>3hg3_A Alpha-galactosidase A; glycoprotein, carbohydrate-binding protein,
glycosidase, Lys enzyme, (beta/alpha)8 barrel, disease
mutation; HET: NAG BMA MAN GLA GLC 2PE; 1.90A {Homo
sapiens} PDB: 3tv8_A* 3lx9_A* 3lxa_A* 3lxb_A* 3lxc_A*
3s5z_A* 1r47_A* 1r46_A* 3gxn_A* 3gxt_A* 3hg2_A* 3hg4_A*
3hg5_A* 3gxp_A* 3s5y_A*
Length = 404
Score = 60.6 bits (146), Expect = 1e-12
Identities = 33/55 (60%), Positives = 43/55 (78%)
Query: 35 PNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDPDMV 89
PN+T I ++CN WRNF DI DSW+S++SI+D+ NQ+ IV AGPG WNDPDM+
Sbjct: 183 PNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDML 237
>1szn_A Alpha-galactosidase; (beta/alpha)8 barrel,TWO domains,
glycoprotein, hydrolase; HET: NAG BMA MAN; 1.54A
{Hypocrea jecorina} SCOP: b.71.1.1 c.1.8.1 PDB: 1t0o_A*
Length = 417
Score = 54.8 bits (131), Expect = 2e-10
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 23 DLIGYTCQAYLIPNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYGNNQDTIVPNAGPGH 82
+++ C F+ WR DDI +W S+ I++ + +
Sbjct: 197 EIVLSMCIWGQADVFSWGNSTGISWRMSDDISPNWGSVTRILNL----NSFKLNSVDFWG 252
Query: 83 WNDPDMV 89
ND DM+
Sbjct: 253 HNDADML 259
>1uas_A Alpha-galactosidase; TIM-barrel, beta-alpha-barrel, greek KEY
motif, hydrolase; HET: GLA; 1.50A {Oryza sativa} SCOP:
b.71.1.1 c.1.8.1
Length = 362
Score = 51.7 bits (123), Expect = 2e-09
Identities = 22/66 (33%), Positives = 28/66 (42%), Gaps = 4/66 (6%)
Query: 23 DLIGYTCQAYLIPNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYGNNQDTIVPNAGPGH 82
++ C+ T N WR DI D+W S+ S + D AGPG
Sbjct: 156 NIFFSLCEWGKENPATWAGRMGNSWRTTGDIADNWGSMTSRA----DENDQWAAYAGPGG 211
Query: 83 WNDPDM 88
WNDPDM
Sbjct: 212 WNDPDM 217
>3lrk_A Alpha-galactosidase 1; tetramer, GH27, glycoprotein, glycosida
hydrolase; HET: NAG BTB; 1.95A {Saccharomyces
cerevisiae} PDB: 3lrl_A* 3lrm_A*
Length = 479
Score = 51.4 bits (122), Expect = 3e-09
Identities = 16/79 (20%), Positives = 21/79 (26%), Gaps = 18/79 (22%)
Query: 29 CQAYLIPNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYGNNQDTIVPN----------- 77
C F N WR D+ + +S G+ D
Sbjct: 186 CNWGQDLTFYWGSGIANSWRMSGDVTAEFTRPDSRCPCDGDEYDCKYAGFHCSIMNILNK 245
Query: 78 -------AGPGHWNDPDMV 89
AG G WND D +
Sbjct: 246 AAPMGQNAGVGGWNDLDNL 264
>3cc1_A BH1870 protein, putative alpha-N-acetylgalactosaminidase;
structural genomic center for structural genomics, JCSG;
HET: MSE PGE PG4 P33; 2.00A {Bacillus halodurans c-125}
Length = 433
Score = 49.0 bits (116), Expect = 2e-08
Identities = 15/58 (25%), Positives = 20/58 (34%), Gaps = 4/58 (6%)
Query: 31 AYLIPNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDPDM 88
I + N+WR DD D W L + + + G GHW D M
Sbjct: 221 PAPIKYAHHFKTNANMWRITDDFWDDWSLLYQMF----ERCEVWEKHIGTGHWPDCGM 274
>3a5v_A Alpha-galactosidase; beta/alpha barrel, N-glycosylation, hydrolase;
HET: MAN NAG BMA 1PG; 2.00A {Umbelopsis vinacea}
Length = 397
Score = 42.9 bits (100), Expect = 3e-06
Identities = 14/79 (17%), Positives = 21/79 (26%), Gaps = 16/79 (20%)
Query: 27 YTCQAYLIPNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYG----------------NN 70
C + N WR D+ D++ + N
Sbjct: 164 SLCNWGEDGPWNFASTISNSWRISGDVYDNFNRPDPACPCTTYDCVLAGFRCSVMNIINK 223
Query: 71 QDTIVPNAGPGHWNDPDMV 89
+ A G WND DM+
Sbjct: 224 AVAVSQKARSGGWNDLDML 242
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 28.3 bits (63), Expect = 0.41
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 6/36 (16%)
Query: 54 QDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDPDMV 89
Q S Q +E++I++ + + G G W D D +
Sbjct: 540 QGSKQDVEALIEFIYDTEKN----GGLG-W-DLDAI 569
>1mqo_A Beta-lactamase II; alpha-beta/BETA-alpha fold, hydrolase; HET: CIT;
1.35A {Bacillus cereus} SCOP: d.157.1.1 PDB: 1bc2_A
1bvt_A* 3i0v_A 3i11_A 3i13_A 3i14_A 3i15_A 2uyx_A 2bc2_A
3bc2_A 2bfl_A 2bfk_A 2bfz_B 2bg2_A 2bg7_A 2bg8_A 1dxk_A
3kns_A 3knr_A 2bfz_A ...
Length = 227
Score = 27.4 bits (61), Expect = 0.60
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 43 HCNLWRNFDDIQDSW-QSLESIIDYYGNNQDTIVPNAGPGHWNDPDMVKSYLDY 95
+L D + W S+E+++ Y N + +VP G G D ++ LD
Sbjct: 175 AKDLGNVADAYVNEWSTSIENVLKRYRNI-NAVVP--GHGEVGDKGLLLHTLDL 225
>2y8b_A Metallo-B-lactamase; hydrolase, cephalosporins, antibiotic
recognition; 1.70A {Pseudomonas aeruginosa} PDB: 2y8a_A
2y87_A 2yz3_A* 2whg_A* 2wrs_A* 1ko3_A 1ko2_A
Length = 265
Score = 27.5 bits (61), Expect = 0.65
Identities = 5/44 (11%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 52 DIQDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDPDMVKSYLDY 95
++ + +++ I Y + ++P G G ++++ +
Sbjct: 214 NLAEWPATIKRIQQRY-PEAEVVIP--GHGLPGGLELLQHTTNV 254
>2cw3_A Pmsod2, iron superoxide dismutase; oxidoreductase; 2.50A {Perkinsus
marinus}
Length = 280
Score = 27.0 bits (60), Expect = 0.83
Identities = 6/27 (22%), Positives = 12/27 (44%)
Query: 58 QSLESIIDYYGNNQDTIVPNAGPGHWN 84
+L+S++ + V NA +N
Sbjct: 126 INLKSLVTLGPDRAGENVFNAAGQIYN 152
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 26.9 bits (59), Expect = 1.00
Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 9/54 (16%)
Query: 5 ISFKTICPVAIGQLTYQV------DLIGYTCQAYLIPNFTSIIEHCNLWRNFDD 52
++ CP V D++ C ++ + +++ + WR F +
Sbjct: 18 LNIVLTCPECKVYPPKIVERFSEGDVVCALC-GLVLSD--KLVDTRSEWRTFSN 68
>2bnx_A Diaphanous protein homolog 1; autoinhibition, actin, nucleation,
cytoskeleton, structural; 2.4A {Mus musculus} SCOP:
a.118.1.23 PDB: 3o4x_A 3obv_A* 2bap_B
Length = 386
Score = 26.4 bits (57), Expect = 1.6
Identities = 10/44 (22%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 35 PNFTSIIEHCNLWRN-FDDIQDSWQSLESIIDYYGNNQDTIVPN 77
P+F SI++H L RN ++ ++ +E + +++ P+
Sbjct: 269 PHFLSILQHLLLVRNDYEARPQYYKLIEECVSQIVLHKNGTDPD 312
>2y69_F Cytochrome C oxidase subunit 5B; electron transport, complex IV,
proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV
DMU; 1.95A {Bos taurus}
Length = 129
Score = 25.4 bits (55), Expect = 3.1
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 72 DTIVPNAGPGHWNDPDMVKSYLDYDY 97
+ + P A G DP++V S +
Sbjct: 63 NILAPKATSGTKEDPNLVPSITNKRI 88
>1f8n_A Lipoxygenase-1; dioxygenase, metalloprotein, fatty acids,
oxidoreductase; 1.40A {Glycine max} SCOP: a.119.1.1
b.12.1.1 PDB: 1yge_A 2sbl_B 3pzw_A 1fgq_A 1fgr_A 3bnd_A
1fgt_A 1fgm_A 3bnb_A 1fgo_A 1y4k_A 3bne_A 3bnc_A 1ik3_A*
1hu9_A* 1jnq_A* 1lnh_A 1n8q_A* 1no3_A* 1rrh_A ...
Length = 839
Score = 25.6 bits (55), Expect = 3.2
Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 3/59 (5%)
Query: 21 QVDLIGYTCQA---YLIPNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYYGNNQDTIVP 76
D + ++ + P F S + + F QD E I + TI+P
Sbjct: 251 SKDALEIGTKSLSQIVQPAFESAFDLKSTPIEFHSFQDVHDLYEGGIKLPRDVISTIIP 309
>1v54_F VI, cytochrome C oxidase polypeptide VB; oxidoreductase; HET: FME
TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: g.41.5.3 PDB: 1oco_F* 1occ_F* 1ocz_F* 1ocr_F*
1v55_F* 2dyr_F* 2dys_F* 2eij_F* 2eik_F* 2eil_F* 2eim_F*
2ein_F* 2occ_F* 2ybb_Q* 2zxw_F* 3abk_F* 3abl_F* 3abm_F*
3ag1_F* 3ag2_F* ...
Length = 98
Score = 24.5 bits (53), Expect = 5.2
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 72 DTIVPNAGPGHWNDPDMVKSYLDYDY 97
+ + P A G DP++V S +
Sbjct: 32 NILAPKATSGTKEDPNLVPSITNKRI 57
>3eg5_B Protein diaphanous homolog 1; protein-protein complex, RHO
proteins, formins, armadillo repeat, G-protein, GTPase,
alternative splicing; HET: GNP; 2.70A {Mus musculus}
PDB: 1z2c_B*
Length = 383
Score = 24.8 bits (53), Expect = 5.3
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 35 PNFTSIIEHCNLWRNFDDI-QDSWQSLESII 64
P+F SI++H L RN + ++ +E +
Sbjct: 331 PHFLSILQHLLLVRNDYEARPQYYKLIEECV 361
>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 = 6.0
Identities = 11/66 (16%), Positives = 19/66 (28%), Gaps = 20/66 (30%)
Query: 8 KTICPVAIGQLTYQVDLIGYTCQAYLIPNFTSIIEHCNLWRNFDDIQDSWQSLESIIDYY 67
T P + +I SI + W N+ + L +II+
Sbjct: 323 LTTNPRRLS-------IIA-----------ESIRDGLATWDNWKHVNCD--KLTTIIESS 362
Query: 68 GNNQDT 73
N +
Sbjct: 363 LNVLEP 368
>3qm3_A Fructose-bisphosphate aldolase; structural genomics, center for
structural genomics of infec diseases, csgid, TIM
beta/alpha-barrel, lyase; 1.85A {Campylobacter jejuni}
Length = 357
Score = 24.6 bits (54), Expect = 6.4
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 49 NFD-DIQDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDPDMVKSY 92
N D D Q W + + +Y N+ + G +D K Y
Sbjct: 285 NIDTDTQ--WAFWDGVREYELKNRAYLQGQIGNPEGDDKPNKKYY 327
>3sbt_A PRE-mRNA-splicing factor 8; rnaseh like domain, VHS like domain, U5
snRNP assembly; 1.80A {Saccharomyces cerevisiae} PDB:
3e66_A 3e9o_A* 3e9p_A
Length = 260
Score = 24.3 bits (52), Expect = 9.1
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 7/43 (16%)
Query: 33 LIPNFTSIIEHCNLWRNFDDIQDSWQSLES-----IIDYYGNN 70
L+ + T I+ +LW +F D Q W ++ES I+ YG
Sbjct: 194 LLSDPTITIKSYHLWPSFTDEQ--WITIESQMRDLILTEYGRK 234
>2v5j_A 2,4-dihydroxyhept-2-ENE-1,7-dioic acid aldolase; lyase, class II
aldolase, homoprotocatechuate, aromatic DEGR aromatic
hydrocarbons catabolism; 1.60A {Escherichia coli} PDB:
2v5k_A
Length = 287
Score = 24.2 bits (53), Expect = 9.8
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 83 WNDPDMVKSYLD 94
WNDP +K LD
Sbjct: 98 WNDPVQIKQLLD 109
>1dxe_A 2-dehydro-3-deoxy-galactarate aldolase; class II aldolase; 1.8A
{Escherichia coli} SCOP: c.1.12.5 PDB: 1dxf_A
Length = 256
Score = 24.1 bits (53), Expect = 10.0
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 83 WNDPDMVKSYLD 94
N+P ++K LD
Sbjct: 78 TNEPVIIKRLLD 89
>1dos_A Aldolase class II; lyase, classii fructose 1,6-bisphosphate
aldolase, glycolysis; 1.67A {Escherichia coli} SCOP:
c.1.10.2 PDB: 1b57_A* 1gyn_A 1zen_A
Length = 358
Score = 23.9 bits (52), Expect = 10.0
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 49 NFD-DIQDSWQSLESIIDYYGNNQDTIVPNAGPGHWNDPDMVKSY 92
N D D Q W + E +++YY N+ + G D K Y
Sbjct: 286 NIDTDTQ--WATWEGVLNYYKANEAYLQGQLGNPKGEDQPNKKYY 328
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
0.322 0.140 0.460
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,648,317
Number of extensions: 82858
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 32
Length of query: 98
Length of database: 6,701,793
Length adjustment: 64
Effective length of query: 34
Effective length of database: 4,914,849
Effective search space: 167104866
Effective search space used: 167104866
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.7 bits)