RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2211
(100 letters)
>3a2b_A Serine palmitoyltransferase; vitamin B6-dependent enzyme fold
type I, acyltransferase, PY phosphate; HET: PLP; 2.30A
{Sphingobacterium multivorum}
Length = 398
Score = 33.7 bits (78), Expect = 0.005
Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 22/79 (27%)
Query: 17 VYRRIVDCFNRPVTSVPGAIITIKDRETPDYGWTFKYTGTESTCLNLASYNYLGFGENTG 76
+Y RP+ S + I R L S +YLG +T
Sbjct: 23 LYAYF-----RPIQSKQDTEVKIDGRRV----------------LMFGSNSYLGLTTDTR 61
Query: 77 LCTERSKESVKQSGCALCS 95
+ + +++++++ G
Sbjct: 62 I-IKAAQDALEKYGTGCAG 79
>1bs0_A Protein (8-amino-7-oxonanoate synthase); PLP-dependent acyl-COA
synthase, biotin biosynthesis, 8-AMIN oxonanoate
synthase; 1.65A {Escherichia coli} SCOP: c.67.1.4 PDB:
2g6w_A* 1dje_A* 1dj9_A*
Length = 384
Score = 33.3 bits (77), Expect = 0.006
Identities = 15/74 (20%), Positives = 24/74 (32%), Gaps = 22/74 (29%)
Query: 18 YRRIVDCFNRPVTSVPGAIITIKDRETPDYGWTFKYTGTESTCLNLASYNYLGFGENTGL 77
RR PV G + DR+ LN +S +YLG + +
Sbjct: 20 LRRR-----YPVAQGAGRWLVADDRQ----------------YLNFSSNDYLGLSHHPQI 58
Query: 78 CTERSKESVKQSGC 91
++ +Q G
Sbjct: 59 -IRAWQQGAEQFGI 71
>3tqx_A 2-amino-3-ketobutyrate coenzyme A ligase; energy metabolism,
transferase; HET: PLP; 2.30A {Coxiella burnetii}
Length = 399
Score = 31.8 bits (73), Expect = 0.020
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 22/73 (30%)
Query: 18 YRRIVDCFNRPVTSVPGAIITIKDRETPDYGWTFKYTGTESTCLNLASYNYLGFGENTGL 77
Y+ R +TS A I + ++E LN + NYLG ++ L
Sbjct: 24 YKSE-----RIITSPQNAEIKVGEKE----------------VLNFCANNYLGLADHPAL 62
Query: 78 CTERSKESVKQSG 90
+ ++ V+Q G
Sbjct: 63 -IKTAQTVVEQYG 74
>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 = 31.0 bits (69), Expect = 0.053
Identities = 20/115 (17%), Positives = 32/115 (27%), Gaps = 39/115 (33%)
Query: 1 GYPDLY--EKFVLFYSRYVYRRIVDCFNRPVTSVPGAIITIKDRETPDYGWTFKYTGTES 58
P +Y K L ++R IVD +N P T D P + +Y
Sbjct: 427 SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS-------DDLIPP--YLDQY----- 472
Query: 59 TCLNLASYNYLGF-------GENTGLCTE--------RSKESVKQSGCALCSPSG 98
Y+++G E L K ++ A +
Sbjct: 473 ------FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK--IRHDSTAWNASGS 519
Score = 26.7 bits (58), Expect = 1.5
Identities = 6/53 (11%), Positives = 15/53 (28%), Gaps = 6/53 (11%)
Query: 19 RRIVDCF-NRPVTSVPGAIITIKDRETPDYGWTFKYTGTES--TCLNLASYNY 68
R+ ++ V + ++ +Y + TE + Y
Sbjct: 65 LRLFWTLLSKQEEMVQKFV---EEVLRINYKFLMSPIKTEQRQPSMMTRMYIE 114
>1fc4_A 2-amino-3-ketobutyrate conenzyme A ligase; 2-amino-3-ketobutyrate
COA ligase, pyridoxal phosphate, COEN transferase,
structural genomics; HET: PLP; 2.00A {Escherichia coli}
SCOP: c.67.1.4
Length = 401
Score = 30.6 bits (70), Expect = 0.059
Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 21/73 (28%)
Query: 18 YRRIVDCFNRPVTSVPGAIITIKDRETPDYGWTFKYTGTESTCLNLASYNYLGFGENTGL 77
++ R +TS A IT+ D G+ +N + NYLG + L
Sbjct: 25 FKEE-----RIITSAQQADITVAD-------------GSH--VINFCANNYLGLANHPDL 64
Query: 78 CTERSKESVKQSG 90
+K + G
Sbjct: 65 -IAAAKAGMDSHG 76
>2bwn_A 5-aminolevulinate synthase; tetrapyrrole biosynthesis, heme
biosynthesis, pyridoxal PHOS dependent, transferase,
acyltransferase; HET: LLP; 2.1A {Rhodobacter
capsulatus} SCOP: c.67.1.4 PDB: 2bwo_A* 2bwp_A*
Length = 401
Score = 27.6 bits (62), Expect = 0.74
Identities = 11/73 (15%), Positives = 21/73 (28%), Gaps = 15/73 (20%)
Query: 18 YRRIVDCFNRPVTSVPGAIITIKDRETPDYGWTFKYTGTESTCLNLASYNYLGFGENTGL 77
YR + GA + G + +YLG G++ +
Sbjct: 20 YRTF-----IDIEREKGAFPKAQWNRP---------DGGKQDITVWCGNDYLGMGQHPVV 65
Query: 78 CTERSKESVKQSG 90
E+++ G
Sbjct: 66 -LAAMHEALEAVG 77
>2w8t_A SPT, serine palmitoyltransferase; HET: LLP; 1.25A {Sphingomonas
paucimobilis} PDB: 2w8u_A* 2w8w_A* 2xbn_A* 2w8j_A*
2w8v_A* 2jg2_A* 2jgt_A 2x8u_A*
Length = 427
Score = 27.2 bits (61), Expect = 0.84
Identities = 8/30 (26%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 61 LNLASYNYLGFGENTGLCTERSKESVKQSG 90
+ L +YNY+G + + KE++++ G
Sbjct: 67 ILLGTYNYMGMTFDPDV-IAAGKEALEKFG 95
>3kki_A CAI-1 autoinducer synthase; quorum sensing, CQSA, P virulence,
acyltransferase, aminotransferase, pyridoxal PHO
transferase; HET: PLP; 1.80A {Vibrio cholerae} PDB:
3hqt_A* 2wk9_A* 2wk8_A* 2wka_A* 2wk7_A
Length = 409
Score = 27.2 bits (61), Expect = 0.97
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 14/70 (20%)
Query: 26 NRPVTSVPGAIITIKDRETPDYGWTFKYTGTESTCLNLASYNYLGFGENTGLCTERSKES 85
N + G + + + +PD + L S +YL + + R +S
Sbjct: 40 NYFDINKNGKHLVLGKQASPDD-------------IILQSNDYLALANHPLI-KARLAKS 85
Query: 86 VKQSGCALCS 95
+ + +L
Sbjct: 86 LLEEQQSLFM 95
>2dm1_A Protein VAV-2; RHO family guanine nucleotide exchange factor,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 73
Score = 25.7 bits (57), Expect = 1.2
Identities = 6/17 (35%), Positives = 8/17 (47%)
Query: 33 PGAIITIKDRETPDYGW 49
G ++ I R D GW
Sbjct: 28 EGDVVRIYSRIGGDQGW 44
>2k9g_A SH3 domain-containing kinase-binding protein 1; CIN85, adaptor
protein, downregulation, CBL, apoptosis, junction,
cytoplasmic vesicle, cytoskeleton; NMR {Homo sapiens}
Length = 73
Score = 25.8 bits (57), Expect = 1.3
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 33 PGAIITIKDRETPDYGW 49
G I+T+ +++ D GW
Sbjct: 30 EGDIVTLINKDCIDVGW 46
>2da9_A SH3-domain kinase binding protein 1; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus}
Length = 70
Score = 25.3 bits (56), Expect = 1.5
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 33 PGAIITIKDRETPDYGW 49
G I+T+ +++ D GW
Sbjct: 28 EGDIVTLINKDCIDVGW 44
>2ydl_A SH3 domain-containing kinase-binding protein 1; signaling
protein; 2.05A {Homo sapiens} PDB: 2k6d_A
Length = 69
Score = 25.3 bits (56), Expect = 1.6
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 33 PGAIITIKDRETPDYGW 49
G I+T+ +++ D GW
Sbjct: 23 EGDIVTLINKDCIDVGW 39
>2jte_A CD2-associated protein; SH3 domain, coiled coil, cytoplasm,
phosphorylation, SH3-binding, signaling protein; NMR
{Mus musculus} PDB: 2kro_A
Length = 64
Score = 24.9 bits (55), Expect = 1.9
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 33 PGAIITIKDRETPDYGW 49
G II + +ET + GW
Sbjct: 27 EGEIIHLISKETGEAGW 43
>1uff_A Intersectin 2; beta barrel, SH3 domain, endocytosis, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens} SCOP: b.34.2.1
Length = 93
Score = 25.1 bits (55), Expect = 3.0
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 33 PGAIITIKDRETPDYGW 49
G II + ++ + GW
Sbjct: 26 SGDIIQVDEKTVGEPGW 42
>2eja_A URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY
diffraction, structural genomics, NPPSFA; 1.90A {Aquifex
aeolicus}
Length = 338
Score = 25.2 bits (56), Expect = 4.1
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 3 PDLYEKFVLFYSRYVYRRIVDCFNRPVT 30
+ Y ++V Y Y+ + D + PV
Sbjct: 208 LEDYGEYVYPYVNYLISELKDFSDTPVI 235
>2dlp_A KIAA1783 protein; SH3 domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 85
Score = 24.3 bits (53), Expect = 4.6
Identities = 5/17 (29%), Positives = 8/17 (47%)
Query: 33 PGAIITIKDRETPDYGW 49
G +I + T + GW
Sbjct: 29 RGDLIKLLPVATLEPGW 45
>1j93_A UROD, uroporphyrinogen decarboxylase; beta barrel, plastidial
enzyme, crystallographic dimer, lyase; 2.30A {Nicotiana
tabacum} SCOP: c.1.22.1
Length = 353
Score = 25.2 bits (56), Expect = 4.8
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 3 PDLYEKFVLFYSRYVYRRIVDCFNRPVTSVP 33
P +E+F L Y ++IVD ++P
Sbjct: 222 PVDFEEFSLPYL----KQIVDSVKLTHPNLP 248
>1x43_A Endophilin B1, SH3 domain GRB2-like protein B1; structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
Length = 81
Score = 23.9 bits (52), Expect = 6.8
Identities = 4/17 (23%), Positives = 6/17 (35%)
Query: 33 PGAIITIKDRETPDYGW 49
+IT+ D W
Sbjct: 38 ADEVITVFSVVGMDSDW 54
>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein;
HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB:
1xec_A* 1xcd_A*
Length = 330
Score = 24.6 bits (54), Expect = 8.1
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 20 RIVDCFNRPVTSVPGAI 36
R+V C + + VP +
Sbjct: 34 RVVQCSDLGLEKVPKDL 50
>1oot_A Hypothetical 40.4 kDa protein in PES4-His2 intergenic region; SH3
domain, sturctural genomics, structural genomics; 1.39A
{Saccharomyces cerevisiae} SCOP: b.34.2.1 PDB: 1ssh_A
2a08_A
Length = 60
Score = 23.3 bits (51), Expect = 8.5
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 33 PGAIITIKDRETPDYGW 49
G +ITI + W
Sbjct: 24 KGDVITILKKSDSQNDW 40
>2inf_A URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta)8 barrel,
eight parallel beta strands surrounded by eight alpha
helices, lyase; 2.30A {Bacillus subtilis}
Length = 359
Score = 24.4 bits (54), Expect = 9.0
Identities = 1/19 (5%), Positives = 6/19 (31%)
Query: 3 PDLYEKFVLFYSRYVYRRI 21
Y ++ ++ +
Sbjct: 222 QADYRTYIKPVMNRIFSEL 240
>1r3s_A URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyrinogen
decarboxylase coproporphyrinogen, X-RAY crystallography,
lyase; HET: 1CP; 1.65A {Homo sapiens} SCOP: c.1.22.1
PDB: 1r3t_A* 1r3r_A 1r3q_A* 1r3y_A* 1uro_A 3gvq_A 3gvr_A
1r3v_A* 3gvv_A 3gvw_A 1jph_A 1r3w_A* 3gw3_A 1jpi_A
1jpk_A 3gw0_A 2q71_A* 2q6z_A*
Length = 367
Score = 24.0 bits (53), Expect = 9.5
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 4/21 (19%)
Query: 3 PDLYEKFVLFYSRYVYRRIVD 23
P L+ KF L Y R +
Sbjct: 226 PQLFNKFALPYI----RDVAK 242
>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex,
leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A
{Homo sapiens} PDB: 1xwd_C*
Length = 350
Score = 24.4 bits (53), Expect = 9.6
Identities = 5/17 (29%), Positives = 8/17 (47%)
Query: 20 RIVDCFNRPVTSVPGAI 36
R+ C VT +P +
Sbjct: 12 RVFLCQESKVTEIPSDL 28
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
0.320 0.139 0.439
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,523,239
Number of extensions: 77273
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 33
Length of query: 100
Length of database: 6,701,793
Length adjustment: 66
Effective length of query: 34
Effective length of database: 4,859,007
Effective search space: 165206238
Effective search space used: 165206238
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 (21.8 bits)
S2: 51 (23.6 bits)