RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15189
(150 letters)
>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 = 31.4 bits (70), Expect = 0.12
Identities = 22/145 (15%), Positives = 47/145 (32%), Gaps = 42/145 (28%)
Query: 7 DPYHKRPMKKGEIGCFLSHYNI--------WNEVVDNNHDIVMVLEDDVRFESFFRQKLA 58
+P R M + F +I W +V+ ++ +V+ + L
Sbjct: 367 EPAEYRKMFD-RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV--------NKLHKYSL- 416
Query: 59 TILKELKTKTLPAWDLIYLGRKKLSEKPDTWVSGSRYLVEA------------------S 100
+ K+ K T+ + + KL + R +V+
Sbjct: 417 -VEKQPKESTISIPSIYLELKVKLENEYAL----HRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 101 YSYWTLGY-LLSRQGARKLTQARPL 124
Y Y +G+ L + + ++T R +
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMV 496
Score = 25.6 bits (55), Expect = 8.2
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 20/85 (23%)
Query: 25 HYNIWNEVVDNNH---DIVMVLEDDVRFESFFRQKLATILKELKTKTLPAWDLIYLGRKK 81
H+++ E ++ + DI+ V ED ++F + + + K + +K D I
Sbjct: 4 HHHMDFETGEHQYQYKDILSVFEDAFV-DNFDCKDVQDMPKSILSKE--EIDHII----- 55
Query: 82 LSEKPDTWVSGSRYLVEASYSYWTL 106
D VSG+ L +WTL
Sbjct: 56 --MSKDA-VSGTLRL------FWTL 71
>2c1l_A Restriction endonuclease; BFII, domain fusion, hydrolase; HET: TAR
TLA SRT MES; 1.9A {Bacillus firmus}
Length = 358
Score = 31.0 bits (69), Expect = 0.14
Identities = 12/60 (20%), Positives = 19/60 (31%)
Query: 29 WNEVVDNNHDIVMVLEDDVRFESFFRQKLATILKELKTKTLPAWDLIYLGRKKLSEKPDT 88
+ ++DNN M + Q T P W+L+Y R +T
Sbjct: 137 ASLLLDNNTTQSMGFSWNDMISEMLNQNWHIHNMTNATDASPGWNLLYDERTTNLTLDET 196
>1c7s_A Beta-N-acetylhexosaminidase; glycosyl hydrolase, chitinolysis,
A/B(TIM)-barrel, site directed mutagenesis; HET: CBS;
1.80A {Serratia marcescens} SCOP: b.1.18.2 b.2.2.3
c.1.8.6 d.92.2.1 PDB: 1c7t_A* 1qba_A 1qbb_A*
Length = 858
Score = 27.8 bits (61), Expect = 1.8
Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 9/79 (11%)
Query: 43 LEDDVRFESFFRQKLATILKELKTKTLPAWDLIYLGRKKLSEKPDTWVSGSRYLVEASYS 102
+ D S+F Q+++ ++K + AW + + SR V
Sbjct: 560 VADMEHLPSYFGQEVSKLVKAHGIDRMQAWQDGLKD-----AESSKAFATSRVGVN---- 610
Query: 103 YWTLGYLLSRQGARKLTQA 121
+W Y
Sbjct: 611 FWDTLYWGGFDSVNDWANK 629
>1b73_A Glutamate racemase; isomerase; 2.30A {Aquifex pyrophilus} SCOP:
c.78.2.1 c.78.2.1 PDB: 1b74_A*
Length = 254
Score = 27.5 bits (62), Expect = 1.8
Identities = 7/20 (35%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
T+LK ++ D++YLG
Sbjct: 14 TVLKAIR-NRYRKVDIVYLG 32
>2vvt_A Glutamate racemase; isomerase, peptidoglycan synthesis, cell WALL
biogenesis/degradation, cell shape, benzyl purine, MURI
inhibitor; HET: I24 DGL; 1.65A {Enterococcus faecalis}
PDB: 2jfp_A* 2jfo_A* 2jfu_A 2jfv_A* 2jfw_A*
Length = 290
Score = 27.2 bits (61), Expect = 2.1
Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
T+LKE K LP LIYLG
Sbjct: 38 TVLKEAL-KQLPNERLIYLG 56
>2oho_A Glutamate racemase; isomerase; 2.25A {Streptococcus pyogenes m1
gas} PDB: 2ohg_A 2ohv_A*
Length = 273
Score = 27.1 bits (61), Expect = 2.3
Identities = 7/20 (35%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
T++ EL + LP ++Y+G
Sbjct: 26 TVVCELI-RQLPHEKIVYIG 44
>3ist_A Glutamate racemase; structural genomics, cell WALL
biogenesis/degradation, isomerase, peptidoglycan
synthesis; HET: MSE; 1.65A {Listeria monocytogenes}
PDB: 3hfr_A* 3isv_A*
Length = 269
Score = 27.1 bits (61), Expect = 2.4
Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
T+++E+ K LP + YLG
Sbjct: 19 TVVREVL-KQLPHEQVYYLG 37
>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 = 27.3 bits (60), Expect = 2.4
Identities = 35/138 (25%), Positives = 49/138 (35%), Gaps = 40/138 (28%)
Query: 7 DPYHKRPMKKGEIGCFLSHYNIWNEVVDNNHDIVMVLEDDVRFESFFRQKLATILKELKT 66
D Y RP+ LSH ++ H + V SFF A+ L+E
Sbjct: 2 DAYSTRPLT-------LSHGSL-------EHVL------LVPTASFFI---ASQLQEQFN 38
Query: 67 KTLPAWDLIYLGRKKLSEKPDTWVSGSRYLVEASYSYWTLGYLLSRQGARKLTQARPLSN 126
K LP + ++P T LV + LGY+ S K+ Q + N
Sbjct: 39 KILPEPTEGFAA----DDEPTTPAE----LV-GKF----LGYVSSLVEPSKVGQFDQVLN 85
Query: 127 LLPVDEFL-PLLSGK--H 141
L + EF L G H
Sbjct: 86 LC-LTEFENCYLEGNDIH 102
Score = 25.8 bits (56), Expect = 7.6
Identities = 3/20 (15%), Positives = 9/20 (45%)
Query: 55 QKLATILKELKTKTLPAWDL 74
+ +L +K + + +L
Sbjct: 1863 DTVTNVLNFIKLQKIDIIEL 1882
>2jfz_A Glutamate racemase; cell WALL, isomerase, cell shape,
peptidoglycan synthesis, peptidoglycan biosynthesis;
HET: 003 DGL; 1.86A {Helicobacter pylori} PDB: 2jfx_A*
2jfy_A* 2w4i_A*
Length = 255
Score = 26.8 bits (60), Expect = 2.7
Identities = 7/20 (35%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
++LK L K ++IY G
Sbjct: 14 SVLKSLL-KARLFDEIIYYG 32
>3uhf_A Glutamate racemase; structural genomics, center for structural
genomics of infec diseases, csgid, alpha-beta sandwich
fold, isomerase; HET: DGL; 1.83A {Campylobacter jejuni}
PDB: 3uho_A* 3uhp_A
Length = 274
Score = 26.4 bits (59), Expect = 3.5
Identities = 6/20 (30%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
++LK L + ++IY G
Sbjct: 38 SVLKSLY-EARLFDEIIYYG 56
>3out_A Glutamate racemase; structural genomics, center for structural
genomics of infec diseases, csgid, MURI, cell envelope;
HET: MSE DGL; 1.65A {Francisella tularensis subsp}
Length = 268
Score = 26.3 bits (59), Expect = 3.7
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
TI+K L LP D+IY G
Sbjct: 21 TIVKNLM-SILPNEDIIYFG 39
>2jfn_A Glutamate racemase; cell WALL, isomerase, cell shape, UDP-
murnac-Ala, peptidoglycan biosynthesis, peptidoglycan
synthesis; HET: GLU UMA; 1.9A {Escherichia coli}
Length = 285
Score = 26.1 bits (58), Expect = 4.5
Identities = 5/20 (25%), Positives = 9/20 (45%), Gaps = 1/20 (5%)
Query: 59 TILKELKTKTLPAWDLIYLG 78
++ E++ LP IY
Sbjct: 35 SVYDEIR-HLLPDLHYIYAF 53
>2j0a_A Beta-1,3-N-acetylglucosaminyltransferase manic FR;
glycosyltransferase, developmental protein,
transmembrane, G apparatus, notch signaling; 1.8A {Mus
musculus} PDB: 2j0b_A*
Length = 280
Score = 26.3 bits (57), Expect = 5.0
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 8/74 (10%)
Query: 75 IYLGRKKLSEKPDTWVSGSRYLV-EASYSYWTLG--YLLSRQGARKLTQARPLSNLLPVD 131
+Y+G+ L+ S+ + + T G + ++RQ A K+ S+ +
Sbjct: 124 VYVGKPSLNRPIHASELQSKQRTKLVRFWFATGGAGFCINRQLALKMVPWASGSHFVDTS 183
Query: 132 EFLPLLSGKHPEDL 145
+ + P+D
Sbjct: 184 ALI-----RLPDDC 192
>3e5n_A D-alanine-D-alanine ligase A; bacterial blight; 2.00A {Xanthomonas
oryzae PV} PDB: 3r5f_A* 3rfc_A*
Length = 386
Score = 25.7 bits (57), Expect = 7.0
Identities = 12/67 (17%), Positives = 24/67 (35%)
Query: 78 GRKKLSEKPDTWVSGSRYLVEASYSYWTLGYLLSRQGARKLTQARPLSNLLPVDEFLPLL 137
G+ +++ + A + LL ++L +P L +D P++
Sbjct: 66 GQWHVNDPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQPEQALAQIDVVFPIV 125
Query: 138 SGKHPED 144
G ED
Sbjct: 126 HGTLGED 132
>1wsc_A Hypothetical protein ST0229; structural genomics, function unknown
protein, unknown function; 2.45A {Sulfolobus tokodaii}
SCOP: d.309.1.1
Length = 230
Score = 25.8 bits (56), Expect = 7.1
Identities = 7/35 (20%), Positives = 11/35 (31%), Gaps = 3/35 (8%)
Query: 16 KGEIGCFLSHYNIWNEVVDNNHDIVMVLEDDVRFE 50
+G IG + + V + D RF
Sbjct: 72 RGCIGYVEAVAPLKEIVSKA---AIAAAFSDPRFP 103
>1zq7_A Hypothetical protein MM0484; X-RAY, NESG, MAR9, Q8PZK8,
structural genomics, PSI, protein structure initiative;
2.11A {Methanosarcina mazei} SCOP: d.309.1.1
Length = 207
Score = 25.6 bits (56), Expect = 7.3
Identities = 7/40 (17%), Positives = 15/40 (37%), Gaps = 3/40 (7%)
Query: 10 HKRPMKKGEIGCFLSHYNIWNEVVDNNHDIVMVLEDDVRF 49
+ + +G IG + ++D+ + D RF
Sbjct: 52 TEGGLLRGCIGHPYPDSTLKEAILDS---AISAATRDPRF 88
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
0.319 0.138 0.429
Gapped
Lambda K H
0.267 0.0530 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,404,841
Number of extensions: 131212
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 291
Number of HSP's successfully gapped: 23
Length of query: 150
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 65
Effective length of database: 4,328,508
Effective search space: 281353020
Effective search space used: 281353020
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 (21.7 bits)
S2: 53 (24.7 bits)