RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5004
(173 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 = 36.8 bits (84), Expect = 0.002
Identities = 36/201 (17%), Positives = 58/201 (28%), Gaps = 72/201 (35%)
Query: 2 KLLVLT--LSLISFVSRCSALLCYQCVSTQPGCGTPF-------KWLWYPSISCPEEDDI 52
K+L+ T + F+S +A + + TP K+L P E +
Sbjct: 267 KILLTTRFKQVTDFLS--AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE--V 322
Query: 53 C------VKIIERKGAEEIITRDCLSTVKAFRTDIPADRYEGCRAAAKDPKLANYVNHSI 106
+ II AE I RD L+T ++ + C KL + S+
Sbjct: 323 LTTNPRRLSII----AESI--RDGLATWDNWK-------HVNC------DKLTTIIESSL 363
Query: 107 PELDVQRPSELKTGYTEEIITRDCLSTVKAFRTD--IPADRYE----------------G 148
L+ P+E + + + F IP
Sbjct: 364 NVLE---PAEYRKMFDRLSV----------FPPSAHIPTILLSLIWFDVIKSDVMVVVNK 410
Query: 149 CR---AAAKDPKLANYVNHSI 166
K PK + SI
Sbjct: 411 LHKYSLVEKQPKESTISIPSI 431
Score = 27.1 bits (59), Expect = 3.8
Identities = 27/166 (16%), Positives = 53/166 (31%), Gaps = 25/166 (15%)
Query: 18 SALLCYQCVSTQPGCGTPFK--WLWYPSISCPEEDDICVKIIERKGAEEIITR-DCLSTV 74
+ + C+S + C FK WL ++ + ++++++ ++ + D T
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFWL---NLKNCNSPETVLEMLQK-----LLYQIDPNWTS 215
Query: 75 KAFRTDIPADRYEGCRAAAKD-PKLANYVNHSIPELD-VQRPSELKT---GYTEEIITRD 129
++ + R +A + K Y N + L VQ + TR
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYEN-CLLVLLNVQNAKAWNAFNLSCKILLTTRF 274
Query: 130 CLSTVKAF-----RTDIPAD-RYEGCRAAAKDPKLANYVNHSIPEL 169
V F T I D L Y++ +L
Sbjct: 275 --KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318
>3laq_U UPAR, U-PAR, urokinase plasminogen activator surface receptor; ATF,
supar, smupar, MATF, disulfide bond, EGF-LIK hydrolase,
kringle; HET: NAG; 3.20A {Mus musculus}
Length = 277
Score = 28.4 bits (62), Expect = 1.3
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 4/44 (9%)
Query: 14 VSRCSALLCYQCVSTQPGCGTPFKWLWYPSISCPEEDDICVKII 57
+ L C C S C S+ C + C++++
Sbjct: 88 FPQGRYLECASCTSLDQSCERG----REQSLQCRYPTEHCIEVV 127
>1ywh_A Urokinase plasminogen activator surface receptor; UPAR,
three-finger fold, protein-peptide complex, hydrolase;
HET: ALC NAG FUC NDG BMA MAN; 2.70A {Homo sapiens} SCOP:
g.7.1.3 g.7.1.3 g.7.1.3
Length = 313
Score = 28.4 bits (62), Expect = 1.4
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 4/44 (9%)
Query: 13 FVSRCSALLCYQCVSTQPGCGTPFKWLWYPSISCPEEDDICVKI 56
SR L C C S+ C + S+ C ++ C+ +
Sbjct: 86 TYSRSRYLECISCGSSDMSCERG----RHQSLQCRSPEEQCLDV 125
>2fd6_U Urokinase plasminogen activator surface receptor; UPAR, ATF,
ATN-615 antibody, FAB, ternary complex, immune SY
hydrolase; HET: PGE NAG FUC NDG PG4; 1.90A {Homo
sapiens} SCOP: g.7.1.3 g.7.1.3 g.7.1.3 PDB: 3bt2_U*
3bt1_U* 2i9b_E* 3u74_U* 3u73_U*
Length = 276
Score = 28.1 bits (61), Expect = 1.7
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 4/46 (8%)
Query: 12 SFVSRCSALLCYQCVSTQPGCGTPFKWLWYPSISCPEEDDICVKII 57
SR L C C S+ C + S+ C ++ C+ ++
Sbjct: 86 VTYSRSRYLECISCGSSDMSCERG----RHQSLQCRSPEEQCLDVV 127
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex,
single-stranded DNA, isomerase/DNA complex; HET: DNA;
2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A*
2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Length = 659
Score = 27.6 bits (62), Expect = 2.3
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 33 GTPFKWLWYPSISCPEEDDICVKIIERKGAEEIITR 68
F +W PS +C D +++ R AE ++ R
Sbjct: 233 DERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNR 268
>2bcf_A Probable D-alanyl-D-alanine carboxypeptidase DACB2;
penicillin-binding protein, DD-2 carboxypeptidase,
directed evolution; 2.30A {Mycobacterium tuberculosis}
Length = 276
Score = 27.2 bits (61), Expect = 2.8
Identities = 13/61 (21%), Positives = 18/61 (29%), Gaps = 19/61 (31%)
Query: 90 RAAAKDPKLANYV---NHSIPELDVQRPSE--------------LKTGYTEEIITRDCLS 132
RAA +P A + + P D ++ KTGYT R
Sbjct: 162 RAAMANPVFAQIIAEPSAMFPSDDGEQLIVNQDELLQRYPGAIGGKTGYTNA--ARKTFV 219
Query: 133 T 133
Sbjct: 220 G 220
>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 = 26.6 bits (58), Expect = 4.3
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 46 CPEEDDICVKIIERKGAEEIITRDC 70
CPE KI+ER +++ C
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALC 48
>3tha_A Tryptophan synthase alpha chain; structural genomics, center for
structural genomics of infec diseases, csgid, lyase;
2.37A {Campylobacter jejuni}
Length = 252
Score = 26.4 bits (59), Expect = 4.4
Identities = 3/33 (9%), Positives = 7/33 (21%), Gaps = 6/33 (18%)
Query: 112 QRPSE--LKTGYTEEIITRDCLSTVKAFRTDIP 142
++ L G + +T
Sbjct: 62 ADAAKIALDQGVD----IHSVFELLARIKTKKA 90
>3hh7_A Muscarinic toxin-like protein 3 homolog; haditoxin, three finger
toxin, snake venom, neurotoxin, nicotinic acetylcholine
receptors; 1.55A {Ophiophagus hannah}
Length = 65
Score = 24.5 bits (53), Expect = 7.5
Identities = 15/53 (28%), Positives = 16/53 (30%), Gaps = 10/53 (18%)
Query: 21 LCYQCVSTQPGCGTPFKWLWYPSISCPEEDDICVKIIERKGAEEIITRDCLST 73
CY ST P CP+ C K G E I R C T
Sbjct: 2 KCYNHQSTTPETTE----------ICPDSGYFCYKSSWIDGREGRIERGCTFT 44
>1lya_A Cathepsin D; lysosomal aspartic protease; HET: NAG BMA MAN; 2.50A
{Homo sapiens} SCOP: b.50.1.2 PDB: 1lyb_A* 1lyw_A*
Length = 97
Score = 25.0 bits (55), Expect = 7.8
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 39 LWYPSISCPEEDDIC 53
LW PSI C D C
Sbjct: 39 LWVPSIHCKLLDIAC 53
>1g0z_A Phospholipase A2; toxin; 2.18A {Bungarus caeruleus} SCOP:
a.133.1.2 PDB: 1u4j_A* 1g2x_A 2osn_A 1dpy_A 1fe5_A
1tc8_A* 1po8_A*
Length = 118
Score = 25.3 bits (55), Expect = 8.2
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 22 CYQCVSTQPGCGTPFKWLWY----PSISCPEEDDICVKII 57
CY + PGC K Y P+I+C + D C + I
Sbjct: 49 CYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFI 88
>3jql_A Phospholipase A2 isoform 3; phospholipase A2, hexapeptide,
hydrolase, calcium, disulfide bond, lipid degradation,
metal-binding, secreted; 1.20A {Naja sagittifera} PDB:
1mf4_A 3jq5_A 1ln8_A 3jti_A 3nju_A* 3osh_A* 3q4y_A
1t37_A 1zm6_A 3gci_A 1yxl_A 1oxr_A 1td7_A* 1sz8_A
1a3d_A 1a3f_A 1psh_A 2osh_A 1poa_A 1pob_A* ...
Length = 119
Score = 25.2 bits (55), Expect = 8.8
Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 22 CYQCVSTQPGCGTPFKWLWY----PSISCPEEDDICVKII 57
CY GC FK Y +++C +++ C +
Sbjct: 50 CYNEAENISGCRPYFKTYSYECTQGTLTCKGDNNACAASV 89
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
0.321 0.136 0.424
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,680,902
Number of extensions: 150892
Number of successful extensions: 403
Number of sequences better than 10.0: 1
Number of HSP's gapped: 401
Number of HSP's successfully gapped: 26
Length of query: 173
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 86
Effective length of database: 4,272,666
Effective search space: 367449276
Effective search space used: 367449276
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: 54 (24.4 bits)