RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13404
(167 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 = 35.2 bits (80), Expect = 0.008
Identities = 20/139 (14%), Positives = 38/139 (27%), Gaps = 44/139 (31%)
Query: 23 DIDVPTPSAIDV-DEEAP-FENEENFNDGDSDIIGAGSPLR--------VEDEDEGSGEE 72
+ D DV D EE II + + + + E ++
Sbjct: 32 NFDCK-----DVQDMPKSILSKEEI-----DHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81
Query: 73 LFGDNLENDYR------------PMPALDRYD--HDQLDD-----SDYSVISADARAEAE 113
+ L +Y+ P Y D+L + + Y+V +
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141
Query: 114 RALRRRDREQ-----AMGG 127
+AL + + G
Sbjct: 142 QALLELRPAKNVLIDGVLG 160
>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 = 28.5 bits (63), Expect = 1.1
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 2 PTSPRTPQTPSDFSPIPPTP--SDIDVPTPSAIDVDEEAPFENEENFNDGDSDI----IG 55
P S R + + F P+ +P S + VP I+ D +N +FN D I
Sbjct: 408 PFSERKLKFSNRFLPV-ASPFHSHLLVPASDLINKDLV---KNNVSFNAKDIQIPVYDTF 463
Query: 56 AGSPLRVEDED 66
GS LRV
Sbjct: 464 DGSDLRVLSGS 474
>4fce_A Bifunctional protein GLMU; GLMU. csgid, niaid, structural genomics,
national institute allergy and infectious diseases; HET:
GP1; 1.96A {Yersinia pseudotuberculosis} PDB: 3fww_A
1hv9_A* 2oi5_A* 2oi6_A* 2oi7_A* 1fxj_A* 1fwy_A*
Length = 459
Score = 27.8 bits (63), Expect = 1.6
Identities = 3/16 (18%), Positives = 7/16 (43%)
Query: 110 AEAERALRRRDREQAM 125
+ ER + E+ +
Sbjct: 236 SALERVFQTEQAEKLL 251
>3gwq_A D-serine deaminase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2, lyase; HET: MSE; 2.00A {Burkholderia xenovorans
LB400}
Length = 426
Score = 27.8 bits (61), Expect = 2.0
Identities = 7/38 (18%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 1 MPTSPRTPQTPSDFSPIPPTPSDIDVPTPSAIDVDEEA 38
+ P T +D + + + DV P+A+ + +
Sbjct: 19 LGMVPGTSIQLTDAARLEWNLLNEDVSLPAAV-LYADR 55
>2v0h_A Bifunctional protein GLMU; cell WALL, magnesium, cell shape,
transferase, peptidoglycan synthesis, associative
mechanism; 1.79A {Haemophilus influenzae} PDB: 2v0i_A*
2v0j_A* 2v0k_A* 2v0l_A* 2vd4_A* 2w0v_A* 2w0w_A* 3twd_A*
Length = 456
Score = 27.8 bits (63), Expect = 2.0
Identities = 3/16 (18%), Positives = 7/16 (43%)
Query: 110 AEAERALRRRDREQAM 125
A ER + + + +
Sbjct: 233 AALERYFQNKQASKLL 248
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.0 bits (59), Expect = 2.5
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 108 ARAEAERALRRRDREQAMGGRRGDADLLYES-DEDEEAPRRKRRAAERAAEGDLGDEEI 165
A + + + RE+A + D + + E E + R A++A D +I
Sbjct: 100 ELDAASKVMEQEWREKA----KKDLEEWNQRQSEQVEKNKINNRIADKAFYQQP-DADI 153
Score = 25.5 bits (55), Expect = 9.7
Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 10/55 (18%)
Query: 103 VISADARAEAERALRRRDREQAMGGRRGDADLLYESDEDEEAPRRKRRAAERAAE 157
+ AD + ++R+ EQ L E D + ++ E+A +
Sbjct: 74 IAQADRLTQEPESIRKWREEQ--------RKRLQELDAASK--VMEQEWREKAKK 118
>1hm9_A GLMU, UDP-N-acetylglucosamine-1-phosphate uridyltransfe;
acetyltransferase, bifunctional, drug design; HET: ACO
UD1; 1.75A {Streptococcus pneumoniae} SCOP: b.81.1.4
c.68.1.5 PDB: 1hm8_A* 1hm0_A* 4ac3_A* 4aaw_A* 1g97_A*
1g95_A*
Length = 468
Score = 27.5 bits (62), Expect = 2.7
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 110 AEAERALRRRDREQAM 125
A AE +RRR + M
Sbjct: 242 ATAESVMRRRINHKHM 257
>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex,
cytoplasm, ribonucleoprotein, structural protein; 3.50A
{Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A
Length = 861
Score = 27.5 bits (60), Expect = 2.9
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 4/62 (6%)
Query: 106 ADARAEAERALRRRDREQAMGGRRGDADLLYESDEDEEAPRRKRRAAERAAEGDLGDEEI 165
A++RAEA R QA + A L E E +K R E + E+
Sbjct: 726 AESRAEAARIEGEGSVLQA----KLKAQALAIETEAELERVKKVREMELIYARAQLELEV 781
Query: 166 NK 167
+K
Sbjct: 782 SK 783
>3st8_A Bifunctional protein GLMU; acetyltransferase, pyrophosphorylase,
rossmann fold, LEFT-handed-beta-helix, cell shape; HET:
COA GP1 UD1; 1.98A {Mycobacterium tuberculosis} PDB:
3spt_A* 3foq_A 3dk5_A 3d8v_A 3d98_A* 3dj4_A 2qkx_A*
Length = 501
Score = 27.1 bits (61), Expect = 3.0
Identities = 5/16 (31%), Positives = 5/16 (31%)
Query: 110 AEAERALRRRDREQAM 125
AE L RR
Sbjct: 251 AELASELNRRVVAAHQ 266
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 26.5 bits (58), Expect = 5.2
Identities = 9/30 (30%), Positives = 11/30 (36%)
Query: 2 PTSPRTPQTPSDFSPIPPTPSDIDVPTPSA 31
PTSP TP + P+ P A
Sbjct: 5 PTSPGTPGVAAATQAANGGPATPAPPALGA 34
Score = 26.1 bits (57), Expect = 7.9
Identities = 11/60 (18%), Positives = 14/60 (23%), Gaps = 1/60 (1%)
Query: 2 PTSPRTPQTPSDFSPIPPTPSDIDVPTPSAIDVDEEAPFENEENFNDGDSDIIGAGSPLR 61
P P P+ P P PTP D + DI +
Sbjct: 27 PAPPALGAAPTG-DPKPKKNKKPKNPTPPRPAGDNATVAAGHATLREHLRDIKAENTDAN 85
>4fx5_A VON willebrand factor type A; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, blood
clotting; HET: MSE; 1.73A {Catenulispora acidiphila}
Length = 464
Score = 26.5 bits (58), Expect = 5.5
Identities = 15/101 (14%), Positives = 30/101 (29%)
Query: 60 LRVEDEDEGSGEELFGDNLENDYRPMPALDRYDHDQLDDSDYSVISADARAEAERALRRR 119
+++ +D G L + + L + ++ A A E A
Sbjct: 337 VQLVAKDAGGATLLGEGKIRAVWTEDTDLSTRINGRVAHYTGQAEMAAAIQEGLDAQAAG 396
Query: 120 DREQAMGGRRGDADLLYESDEDEEAPRRKRRAAERAAEGDL 160
D + A DL ES ++ ++ A +
Sbjct: 397 DLDTATARLGRAMDLAVESGHEDTVKMLRKVTEVDPATSKV 437
>3ne5_B Cation efflux system protein CUSB; transmembrane helix, metal
transport; 2.90A {Escherichia coli} PDB: 3ooc_A 3opo_A
3ow7_A 3h9i_A 3h94_A 3h9t_B
Length = 413
Score = 26.3 bits (58), Expect = 6.4
Identities = 6/54 (11%), Positives = 12/54 (22%)
Query: 101 YSVISADARAEAERALRRRDREQAMGGRRGDADLLYESDEDEEAPRRKRRAAER 154
+A++E G L + D ++ R
Sbjct: 154 TIPDWVEAQSEYLLLRETGGTATQTEGILERLRLAGMPEADIRRLIATQKIQTR 207
>1x5i_A Neogenin; RGM binding, fibronectin type III domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
SCOP: b.1.2.1
Length = 126
Score = 25.1 bits (55), Expect = 8.3
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 2 PTSPRTPQTPSDFSPIPPTPSDIDV-PTPSAIDV 34
S T ++ D + +P PS + V P ++I V
Sbjct: 12 WLSAETFESDLDETRVPEVPSSLHVRPLVTSIVV 45
>2v5y_A Receptor-type tyrosine-protein phosphatase MU; membrane, hydrolase,
glycoprotein, receptor protei tyrosine phosphatase, cell
adhesion; HET: NAG; 3.10A {Homo sapiens}
Length = 731
Score = 25.9 bits (56), Expect = 9.8
Identities = 7/33 (21%), Positives = 9/33 (27%)
Query: 2 PTSPRTPQTPSDFSPIPPTPSDIDVPTPSAIDV 34
+ QT D PT S I +
Sbjct: 449 ESQELIVQTDEDLPGAVPTESIQGSTFEEKIFL 481
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
0.308 0.132 0.374
Gapped
Lambda K H
0.267 0.0561 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,877,243
Number of extensions: 189749
Number of successful extensions: 360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 60
Length of query: 167
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 80
Effective length of database: 4,272,666
Effective search space: 341813280
Effective search space used: 341813280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 54 (25.0 bits)