RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16704
(146 letters)
>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like
repeat, protein transport; 2.90A {Saccharomyces
cerevisiae} SCOP: a.118.8.1
Length = 292
Score = 127 bits (319), Expect = 7e-37
Identities = 43/110 (39%), Positives = 61/110 (55%), Gaps = 1/110 (0%)
Query: 36 LFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYK 94
++ K++ N L +++ K+YF K GLC L D + + L P F D+RE
Sbjct: 180 IYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESN 239
Query: 95 FLLKLIESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQISTNED 144
FL LI+++ E DS+ SE KEFD+ RLD+W T+L KIK I ED
Sbjct: 240 FLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKWKITILNKIKESIQQQED 289
>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein
structure initiative, PSI, center for eukaryotic
structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}
Length = 307
Score = 91.5 bits (227), Expect = 2e-23
Identities = 13/96 (13%), Positives = 34/96 (35%), Gaps = 3/96 (3%)
Query: 46 ENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLE 104
+ + L L D + Q+ + + P F + + L L+++ +
Sbjct: 186 KEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESYSI-PGFSGSEDCAALEDLLQAYD 244
Query: 105 EEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQIS 140
E+D + + ++ +D Y + + +K
Sbjct: 245 EQDEEQLLRVCRS-PLVTYMDNDYAKLAISLKVPGG 279
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 33.6 bits (76), Expect = 0.011
Identities = 7/52 (13%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 91 REYKFLLKLIESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQISTN 142
E + K ++ L+ E ++ L++W ++++ N
Sbjct: 92 EEQR---KRLQELDAASKVMEQEWREKAKK--DLEEWNQRQSEQVEKNKINN 138
>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 = 31.7 bits (71), Expect = 0.068
Identities = 22/108 (20%), Positives = 40/108 (37%), Gaps = 22/108 (20%)
Query: 38 YSTGKAATENSLMKYNSKEYFFKAGLCHLCIDLLNCQQALSRYIDLSPAFQDTREYKFL- 96
Y+ K + L+ +YF+ H+ L N + R F D ++FL
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFY----SHIGHHLKNIEHP-ERMTLFRMVFLD---FRFLE 504
Query: 97 LKLIESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQISTNED 144
K+ DS A++ + +++ +L Y K I N+
Sbjct: 505 QKIR-----HDSTAWNASGSILNTLQQLKF-Y-------KPYICDNDP 539
Score = 31.0 bits (69), Expect = 0.13
Identities = 17/105 (16%), Positives = 33/105 (31%), Gaps = 27/105 (25%)
Query: 40 TGK-------AATENSLMKYNSKEYFFKAGLCHLCIDLLNCQQALSRYIDLSPAFQDTRE 92
+GK + K + K ++ C+ +L Q L ID P + +
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID--PNWTSRSD 218
Query: 93 YKFLLKL-IESLEEEDSDAF-----------------SETVKEFD 119
+ +KL I S++ E ++ F+
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN 263
Score = 28.7 bits (63), Expect = 0.84
Identities = 12/89 (13%), Positives = 29/89 (32%), Gaps = 13/89 (14%)
Query: 66 LCIDLLNCQQALSRYIDLSPAFQ-DTR-EYKFLLKLIESLEEEDSDAFSETVKEFDSISR 123
+++L + + LS F L + + + D V + S
Sbjct: 361 SSLNVLEPAEYRKMFDRLS-VFPPSAHIPTILLSLIWFDVIKSDVM---VVVNKLHKYSL 416
Query: 124 LDQW---YTTML----LKIKRQISTNEDL 145
+++ T + L++K ++ L
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYAL 445
Score = 27.9 bits (61), Expect = 1.7
Identities = 20/112 (17%), Positives = 37/112 (33%), Gaps = 20/112 (17%)
Query: 45 TENSLMKYNSKEYF------FKAGL-CHLCIDLLNCQQALSR----YIDLSPAFQDTREY 93
E +Y K+ F C D+ + LS+ +I +S +
Sbjct: 9 FETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMP--KSILSKEEIDHIIMSKD-AVSGTL 65
Query: 94 KFLLKLIESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQISTNEDL 145
L + S +EE F E V + ++ + + +RQ S +
Sbjct: 66 -RLFWTLLSKQEEMVQKFVEEVLRINY-----KFLMSPIKTEQRQPSMMTRM 111
Score = 25.6 bits (55), Expect = 8.0
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 9/55 (16%)
Query: 94 KFLLKLIESLEEEDSDA-------FSETVKEFDSISRLDQWYTTMLLKIKRQIST 141
K+L + L E +E++++ ++ D W K+ I +
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAESIRDG--LATWDNWKHVNCDKLTTIIES 361
>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 = 30.0 bits (67), Expect = 0.32
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 15/63 (23%)
Query: 94 KFLLKLIESLEEEDSDAFSETVK----EFDS-----------ISRLDQWYTTMLLKIKRQ 138
KFL + +E F + + EF++ ++L Q T L+K K
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 139 IST 141
I
Sbjct: 123 IKN 125
>1nrf_A Regulatory protein BLAR1; penicillin-receptor, beta-lactamase
induction, penicillin-binding protein, membrane
protein; 2.50A {Bacillus licheniformis} SCOP: e.3.1.1
Length = 262
Score = 27.5 bits (61), Expect = 1.5
Identities = 8/34 (23%), Positives = 18/34 (52%)
Query: 28 TFRIVYSLLFYSTGKAATENSLMKYNSKEYFFKA 61
T+++ +LL +G +S M ++ +Y +K
Sbjct: 64 TYKVFSALLALESGIITKNDSHMTWDGTQYPYKE 97
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 27.6 bits (62), Expect = 1.7
Identities = 8/36 (22%), Positives = 12/36 (33%), Gaps = 1/36 (2%)
Query: 75 QALSR-YIDLSPAFQDTREYKFLLKLIESLEEEDSD 109
+ Y + T K + IE L EE +
Sbjct: 23 KNYGMEYAKIEEIENITNRIKETQEFIELLREEGEN 58
>3p1v_A Metallo-endopeptidase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-biology; HET: MSE; 1.93A {Bacteroides ovatus atcc
8483} PDB: 4df9_A*
Length = 407
Score = 26.5 bits (58), Expect = 3.5
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 11/39 (28%)
Query: 45 TENSLMKYNSKEYFFKAGLCHLCIDLLNCQQALSRYIDL 83
+ MK N F C + CQ+A+ R I+
Sbjct: 377 AYDCRMKTNEYPEF-----CPV------CQRAIRRMIEF 404
>2iwb_A Methicillin resistance MECR1 protein; antibiotic resistance,
bacterial antibiotic resistance, methicillin
resistance, beta-lactamic antibiotics, MRSA; 1.8A
{Staphylococcus aureus} PDB: 2iwc_A* 2iwd_A*
Length = 246
Score = 26.0 bits (57), Expect = 5.3
Identities = 6/34 (17%), Positives = 18/34 (52%)
Query: 28 TFRIVYSLLFYSTGKAATENSLMKYNSKEYFFKA 61
T++I +L+ + + ++ +++ +Y FK
Sbjct: 53 TYKIYLALMAFDQNLLSLNHTEQQWDKHQYPFKE 86
>2qj6_A Toxin A; clostridial repetitive oligo peptides; 2.50A {Clostridium
difficile}
Length = 332
Score = 26.0 bits (57), Expect = 6.0
Identities = 6/25 (24%), Positives = 8/25 (32%)
Query: 37 FYSTGKAATENSLMKYNSKEYFFKA 61
F A L + + YFF
Sbjct: 302 FMPDTAMAAAGGLFEIDGVIYFFGV 326
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
mimicry, translation; 1.81A {Escherichia coli} SCOP:
e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Length = 365
Score = 25.3 bits (56), Expect = 8.9
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 74 QQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETVKEFDSI-SRLDQWYTTML 132
+ + + +D LL+L E +D + F+E V E D++ +L Q +
Sbjct: 64 EAVVDTLDQMKQGLEDVSG---LLELAV--EADDEETFNEAVAELDALEEKLAQLEFRRM 118
Query: 133 L 133
Sbjct: 119 F 119
>1r6f_A Virulence-associated V antigen; coiled-coil, protein binding; 2.17A
{Yersinia pestis} SCOP: e.46.1.1
Length = 310
Score = 25.2 bits (54), Expect = 9.0
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 85 PAFQDTREYKFLLKLIESLEEED-SDAFSETVKEF 118
F+ + EYK L K+ ++ + D S+ ++K+F
Sbjct: 183 EIFKASAEYKILEKMPQTTIQVDGSEKKIVSIKDF 217
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
0.329 0.139 0.400
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,104,332
Number of extensions: 111766
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 287
Number of HSP's successfully gapped: 25
Length of query: 146
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 61
Effective length of database: 4,328,508
Effective search space: 264038988
Effective search space used: 264038988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)