RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7554
(115 letters)
>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation,
ATP-binding, cytoplasm, mitochondrion,
nucleotide-binding, nucleus; 2.95A {Saccharomyces
cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*
Length = 409
Score = 82.8 bits (205), Expect = 4e-20
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 59 VYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALK 103
VYK + +ITNK +E EGIPHH+++ +D + + + +
Sbjct: 38 VYKDIPIITNKHPLQEREGIPHHVMNHVDWSEEYYSHRFETECMN 82
>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP;
2.37A {Humulus lupulus}
Length = 339
Score = 77.3 bits (190), Expect = 2e-18
Identities = 22/46 (47%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 59 VYKGLDVITNKVTPEEAEGIPHHLLDFLDP-NTRFTVVDYRNRALK 103
VYKGLD+ TNK++ + G+PHHLL +DP T D+R+ A K
Sbjct: 76 VYKGLDITTNKISVPDRGGVPHHLLGEVDPARGELTPADFRSLAGK 121
>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside
modification, isopentenyl-tRNA transferase,
transferase-RNA complex; 2.50A {Escherichia coli k-12}
PDB: 2zxu_A* 2zm5_A
Length = 316
Score = 73.3 bits (181), Expect = 6e-17
Identities = 19/46 (41%), Positives = 27/46 (58%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALK 103
++YKG+D+ T K EE PH LLD DP+ ++ D+R AL
Sbjct: 45 LIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALA 90
>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding,
nucleotide-binding, nucleotidyltransferase, tRNA
processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A
3crr_A
Length = 323
Score = 72.9 bits (180), Expect = 7e-17
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALK 103
++Y+G+D+ T K + E PH L+D DP ++ ++R AL
Sbjct: 40 LIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESYSAAEFRADALA 85
>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2, protein structure
initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A
Length = 322
Score = 71.8 bits (177), Expect = 2e-16
Identities = 21/46 (45%), Positives = 33/46 (71%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALK 103
VY+G+D+ T K+T EE +G+PHHL+D DP+ F+V D+++ A
Sbjct: 38 QVYRGMDIGTAKITAEEMDGVPHHLIDIKDPSESFSVADFQDLATP 83
>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2; 2.70A
{Staphylococcus epidermidis atcc 12228}
Length = 340
Score = 71.1 bits (175), Expect = 5e-16
Identities = 22/46 (47%), Positives = 33/46 (71%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALK 103
VY+G+D+ T KVT EE EGIPH+++D L P+ F+ +++ RA K
Sbjct: 42 QVYQGMDIGTAKVTTEEMEGIPHYMIDILPPDASFSAYEFKKRAEK 87
>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis;
HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB:
2ze5_A* 2ze7_A* 2ze8_A
Length = 253
Score = 65.2 bits (159), Expect = 3e-14
Identities = 5/46 (10%), Positives = 11/46 (23%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALK 103
+ + + E + LD + +R L
Sbjct: 36 QCCPQIATGSGRPLESELQSTRRIYLDSRPLTEGILDAESAHRRLI 81
>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 = 33.5 bits (76), Expect = 0.011
Identities = 17/103 (16%), Positives = 36/103 (34%), Gaps = 22/103 (21%)
Query: 24 SYLSCLPDSVCPHAHQVDLT-DGPDLFCRTYQVYLMVYKGLDV--ITNKVTPEEAEGI-- 78
L D + + +++ + D+ VY + G D+ ++ ++ + I
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQI---PVYD-TFDGSDLRVLSGSISERIVDCIIR 485
Query: 79 ------------PHHLLDFLDPNTRFTVVDYRNRALKHTGLKV 109
H+LDF P + +R TG++V
Sbjct: 486 LPVKWETTTQFKATHILDF-GPGGASGLGVLTHRNKDGTGVRV 527
Score = 27.3 bits (60), Expect = 1.4
Identities = 28/119 (23%), Positives = 40/119 (33%), Gaps = 30/119 (25%)
Query: 8 HYQV--NLLTGTPDQVYLSYLSCLPDSVCPH----AHQVDLTDGPD------------LF 49
HY V LL TP ++ SYL + A + TD + LF
Sbjct: 248 HYVVTAKLLGFTPGELR-SYLKGA--TGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF 304
Query: 50 ---CRTYQVYLMVYKGLDVITNKVTPEEAEGIPHHLL---DFLDPNTRFTVVDYRNRAL 102
R Y+ Y L + + E EG+P +L + L V+ N L
Sbjct: 305 FIGVRCYEAYPNTS--LPPSILEDSLENNEGVPSPMLSISN-LTQEQVQDYVNKTNSHL 360
>2ejx_A ST0812; arcaea, unknown function, NPPSFA; 1.79A {Sulfolobus
tokodaii str}
Length = 139
Score = 27.0 bits (59), Expect = 1.2
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 52 TYQVYLMVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNR 100
+Y+V VYKG+D + + GI + + D NT ++++ N+
Sbjct: 59 SYKVKGRVYKGVDEVRIIYDSDRGNGILY--IRKKDNNTLQIILEHDNK 105
>1x7f_A Outer surface protein; structural genomics, unknown function, MCSG,
PSI, midwest center for struct genomics; 2.30A {Bacillus
cereus atcc 14579} SCOP: b.62.1.2 c.1.8.12
Length = 385
Score = 26.7 bits (59), Expect = 2.1
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 69 KVTPEEAEGIPHHLLDFLDPNTRFTVVD 96
+ EE LLD++ T+FT V+
Sbjct: 363 TIAEEE-----LFLLDYVGAWTQFTCVE 385
>3n6x_A Putative glutathionylspermidine synthase; domain of unknown
function (DUF404), structural genomics; 2.35A
{Methylobacillus flagellatus}
Length = 474
Score = 26.1 bits (57), Expect = 3.4
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 14/52 (26%)
Query: 40 VDLTDGPDLFCRTYQVYLMVYKGL---DVITNKVTPEEAEGIPHHLLDFLDP 88
++L +G DLF R VY+ +G DVI ++ DF+DP
Sbjct: 244 IELVEGQDLFVRNNAVYMRTTEGPKRVDVIYRRIDD-----------DFIDP 284
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 26.2 bits (57), Expect = 3.6
Identities = 14/93 (15%), Positives = 28/93 (30%), Gaps = 7/93 (7%)
Query: 13 LLTGTPDQVYLSYLSCLPDSVCPHAHQVDLTDGPDLFCRTYQVYLMVYKGLD--VITNKV 70
LLT TP+Q+ + + P + F + Y V + + NK+
Sbjct: 311 LLTATPEQLGMESHFARLRLLDP-----NRFHDFAQFVEEQKNYCPVADAVAMLLAGNKL 365
Query: 71 TPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALK 103
+ +E + + + A
Sbjct: 366 SNDELNMLGEMIGEQDIEPLLQAANSDSEDAQS 398
>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 = 25.7 bits (56), Expect = 3.8
Identities = 6/22 (27%), Positives = 7/22 (31%)
Query: 80 HHLLDFLDPNTRFTVVDYRNRA 101
+D L F VV A
Sbjct: 105 KVAIDTLTDGAFFAVVAGTEGA 126
>1nf2_A Phosphatase; structural proteomics, HAD NEW fold, structural
genomics, BSGC structure funded by NIH structure
initiative, PSI; 2.20A {Thermotoga maritima} SCOP:
c.108.1.10
Length = 268
Score = 25.6 bits (57), Expect = 4.6
Identities = 5/40 (12%), Positives = 13/40 (32%), Gaps = 2/40 (5%)
Query: 36 HAHQVDLTDGPDL--FCRTYQVYLMVYKGLDVITNKVTPE 73
++ D+ + + V+ Y + + K E
Sbjct: 79 LNEKIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEKDNEE 118
>4dw8_A Haloacid dehalogenase-like hydrolase; HAD, putative phosphatase,
enzyme function initiative, EFI, structural genomics;
1.50A {Bacteroides thetaiotaomicron} PDB: 3niw_A 4dwo_A
Length = 279
Score = 24.8 bits (55), Expect = 6.8
Identities = 8/68 (11%), Positives = 21/68 (30%), Gaps = 8/68 (11%)
Query: 36 HAHQVDLTDGPDL--FCRTYQVYLMVYKGLDVITNKVTPEEAE------GIPHHLLDFLD 87
+ + + P L RT + ++ Y G +++T + + +
Sbjct: 86 YENVLPNEVVPVLYECARTNHLSILTYDGAEIVTENSLDPYVQKEAFLNKMAIRETNDFL 145
Query: 88 PNTRFTVV 95
+ V
Sbjct: 146 TDITLPVA 153
>2pmi_A Negative RE, cyclin-dependent protein kinase PHO85;
cyclin-dependent kinase, signaling protein,transfera
cycle complex; HET: MES AGS; 2.90A {Saccharomyces
cerevisiae} PDB: 2pk9_A*
Length = 317
Score = 24.9 bits (55), Expect = 7.4
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 9/34 (26%)
Query: 52 TYQVYLMVYKGLDVITN------KVTPEEAEGIP 79
TY VYKGL+ T +V + EG P
Sbjct: 17 TYAT---VYKGLNKTTGVYVALKEVKLDSEEGTP 47
>2gwm_A 65 kDa virulence protein; SPVB, ADP-ribosyltransferase,
transferase, toxin; 1.50A {Salmonella typhimurium} PDB:
2gwl_A*
Length = 200
Score = 24.8 bits (53), Expect = 8.0
Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 7/40 (17%)
Query: 61 KGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNR 100
KG + EAE +L PNT+ + N
Sbjct: 133 KGRILGDVAHFKGEAE-----ML--FPPNTKLKIESIVNC 165
>1kut_A Phosphoribosylaminoimidazole-succinocarboxamide synthase;
structural genomics, saicar synthetase, PSI, protein
structure initiative; 2.20A {Thermotoga maritima} SCOP:
d.143.1.1
Length = 230
Score = 24.9 bits (55), Expect = 8.2
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 74 EAEGIPHHLLDFLDPNT 90
+GI HL++++ P T
Sbjct: 55 SEKGIKTHLVEYIPPRT 71
>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 = 24.8 bits (53), Expect = 10.0
Identities = 17/93 (18%), Positives = 30/93 (32%), Gaps = 30/93 (32%)
Query: 7 THYQV-------NLLTGTPDQVYLSYLSCLPDSVCPHAHQVDLTDGPDLFCRTYQVYLMV 59
HY + +L+ DQ + S++ H ++ + LF +
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGH-------HLKNIEHPERMTLFRMVF------ 497
Query: 60 YKGLDV--ITNKV----TPEEAEG-IPHHLLDF 85
LD + K+ T A G I + L
Sbjct: 498 ---LDFRFLEQKIRHDSTAWNASGSILNTLQQL 527
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 0.138 0.426
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: 1,879,921
Number of extensions: 105989
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 35
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
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 (23.8 bits)