RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045812
(105 letters)
>3qas_B Undecaprenyl pyrophosphate synthase; alpha-helix, isoprenoid
biosynthesis, transferase; 1.70A {Escherichia coli} PDB:
1jp3_A* 1v7u_A* 1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A*
2e9c_A* 2e9d_A* 1ueh_A 1x09_A* 1x08_A*
Length = 253
Score = 139 bits (352), Expect = 8e-43
Identities = 37/86 (43%), Positives = 55/86 (63%), Gaps = 4/86 (4%)
Query: 24 MPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNW- 82
RHVA+IMDGN RWA+++G + GH+AG +S+R V G++ LT++AFS +NW
Sbjct: 17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWN 76
Query: 83 ---VEVEFLMKLFEKSIKSELEGFIR 105
EV LM+LF ++ SE++ R
Sbjct: 77 RPAQEVSALMELFVWALDSEVKSLHR 102
>1f75_A Undecaprenyl pyrophosphate synthetase; parallel beta sheet, NEW
fold for isoprenoid synthase, peptidoglycan synthesis,
transferase; 2.20A {Micrococcus luteus} SCOP: c.101.1.1
Length = 249
Score = 138 bits (350), Expect = 1e-42
Identities = 36/91 (39%), Positives = 56/91 (61%), Gaps = 4/91 (4%)
Query: 19 LNREAMPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFS 78
+N +P+H+A+IMDGN RWA+Q+ +P GH G++++R++ GVK LT++AFS
Sbjct: 15 INAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFS 74
Query: 79 YDNW----VEVEFLMKLFEKSIKSELEGFIR 105
+NW EV +LMKL + + L I
Sbjct: 75 TENWSRPKDEVNYLMKLPGDFLNTFLPELIE 105
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 137 bits (348), Expect = 7e-42
Identities = 31/91 (34%), Positives = 50/91 (54%), Gaps = 4/91 (4%)
Query: 19 LNREAMPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFS 78
+ + +P HVA++MDGN RWA QRGL + GH+ G + ++ G+K L+++AFS
Sbjct: 50 IPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFS 109
Query: 79 YDNW----VEVEFLMKLFEKSIKSELEGFIR 105
+NW EV FLM ++ + +
Sbjct: 110 TENWKRSPEEVRFLMGFNRDVVRRRRDTLKK 140
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase,
transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 134 bits (339), Expect = 6e-41
Identities = 32/91 (35%), Positives = 57/91 (62%), Gaps = 4/91 (4%)
Query: 19 LNREAMPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFS 78
++ +H+A+IMDGN RWA+ + + GH+ GV++L+++ C ++ LT++AFS
Sbjct: 10 EKLDSTLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYAFS 69
Query: 79 YDNW----VEVEFLMKLFEKSIKSELEGFIR 105
+NW EV+FLMK+ +K +K E ++
Sbjct: 70 TENWKRPKSEVDFLMKMLKKYLKDERSTYLD 100
>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural
genomics, center for structural GEN infectious diseases;
HET: FFT; 2.46A {Campylobacter jejuni}
Length = 225
Score = 133 bits (337), Expect = 8e-41
Identities = 31/85 (36%), Positives = 56/85 (65%), Gaps = 4/85 (4%)
Query: 25 PRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNW-- 82
+H+AV+MDGN RWAR +G + G+ GV+++++L+E+C + L++FAFS +NW
Sbjct: 7 LKHLAVVMDGNRRWARAKGFLAKLGYSQGVKTMQKLMEVCMEENISNLSLFAFSTENWKR 66
Query: 83 --VEVEFLMKLFEKSIKSELEGFIR 105
E++F+ +L ++ + LE F +
Sbjct: 67 PKDEIDFIFELLDRCLDEALEKFEK 91
>2vg0_A Short-chain Z-isoprenyl diphosphate synthetase; peptidoglycan
synthesis, cell WALL biogenesis/degradation, secreted,
cell shape; HET: GPP; 1.7A {Mycobacterium tuberculosis}
PDB: 2vfw_A* 2vg1_A*
Length = 227
Score = 129 bits (326), Expect = 4e-39
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 24 MPRHVAVIMDGNVRWARQRGLP-SSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNW 82
+PRH+AV+ DGN RWAR G S G+ G + E++ C G+++ TV+ S +N
Sbjct: 2 LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENL 61
Query: 83 ----VEVEFLMKLFEKSIKSELE 101
E+ L+++ ++
Sbjct: 62 QRDPDELAALIEIITDVVEEICA 84
>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 = 31.6 bits (71), Expect = 0.038
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 14/38 (36%)
Query: 40 RQRGL-PSS---AGH---E-------AGVRSLRELVEL 63
+ +GL P+ AGH E A V S+ LVE+
Sbjct: 1748 KSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEV 1785
Score = 26.2 bits (57), Expect = 3.0
Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 12/76 (15%)
Query: 19 LNREAMPRHVAVIMDGNVRWARQRGLPSS------AGHEAGVRSL-RELVELCCRWGVKV 71
L+ R V I+ V+W ++ G +G+ L + GV+V
Sbjct: 471 LSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGT---GVRV 527
Query: 72 LTVFAFSYDNWVEVEF 87
+ A + D + ++
Sbjct: 528 --IVAGTLDINPDDDY 541
>3tva_A Xylose isomerase domain protein TIM barrel; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG;
HET: MSE; 2.15A {Planctomyces limnophilus}
Length = 290
Score = 28.6 bits (64), Expect = 0.28
Identities = 7/49 (14%), Positives = 16/49 (32%)
Query: 39 ARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNWVEVEF 87
AR GL + V ++E+ + G + + ++
Sbjct: 86 ARTVGLVPLETRASRVAEMKEISDFASWVGCPAIGLHIGFVPESSSPDY 134
>1qzm_A ATP-dependent protease LA; oligomerization domain, AAA+ protein,
hydrolase; 1.90A {Escherichia coli} SCOP: c.37.1.20
Length = 94
Score = 26.7 bits (60), Expect = 0.76
Identities = 10/15 (66%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 51 EAGVRSL-RELVELC 64
EAGVR L RE+ +LC
Sbjct: 48 EAGVRGLEREISKLC 62
>3v8h_A TS, tsase, thymidylate synthase; ssgcid, structural genomics,
seattle S genomics center for infectious disease,
transferase; HET: CIT; 1.65A {Burkholderia
thailandensis}
Length = 327
Score = 27.4 bits (61), Expect = 0.82
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 66 RWGVKVLTVFAFSYDNWVEVEF-LM---KLFEKSIKSELEGFIR 105
R G++ + + ++ F + KL KS EL GF+R
Sbjct: 25 RTGIRTIGIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELVGFLR 68
>3dx5_A Uncharacterized protein ASBF; beta-alpha barrel, petrobactin
synthesis, ASB locus, structu genomics, PSI-2, protein
structure initiative; HET: MSE DHB TRS; 2.12A {Bacillus
anthracis}
Length = 286
Score = 27.4 bits (61), Expect = 0.89
Identities = 6/75 (8%), Positives = 17/75 (22%), Gaps = 15/75 (20%)
Query: 21 REAMPRHVAVIMDGNV----RWARQRGLPSSAG-----------HEAGVRSLRELVELCC 65
+++ + + + L + E + +L L
Sbjct: 35 WGTHAQNLYMQEYETTERELNCLKDKTLEITMISDYLDISLSADFEKTIEKCEQLAILAN 94
Query: 66 RWGVKVLTVFAFSYD 80
+ + FA
Sbjct: 95 WFKTNKIRTFAGQKG 109
>3vni_A Xylose isomerase domain protein TIM barrel; D-psicose 3-epimerase,
ketohexose; 1.98A {Clostridium cellulolyticum} PDB:
3vnj_A* 3vnl_A* 3vnk_A* 3vnm_A*
Length = 294
Score = 26.7 bits (59), Expect = 1.3
Identities = 7/47 (14%), Positives = 15/47 (31%)
Query: 26 RHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVL 72
+ + + + E V S+RE+ ++ GV
Sbjct: 103 HLIGGALYSYWPIDYTKTIDKKGDWERSVESVREVAKVAEACGVDFC 149
>1igl_A Insulin-like growth factor II; NMR {Homo sapiens} SCOP: g.1.1.1
PDB: 2l29_B 2v5p_C* 3e4z_C 3kr3_D
Length = 67
Score = 25.1 bits (54), Expect = 2.5
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 41 QRGLPSSAGHEAGVRSLRELVELCC 65
RG S R R +VE CC
Sbjct: 23 DRGFYFSRPASRVSRRSRGIVEECC 47
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices,
helix-hairpin-helix motif, iron-sulfur cluste hydrolase;
2.30A {Homo sapiens}
Length = 287
Score = 25.7 bits (57), Expect = 3.3
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 29 AVIMDGNVR--WARQRGLPSSAGHEAGVRSLRELVE 62
++DGNV R R + + + L L +
Sbjct: 154 TGVVDGNVARVLCRVRAIGADPSSTLVSQQLWGLAQ 189
>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase,
nucleotide-binding, Pro serine protease, stress
response; HET: ADP; 3.40A {Bacillus subtilis} PDB:
1x37_A
Length = 543
Score = 25.5 bits (57), Expect = 3.3
Identities = 10/15 (66%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 51 EAGVRSL-RELVELC 64
EAGVRSL R+L +C
Sbjct: 298 EAGVRSLERQLAAIC 312
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A
{Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A
1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A*
1wef_A* 1kg7_A 1kqj_A
Length = 225
Score = 25.6 bits (57), Expect = 3.5
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 29 AVIMDGNVR--WARQRGLPSSAGHEAGVRSLRELVE 62
I+DGNV+ AR + G + L L E
Sbjct: 134 FPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSE 169
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding
protein; 2.20A {Bovine immunodeficiency virus} PDB:
3kkr_A
Length = 152
Score = 25.0 bits (55), Expect = 4.0
Identities = 7/48 (14%), Positives = 17/48 (35%), Gaps = 4/48 (8%)
Query: 26 RHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLT 73
+ V ++ N + +P + +++L R+ V L
Sbjct: 15 TIIWVAVETNSGLVEAQVIPEETALQV----ALCILQLIQRYTVLHLH 58
>1o7b_T Tumor necrosis factor-inducible protein TSG-6; hyaluronan-binding
domain, carbohydrate-binding domain, LINK module, cell
adhesion, glycoprotein; NMR {Homo sapiens} SCOP:
d.169.1.4 PDB: 1o7c_T 2pf5_A*
Length = 98
Score = 24.4 bits (53), Expect = 5.2
Identities = 6/39 (15%), Positives = 13/39 (33%)
Query: 31 IMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGV 69
+ G V + + P+ + G+ + RW
Sbjct: 52 MAKGRVGYPIVKPGPNCGFGKTGIIDYGIRLNRSERWDA 90
>3cqj_A L-ribulose-5-phosphate 3-epimerase ULAE; TIM-barrel, isomerase,
phosphate-binding motif; 2.04A {Escherichia coli} PDB:
3cqi_A 3cqh_A 3cqk_A
Length = 295
Score = 25.0 bits (55), Expect = 5.7
Identities = 8/55 (14%), Positives = 20/55 (36%)
Query: 43 GLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNWVEVEFLMKLFEKSIK 97
G A G+ +R+ ++ G++V+ + + + F +K
Sbjct: 96 GSEDDAVRAQGLEIMRKAIQFAQDVGIRVIQLAGYDVYYQEANNETRRRFRDGLK 150
>4dqv_A Probable peptide synthetase NRP (peptide synthase; GXXGXXG motif,
rossmann fold, short chain dehydrogenase/REDU family,
reductase; 2.30A {Mycobacterium tuberculosis}
Length = 478
Score = 24.9 bits (54), Expect = 7.6
Identities = 7/56 (12%), Positives = 11/56 (19%), Gaps = 9/56 (16%)
Query: 35 NVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVL----TVFAFSYDNWVEVE 86
V P V EL+ + +K T +
Sbjct: 177 MVNA-----FPYHELFGPNVAGTAELIRIALTTKLKPFTYVSTADVGAAIEPSAFT 227
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA
glycosylase, transition state analog, DNA repair; HET:
NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A*
1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Length = 369
Score = 24.6 bits (54), Expect = 9.1
Identities = 6/36 (16%), Positives = 13/36 (36%), Gaps = 2/36 (5%)
Query: 29 AVIMDGNVR--WARQRGLPSSAGHEAGVRSLRELVE 62
+DGNV +R + + + ++V
Sbjct: 143 EPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVR 178
>3nkl_A UDP-D-quinovosamine 4-dehydrogenase; alpha-beta fold, structural
genomics, PSI-2, protein structu initiative; HET: MSE
GOL; 1.90A {Vibrio fischeri}
Length = 141
Score = 24.0 bits (53), Expect = 9.5
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 44 LPSSAGHEAGVRSLRELVELCCRWGVKVLTV 74
+PS A + ++E + V+VLT+
Sbjct: 73 VPS-----ASQVQKKVIIESLAKLHVEVLTI 98
>3vte_A Tetrahydrocannabinolic acid synthase; BI-covalent flavinylation,
oxidoreductase; HET: NAG FAD; 2.75A {Cannabis sativa}
Length = 518
Score = 24.6 bits (53), Expect = 9.6
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 23 AMPRHVAVIMDGNVRWARQRGLPSSA---GHEAGVRSLR 58
P + + I + +++ GL GH+A S
Sbjct: 58 VTPSNNSHIQA-TILCSKKVGLQIRTRSGGHDAEGMSYI 95
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
0.324 0.139 0.427
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,679,613
Number of extensions: 93059
Number of successful extensions: 452
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 34
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.7 bits)