RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3587
(195 letters)
>1puj_A YLQF, conserved hypothetical protein YLQF; structural genomics,
nysgxrc T18, GTPase, PSI, protein structure initiative;
HET: GNP; 2.00A {Bacillus subtilis} SCOP: c.37.1.8
Length = 282
Score = 58.9 bits (143), Expect = 7e-11
Identities = 23/141 (16%), Positives = 46/141 (32%), Gaps = 22/141 (15%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQ----VLMGSFPIAQLREP 98
+ PG T Q + + + L D PG+++P K L + G+ I
Sbjct: 145 IAKTGDRPGITTSQQWVKVGKELELLDTPGILWP-KFEDELVGLRLAVTGA--IKDSIIN 201
Query: 99 YSTV-QYLAERM------DLIKLLHIKHPDDDEYWCAMDICDGWAQKRSYMTAKTGRYDS 151
V + + L + + +D ++ D +KR + G +
Sbjct: 202 LQDVAVFGLRFLEEHYPERLKERYGLDEIPED----IAELFDAIGEKRGCLM-SGGLINY 256
Query: 152 YRAANELL---RMATEGRICL 169
+ ++ R GR+
Sbjct: 257 DKTTEVIIRDIRTEKFGRLSF 277
>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP,
signaling protein; HET: GNP; 2.00A {Thermotoga maritima}
PDB: 3cnn_A* 3cno_A*
Length = 262
Score = 55.7 bits (135), Expect = 7e-10
Identities = 27/134 (20%), Positives = 51/134 (38%), Gaps = 19/134 (14%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQ----VLMGSFPIAQLREP 98
SV PG TK Q L + +++ D PG+++ + +L+GS P+ ++ +
Sbjct: 124 ASSVGAQPGITKGIQWFSLENGVKILDTPGILYK-NIFSEDLAAKLLLVGSLPVERIEDQ 182
Query: 99 YSTVQYLAERMDLIKLLHIKHPDDDEYWCAMDICDGWAQKRSYMTAKTGRYDSYRAANEL 158
+ ER ++ + + + +A+KR + K G D RA
Sbjct: 183 -----RIFER--AFEIFARSIGIESS---FSEFFEDFARKRGLLK-KGGVPDIERALMLF 231
Query: 159 L---RMATEGRICL 169
GR+
Sbjct: 232 FTEVAQGKAGRVSF 245
>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved
in replication initiation, csgid, IDP90222; HET: DGI;
1.80A {Bacillus anthracis str}
Length = 368
Score = 38.4 bits (89), Expect = 9e-04
Identities = 11/49 (22%), Positives = 20/49 (40%)
Query: 35 SKVPKPLQVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPL 83
+ V++ S PG T I L + L D PG++ ++ +
Sbjct: 183 EFSDETENVITTSHFPGTTLDLIDIPLDEESSLYDTPGIINHHQMAHYV 231
Score = 37.3 bits (86), Expect = 0.002
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPL 41
V++ S PG T I L + L D PG++ ++ +
Sbjct: 191 VITTSHFPGTTLDLIDIPLDEESSLYDTPGIINHHQMAHYV 231
>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling
protein; HET: GDP; 2.36A {Geobacillus
stearothermophilus}
Length = 369
Score = 37.2 bits (86), Expect = 0.002
Identities = 11/41 (26%), Positives = 16/41 (39%)
Query: 36 KVPKPLQVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFP 76
+ V++ S PG T I L L D PG++
Sbjct: 185 EATGKGNVITTSYFPGTTLDMIEIPLESGATLYDTPGIINH 225
Score = 36.8 bits (85), Expect = 0.003
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFP 34
V++ S PG T I L L D PG++
Sbjct: 192 VITTSYFPGTTLDMIEIPLESGATLYDTPGIINH 225
>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA,
national P protein structural and functional analyses;
HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8
Length = 190
Score = 33.8 bits (78), Expect = 0.019
Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 15/73 (20%)
Query: 44 VSVSRTPGHTKHFQTI--FLTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYST 101
V + PG T + I N ++ D PG F +PK +Q +
Sbjct: 26 VRRGKRPGVT---RKIIEIEWKNHKIIDMPGFGFMMGLPKEVQERIKDE----------I 72
Query: 102 VQYLAERMDLIKL 114
V ++ + I +
Sbjct: 73 VHFIEDNAKNIDV 85
Score = 31.1 bits (71), Expect = 0.13
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 2 VSVSRTPGHTKHFQTI--FLTDNIRLCDCPGLVFPSKVPKPLQ 42
V + PG T + I N ++ D PG F +PK +Q
Sbjct: 26 VRRGKRPGVT---RKIIEIEWKNHKIIDMPGFGFMMGLPKEVQ 65
>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 = 34.3 bits (78), Expect = 0.020
Identities = 38/218 (17%), Positives = 66/218 (30%), Gaps = 73/218 (33%)
Query: 12 KHFQTIFLTDNIRLCDCPGLV--FPSKVPKPL-----------QVVSVSRTPGHTKHFQT 58
F+ +L N D L + L +++ P K
Sbjct: 89 TEFENCYLEGN----DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSA 144
Query: 59 IF---LTDNIRLCDCPGLVFPSKVPKPLQVLMGS----FPIAQLREPYSTVQYLAERMDL 111
+F N +L +F Q G+ F +LR+ Y T L DL
Sbjct: 145 LFRAVGEGNAQLV----AIFGG------Q---GNTDDYFE--ELRDLYQTYHVLVG--DL 187
Query: 112 I----KLLH--IKHPDDDEYWC--AMDICDGWAQKRS------YMTAKTGRYDSYRAA-- 155
I + L I+ D E ++I + W + S Y+ +
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILE-WLENPSNTPDKDYLLS---------IPIS 237
Query: 156 ---NELLRMATEGRIC--LCLMPPQYLSK-QGVSKHSR 187
++++A L P + S +G + HS+
Sbjct: 238 CPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ 275
>3i2k_A Cocaine esterase; alpha/beta hydrolase, hydrolase; HET: DBC GOL;
1.51A {Rhodococcus SP} PDB: 3i2j_A* 3puh_A 3i2h_A*
3i2i_A* 3i2g_A* 3ida_A* 3i2f_A* 3pui_A 1ju3_A 1ju4_A
1l7q_A 1l7r_A
Length = 587
Score = 31.9 bits (72), Expect = 0.12
Identities = 15/90 (16%), Positives = 32/90 (35%)
Query: 83 LQVLMGSFPIAQLREPYSTVQYLAERMDLIKLLHIKHPDDDEYWCAMDICDGWAQKRSYM 142
L ++ A P + L + + + HPD+DE W ++ + + +
Sbjct: 192 LAAILNDVAGAASVTPLAEQPLLGRLIPWVIDQVVDHPDNDESWQSISLFERLGGLATPA 251
Query: 143 TAKTGRYDSYRAANELLRMATEGRICLCLM 172
G YD + + +A + L+
Sbjct: 252 LITAGWYDGFVGESLRTFVAVKDNADARLV 281
>3tp9_A Beta-lactamase and rhodanese domain protein; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG;
2.70A {Alicyclobacillus acidocaldarius subsp}
Length = 474
Score = 31.5 bits (71), Expect = 0.17
Identities = 24/122 (19%), Positives = 37/122 (30%), Gaps = 15/122 (12%)
Query: 49 TPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYSTVQYLAER 108
TPGHT + L D D P +F V +G L E + +E
Sbjct: 120 TPGHTPEHVSYLLYDGKTSPDVPMALFSGDF-----VFVGDVGRPDLLERVAGESGSSE- 173
Query: 109 MDLIKLLHIKH------PDDDEYWCAMDICDGWAQKRSYMTAKTGRYDSYRAANELLRMA 162
L + + PD + A + + + T Y + N L+
Sbjct: 174 -ALARQMFRSLRKFEALPDHVQVLPAHGAGSACGKALGAVPSSTVGY--EKLVNWALQHK 230
Query: 163 TE 164
E
Sbjct: 231 DE 232
Score = 28.8 bits (64), Expect = 1.2
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 7 TPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVVSVSRT 49
TPGHT + L D D P +F + V V R
Sbjct: 120 TPGHTPEHVSYLLYDGKTSPDVPMALFSGDF---VFVGDVGRP 159
>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell
cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima}
PDB: 3pr1_A
Length = 195
Score = 30.6 bits (70), Expect = 0.21
Identities = 20/87 (22%), Positives = 31/87 (35%), Gaps = 22/87 (25%)
Query: 46 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYSTV 102
VS+TPG T ++I + + D PG + +KV K ++L
Sbjct: 51 VSKTPGKT---RSINFYLVNSKYYFVDLPGYGY-AKVSKKERMLWKRL----------VE 96
Query: 103 QYLAERMDLIKLLH---IKHP--DDDE 124
Y R L + + P D D
Sbjct: 97 DYFKNRWSLQMVFLLVDGRIPPQDSDL 123
Score = 27.9 bits (63), Expect = 1.9
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 4 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPK 39
VS+TPG T ++I + + D PG + +KV K
Sbjct: 51 VSKTPGKT---RSINFYLVNSKYYFVDLPGYGY-AKVSK 85
>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP;
1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A*
1svw_A*
Length = 195
Score = 30.6 bits (70), Expect = 0.24
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 22/87 (25%)
Query: 46 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYSTV 102
S PG T QT+ + + D + D PG F +KV K + G
Sbjct: 52 TSSKPGKT---QTLNFYIINDELHFVDVPGYGF-AKVSKSEREAWGRM----------IE 97
Query: 103 QYLAERMDLIKLLH---IKHP--DDDE 124
Y+ R +L ++ ++H +DD
Sbjct: 98 TYITTREELKAVVQIVDLRHAPSNDDV 124
Score = 27.5 bits (62), Expect = 2.0
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 7/39 (17%)
Query: 4 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPK 39
S PG T QT+ + + D + D PG F +KV K
Sbjct: 52 TSSKPGKT---QTLNFYIINDELHFVDVPGYGF-AKVSK 86
>3r2u_A Metallo-beta-lactamase family protein; structural genomics, for
structural genomics of infectious diseases, csgid, HYDR;
2.10A {Staphylococcus aureus}
Length = 466
Score = 30.4 bits (68), Expect = 0.33
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 7 TPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVVSVSRT 49
TPGHT + LTD P +F + V + R
Sbjct: 140 TPGHTPESISFLLTDEGAGAQVPMGLFSGDF---IFVGDIGRP 179
Score = 30.0 bits (67), Expect = 0.57
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 49 TPGHTKHFQTIFLTDNIRLCDCPGLVF 75
TPGHT + LTD P +F
Sbjct: 140 TPGHTPESISFLLTDEGAGAQVPMGLF 166
>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 = 30.6 bits (68), Expect = 0.33
Identities = 22/146 (15%), Positives = 40/146 (27%), Gaps = 29/146 (19%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPK--PLQV----VSVSRTPGHTK 54
+ + T + L C L P +V P ++ S+
Sbjct: 289 ISLDHHSMTLTPD-EVKSLLLKYLDCRPQDL--PREVLTTNPRRLSIIAESIRDGLATWD 345
Query: 55 HFQTIF---LTDNIRLC-DC--PGL---------VFPSKVPKPLQVLMGSFPIAQLREPY 99
+++ + LT I + P VFP P +L +
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLS----LIWFDVIK 401
Query: 100 STVQYLAERMDLIKLLHIKHPDDDEY 125
S V + ++ L K P +
Sbjct: 402 SDVMVVVNKL-HKYSLVEKQPKESTI 426
>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics,
nysgxrc T16, GTPase, PSI, protein structure initiative;
2.00A {Escherichia coli} SCOP: c.37.1.8
Length = 210
Score = 29.9 bits (68), Expect = 0.38
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 22/87 (25%)
Query: 46 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYSTV 102
S+TPG T Q I F + D RL D PG + ++VP+ ++
Sbjct: 55 TSKTPGRT---QLINLFEVADGKRLVDLPGYGY-AEVPEEMKRKWQRA----------LG 100
Query: 103 QYLAERMDL---IKLLHIKHP--DDDE 124
+YL +R L + L+ I+HP D D+
Sbjct: 101 EYLEKRQSLQGLVVLMDIRHPLKDLDQ 127
Score = 27.6 bits (62), Expect = 2.5
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 7/42 (16%)
Query: 4 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPKPLQ 42
S+TPG T Q I F + D RL D PG + ++VP+ ++
Sbjct: 55 TSKTPGRT---QLINLFEVADGKRLVDLPGYGY-AEVPEEMK 92
>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase,
cell division, cell cycle, SEP GTP-binding; 2.20A
{Burkholderia thailandensis}
Length = 223
Score = 28.0 bits (63), Expect = 1.6
Identities = 20/91 (21%), Positives = 29/91 (31%), Gaps = 26/91 (28%)
Query: 46 VSRTPGHTKHFQTI--FL-----TDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREP 98
S+TPG T Q I F L D PG + ++VP +
Sbjct: 58 ASKTPGRT---QHINYFSVGPAAEPVAHLVDLPGYGY-AEVPGAAKAHWEQL-------- 105
Query: 99 YSTVQYLAERMDLIKLLH---IKHP--DDDE 124
YL R L ++ + P + D
Sbjct: 106 --LSSYLQTRPQLCGMILMMDARRPLTELDR 134
>1pg4_A Acetyl-COA synthetase; AMP-forming, adenylate-forming,
thioester-forming, ligase; HET: COA PRX; 1.75A
{Salmonella enterica} SCOP: e.23.1.1 PDB: 1pg3_A*
2p2f_A* 2p2b_A* 2p2q_A* 2p2j_A* 2p20_A* 2p2m_A*
Length = 652
Score = 27.9 bits (63), Expect = 2.2
Identities = 9/23 (39%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 121 DDDEYWCAMDICDGWAQKRSYMT 143
D YWC D+ GW SY+
Sbjct: 297 PGDIYWCTADV--GWVTGHSYLL 317
>1ry2_A Acetyl-coenzyme A synthetase 1, acyl-activating enzyme 1; AMP
forming, related to firefly luciferase, ligase; HET:
AMP; 2.30A {Saccharomyces cerevisiae} SCOP: e.23.1.1
Length = 663
Score = 27.5 bits (62), Expect = 3.1
Identities = 7/23 (30%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 121 DDDEYWCAMDICDGWAQKRSYMT 143
+D ++ A DI GW +Y+
Sbjct: 303 QEDVFFTAGDI--GWITGHTYVV 323
>2b9v_A Alpha-amino acid ester hydrolase; catalytic triad,
alpha/beta-hydrolase; 2.00A {Acetobacter pasteurianus}
SCOP: b.18.1.13 c.69.1.21 PDB: 2b4k_A 1nx9_A* 1ryy_A
Length = 652
Score = 27.0 bits (59), Expect = 4.7
Identities = 13/68 (19%), Positives = 22/68 (32%), Gaps = 8/68 (11%)
Query: 116 HIKHPDDDEYWCAMDICDGWAQKRS--YMTAKTGRYDSY------RAANELLRMATEGRI 167
HP D +W + AQ++ M + G +D A L +
Sbjct: 262 MHAHPAYDAFWQGQALDKILAQRKPTVPMLWEQGLWDQEDMWGAIHAWQALKDADVKAPN 321
Query: 168 CLCLMPPQ 175
L + P +
Sbjct: 322 TLVMGPWR 329
>1t4y_A Adaptive-response sensory-kinase SASA; alpha/beta protein,
thioredoxin fold, transferase; NMR {Synechococcus
elongatus} SCOP: c.47.1.15 PDB: 1t4z_A
Length = 105
Score = 25.4 bits (55), Expect = 7.5
Identities = 22/93 (23%), Positives = 31/93 (33%), Gaps = 20/93 (21%)
Query: 4 VSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVVSVSRTPGHTKHFQTIFLTD 63
V P Q + NI VP LQV++V+ P ++++ +
Sbjct: 19 VDTRPLSQHIVQRVK---NILAAVEAT------VPISLQVINVADQPQLVEYYRLVVT-- 67
Query: 64 NIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLR 96
P LV P QVL G QL
Sbjct: 68 -------PALV--KIGPGSRQVLSGIDLTDQLA 91
>3kw0_A Cysteine peptidase; structural genomics, joint center for ST
genomics, JCSG, protein structure initiative, PSI-2,
hydrol; HET: LYS; 2.50A {Bacillus cereus}
Length = 214
Score = 25.9 bits (56), Expect = 7.7
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 90 FPIAQLREPYSTVQYLAERMDLIKLLHIKHPDDDEYWCA 128
+ L Y +A+ + I L +H D++EY C+
Sbjct: 137 VGFSLLNSGYDK-NEIAQIVARIGLGIGRHEDNNEYICS 174
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 0.138 0.439
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,944,559
Number of extensions: 163506
Number of successful extensions: 410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 404
Number of HSP's successfully gapped: 30
Length of query: 195
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 106
Effective length of database: 4,216,824
Effective search space: 446983344
Effective search space used: 446983344
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: 55 (25.0 bits)