RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029850
(186 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 234 bits (598), Expect = 2e-79
Identities = 123/169 (72%), Positives = 145/169 (85%)
Query: 11 VGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHYQ 70
VGFEM+D IA + I MNTIQSK+L+GIGSIGEVP+L+ KPQ+YMN+SGE++GPLAA+YQ
Sbjct: 37 VGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVKPQSYMNYSGEAIGPLAAYYQ 96
Query: 71 VPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPGK 130
VPLRHIL+IYD+ SL NGVLRLQ KGGHG HNGL++V+ HLDG REFPRL IGIG+PPGK
Sbjct: 97 VPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIEHLDGRREFPRLSIGIGSPPGK 156
Query: 131 MDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFNMGQ 179
MD +A+LLQKFS ER QID ALEQGV+AVRTLVL GF + RFN+ Q
Sbjct: 157 MDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFSGSTERFNLVQ 205
>2z2i_A PTH, peptidyl-tRNA hydrolase; protein synthesis; 1.98A
{Mycobacterium tuberculosis} PDB: 2z2j_A 2z2k_A 3tck_A
3tcn_A 3td2_A 3td6_A 2jrc_A 3p2j_A 3kk0_A 3kjz_A
Length = 191
Score = 208 bits (533), Expect = 1e-69
Identities = 63/167 (37%), Positives = 96/167 (57%), Gaps = 2/167 (1%)
Query: 11 VGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
+GF + D +A +S A + G ++LAKP+ YMN SG +GPLA Y
Sbjct: 24 LGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFY 83
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
V +I+VI+D++ L G +RL+ GG G HNGL+SV+ L G ++F R+ IGIG PPG
Sbjct: 84 SVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAAL-GTKDFQRVRIGIGRPPG 142
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFN 176
+ D A++L+ F+P ER ++ EQ +A L+ G + +R +
Sbjct: 143 RKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPAQNRVH 189
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 202 bits (516), Expect = 6e-67
Identities = 47/167 (28%), Positives = 87/167 (52%), Gaps = 1/167 (0%)
Query: 11 VGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
G ++ +A AQ +++ + L+G S + L P YMN SG+SV LA +
Sbjct: 24 AGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFF 83
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
++ ILV +DE+ + GV +L+ GGHG HNGL+ ++ L F RL +GIG+P
Sbjct: 84 RIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGH 143
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFN 176
+ Y+L + E+E +D +++ + + ++ + + + + +
Sbjct: 144 SSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLH 190
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 196 bits (502), Expect = 6e-65
Identities = 48/167 (28%), Positives = 84/167 (50%), Gaps = 1/167 (0%)
Query: 11 VGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
G +D +A+ R + + ++G + L P +MN SG++V +A+ +
Sbjct: 22 AGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFF 81
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
++ ILV +DE+ L GV + + GGHG HNGLK +++ L F RL IGIG+P
Sbjct: 82 RINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGD 141
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFN 176
K + ++L K E++ ID A+++ +G + +R +
Sbjct: 142 KNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLH 188
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 182 bits (464), Expect = 5e-59
Identities = 53/166 (31%), Positives = 91/166 (54%), Gaps = 2/166 (1%)
Query: 11 VGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
VG I IAQ + ++ + + SI ++L P YMN SG +V +A Y
Sbjct: 43 VGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVVLVFPTTYMNNSGLAVSKVANFY 102
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
++ ILV++DE+ + +G +RL+ GGHG HNGL+S+ HL G ++ RL IGIG+P
Sbjct: 103 KIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRSINQHL-GTNDYLRLRIGIGHPGH 161
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRF 175
K + Y+L S +++ ID+A++ G+ + ++ + + +
Sbjct: 162 KSKVANYVLSNPSIAQKKDIDSAIDNGICFLDDIINYKLEPVMQKL 207
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 179 bits (456), Expect = 5e-58
Identities = 55/167 (32%), Positives = 89/167 (53%), Gaps = 3/167 (1%)
Query: 11 VGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
GF ++ +A I + + + G G+I + L P YMN SG+SV P + Y
Sbjct: 24 AGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLLPMTYMNRSGQSVVPFSKFY 83
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPPG 129
Q+ IL+ +DE+ + GV+RL+ GGHG HNGL+ ++ H+ F RL IGIG+P
Sbjct: 84 QIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVPHIG--PNFHRLRIGIGHPGS 141
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFN 176
K + ++L K E+ +D A++ + V+ LV Q +++ N
Sbjct: 142 KERVSGHVLGKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQAMNQIN 188
>3v2i_A PTH, peptidyl-tRNA hydrolase; ssgcid, seattle structural genomics
center for infectious DI RNA; HET: CIT; 1.65A
{Burkholderia thailandensis E264}
Length = 222
Score = 179 bits (457), Expect = 1e-57
Identities = 51/177 (28%), Positives = 90/177 (50%), Gaps = 12/177 (6%)
Query: 11 VGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAKPQAYMNFSGESVGPLAAHY 69
GF ++D +A+ + + + + L +PQ YMN SG+SV LA +
Sbjct: 43 AGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLEPQTYMNRSGQSVVALAHFF 102
Query: 70 QVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNHLDGCREFPRLCIGIGNPP- 128
++ ILV +DE+ L G ++L+ GG G HNGLK + HL +++ RL IGIG+P
Sbjct: 103 KILPNEILVAHDELDLPPGAVKLKLGGGSGGHNGLKDISAHL-SSQQYWRLRIGIGHPRD 161
Query: 129 ---------GKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQNISRFN 176
K D+ ++L+ E++ IDAA+E+ + + +V ++ + + +
Sbjct: 162 MIPESARAGAKPDVANFVLKPPRKEEQDVIDAAIERALAVMPAVVKGETERAMMQLH 218
>2y2w_A Arabinofuranosidase; hydrolase, arabinoxylan, glycoside hydrolase
family 51; 2.50A {Bifidobacterium longum}
Length = 574
Score = 28.0 bits (61), Expect = 2.2
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 89 VLRLQPKGGHGHHN 102
+ KG H HH+
Sbjct: 561 SVEFHGKGHHHHHH 574
>2v6z_M DNA polymerase epsilon subunit 2; DNA replication, DPOE2,
transferase, AAA protein family; HET: DNA; NMR {Homo
sapiens}
Length = 99
Score = 26.2 bits (57), Expect = 3.3
Identities = 8/38 (21%), Positives = 17/38 (44%)
Query: 130 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNG 167
+ + YL + I +++ LE+ + AV L+
Sbjct: 46 RGEAIKYLTEALQSISELELEDKLEKIINAVEKQPLSS 83
>3nxu_A Cytochrome P450 3A4; alpha beta protein, cytochrome P450 fold,
hemoprotein, monoo cytochrome P450 reductase,
endoplasmic reticulum; HET: HEM RIT; 2.00A {Homo
sapiens} PDB: 1w0e_A* 1w0g_A* 2j0d_A* 2v0m_A* 1w0f_A*
1tqn_A* 3ua1_A* 3tjs_A*
Length = 485
Score = 27.2 bits (61), Expect = 3.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 118 PRLCIGIGNPPGKMDMK---AYLLQKF--SPIEREQI 149
PR C IG M+MK +LQ F P + QI
Sbjct: 417 PRNC--IGMRFALMNMKLALIRVLQNFSFKPCKETQI 451
>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 = 26.7 bits (60), Expect = 4.4
Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 8/49 (16%)
Query: 71 VPLRHILVIYDEMSLMNG---VLRLQPKGGHGHHNGLKSVMNHLDGCRE 116
+P RHI V+ D N +G+ G + L C E
Sbjct: 2 LP-RHIAVLCDG----NRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHE 45
>3fi9_A Malate dehydrogenase; structural genomics, oxidoreductase, PSI-2,
protein structur initiative; 1.90A {Porphyromonas
gingivalis}
Length = 343
Score = 26.4 bits (59), Expect = 5.5
Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 122 IGIGNPPGKMDMKAYLLQKFSPIEREQI 149
I I NP D+ + +S ++ Q+
Sbjct: 123 IIIFNP---ADITGLVTLIYSGLKPSQV 147
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
0.323 0.140 0.413
Gapped
Lambda K H
0.267 0.0826 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,960,115
Number of extensions: 180145
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 24
Length of query: 186
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 98
Effective length of database: 4,244,745
Effective search space: 415985010
Effective search space used: 415985010
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 (21.9 bits)
S2: 54 (24.4 bits)