RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026076
(244 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 291 bits (748), Expect = e-101
Identities = 144/193 (74%), Positives = 167/193 (86%)
Query: 45 VEYTPWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNTIQSKALIGIGSIGEVPI 104
VEYTPWLI GLGNPG KY+GTRHNVGFEM+D IA + I MNTIQSK+L+GIGSIGEVP+
Sbjct: 13 VEYTPWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPV 72
Query: 105 LLAKPQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKS 164
L+ KPQ+YMN+SGE++GPLAA+YQVPLRHIL+IYD+ SL NGVLRLQ KGGHG HNGL++
Sbjct: 73 LVVKPQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQN 132
Query: 165 VMNHLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLN 224
V+ HLDG REFPRL IGIG+PPGKMD +A+LLQKFS ER QID ALEQGV+AVRTLVL
Sbjct: 133 VIEHLDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLK 192
Query: 225 GFDQNISRFNMGQ 237
GF + RFN+ Q
Sbjct: 193 GFSGSTERFNLVQ 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 = 260 bits (667), Expect = 4e-89
Identities = 77/187 (41%), Positives = 111/187 (59%), Gaps = 2/187 (1%)
Query: 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLA 107
P L+VGLGNPG Y TRHN+GF + D +A +S A + G ++LA
Sbjct: 4 PLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLA 63
Query: 108 KPQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMN 167
KP+ YMN SG +GPLA Y V +I+VI+D++ L G +RL+ GG G HNGL+SV+
Sbjct: 64 KPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVA 123
Query: 168 HLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFD 227
L G ++F R+ IGIG PPG+ D A++L+ F+P ER ++ EQ +A L+ G +
Sbjct: 124 AL-GTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGME 182
Query: 228 QNISRFN 234
+R +
Sbjct: 183 PAQNRVH 189
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 251 bits (643), Expect = 2e-85
Identities = 61/187 (32%), Positives = 102/187 (54%), Gaps = 1/187 (0%)
Query: 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLA 107
LIVGLGNPG +Y TRHN G ++ +A AQ +++ + L+G S + L
Sbjct: 4 VQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLL 63
Query: 108 KPQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMN 167
P YMN SG+SV LA +++ ILV +DE+ + GV +L+ GGHG HNGL+ ++
Sbjct: 64 IPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIA 123
Query: 168 HLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFD 227
L F RL +GIG+P + Y+L + E+E +D +++ + + ++ +
Sbjct: 124 QLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWT 183
Query: 228 QNISRFN 234
+ + + +
Sbjct: 184 RAMQKLH 190
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 243 bits (624), Expect = 2e-82
Identities = 61/186 (32%), Positives = 98/186 (52%), Gaps = 1/186 (0%)
Query: 50 WLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAK 108
LIVGL NPG +Y TRHN G +D +A+ R + + ++G + L
Sbjct: 3 KLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLV 62
Query: 109 PQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNH 168
P +MN SG++V +A+ +++ ILV +DE+ L GV + + GGHG HNGLK +++
Sbjct: 63 PTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISK 122
Query: 169 LDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQ 228
L F RL IGIG+P K + ++L K E++ ID A+++ +G +
Sbjct: 123 LGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTK 182
Query: 229 NISRFN 234
+R +
Sbjct: 183 ATNRLH 188
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 230 bits (588), Expect = 6e-77
Identities = 64/186 (34%), Positives = 105/186 (56%), Gaps = 2/186 (1%)
Query: 49 PWLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLA 107
+I+GLGN G +Y TRHNVG I IAQ + ++ + + SI ++L
Sbjct: 23 IKMIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVVLV 82
Query: 108 KPQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMN 167
P YMN SG +V +A Y++ ILV++DE+ + +G +RL+ GGHG HNGL+S+
Sbjct: 83 FPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRSINQ 142
Query: 168 HLDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFD 227
HL G ++ RL IGIG+P K + Y+L S +++ ID+A++ G+ + ++ +
Sbjct: 143 HL-GTNDYLRLRIGIGHPGHKSKVANYVLSNPSIAQKKDIDSAIDNGICFLDDIINYKLE 201
Query: 228 QNISRF 233
+ +
Sbjct: 202 PVMQKL 207
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 227 bits (580), Expect = 7e-76
Identities = 69/186 (37%), Positives = 104/186 (55%), Gaps = 3/186 (1%)
Query: 50 WLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAK 108
LIVGLGNPG +Y TRHN GF ++ +A I + + + G G+I + L
Sbjct: 5 SLIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLL 64
Query: 109 PQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNH 168
P YMN SG+SV P + YQ+ IL+ +DE+ + GV+RL+ GGHG HNGL+ ++ H
Sbjct: 65 PMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVPH 124
Query: 169 LDGCREFPRLCIGIGNPPGKMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNGFDQ 228
+ F RL IGIG+P K + ++L K E+ +D A++ + V+ LV Q
Sbjct: 125 IG--PNFHRLRIGIGHPGSKERVSGHVLGKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQ 182
Query: 229 NISRFN 234
+++ N
Sbjct: 183 AMNQIN 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 = 227 bits (580), Expect = 2e-75
Identities = 65/196 (33%), Positives = 105/196 (53%), Gaps = 12/196 (6%)
Query: 50 WLIVGLGNPGIKYHGTRHNVGFEMIDHIAQAQRIAMNT-IQSKALIGIGSIGEVPILLAK 108
LIVGLGNPG +Y TRHN GF ++D +A+ + + + + L +
Sbjct: 24 KLIVGLGNPGAEYTATRHNAGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLE 83
Query: 109 PQAYMNFSGESVGPLAAHYQVPLRHILVIYDEMSLMNGVLRLQPKGGHGHHNGLKSVMNH 168
PQ YMN SG+SV LA +++ ILV +DE+ L G ++L+ GG G HNGLK + H
Sbjct: 84 PQTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKLKLGGGSGGHNGLKDISAH 143
Query: 169 LDGCREFPRLCIGIGNPP----------GKMDMKAYLLQKFSPIEREQIDAALEQGVEAV 218
L +++ RL IGIG+P K D+ ++L+ E++ IDAA+E+ + +
Sbjct: 144 L-SSQQYWRLRIGIGHPRDMIPESARAGAKPDVANFVLKPPRKEEQDVIDAAIERALAVM 202
Query: 219 RTLVLNGFDQNISRFN 234
+V ++ + + +
Sbjct: 203 PAVVKGETERAMMQLH 218
>2v6z_M DNA polymerase epsilon subunit 2; DNA replication, DPOE2,
transferase, AAA protein family; HET: DNA; NMR {Homo
sapiens}
Length = 99
Score = 26.6 bits (58), Expect = 3.0
Identities = 8/38 (21%), Positives = 17/38 (44%)
Query: 188 KMDMKAYLLQKFSPIEREQIDAALEQGVEAVRTLVLNG 225
+ + 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 = 5.1
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 176 PRLCIGIGNPPGKMDMK---AYLLQKF--SPIEREQI 207
PR C IG M+MK +LQ F P + QI
Sbjct: 417 PRNC--IGMRFALMNMKLALIRVLQNFSFKPCKETQI 451
>2y2w_A Arabinofuranosidase; hydrolase, arabinoxylan, glycoside hydrolase
family 51; 2.50A {Bifidobacterium longum}
Length = 574
Score = 27.3 bits (59), Expect = 5.1
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 147 VLRLQPKGGHGHHN 160
+ KG H HH+
Sbjct: 561 SVEFHGKGHHHHHH 574
>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 = 27.1 bits (61), Expect = 5.4
Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 12/51 (23%)
Query: 129 VPLRHILVIYDEMSLM--NG---VLRLQPKGGHGHHNGLKSVMNHLDGCRE 174
+P RHI V+ N +G+ G + L C E
Sbjct: 2 LP-RHIAVL------CDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHE 45
>3fi9_A Malate dehydrogenase; structural genomics, oxidoreductase, PSI-2,
protein structur initiative; 1.90A {Porphyromonas
gingivalis}
Length = 343
Score = 27.2 bits (61), Expect = 5.9
Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 180 IGIGNPPGKMDMKAYLLQKFSPIEREQI 207
I I NP D+ + +S ++ Q+
Sbjct: 123 IIIFNP---ADITGLVTLIYSGLKPSQV 147
>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus
subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A
Length = 245
Score = 26.1 bits (58), Expect = 9.8
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 11/47 (23%)
Query: 187 GKMDMKAYL--------LQ---KFSPIEREQIDAALEQGVEAVRTLV 222
++DM + LQ + + RE ++ L + ++ L+
Sbjct: 184 AEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELI 230
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
0.322 0.140 0.431
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: 3,847,246
Number of extensions: 236384
Number of successful extensions: 562
Number of sequences better than 10.0: 1
Number of HSP's gapped: 550
Number of HSP's successfully gapped: 17
Length of query: 244
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 153
Effective length of database: 4,160,982
Effective search space: 636630246
Effective search space used: 636630246
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: 56 (25.2 bits)