BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy1690
(218 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RQ0|A Chain A, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|B Chain B, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|C Chain C, Crystal Structure Of Peptide Releasing Factor 1
Length = 342
Score = 127 bits (318), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 79/219 (36%), Positives = 120/219 (54%), Gaps = 46/219 (21%)
Query: 1 VQRVPKTEKSGRLHTSTVSVAVLPQPKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAV 60
VQRVP TE GR+HTST +VAVLP+ ++ ++ + +DLK+ET RA+G GGQ+VN T+SAV
Sbjct: 161 VQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAV 220
Query: 61 RMTHIPTGISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQENRWVVRLVTKRSARTII 120
R+TH+PTGI V Q +RSQ +N+ AL L+ +Y++Q E++E R I
Sbjct: 221 RITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKE-------------REIS 267
Query: 121 HRTESPIIAFREPCTTLPSSCPAVHLEEKDLKVETKRATGAGGQHVNTTD-SADRITDHR 179
+ +S I TG + + T + +R+TDHR
Sbjct: 268 QKRKSQI------------------------------GTGERSEKIRTYNFPQNRVTDHR 297
Query: 180 IQRTVYNVAEFMSGGAMLHELISDIRQHDYQFRIDQLLS 218
I T Y + E + G L E+IS + +HD + ++++L
Sbjct: 298 INYTSYRLQEILDGD--LDEIISKLIEHDIENNLEEVLG 334
>pdb|2FVO|A Chain A, Docking Of The Modified Rf1 X-ray Structure Into The Low
Resolution Cryo-em Map Of E.coli 70s Ribosome Bound With
Rf1
Length = 333
Score = 126 bits (317), Expect = 8e-30, Method: Compositional matrix adjust.
Identities = 79/218 (36%), Positives = 120/218 (55%), Gaps = 46/218 (21%)
Query: 1 VQRVPKTEKSGRLHTSTVSVAVLPQPKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAV 60
VQRVP TE GR+HTST +VAVLP+ ++ ++ + +DLK+ET RA+G GGQ+VN T+SAV
Sbjct: 161 VQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAV 220
Query: 61 RMTHIPTGISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQENRWVVRLVTKRSARTII 120
R+TH+PTGI V Q +RSQ +N+ AL L+ +Y++Q E++E R I
Sbjct: 221 RITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKE-------------REIS 267
Query: 121 HRTESPIIAFREPCTTLPSSCPAVHLEEKDLKVETKRATGAGGQHVNTTD-SADRITDHR 179
+ +S I TG + + T + +R+TDHR
Sbjct: 268 QKRKSQI------------------------------GTGERSEKIRTYNFPQNRVTDHR 297
Query: 180 IQRTVYNVAEFMSGGAMLHELISDIRQHDYQFRIDQLL 217
I T Y + E + G L E+IS + +HD + ++++L
Sbjct: 298 INYTSYRLQEILDGD--LDEIISKLIEHDIENNLEEVL 333
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 113 bits (283), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 73/194 (37%), Positives = 100/194 (51%), Gaps = 43/194 (22%)
Query: 1 VQRVPKTEKSGRLHTSTVSVAVLPQPKDIEV-HLDEKDLKVETKRATGAGGQHVNTTDSA 59
VQRVP TE GR+HTS +VAV+P+ D E+ ++ DL+++T R++GAGGQHVNTTDSA
Sbjct: 184 VQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSA 243
Query: 60 VRMTHIPTGISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQENRWVVRLVTKRSARTI 119
+R+TH+PTGI VE Q++RSQ KN+A AL+ L I+ E R T+R+
Sbjct: 244 IRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAA---EMAKRQQAEASTRRNLLGS 300
Query: 120 IHRTESPIIAFREPCTTLPSSCPAVHLEEKDLKVETKRATGAGGQHVNTTDSADRITDHR 179
R++ R P R+TDHR
Sbjct: 301 GDRSD------RNRTYNFPQG---------------------------------RVTDHR 321
Query: 180 IQRTVYNVAEFMSG 193
I T+Y + E M G
Sbjct: 322 INLTLYRLDEVMEG 335
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 46/81 (56%), Gaps = 9/81 (11%)
Query: 97 IQFEEQENRWVVRLVTKRSARTIIHRTESPIIAFRE-PCTTLPSSCPAVHLEEKDLKVET 155
++FE +R V+ V ++ IH + + E P LP PA DL+++T
Sbjct: 175 LKFESGGHR--VQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPA------DLRIDT 226
Query: 156 KRATGAGGQHVNTTDSADRIT 176
R++GAGGQHVNTTDSA RIT
Sbjct: 227 FRSSGAGGQHVNTTDSAIRIT 247
>pdb|2B64|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Subunit, Trnas, Mrna And
Release Factor Rf1 From A Crystal Structure Of The Whole
Ribosomal Complex". The Entire Crystal Structure
Contains One 70s Ribosome, Trnas, Mrna And Release
Factor Rf1 And Is Described In Remark 400.
pdb|3D5A|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3MR8|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|3MS0|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (30s) And 3ms1 (50s)
Length = 354
Score = 109 bits (272), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 54/106 (50%), Positives = 75/106 (70%)
Query: 1 VQRVPKTEKSGRLHTSTVSVAVLPQPKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAV 60
VQRVP TE GR+HTST +VAVLP+ ++ + L+ +++++ RA+G GGQ VNTTDSAV
Sbjct: 180 VQRVPVTETQGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAV 239
Query: 61 RMTHIPTGISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQENRW 106
R+ H+PTGI V Q+ RSQIKNR AL L+ + E++ E+ R
Sbjct: 240 RVVHLPTGIMVTCQDSRSQIKNREKALMILRSRLLEMKRAEEAERL 285
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 36/153 (23%), Positives = 65/153 (42%), Gaps = 12/153 (7%)
Query: 26 PKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIPTGISVESQEDRSQIKNRAN 85
PKD +DE+D VE + TG + D + E++ + +
Sbjct: 98 PKD---PMDERDAIVEIRAGTGGEEAALFARDLFNMYLRFAEEMGFETE----VLDSHPT 150
Query: 86 ALAKLKRLIYEIQFEEQENRWVVRLVTKRSARTIIHRTESPIIAFREPCTTLPSSCP--- 142
L ++++E++ + R R + T+ I LP +
Sbjct: 151 DLGGFSKVVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGRIHTSTATVAVLPKAEEEDF 210
Query: 143 AVHLEEKDLKVETKRATGAGGQHVNTTDSADRI 175
A++++E ++++ RA+G GGQ VNTTDSA R+
Sbjct: 211 ALNMDE--IRIDVMRASGPGGQGVNTTDSAVRV 241
>pdb|1MI6|A Chain A, Docking Of The Modified Rf2 X-Ray Structure Into The Low
Resolution Cryo-Em Map Of Rf2 E.Coli 70s Ribosome
Length = 365
Score = 96.3 bits (238), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 45/96 (46%), Positives = 68/96 (70%), Gaps = 1/96 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQ-PKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ GR HTS S V P+ DI++ ++ DL+++ RA+GAGGQHVN T+SAVR+THIP
Sbjct: 208 DSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIP 267
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQ 102
TGI + Q DRSQ KN+ A+ ++K +YE++ +++
Sbjct: 268 TGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKK 303
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/33 (54%), Positives = 25/33 (75%)
Query: 144 VHLEEKDLKVETKRATGAGGQHVNTTDSADRIT 176
+ + DL+++ RA+GAGGQHVN T+SA RIT
Sbjct: 232 IEINPADLRIDVYRASGAGGQHVNRTESAVRIT 264
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 94.4 bits (233), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 44/96 (45%), Positives = 67/96 (69%), Gaps = 1/96 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQ-PKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ GR HTS S V P+ DI++ ++ DL+++ R +GAGGQHVN T+SAVR+THIP
Sbjct: 208 DSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIP 267
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQ 102
TGI + Q DRSQ KN+ A+ ++K +YE++ +++
Sbjct: 268 TGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKK 303
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 24/33 (72%)
Query: 144 VHLEEKDLKVETKRATGAGGQHVNTTDSADRIT 176
+ + DL+++ R +GAGGQHVN T+SA RIT
Sbjct: 232 IEINPADLRIDVYRTSGAGGQHVNRTESAVRIT 264
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 92.4 bits (228), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 45/92 (48%), Positives = 63/92 (68%), Gaps = 1/92 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQ-PKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ GR HTS S V P+ DI++ ++ DL+++ RA+GAGGQHVN T+SAVR+THIP
Sbjct: 208 DSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIP 267
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIYEIQ 98
TGI + Q DRSQ KN+ A + K +YE++
Sbjct: 268 TGIVTQCQNDRSQHKNKDQAXKQXKAKLYEVE 299
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/33 (54%), Positives = 25/33 (75%)
Query: 144 VHLEEKDLKVETKRATGAGGQHVNTTDSADRIT 176
+ + DL+++ RA+GAGGQHVN T+SA RIT
Sbjct: 232 IEINPADLRIDVYRASGAGGQHVNRTESAVRIT 264
>pdb|1ZBT|A Chain A, Crystal Structure Of Peptide Chain Release Factor 1 (rf-1)
(smu.1085) From Streptococcus Mutans At 2.34 A
Resolution
Length = 371
Score = 84.3 bits (207), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 47/86 (54%), Positives = 63/86 (73%)
Query: 1 VQRVPKTEKSGRLHTSTVSVAVLPQPKDIEVHLDEKDLKVETKRATGAGGQHVNTTDSAV 60
VQRVP TE GR+HTST +V V P+ +++E +D KDL+V+ A+GAGGQ+VN +AV
Sbjct: 198 VQRVPVTESQGRVHTSTATVLVXPEVEEVEYEIDPKDLRVDIYHASGAGGQNVNKVATAV 257
Query: 61 RMTHIPTGISVESQEDRSQIKNRANA 86
R+ H+PT I VE QE+R+Q KNR A
Sbjct: 258 RIIHLPTNIKVEXQEERTQQKNRDKA 283
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 22/30 (73%)
Query: 146 LEEKDLKVETKRATGAGGQHVNTTDSADRI 175
++ KDL+V+ A+GAGGQ+VN +A RI
Sbjct: 230 IDPKDLRVDIYHASGAGGQNVNKVATAVRI 259
>pdb|3F1E|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400
Length = 378
Score = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 44/89 (49%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQPKDIEVH-LDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ SGR HTS V V+P+ + L ++L+++ RA+G GGQ VNTTDSAVR+ H+P
Sbjct: 209 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 268
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIY 95
TGI+V Q RSQIKN+ AL LK +Y
Sbjct: 269 TGITVTCQTTRSQIKNKELALKILKARLY 297
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 24/30 (80%)
Query: 146 LEEKDLKVETKRATGAGGQHVNTTDSADRI 175
L+ ++L+++ RA+G GGQ VNTTDSA R+
Sbjct: 235 LKPEELRIDVMRASGPGGQGVNTTDSAVRV 264
>pdb|2X9R|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
Length = 351
Score = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 44/89 (49%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQPKDIEVH-LDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ SGR HTS V V+P+ + L ++L+++ RA+G GGQ VNTTDSAVR+ H+P
Sbjct: 191 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 250
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIY 95
TGI+V Q RSQIKN+ AL LK +Y
Sbjct: 251 TGITVTCQTTRSQIKNKELALKILKARLY 279
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 24/30 (80%)
Query: 146 LEEKDLKVETKRATGAGGQHVNTTDSADRI 175
L+ ++L+++ RA+G GGQ VNTTDSA R+
Sbjct: 217 LKPEELRIDVMRASGPGGQGVNTTDSAVRV 246
>pdb|2WH1|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH3|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome). This File Contains The
30s Subunit
Length = 351
Score = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 44/89 (49%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQPKDIEVH-LDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ SGR HTS V V+P+ + L ++L+++ RA+G GGQ VNTTDSAVR+ H+P
Sbjct: 191 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 250
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIY 95
TGI+V Q RSQIKN+ AL LK +Y
Sbjct: 251 TGITVTCQTTRSQIKNKELALKILKARLY 279
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 24/30 (80%)
Query: 146 LEEKDLKVETKRATGAGGQHVNTTDSADRI 175
L+ ++L+++ RA+G GGQ VNTTDSA R+
Sbjct: 217 LKPEELRIDVMRASGPGGQGVNTTDSAVRV 246
>pdb|2B9M|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Ribosomal Subunit, Trnas,
Mrna And Release Factor Rf2 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf2 And Is Described In Remark 400
Length = 365
Score = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 44/89 (49%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQPKDIEVH-LDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ SGR HTS V V+P+ + L ++L+++ RA+G GGQ VNTTDSAVR+ H+P
Sbjct: 196 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 255
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIY 95
TGI+V Q RSQIKN+ AL LK +Y
Sbjct: 256 TGITVTCQTTRSQIKNKELALKILKARLY 284
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 24/30 (80%)
Query: 146 LEEKDLKVETKRATGAGGQHVNTTDSADRI 175
L+ ++L+++ RA+G GGQ VNTTDSA R+
Sbjct: 222 LKPEELRIDVMRASGPGGQGVNTTDSAVRV 251
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 44/89 (49%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 8 EKSGRLHTSTVSVAVLPQPKDIEVH-LDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIP 66
+ SGR HTS V V+P+ + L ++L+++ RA+G GGQ VNTTDSAVR+ H+P
Sbjct: 196 DASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLP 255
Query: 67 TGISVESQEDRSQIKNRANALAKLKRLIY 95
TGI+V Q RSQIKN+ AL LK +Y
Sbjct: 256 TGITVTCQTTRSQIKNKELALKILKARLY 284
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 24/30 (80%)
Query: 146 LEEKDLKVETKRATGAGGQHVNTTDSADRI 175
L+ ++L+++ RA+G GGQ VNTTDSA R+
Sbjct: 222 LKPEELRIDVMRASGPGGQGVNTTDSAVRV 251
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 32/99 (32%), Positives = 49/99 (49%), Gaps = 24/99 (24%)
Query: 31 VHLDEKDLKVETKRATGAGGQHVNTTDSA------VRMTHIPTG---------------- 68
V + + +L++ RA GAGGQHVN T SA +R + +P
Sbjct: 8 VSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDD 67
Query: 69 --ISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQENR 105
I +++QE RSQ NR A+A+L +I E+ E++ R
Sbjct: 68 GVIIIKAQEFRSQELNREAAIARLVAVIKELTAEQKSRR 106
Score = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 20/29 (68%)
Query: 144 VHLEEKDLKVETKRATGAGGQHVNTTDSA 172
V + + +L++ RA GAGGQHVN T SA
Sbjct: 8 VSIADNELEITAIRAQGAGGQHVNKTSSA 36
>pdb|4DH9|Y Chain Y, Crystal Structure Of Yaej Bound To The 70s Ribosome
Length = 140
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 32/99 (32%), Positives = 49/99 (49%), Gaps = 24/99 (24%)
Query: 31 VHLDEKDLKVETKRATGAGGQHVNTTDSA------VRMTHIPTG---------------- 68
V + + +L++ RA GAGGQHVN T +A +R + +P
Sbjct: 8 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSD 67
Query: 69 --ISVESQEDRSQIKNRANALAKLKRLIYEIQFEEQENR 105
I +++QE RSQ NR ALA+L +I E+ E++ R
Sbjct: 68 GVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKARR 106
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 144 VHLEEKDLKVETKRATGAGGQHVNTTDSA 172
V + + +L++ RA GAGGQHVN T +A
Sbjct: 8 VAIPDGELEITAIRAQGAGGQHVNKTSTA 36
>pdb|2RSM|A Chain A, Solution Structure And Sirna-Mediated Knockdown Analysis
Of The Mitochondrial Disease-Related Protein C12orf65
(Ict2)
Length = 115
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 31/51 (60%)
Query: 33 LDEKDLKVETKRATGAGGQHVNTTDSAVRMTHIPTGISVESQEDRSQIKNR 83
L+E +L+ + + G GGQ N T + V + H+P+GI V+ + RS +NR
Sbjct: 43 LNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNR 93
>pdb|2JVA|A Chain A, Nmr Solution Structure Of Peptidyl-Trna Hydrolase Domain
Protein From Pseudomonas Syringae Pv. Tomato. Northeast
Structural Genomics Consortium Target Psr211
Length = 108
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 24/88 (27%)
Query: 31 VHLDEKDLKVETKRATGAGGQHVNTTDSAVRM------THIPTG---------------- 68
VHL + ++++ RA GAGGQ+VN SA+ + + +P
Sbjct: 8 VHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSD 67
Query: 69 --ISVESQEDRSQIKNRANALAKLKRLI 94
I +++Q+ R+Q +NRA+AL +L LI
Sbjct: 68 GVIVLKAQQYRTQEQNRADALLRLSELI 95
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 144 VHLEEKDLKVETKRATGAGGQHVNTTDSA 172
VHL + ++++ RA GAGGQ+VN SA
Sbjct: 8 VHLPDAEIELTAIRAQGAGGQNVNKVSSA 36
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.129 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,872,088
Number of Sequences: 62578
Number of extensions: 212586
Number of successful extensions: 487
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 434
Number of HSP's gapped (non-prelim): 38
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)