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= 032666
(136 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RYB|A Chain A, Crystal Structure Of The Chloroplast Group Ii Intron
Splicing Factor Crs2
Length = 205
Score = 145 bits (367), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 63/103 (61%), Positives = 80/103 (77%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK 77
PWL GLGNPG+KY GTRHNVGFEM+D A +GI+MNT+ K+ G G +G+ PVL+ K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVK 76
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
PQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQ 119
>pdb|1RYM|A Chain A, Structure Of The Group Ii Intron Splicing Factor Crs2
Length = 212
Score = 144 bits (362), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 63/103 (61%), Positives = 79/103 (76%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK 77
PWL GLGNPG+KY GTRHNVGFEM+D A +GI+MNT K+ G G +G+ PVL+ K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTEQSKSLLGIGSIGEVPVLVVK 76
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
PQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQ 119
>pdb|1RYN|A Chain A, Structure Of The Chloroplast Group Ii Intron Splicing
Factor Crs2
Length = 202
Score = 143 bits (360), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 63/103 (61%), Positives = 79/103 (76%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK 77
PWL GLGNPG+KY GTRHNVGFEM+D A +GI+MNT K+ G G +G+ PVL+ K
Sbjct: 5 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTNQFKSLLGTGSIGEVPVLVVK 64
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
PQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+
Sbjct: 65 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQ 107
>pdb|2LGJ|A Chain A, Solution Structure Of Mspth
Length = 191
Score = 88.2 bits (217), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 48/108 (44%), Positives = 64/108 (59%), Gaps = 3/108 (2%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCK--ATFGQGFVGDAP 72
+A P L VGLGNPG Y TRHN+GF + D A G S VH K A G +
Sbjct: 1 MAEPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIG-SAFKVHKKSGAEVVTGRLAGTS 59
Query: 73 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
V+LAKP+ YMN SG GPLA +Y +P +++V HD++ + G +RL+
Sbjct: 60 VVLAKPRCYMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRLK 107
>pdb|3KJZ|A Chain A, Crystal Structure Of Native Peptidyl-Trna Hydrolase From
Mycobacterium Smegmatis
pdb|3KK0|A Chain A, Crystal Structure Of Partially Folded Intermediate State
Of Peptidyl- Trna Hydrolase From Mycobacterium Smegmatis
pdb|3P2J|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Mycobacterium Smegmatis At 2.2 A Resolution
Length = 191
Score = 85.9 bits (211), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 47/108 (43%), Positives = 63/108 (58%), Gaps = 3/108 (2%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCK--ATFGQGFVGDAP 72
+A P L VGLGNPG Y TRHN+GF + D A G S VH K A G +
Sbjct: 1 MAEPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIG-SAFKVHKKSGAEVVTGRLAGTT 59
Query: 73 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
V+LAKP+ MN SG GPLA +Y +P +++V HD++ + G +RL+
Sbjct: 60 VVLAKPRISMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRLK 107
>pdb|2JRC|A Chain A, Solution Structure Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis H37rv
Length = 204
Score = 82.4 bits (202), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 44/107 (41%), Positives = 57/107 (53%), Gaps = 1/107 (0%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNT-VHCKATFGQGFVGDAPV 73
+A P L VGLGNPG Y TRHN+GF + D A G A G +
Sbjct: 1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSL 60
Query: 74 LLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
+LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +RL+
Sbjct: 61 VLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLK 107
>pdb|2Z2I|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis
pdb|2Z2J|A Chain A, Crystal Structure Of Peptidyl-trna Hydrolase From
Mycobacterium Tuberculosis
pdb|2Z2J|B Chain B, Crystal Structure Of Peptidyl-trna Hydrolase From
Mycobacterium Tuberculosis
pdb|2Z2K|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis
pdb|3TCK|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis - Form 4
pdb|3TCN|A Chain A, Crystal Structures Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis - Form 2 Grown In Presence Of
Pentaglycine
pdb|3TCN|B Chain B, Crystal Structures Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis - Form 2 Grown In Presence Of
Pentaglycine
pdb|3TD2|A Chain A, Crystal Structures Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis - Form 5
pdb|3TD6|A Chain A, Peptidyl-Trna Hydrolase From Mycobacterium Tuberculosis
From Trigonal Partially Dehydrated Crystal
Length = 191
Score = 82.4 bits (202), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 44/107 (41%), Positives = 57/107 (53%), Gaps = 1/107 (0%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNT-VHCKATFGQGFVGDAPV 73
+A P L VGLGNPG Y TRHN+GF + D A G A G +
Sbjct: 1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSL 60
Query: 74 LLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
+LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +RL+
Sbjct: 61 VLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLK 107
>pdb|3V2I|A Chain A, Structure Of A Peptidyl-Trna Hydrolase (Pth) From
Burkholderia Thailandensis
Length = 222
Score = 82.0 bits (201), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 41/102 (40%), Positives = 61/102 (59%), Gaps = 1/102 (0%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAKP 78
L VGLGNPG +Y TRHN GF ++D A G ++ + + + + V L +P
Sbjct: 25 LIVGLGNPGAEYTATRHNAGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLEP 84
Query: 79 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
QTYMN SG+S LA ++K+ N +LV HD++ LP G ++L+
Sbjct: 85 QTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKLK 126
>pdb|4FOP|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Acinetobacter Baumannii At 1.86 A Resolution
pdb|4FOT|A Chain A, Crystal Structure Of Peptidyl- Trna Hydrolase From
Acinetobacter Baumannii At 2.20 A Resolution
pdb|4HOY|A Chain A, Crystal Structure Of Peptidyl- Trna Hydrolase From
Acinetobacter Baumannii At 1.78 A Resolution
pdb|4IKO|A Chain A, Structure Of Peptidyl- Trna Hydrolase From Acinetobacter
Baumannii At 1.90 A Resolution
Length = 193
Score = 79.3 bits (194), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 40/102 (39%), Positives = 60/102 (58%), Gaps = 1/102 (0%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAKP 78
L VGLGNPG +Y TRHN GF ++ A+ GI++ N G+G + V L P
Sbjct: 6 LIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLLP 65
Query: 79 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
TYMN SG+S P + +Y++ +L+ HD++ + GV+RL+
Sbjct: 66 MTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLK 107
>pdb|4DHW|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Pseudomonas Aeruginosa With Adipic Acid At 2.4 Angstrom
Resolution
pdb|4DHW|B Chain B, Crystal Structure Of Peptidyl-Trna Hydrolase From
Pseudomonas Aeruginosa With Adipic Acid At 2.4 Angstrom
Resolution
pdb|4DJJ|A Chain A, Crystal Structure Of The Complex Of Peptidyl-Trna
Hydrolase From Pseudomonas Aeruginosa With Pimelic Acid
At 2.9 Angstrom Resolution
pdb|4DJJ|B Chain B, Crystal Structure Of The Complex Of Peptidyl-Trna
Hydrolase From Pseudomonas Aeruginosa With Pimelic Acid
At 2.9 Angstrom Resolution
pdb|4ERX|A Chain A, Crystal Structure Of The Complex Of Peptidyl-Trna
Hydrolase From Pseudomonas Aeruginosa With Diethylene
Glycol At 2.5 Angstrom Resolution
pdb|4ERX|B Chain B, Crystal Structure Of The Complex Of Peptidyl-Trna
Hydrolase From Pseudomonas Aeruginosa With Diethylene
Glycol At 2.5 Angstrom Resolution
pdb|4FNO|A Chain A, Crystal Structure Of Peptidyl T-Rna Hydrolase From
Pseudomonas Aeruginosa At 2.2 Angstrom Resolution
pdb|4FNO|B Chain B, Crystal Structure Of Peptidyl T-Rna Hydrolase From
Pseudomonas Aeruginosa At 2.2 Angstrom Resolution
Length = 194
Score = 75.9 bits (185), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 62/106 (58%), Gaps = 9/106 (8%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-----APVL 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ V + FG VG V
Sbjct: 6 LIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSL--VADRKYFG--LVGKFSHQGKDVR 61
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +L+
Sbjct: 62 LLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLK 107
>pdb|4FYJ|A Chain A, Crystal Structure Of P. Aeruginosa Peptidyl-Trna Hydrolase
Length = 199
Score = 75.9 bits (185), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 43/106 (40%), Positives = 62/106 (58%), Gaps = 9/106 (8%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-----APVL 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ V + FG VG V
Sbjct: 12 LIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSL--VADRKYFG--LVGKFSHQGKDVR 67
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +L+
Sbjct: 68 LLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLK 113
>pdb|2PTH|A Chain A, Peptidyl-Trna Hydrolase From Escherichia Coli
Length = 193
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 37/105 (35%), Positives = 58/105 (55%), Gaps = 7/105 (6%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATF----GQGFVGDAPVLL 75
L VGL NPG +Y TRHN G +D AE + +A F + +G V L
Sbjct: 4 LIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLRE---EAKFFGYTSRVTLGGEDVRL 60
Query: 76 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
P T+MNLSG++ +A+++++ + +LV HD++ LP GV + +
Sbjct: 61 LVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFK 105
>pdb|3VJR|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli In Complex With The
Cca-Acceptor-T[psi]c Domain Of Trna
pdb|3VJR|C Chain C, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli In Complex With The
Cca-Acceptor-T[psi]c Domain Of Trna
Length = 197
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 37/105 (35%), Positives = 58/105 (55%), Gaps = 7/105 (6%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATF----GQGFVGDAPVLL 75
L VGL NPG +Y TRHN G +D AE + +A F + +G V L
Sbjct: 8 LIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLRE---EAKFFGYTSRVTLGGEDVRL 64
Query: 76 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
P T+MNLSG++ +A+++++ + +LV HD++ LP GV + +
Sbjct: 65 LVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFK 109
>pdb|3OFV|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli, I222 Crystal Form
pdb|3OFV|B Chain B, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli, I222 Crystal Form
pdb|3OFV|C Chain C, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli, I222 Crystal Form
Length = 211
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 37/105 (35%), Positives = 58/105 (55%), Gaps = 7/105 (6%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATF----GQGFVGDAPVLL 75
L VGL NPG +Y TRHN G +D AE + +A F + +G V L
Sbjct: 25 LIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLRE---EAKFFGYTSRVTLGGEDVRL 81
Query: 76 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
P T+MNLSG++ +A+++++ + +LV HD++ LP GV + +
Sbjct: 82 LVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFK 126
>pdb|3NEA|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Francisella Tularensis
Length = 207
Score = 63.5 bits (153), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 35/104 (33%), Positives = 57/104 (54%), Gaps = 5/104 (4%)
Query: 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNT---VHCKATFGQGFVGDAPVLLA 76
+ +GLGN G +Y+ TRHNVG I A+ S ++ ++C + + V+L
Sbjct: 25 MIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNC--NLAKVSIDYNNVVLV 82
Query: 77 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120
P TYMN SG + +A +YK+ +LV HD++ + G +RL+
Sbjct: 83 FPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLK 126
>pdb|3S5T|A Chain A, Crystal Structure Of A Member Of Duf3298 Family (Bf2082)
From Bacteroides Fragilis Nctc 9343 At 2.30 A
Resolution
Length = 265
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 53 SMNTVHCKATFGQGFVGDAPVLLAKPQT 80
S+N+ A FG+G++G+ P + K T
Sbjct: 56 SLNSYFIAACFGEGYIGEKPAQVVKEYT 83
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
0.327 0.143 0.467
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,976,859
Number of Sequences: 62578
Number of extensions: 150459
Number of successful extensions: 339
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 307
Number of HSP's gapped (non-prelim): 22
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)