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= 029635
(190 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RYN|A Chain A, Structure Of The Chloroplast Group Ii Intron Splicing
Factor Crs2
Length = 202
Score = 149 bits (375), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 65/115 (56%), Positives = 88/115 (76%)
Query: 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAK 134
PWLI GLGNPG +Y GTRHNVGFEMVD IA EGI++++ FK+ G G IG VPV++ K
Sbjct: 5 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTNQFKSLLGTGSIGEVPVLVVK 64
Query: 135 PQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189
PQ++MN SG+++G + +YY++PL+ +L+I+DD LP +RL KGGHG HNG +
Sbjct: 65 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQ 119
>pdb|1RYB|A Chain A, Crystal Structure Of The Chloroplast Group Ii Intron
Splicing Factor Crs2
Length = 205
Score = 147 bits (370), Expect = 4e-36, Method: Compositional matrix adjust.
Identities = 64/115 (55%), Positives = 88/115 (76%)
Query: 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAK 134
PWLI GLGNPG +Y GTRHNVGFEMVD IA EGI+++++ K+ G G IG VPV++ K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVK 76
Query: 135 PQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189
PQ++MN SG+++G + +YY++PL+ +L+I+DD LP +RL KGGHG HNG +
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQ 131
>pdb|1RYM|A Chain A, Structure Of The Group Ii Intron Splicing Factor Crs2
Length = 212
Score = 145 bits (366), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 64/115 (55%), Positives = 87/115 (75%)
Query: 75 PWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAHFGKGFIGNVPVMLAK 134
PWLI GLGNPG +Y GTRHNVGFEMVD IA EGI++++ K+ G G IG VPV++ K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTEQSKSLLGIGSIGEVPVLVVK 76
Query: 135 PQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRLLPKGGHGGHNGYK 189
PQ++MN SG+++G + +YY++PL+ +L+I+DD LP +RL KGGHG HNG +
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQ 131
>pdb|2LGJ|A Chain A, Solution Structure Of Mspth
Length = 191
Score = 89.4 bits (220), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 46/105 (43%), Positives = 66/105 (62%), Gaps = 3/105 (2%)
Query: 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFK--AHFGKGFIGNVPVM 131
P L+VGLGNPG Y TRHN+GF + D +A G S V+ K A G + V+
Sbjct: 3 EPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIG-SAFKVHKKSGAEVVTGRLAGTSVV 61
Query: 132 LAKPQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRL 176
LAKP+ +MN SG+ VG + +Y +P +Q++VI D+LD+ F ++RL
Sbjct: 62 LAKPRCYMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRL 106
>pdb|3V2I|A Chain A, Structure Of A Peptidyl-Trna Hydrolase (Pth) From
Burkholderia Thailandensis
Length = 222
Score = 87.4 bits (215), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 44/101 (43%), Positives = 62/101 (61%), Gaps = 1/101 (0%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISV-SSVNFKAHFGKGFIGNVPVMLAKP 135
LIVGLGNPG +Y TRHN GF +VD +A G ++ F + K + V L +P
Sbjct: 25 LIVGLGNPGAEYTATRHNAGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLEP 84
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRL 176
QT+MN SGQSV ++ ++KI ++LV D+LDLP ++L
Sbjct: 85 QTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKL 125
>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 = 87.0 bits (214), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 46/105 (43%), Positives = 65/105 (61%), Gaps = 3/105 (2%)
Query: 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFK--AHFGKGFIGNVPVM 131
P L+VGLGNPG Y TRHN+GF + D +A G S V+ K A G + V+
Sbjct: 3 EPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIG-SAFKVHKKSGAEVVTGRLAGTTVV 61
Query: 132 LAKPQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRL 176
LAKP+ MN SG+ VG + +Y +P +Q++VI D+LD+ F ++RL
Sbjct: 62 LAKPRISMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRL 106
>pdb|2JRC|A Chain A, Solution Structure Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis H37rv
Length = 204
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 44/109 (40%), Positives = 61/109 (55%), Gaps = 11/109 (10%)
Query: 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAH------FGKGFIGN 127
P L+VGLGNPG Y TRHN+GF + D +A G FKAH G
Sbjct: 3 EPLLVVGLGNPGANYARTRHNLGFVVADLLAARLG-----AKFKAHKRSGAEVATGRSAG 57
Query: 128 VPVMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRL 176
++LAKP+ +MN SG+ +G + +Y + ++VI DDLDL F ++RL
Sbjct: 58 RSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRL 106
>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 = 85.5 bits (210), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 44/109 (40%), Positives = 61/109 (55%), Gaps = 11/109 (10%)
Query: 74 HPWLIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSVNFKAH------FGKGFIGN 127
P L+VGLGNPG Y TRHN+GF + D +A G FKAH G
Sbjct: 3 EPLLVVGLGNPGANYARTRHNLGFVVADLLAARLG-----AKFKAHKRSGAEVATGRSAG 57
Query: 128 VPVMLAKPQTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRL 176
++LAKP+ +MN SG+ +G + +Y + ++VI DDLDL F ++RL
Sbjct: 58 RSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRL 106
>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 = 76.3 bits (186), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 41/95 (43%), Positives = 58/95 (61%), Gaps = 1/95 (1%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGIS-VSSVNFKAHFGKGFIGNVPVMLAKP 135
LIVGLGNPG +Y+ TRHN G V+ +A A+G+S V+ + GK V L P
Sbjct: 6 LIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIP 65
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLP 170
T+MN SGQSV ++ +++I +LV D+LD+P
Sbjct: 66 TTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMP 100
>pdb|4FYJ|A Chain A, Crystal Structure Of P. Aeruginosa Peptidyl-Trna Hydrolase
Length = 199
Score = 76.3 bits (186), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 41/95 (43%), Positives = 58/95 (61%), Gaps = 1/95 (1%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGIS-VSSVNFKAHFGKGFIGNVPVMLAKP 135
LIVGLGNPG +Y+ TRHN G V+ +A A+G+S V+ + GK V L P
Sbjct: 12 LIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIP 71
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLP 170
T+MN SGQSV ++ +++I +LV D+LD+P
Sbjct: 72 TTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMP 106
>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 = 75.9 bits (185), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 43/101 (42%), Positives = 60/101 (59%), Gaps = 1/101 (0%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISV-SSVNFKAHFGKGFIGNVPVMLAKP 135
LIVGLGNPG +Y TRHN GF V+ +A+ GI++ + F G+G I V L P
Sbjct: 6 LIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLLP 65
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRL 176
T+MN SGQSV +Y+I + +L+ D+LD+ +RL
Sbjct: 66 MTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRL 106
>pdb|2PTH|A Chain A, Peptidyl-Trna Hydrolase From Escherichia Coli
Length = 193
Score = 73.9 bits (180), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 39/95 (41%), Positives = 55/95 (57%), Gaps = 1/95 (1%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISV-SSVNFKAHFGKGFIGNVPVMLAKP 135
LIVGL NPG +Y TRHN G VD +AE + F + + +G V L P
Sbjct: 4 LIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVP 63
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLP 170
TFMN SG++V ++ S+++I ++LV D+LDLP
Sbjct: 64 TTFMNLSGKAVAAMASFFRINPDEILVAHDELDLP 98
>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 = 73.9 bits (180), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 39/95 (41%), Positives = 55/95 (57%), Gaps = 1/95 (1%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISV-SSVNFKAHFGKGFIGNVPVMLAKP 135
LIVGL NPG +Y TRHN G VD +AE + F + + +G V L P
Sbjct: 8 LIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVP 67
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLP 170
TFMN SG++V ++ S+++I ++LV D+LDLP
Sbjct: 68 TTFMNLSGKAVAAMASFFRINPDEILVAHDELDLP 102
>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 = 73.6 bits (179), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 39/95 (41%), Positives = 55/95 (57%), Gaps = 1/95 (1%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISV-SSVNFKAHFGKGFIGNVPVMLAKP 135
LIVGL NPG +Y TRHN G VD +AE + F + + +G V L P
Sbjct: 25 LIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVP 84
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLP 170
TFMN SG++V ++ S+++I ++LV D+LDLP
Sbjct: 85 TTFMNLSGKAVAAMASFFRINPDEILVAHDELDLP 119
>pdb|3NEA|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Francisella Tularensis
Length = 207
Score = 72.4 bits (176), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 40/101 (39%), Positives = 59/101 (58%), Gaps = 1/101 (0%)
Query: 77 LIVGLGNPGKQYNGTRHNVGFEMVDAIAEAEGISVSSV-NFKAHFGKGFIGNVPVMLAKP 135
+I+GLGN GK+Y TRHNVG + IA+ S SS + K I V+L P
Sbjct: 25 MIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVVLVFP 84
Query: 136 QTFMNASGQSVGSIVSYYKIPLKQVLVIFDDLDLPFSKMRL 176
T+MN SG +V + ++YKI ++LV+ D+LD+ ++RL
Sbjct: 85 TTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRL 125
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
0.322 0.138 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,643,098
Number of Sequences: 62578
Number of extensions: 209060
Number of successful extensions: 387
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 360
Number of HSP's gapped (non-prelim): 19
length of query: 190
length of database: 14,973,337
effective HSP length: 93
effective length of query: 97
effective length of database: 9,153,583
effective search space: 887897551
effective search space used: 887897551
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)