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= 028433
(209 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RYM|A Chain A, Structure Of The Group Ii Intron Splicing Factor Crs2
Length = 212
Score = 196 bits (497), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 96/197 (48%), Positives = 129/197 (65%), Gaps = 11/197 (5%)
Query: 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLA 77
PWL GLGNPG+KY GTRHN VGFEM+D A +GI+MNT K+ G G +G+ PVL+
Sbjct: 17 PWLIAGLGNPGNKYYGTRHN-VGFEMVDRIAAEEGITMNTEQSKSLLGIGSIGEVPVLVV 75
Query: 78 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSVMN 137
KPQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GV ++V+
Sbjct: 76 KPQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIE 135
Query: 138 NFR----------GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 187
+ GIG PPG+MDP+AFLLQKF++ R +IDTAL++GV+ ++ L+ KG +
Sbjct: 136 HLDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFS 195
Query: 188 ESARHFNTIQKYKHIRL 204
S FN +QKYK R+
Sbjct: 196 GSTERFNLVQKYKFHRV 212
>pdb|1RYB|A Chain A, Crystal Structure Of The Chloroplast Group Ii Intron
Splicing Factor Crs2
Length = 205
Score = 191 bits (484), Expect = 3e-49, Method: Compositional matrix adjust.
Identities = 92/190 (48%), Positives = 125/190 (65%), Gaps = 11/190 (5%)
Query: 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLA 77
PWL GLGNPG+KY GTRHN VGFEM+D A +GI+MNT+ K+ G G +G+ PVL+
Sbjct: 17 PWLIAGLGNPGNKYYGTRHN-VGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVV 75
Query: 78 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSVMN 137
KPQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GV ++V+
Sbjct: 76 KPQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIE 135
Query: 138 NFR----------GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 187
+ GIG PPG+MDP+AFLLQKF++ R +IDTAL++GV+ ++ L+ KG +
Sbjct: 136 HLDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFS 195
Query: 188 ESARHFNTIQ 197
S FN +Q
Sbjct: 196 GSTERFNLVQ 205
>pdb|1RYN|A Chain A, Structure Of The Chloroplast Group Ii Intron Splicing
Factor Crs2
Length = 202
Score = 190 bits (482), Expect = 6e-49, Method: Compositional matrix adjust.
Identities = 93/191 (48%), Positives = 125/191 (65%), Gaps = 11/191 (5%)
Query: 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLA 77
PWL GLGNPG+KY GTRHN VGFEM+D A +GI+MNT K+ G G +G+ PVL+
Sbjct: 5 PWLIAGLGNPGNKYYGTRHN-VGFEMVDRIAAEEGITMNTNQFKSLLGTGSIGEVPVLVV 63
Query: 78 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSVMN 137
KPQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GV ++V+
Sbjct: 64 KPQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIE 123
Query: 138 NFR----------GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLT 187
+ GIG PPG+MDP+AFLLQKF++ R +IDTAL++GV+ ++ L+ KG +
Sbjct: 124 HLDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFS 183
Query: 188 ESARHFNTIQK 198
S FN +QK
Sbjct: 184 GSTERFNLVQK 194
>pdb|2LGJ|A Chain A, Solution Structure Of Mspth
Length = 191
Score = 114 bits (285), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 73/196 (37%), Positives = 105/196 (53%), Gaps = 16/196 (8%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCK--ATFGQGFVGDA 72
+A P L VGLGNPG Y TRHN +GF + D A G S VH K A G +
Sbjct: 1 MAEPLLVVGLGNPGPTYAKTRHN-LGFMVADVLAGRIG-SAFKVHKKSGAEVVTGRLAGT 58
Query: 73 PVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXX 132
V+LAKP+ YMN SG GPLA +Y +P +++V HD++ + G
Sbjct: 59 SVVLAKPRCYMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRLKLGGGEGGHNGL 118
Query: 133 KSVMN-----NFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLS 183
+SV + NF G+GRPPG+ DP AF+L+ F A R + T +++ + +LL++
Sbjct: 119 RSVASALGTKNFHRVRIGVGRPPGRKDPAAFVLENFTAAERAEVPTIVEQAADATELLIA 178
Query: 184 KGLTESARHFNTIQKY 199
+GL E A+ NT+ +
Sbjct: 179 QGL-EPAQ--NTVHAW 191
>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 = 110 bits (275), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 71/196 (36%), Positives = 104/196 (53%), Gaps = 16/196 (8%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCK--ATFGQGFVGDA 72
+A P L VGLGNPG Y TRHN +GF + D A G S VH K A G +
Sbjct: 1 MAEPLLVVGLGNPGPTYAKTRHN-LGFMVADVLAGRIG-SAFKVHKKSGAEVVTGRLAGT 58
Query: 73 PVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXX 132
V+LAKP+ MN SG GPLA +Y +P +++V HD++ + G
Sbjct: 59 TVVLAKPRISMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRLKLGGGEGGHNGL 118
Query: 133 KSVMN-----NFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLS 183
+SV + NF G+GRPPG+ DP AF+L+ F + R + T +++ + +LL++
Sbjct: 119 RSVASALGTKNFHRVRIGVGRPPGRKDPAAFVLENFTSAERAEVPTIVEQAADATELLIA 178
Query: 184 KGLTESARHFNTIQKY 199
+GL E A+ NT+ +
Sbjct: 179 QGL-EPAQ--NTVHAW 191
>pdb|2JRC|A Chain A, Solution Structure Of Peptidyl-Trna Hydrolase From
Mycobacterium Tuberculosis H37rv
Length = 204
Score = 103 bits (258), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 63/182 (34%), Positives = 89/182 (48%), Gaps = 11/182 (6%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNT-VHCKATFGQGFVGDAP 73
+A P L VGLGNPG Y TRHN +GF + D A G A G
Sbjct: 1 MAEPLLVVGLGNPGANYARTRHN-LGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRS 59
Query: 74 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXK 133
++LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +
Sbjct: 60 LVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLR 119
Query: 134 SVM-----NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSK 184
SV+ +F+ GIGRPPG+ DP AF+L+ F R + T ++ + +LL+ +
Sbjct: 120 SVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQ 179
Query: 185 GL 186
G+
Sbjct: 180 GM 181
>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 = 103 bits (258), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 63/182 (34%), Positives = 89/182 (48%), Gaps = 11/182 (6%)
Query: 15 VARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNT-VHCKATFGQGFVGDAP 73
+A P L VGLGNPG Y TRHN +GF + D A G A G
Sbjct: 1 MAEPLLVVGLGNPGANYARTRHN-LGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRS 59
Query: 74 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXK 133
++LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +
Sbjct: 60 LVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLR 119
Query: 134 SVM-----NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSK 184
SV+ +F+ GIGRPPG+ DP AF+L+ F R + T ++ + +LL+ +
Sbjct: 120 SVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQ 179
Query: 185 GL 186
G+
Sbjct: 180 GM 181
>pdb|3V2I|A Chain A, Structure Of A Peptidyl-Trna Hydrolase (Pth) From
Burkholderia Thailandensis
Length = 222
Score = 77.0 bits (188), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 57/191 (29%), Positives = 87/191 (45%), Gaps = 22/191 (11%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAK 78
L VGLGNPG +Y TRHN GF ++D A G ++ + + + + V L +
Sbjct: 25 LIVGLGNPGAEYTATRHN-AGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLE 83
Query: 79 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSVMNN 138
PQTYMN SG+S LA ++K+ N +LV HD++ LP G K + +
Sbjct: 84 PQTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKLKLGGGSGGHNGLKDISAH 143
Query: 139 FR---------GIGRPPGQM----------DPKAFLLQKFNAIARERIDTALQEGVEVLK 179
GIG P + D F+L+ ++ ID A++ + V+
Sbjct: 144 LSSQQYWRLRIGIGHPRDMIPESARAGAKPDVANFVLKPPRKEEQDVIDAAIERALAVMP 203
Query: 180 LLLSKGLTESA 190
++ KG TE A
Sbjct: 204 AVV-KGETERA 213
>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 = 2e-14, Method: Compositional matrix adjust.
Identities = 55/190 (28%), Positives = 88/190 (46%), Gaps = 13/190 (6%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAK 78
L VGLGNPG +Y TRHN GF ++ A+ GI++ N G+G + V L
Sbjct: 6 LIVGLGNPGSEYAQTRHN-AGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLL 64
Query: 79 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSVM-- 136
P TYMN SG+S P + +Y++ +L+ HD++ + GV + ++
Sbjct: 65 PMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVPH 124
Query: 137 --NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESA 190
NF GIG P + +L K + + +D A+ + +KLL+ + ++
Sbjct: 125 IGPNFHRLRIGIGHPGSKERVSGHVLGKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQA- 183
Query: 191 RHFNTIQKYK 200
N I YK
Sbjct: 184 --MNQINAYK 191
>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 = 54/192 (28%), Positives = 88/192 (45%), Gaps = 18/192 (9%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATF----GQGFVGDAPVL 75
L VGL NPG +Y TRHN G +D AE + +A F + +G V
Sbjct: 8 LIVGLANPGAEYAATRHN-AGAWFVDLLAERLRAPLRE---EAKFFGYTSRVTLGGEDVR 63
Query: 76 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSV 135
L P T+MNLSG++ +A+++++ + +LV HD++ LP GV K +
Sbjct: 64 LLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDI 123
Query: 136 MN------NFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 185
++ NF GIG P + F+L K ++ ID A+ E ++ + G
Sbjct: 124 ISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDG 183
Query: 186 LTESARHFNTIQ 197
LT++ + +
Sbjct: 184 LTKATNRLHAFK 195
>pdb|2PTH|A Chain A, Peptidyl-Trna Hydrolase From Escherichia Coli
Length = 193
Score = 73.9 bits (180), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 54/192 (28%), Positives = 88/192 (45%), Gaps = 18/192 (9%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATF----GQGFVGDAPVL 75
L VGL NPG +Y TRHN G +D AE + +A F + +G V
Sbjct: 4 LIVGLANPGAEYAATRHN-AGAWFVDLLAERLRAPLRE---EAKFFGYTSRVTLGGEDVR 59
Query: 76 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSV 135
L P T+MNLSG++ +A+++++ + +LV HD++ LP GV K +
Sbjct: 60 LLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDI 119
Query: 136 MN------NFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 185
++ NF GIG P + F+L K ++ ID A+ E ++ + G
Sbjct: 120 ISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDG 179
Query: 186 LTESARHFNTIQ 197
LT++ + +
Sbjct: 180 LTKATNRLHAFK 191
>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 = 73.6 bits (179), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 56/191 (29%), Positives = 91/191 (47%), Gaps = 20/191 (10%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-----APV 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ V + FG VG V
Sbjct: 6 LIVGLGNPGPEYDQTRHN-AGALFVERLAHAQGVSL--VADRKYFG--LVGKFSHQGKDV 60
Query: 75 LLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKS 134
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +
Sbjct: 61 RLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRD 120
Query: 135 VM------NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSK 184
++ N+F GIG P ++L + +E +DT++ + VL +L+
Sbjct: 121 IIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAG 180
Query: 185 GLTESARHFNT 195
T + + ++
Sbjct: 181 DWTRAMQKLHS 191
>pdb|4FYJ|A Chain A, Crystal Structure Of P. Aeruginosa Peptidyl-Trna Hydrolase
Length = 199
Score = 73.6 bits (179), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 56/191 (29%), Positives = 91/191 (47%), Gaps = 20/191 (10%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-----APV 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ V + FG VG V
Sbjct: 12 LIVGLGNPGPEYDQTRHN-AGALFVERLAHAQGVSL--VADRKYFG--LVGKFSHQGKDV 66
Query: 75 LLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKS 134
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +
Sbjct: 67 RLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRD 126
Query: 135 VM------NNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSK 184
++ N+F GIG P ++L + +E +DT++ + VL +L+
Sbjct: 127 IIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAG 186
Query: 185 GLTESARHFNT 195
T + + ++
Sbjct: 187 DWTRAMQKLHS 197
>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 = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 54/190 (28%), Positives = 87/190 (45%), Gaps = 18/190 (9%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATF----GQGFVGDAPVL 75
L VGL NPG +Y TRHN G +D AE + +A F + +G V
Sbjct: 25 LIVGLANPGAEYAATRHN-AGAWFVDLLAERLRAPLRE---EAKFFGYTSRVTLGGEDVR 80
Query: 76 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSV 135
L P T+MNLSG++ +A+++++ + +LV HD++ LP GV K +
Sbjct: 81 LLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDI 140
Query: 136 MN------NFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 185
++ NF GIG P + F+L K ++ ID A+ E ++ + G
Sbjct: 141 ISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDG 200
Query: 186 LTESARHFNT 195
LT++ +
Sbjct: 201 LTKATNRLHA 210
>pdb|3NEA|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Francisella Tularensis
Length = 207
Score = 59.3 bits (142), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 46/179 (25%), Positives = 82/179 (45%), Gaps = 15/179 (8%)
Query: 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNT---VHCKATFGQGFVGDAPVLL 76
+ +GLGN G +Y+ TRHN VG I A+ S ++ ++C + + V+L
Sbjct: 25 MIIGLGNIGKEYQDTRHN-VGEWFIAKIAQDNNQSFSSNPKLNC--NLAKVSIDYNNVVL 81
Query: 77 AKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVXXXXXXXXXXXXXXXKSV- 135
P TYMN SG + +A +YK+ +LV HD++ + G +S+
Sbjct: 82 VFPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRSIN 141
Query: 136 ----MNNFR----GIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGL 186
N++ GIG P + ++L + ++ ID+A+ G+ L +++ L
Sbjct: 142 QHLGTNDYLRLRIGIGHPGHKSKVANYVLSNPSIAQKKDIDSAIDNGICFLDDIINYKL 200
>pdb|1Y4T|A Chain A, Ferric Binding Protein From Campylobacter Jejuni
pdb|1Y4T|D Chain D, Ferric Binding Protein From Campylobacter Jejuni
pdb|3E13|X Chain X, Iron Reconstituted Ferric Binding Protein From
Campylobacter Jejuni
Length = 322
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 33 GTRHNQVGFEMIDAFAESQGISMNTVHCKAT 63
RH FE+I F E GI +N KA+
Sbjct: 8 SARHYNADFEIIKKFEEKTGIKVNHTQAKAS 38
>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 = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 54 SMNTVHCKATFGQGFVGDAPVLLAKPQT 81
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
0.323 0.140 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,733,189
Number of Sequences: 62578
Number of extensions: 207658
Number of successful extensions: 443
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: 393
Number of HSP's gapped (non-prelim): 17
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)