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= 042110
(287 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Q5H|A Chain A, Crystal Structure Of Apo-Wildtype Glycyl-Trna Synthetase
Length = 691
Score = 162 bits (410), Expect = 2e-40, Method: Compositional matrix adjust.
Identities = 95/253 (37%), Positives = 141/253 (55%), Gaps = 24/253 (9%)
Query: 12 VALVAQEKFSEPREVEKLVIAPVK----------KELALEAM---NEKEALGMKATLESK 58
V LVA++ EP+ V + P K +L +E + +E M+ L K
Sbjct: 424 VPLVAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEK 483
Query: 59 GEVEFYVRKLGKNVCIKKNMLLISKEKKKEFQRVFTPSVIEPSSGIDRIIYCLCEHCFYR 118
GE F + GK + K+M+ + + +K + P+VIEPS G+ RI+Y + EH F+
Sbjct: 484 GE--FTIETEGKTFQLTKDMINVKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHV 541
Query: 119 RPSKAGDEQLNVFRFPPLVAPIKCTVFTLVQNQQYEEVAKVISESLSVAGISHKIDITGA 178
R GDEQ F FP +VAP KC+V L QNQ++ K +SE+L+ G+SHK+D +
Sbjct: 542 R---EGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSG 598
Query: 179 SIGKRYARTDELGVPCAITVD------STSSVTIRERDSKDQMRVHVDDVASIVKALTDG 232
SIG+RYARTDE+GV +T+D + + T+R+RDS Q+R + ++ SIV+ L +G
Sbjct: 599 SIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANG 658
Query: 233 QRTWEDVWANSPF 245
TW DV A P
Sbjct: 659 NITWADVEARYPL 671
>pdb|2PME|A Chain A, The Apo Crystal Structure Of The Glycyl-Trna Synthetase
pdb|2ZT5|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
In Complex With Ap4a (Cocrystallized With Atp)
pdb|2ZT6|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
In Complex With Ampcpp
pdb|2ZT7|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
In Complex With Glycine And Atp
pdb|2ZT8|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
In Complex With Gly-Amp Analog
pdb|2ZXF|A Chain A, Crystal Structure Of Human Glycyl-Trna Synthetase (Glyrs)
In Complex With Ap4a (Cocrystallized With Ap4a)
Length = 693
Score = 162 bits (410), Expect = 2e-40, Method: Compositional matrix adjust.
Identities = 95/253 (37%), Positives = 141/253 (55%), Gaps = 24/253 (9%)
Query: 12 VALVAQEKFSEPREVEKLVIAPVK----------KELALEAM---NEKEALGMKATLESK 58
V LVA++ EP+ V + P K +L +E + +E M+ L K
Sbjct: 424 VPLVAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEK 483
Query: 59 GEVEFYVRKLGKNVCIKKNMLLISKEKKKEFQRVFTPSVIEPSSGIDRIIYCLCEHCFYR 118
GE F + GK + K+M+ + + +K + P+VIEPS G+ RI+Y + EH F+
Sbjct: 484 GE--FTIETEGKTFQLTKDMINVKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHV 541
Query: 119 RPSKAGDEQLNVFRFPPLVAPIKCTVFTLVQNQQYEEVAKVISESLSVAGISHKIDITGA 178
R GDEQ F FP +VAP KC+V L QNQ++ K +SE+L+ G+SHK+D +
Sbjct: 542 R---EGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSG 598
Query: 179 SIGKRYARTDELGVPCAITVD------STSSVTIRERDSKDQMRVHVDDVASIVKALTDG 232
SIG+RYARTDE+GV +T+D + + T+R+RDS Q+R + ++ SIV+ L +G
Sbjct: 599 SIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANG 658
Query: 233 QRTWEDVWANSPF 245
TW DV A P
Sbjct: 659 NITWADVEARYPL 671
>pdb|2Q5I|A Chain A, Crystal Structure Of Apo S581l Glycyl-Trna Synthetase
Mutant
Length = 691
Score = 160 bits (404), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 94/253 (37%), Positives = 140/253 (55%), Gaps = 24/253 (9%)
Query: 12 VALVAQEKFSEPREVEKLVIAPVK----------KELALEAM---NEKEALGMKATLESK 58
V LVA++ EP+ V + P K +L +E + +E M+ L K
Sbjct: 424 VPLVAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEK 483
Query: 59 GEVEFYVRKLGKNVCIKKNMLLISKEKKKEFQRVFTPSVIEPSSGIDRIIYCLCEHCFYR 118
GE F + GK + K+M+ + + +K + P+VIEPS G+ RI+Y + EH F+
Sbjct: 484 GE--FTIETEGKTFQLTKDMINVKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHV 541
Query: 119 RPSKAGDEQLNVFRFPPLVAPIKCTVFTLVQNQQYEEVAKVISESLSVAGISHKIDITGA 178
R GDEQ F FP +VAP KC+V L QNQ++ K + E+L+ G+SHK+D +
Sbjct: 542 R---EGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELLEALTRHGVSHKVDDSSG 598
Query: 179 SIGKRYARTDELGVPCAITVD------STSSVTIRERDSKDQMRVHVDDVASIVKALTDG 232
SIG+RYARTDE+GV +T+D + + T+R+RDS Q+R + ++ SIV+ L +G
Sbjct: 599 SIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANG 658
Query: 233 QRTWEDVWANSPF 245
TW DV A P
Sbjct: 659 NITWADVEARYPL 671
>pdb|2PMF|A Chain A, The Crystal Structure Of A Human Glycyl-trna Synthetase
Mutant
Length = 693
Score = 159 bits (401), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 94/253 (37%), Positives = 140/253 (55%), Gaps = 24/253 (9%)
Query: 12 VALVAQEKFSEPREVEKLVIAPVK----------KELALEAM---NEKEALGMKATLESK 58
V LVA++ EP+ V + P K +L +E + +E M+ L K
Sbjct: 424 VPLVAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEK 483
Query: 59 GEVEFYVRKLGKNVCIKKNMLLISKEKKKEFQRVFTPSVIEPSSGIDRIIYCLCEHCFYR 118
GE F + GK + K+M+ + + +K + P+VIEPS + RI+Y + EH F+
Sbjct: 484 GE--FTIETEGKTFQLTKDMINVKRFQKTLYVEEVVPNVIEPSFRLGRIMYTVFEHTFHV 541
Query: 119 RPSKAGDEQLNVFRFPPLVAPIKCTVFTLVQNQQYEEVAKVISESLSVAGISHKIDITGA 178
R GDEQ F FP +VAP KC+V L QNQ++ K +SE+L+ G+SHK+D +
Sbjct: 542 R---EGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSG 598
Query: 179 SIGKRYARTDELGVPCAITVD------STSSVTIRERDSKDQMRVHVDDVASIVKALTDG 232
SIG+RYARTDE+GV +T+D + + T+R+RDS Q+R + ++ SIV+ L +G
Sbjct: 599 SIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANG 658
Query: 233 QRTWEDVWANSPF 245
TW DV A P
Sbjct: 659 NITWADVEARYPL 671
>pdb|1ATI|A Chain A, Crystal Structure Of Glycyl-Trna Synthetase From Thermus
Thermophilus
pdb|1ATI|B Chain B, Crystal Structure Of Glycyl-Trna Synthetase From Thermus
Thermophilus
Length = 505
Score = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 53/149 (35%), Positives = 82/149 (55%), Gaps = 15/149 (10%)
Query: 93 FTPSVIEPSSGIDRIIYCLCEHCFYRRPSKAGDEQLNVFRFPPLVAPIKCTVFTLVQNQ- 151
F P VIEPS+G+DR + L F R G+E++ V + P +APIK V LV+N+
Sbjct: 353 FVPYVIEPSAGVDRGVLALLAEAFTREELPNGEERI-VLKLKPQLAPIKVAVIPLVKNRP 411
Query: 152 QYEEVAKVISESLSVAGISHKIDITGASIGKRYARTDELGVPCAITVDSTS--------- 202
+ E AK + L G+ + +IGK Y R DE+G P A+TVD +
Sbjct: 412 EITEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTIGQSKDGTT 471
Query: 203 ----SVTIRERDSKDQMRVHVDDVASIVK 227
+VT+R+RD+ +Q+R+HVD++ ++
Sbjct: 472 RLKDTVTVRDRDTMEQIRLHVDELEGFLR 500
>pdb|1GGM|A Chain A, Glycyl-Trna Synthetase From Thermus Thermophilus Complexed
With Glycyl-Adenylate
pdb|1GGM|B Chain B, Glycyl-Trna Synthetase From Thermus Thermophilus Complexed
With Glycyl-Adenylate
pdb|1B76|A Chain A, Glycyl-trna Synthetase From Thermus Thermophilus Complexed
With Atp
pdb|1B76|B Chain B, Glycyl-trna Synthetase From Thermus Thermophilus Complexed
With Atp
Length = 442
Score = 94.7 bits (234), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 53/149 (35%), Positives = 82/149 (55%), Gaps = 15/149 (10%)
Query: 93 FTPSVIEPSSGIDRIIYCLCEHCFYRRPSKAGDEQLNVFRFPPLVAPIKCTVFTLVQNQ- 151
F P VIEPS+G+DR + L F R G+E++ V + P +APIK V LV+N+
Sbjct: 290 FVPYVIEPSAGVDRGVLALLAEAFTREELPNGEERI-VLKLKPQLAPIKVAVIPLVKNRP 348
Query: 152 QYEEVAKVISESLSVAGISHKIDITGASIGKRYARTDELGVPCAITVDSTS--------- 202
+ E AK + L G+ + +IGK Y R DE+G P A+TVD +
Sbjct: 349 EITEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTIGQSKDGTT 408
Query: 203 ----SVTIRERDSKDQMRVHVDDVASIVK 227
+VT+R+RD+ +Q+R+HVD++ ++
Sbjct: 409 RLKDTVTVRDRDTMEQIRLHVDELEGFLR 437
>pdb|1NJ8|A Chain A, Crystal Structure Of Prolyl-Trna Synthetase From
Methanocaldococcus Janaschii
pdb|1NJ8|B Chain B, Crystal Structure Of Prolyl-Trna Synthetase From
Methanocaldococcus Janaschii
pdb|1NJ8|C Chain C, Crystal Structure Of Prolyl-Trna Synthetase From
Methanocaldococcus Janaschii
pdb|1NJ8|D Chain D, Crystal Structure Of Prolyl-Trna Synthetase From
Methanocaldococcus Janaschii
Length = 459
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 33/127 (25%), Positives = 55/127 (43%), Gaps = 16/127 (12%)
Query: 124 GDEQLNVFRFPPLVAPIKCTVFTLVQNQQYE---EVAKVISESLSVAGISHKIDITGASI 180
GDE+ + PP+VAPI+ + L+ + + E AK I E L H ID
Sbjct: 269 GDEKGLIL--PPIVAPIQVVIVPLIFKGKEDIVMEKAKEIYEKLKGKFRVH-IDDRDIRP 325
Query: 181 GKRYARTDELGVPCAITVD----STSSVTIRERDSKDQMRVHVDDVASIVKALTDG---- 232
G+++ + GVP I V +T+ RD+ ++ +V + +V+ +
Sbjct: 326 GRKFNDWEIKGVPLRIEVGPKDIENKKITLFRRDTMEKFQVDETQLMEVVEKTLNNIMEN 385
Query: 233 --QRTWE 237
R WE
Sbjct: 386 IKNRAWE 392
>pdb|3EOJ|A Chain A, Fmo Protein From Prosthecochloris Aestuarii 2k At 1.3a
Resolution
Length = 366
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 43/168 (25%), Positives = 63/168 (37%), Gaps = 36/168 (21%)
Query: 108 IYCLCEHCFYRRPSKAGDEQLNVFRFP----PLVAPIKCTVFTLVQ--NQQYEEVAKVIS 161
I L C R +K D Q V RF +V +K T+ V N+ + V
Sbjct: 41 IPLLPTDCNIRIDAKPLDAQKGVVRFTTKIESVVDSVKNTLNVEVDIANETKDRRIAVGE 100
Query: 162 ESLSVAGISHKIDITGASIGKRYARTDELGVPCAITVDSTSSVTIRERDSKD-QMRVHVD 220
SLSV SH G+ + Y R+D A+ + + + ++ R D M+V +D
Sbjct: 101 GSLSVGDFSHSFSFEGSVVNMYYYRSD------AVRRNIPNPIYMQGRQFHDILMKVPLD 154
Query: 221 DVASIVKALTDGQRTWEDVWANSPFPIPNPPNLLRNEMSNGGENFNLW 268
+ L D TWE + +S GG NF W
Sbjct: 155 N-----NDLVD---TWEG---------------FQQSISGGGANFGDW 179
>pdb|3VDI|A Chain A, Structure Of The Fmo Protein From Pelodictyon Phaeum
Length = 367
Score = 30.8 bits (68), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 40/166 (24%), Positives = 61/166 (36%), Gaps = 36/166 (21%)
Query: 110 CLCEHCFYRRPSKAGDEQLNVFRFPPLVAPI------KCTVFTLVQNQQYEEVAKVISES 163
L C + +K D Q V RF + I K V + N+ + V
Sbjct: 44 LLPADCNIKIEAKPLDAQKGVVRFTSQIESIVDSTKNKLVVEVDIANETKDRRIAVGEGE 103
Query: 164 LSVAGISHKIDITGASIGKRYARTDELGVPCAITVDSTSSVTIRERDSKD-QMRVHVDDV 222
+SV SHK G+ + Y R+D A+ + + V ++ R D M+V +D+
Sbjct: 104 VSVGDFSHKFSFEGSVVNMYYYRSD------AVRRNVPNPVYMQGRQFHDIMMKVPLDN- 156
Query: 223 ASIVKALTDGQRTWEDVWANSPFPIPNPPNLLRNEMSNGGENFNLW 268
K L + TWE + +S GG NF W
Sbjct: 157 ----KDLIE---TWEG---------------FQQSISGGGVNFGDW 180
>pdb|1NJ1|A Chain A, Crystal Structure Of Prolyl-Trna Synthetase From
Methanothermobacter Thermautotrophicus Bound To Cysteine
Sulfamoyl Adenylate
pdb|1NJ2|A Chain A, Crystal Structure Of Prolyl-Trna Synthetase From
Methanothermobacter Thermautotrophicus
pdb|1NJ5|A Chain A, Crystal Structure Of Prolyl-trna Synthetase From
Methanothermobacter Thermautotrophicus Bound To Proline
Sulfamoyl Adenylate
pdb|1NJ6|A Chain A, Crystal Structure Of Prolyl-Trna Synthetase From
Methanothermobacter Thermautotrophicus Bound To Alanine
Sulfamoyl Adenylate
Length = 501
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 24/118 (20%), Positives = 45/118 (38%), Gaps = 13/118 (11%)
Query: 133 FPPLVAPIKCTVFTLVQNQQYEEVAKVISE---SLSVAGISHKIDITGASIGKRYARTDE 189
PP VA + + ++ + EEV + E L AG +D G++Y +
Sbjct: 308 LPPDVAAHQVVIVPIIFKKAAEEVMEACRELRSRLEAAGFRVHLDDRDIRAGRKYYEWEM 367
Query: 190 LGVPCAITVD----STSSVTIRERDSKDQMRVHVDDVASIVKALTDG------QRTWE 237
GVP + + + I RD+ +++ + + ++ L R WE
Sbjct: 368 RGVPLRVEIGPRDLEKGAAVISRRDTGEKVTADLQGIEETLRELMKDILENLRTRAWE 425
>pdb|2J3L|A Chain A, Prolyl-Trna Synthetase From Enterococcus Faecalis
Complexed With A Prolyl-Adenylate Analogue
('5'-O-(N-(L-Prolyl)- Sulfamoyl)adenosine)
pdb|2J3L|B Chain B, Prolyl-Trna Synthetase From Enterococcus Faecalis
Complexed With A Prolyl-Adenylate Analogue
('5'-O-(N-(L-Prolyl)- Sulfamoyl)adenosine)
pdb|2J3M|A Chain A, Prolyl-Trna Synthetase From Enterococcus Faecalis
Complexed With Atp, Manganese And Prolinol
pdb|2J3M|B Chain B, Prolyl-Trna Synthetase From Enterococcus Faecalis
Complexed With Atp, Manganese And Prolinol
Length = 572
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 11/97 (11%)
Query: 103 GIDRIIYCLCEHCFYRRPSKAGDEQLNVFRFPPLVAPIKCTVFTLVQNQQYE-EVAKVIS 161
G+ R++ + E A + +N +P +AP V + +Y+ ++++ +
Sbjct: 444 GVSRLLSAIVEQ-------NADERGIN---WPTGIAPFDLHVVQMNVKDEYQTKLSQEVE 493
Query: 162 ESLSVAGISHKIDITGASIGKRYARTDELGVPCAITV 198
++ AG +D G ++A D +G P ITV
Sbjct: 494 AMMTEAGYEVLVDDRNERAGVKFADADLIGCPIRITV 530
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
0.317 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,278,479
Number of Sequences: 62578
Number of extensions: 335477
Number of successful extensions: 814
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 792
Number of HSP's gapped (non-prelim): 19
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)