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= 041441
(310 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 362 bits (930), Expect = e-100, Method: Compositional matrix adjust.
Identities = 172/306 (56%), Positives = 216/306 (70%), Gaps = 1/306 (0%)
Query: 1 HFLLKENMLEVRSPCVTPEVVLKASGHVEKLTDQMVKDEKTGTFYRADQLLKDFCNEKLR 60
HF+ +E +LE+ +TPE VLK SGHV+K D MVKD K G +RAD LLK +KL
Sbjct: 114 HFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHL-QKLM 172
Query: 61 EDVRLSLEQAAELRRTLAMMDDLSVEELGAKIKEYGITAPDTKNPLSDPYPFNLMFQTSV 120
D + S+E+ +E+ LA +D+ +EL Y + +P T N LS P FNLMF+T +
Sbjct: 173 SDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFI 232
Query: 121 GPSGLTAAYVRPETAPGIFVNFKDLYYNNGNKLPFAAAQIGQAFRNEISPRQGFSRVREF 180
GP G Y+RPETA GIF+NFK L N KLPFAAAQIG +FRNEISPR G RVREF
Sbjct: 233 GPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREF 292
Query: 181 TLAEIEHFVDPKDKSHPKFSEVKNLEFLMFPREEQMSAQSAKKIRLGEAVSRGIVNNETI 240
T+AEIEHFVDP +K HPKF V +L ++ + Q+S QSA+K+RLG+AV +G++NN +
Sbjct: 293 TMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVL 352
Query: 241 GYFIGRVYLFLSRLGIDQDHLRFRQHLANEMAHYAADCWDAEIECSYGWIECVGIADRSA 300
GYFIGR+YL+L+++GI D LRFRQH+ NEMAHYA DCWDAE + SYGWIE VG ADRS
Sbjct: 353 GYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSC 412
Query: 301 YDLRAH 306
YDL H
Sbjct: 413 YDLSCH 418
>pdb|2PMF|A Chain A, The Crystal Structure Of A Human Glycyl-trna Synthetase
Mutant
Length = 693
Score = 362 bits (930), Expect = e-100, Method: Compositional matrix adjust.
Identities = 172/306 (56%), Positives = 216/306 (70%), Gaps = 1/306 (0%)
Query: 1 HFLLKENMLEVRSPCVTPEVVLKASGHVEKLTDQMVKDEKTGTFYRADQLLKDFCNEKLR 60
HF+ +E +LE+ +TPE VLK SGHV+K D MVKD K G +RAD LLK +KL
Sbjct: 114 HFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHL-QKLM 172
Query: 61 EDVRLSLEQAAELRRTLAMMDDLSVEELGAKIKEYGITAPDTKNPLSDPYPFNLMFQTSV 120
D + S+E+ +E+ LA +D+ +EL Y + +P T N LS P FNLMF+T +
Sbjct: 173 SDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFI 232
Query: 121 GPSGLTAAYVRPETAPGIFVNFKDLYYNNGNKLPFAAAQIGQAFRNEISPRQGFSRVREF 180
GP G Y+RPETA GIF+NFK L N KLPFAAAQIG +FRNEISPR G RVREF
Sbjct: 233 GPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREF 292
Query: 181 TLAEIEHFVDPKDKSHPKFSEVKNLEFLMFPREEQMSAQSAKKIRLGEAVSRGIVNNETI 240
T+AEIEHFVDP +K HPKF V +L ++ + Q+S QSA+K+RLG+AV +G++NN +
Sbjct: 293 TMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVL 352
Query: 241 GYFIGRVYLFLSRLGIDQDHLRFRQHLANEMAHYAADCWDAEIECSYGWIECVGIADRSA 300
GYFIGR+YL+L+++GI D LRFRQH+ NEMAHYA DCWDAE + SYGWIE VG ADRS
Sbjct: 353 GYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSC 412
Query: 301 YDLRAH 306
YDL H
Sbjct: 413 YDLSCH 418
>pdb|2Q5I|A Chain A, Crystal Structure Of Apo S581l Glycyl-Trna Synthetase
Mutant
Length = 691
Score = 362 bits (929), Expect = e-100, Method: Compositional matrix adjust.
Identities = 172/306 (56%), Positives = 216/306 (70%), Gaps = 1/306 (0%)
Query: 1 HFLLKENMLEVRSPCVTPEVVLKASGHVEKLTDQMVKDEKTGTFYRADQLLKDFCNEKLR 60
HF+ +E +LE+ +TPE VLK SGHV+K D MVKD K G +RAD LLK +KL
Sbjct: 114 HFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHL-QKLM 172
Query: 61 EDVRLSLEQAAELRRTLAMMDDLSVEELGAKIKEYGITAPDTKNPLSDPYPFNLMFQTSV 120
D + S+E+ +E+ LA +D+ +EL Y + +P T N LS P FNLMF+T +
Sbjct: 173 SDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFI 232
Query: 121 GPSGLTAAYVRPETAPGIFVNFKDLYYNNGNKLPFAAAQIGQAFRNEISPRQGFSRVREF 180
GP G Y+RPETA GIF+NFK L N KLPFAAAQIG +FRNEISPR G RVREF
Sbjct: 233 GPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREF 292
Query: 181 TLAEIEHFVDPKDKSHPKFSEVKNLEFLMFPREEQMSAQSAKKIRLGEAVSRGIVNNETI 240
T+AEIEHFVDP +K HPKF V +L ++ + Q+S QSA+K+RLG+AV +G++NN +
Sbjct: 293 TMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVL 352
Query: 241 GYFIGRVYLFLSRLGIDQDHLRFRQHLANEMAHYAADCWDAEIECSYGWIECVGIADRSA 300
GYFIGR+YL+L+++GI D LRFRQH+ NEMAHYA DCWDAE + SYGWIE VG ADRS
Sbjct: 353 GYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSC 412
Query: 301 YDLRAH 306
YDL H
Sbjct: 413 YDLSCH 418
>pdb|2Q5H|A Chain A, Crystal Structure Of Apo-Wildtype Glycyl-Trna Synthetase
Length = 691
Score = 362 bits (929), Expect = e-100, Method: Compositional matrix adjust.
Identities = 172/306 (56%), Positives = 216/306 (70%), Gaps = 1/306 (0%)
Query: 1 HFLLKENMLEVRSPCVTPEVVLKASGHVEKLTDQMVKDEKTGTFYRADQLLKDFCNEKLR 60
HF+ +E +LE+ +TPE VLK SGHV+K D MVKD K G +RAD LLK +KL
Sbjct: 114 HFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHL-QKLM 172
Query: 61 EDVRLSLEQAAELRRTLAMMDDLSVEELGAKIKEYGITAPDTKNPLSDPYPFNLMFQTSV 120
D + S+E+ +E+ LA +D+ +EL Y + +P T N LS P FNLMF+T +
Sbjct: 173 SDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFI 232
Query: 121 GPSGLTAAYVRPETAPGIFVNFKDLYYNNGNKLPFAAAQIGQAFRNEISPRQGFSRVREF 180
GP G Y+RPETA GIF+NFK L N KLPFAAAQIG +FRNEISPR G RVREF
Sbjct: 233 GPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREF 292
Query: 181 TLAEIEHFVDPKDKSHPKFSEVKNLEFLMFPREEQMSAQSAKKIRLGEAVSRGIVNNETI 240
T+AEIEHFVDP +K HPKF V +L ++ + Q+S QSA+K+RLG+AV +G++NN +
Sbjct: 293 TMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVL 352
Query: 241 GYFIGRVYLFLSRLGIDQDHLRFRQHLANEMAHYAADCWDAEIECSYGWIECVGIADRSA 300
GYFIGR+YL+L+++GI D LRFRQH+ NEMAHYA DCWDAE + SYGWIE VG ADRS
Sbjct: 353 GYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSC 412
Query: 301 YDLRAH 306
YDL H
Sbjct: 413 YDLSCH 418
>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 = 127 bits (320), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 98/308 (31%), Positives = 140/308 (45%), Gaps = 49/308 (15%)
Query: 5 KENMLEVRSPCVTPEVVLKASGHVEKLTDQMVKDEKTGTFYRADQLLKDFCNEKLREDVR 64
+++M + + +T +VL SGH D MV + T YR D LLK+ E L+ R
Sbjct: 57 RDDMEGLDASVLTHRLVLHYSGHEATFADPMVDNRITKKRYRLDHLLKEQPEEVLKRLYR 116
Query: 65 -LSLEQAAELRRTLAMMDDLSVEELGAKIKEYGITAPDTKNP--LSDPYPFNLMFQTSVG 121
+ +E+ AMM + E G + G+ P + P + P FN+MFQ G
Sbjct: 117 AMEVEEENLHALVQAMMQ--APERAGGAMTAAGVLDPASGEPGDWTPPRYFNMMFQDLRG 174
Query: 122 PSGLTA--AYVRPETAPGIFVNFKDLYYNNGNKLPFAAAQIGQAFRNEISPRQGFSRVRE 179
P G AY+RPETA GIFVNFK++ KL F AQIG+AFRNEI+PR RVRE
Sbjct: 175 PRGGRGLLAYLRPETAQGIFVNFKNVLDATSRKLGFGIAQIGKAFRNEITPRNFIFRVRE 234
Query: 180 FTLAEIEHFVDPKDKSHPKFSEVKNLEFLMFPREEQMSAQSAKKIRLGEAVSRGIVNNET 239
F EIE+FV P + + + + EE++
Sbjct: 235 FEQMEIEYFVRPGEDEY----------WHRYWVEERLK---------------------- 262
Query: 240 IGYFIGRVYLFLSRLGIDQDHLRFRQHLANEMAHYAADCWDAEIECSYGWIECVGIADRS 299
+ +G+ +++L Q AHYA D +G +E GIA R+
Sbjct: 263 ----------WWQEMGLSRENLVPYQQPPESSAHYAKATVDILYRFPHGSLELEGIAQRT 312
Query: 300 AYDLRAHT 307
+DL +HT
Sbjct: 313 DFDLGSHT 320
>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 = 100 bits (250), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 69/203 (33%), Positives = 94/203 (46%), Gaps = 44/203 (21%)
Query: 107 SDPYPFNLMFQTSVGPSGLTA--AYVRPETAPGIFVNFKDLYYNNGNKLPFAAAQIGQAF 164
+ P FN+MFQ GP G AY+RPETA GIFVNFK++ KL F AQIG+AF
Sbjct: 97 TPPRYFNMMFQDLRGPRGGRGLLAYLRPETAQGIFVNFKNVLDATSRKLGFGIAQIGKAF 156
Query: 165 RNEISPRQGFSRVREFTLAEIEHFVDPKDKSHPKFSEVKNLEFLMFPREEQMSAQSAKKI 224
RNEI+PR RVREF EIE+FV P + + + + EE++
Sbjct: 157 RNEITPRNFIFRVREFEQMEIEYFVRPGEDEY----------WHRYWVEERLK------- 199
Query: 225 RLGEAVSRGIVNNETIGYFIGRVYLFLSRLGIDQDHLRFRQHLANEMAHYAADCWDAEIE 284
+ +G+ +++L Q AHYA D
Sbjct: 200 -------------------------WWQEMGLSRENLVPYQQPPESSAHYAKATVDILYR 234
Query: 285 CSYGWIECVGIADRSAYDLRAHT 307
+G +E GIA R+ +DL +HT
Sbjct: 235 FPHGSLELEGIAQRTDFDLGSHT 257
>pdb|2WJ3|A Chain A, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a
pdb|2WJ3|B Chain B, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a
pdb|2WJ3|C Chain C, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a
pdb|2WJ3|D Chain D, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a
pdb|2WJ4|A Chain A, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Anaerobically Complexed With Its
Natural Substrate 1-H-3-Hydroxy-4-Oxoquinaldine
pdb|2WJ4|B Chain B, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Anaerobically Complexed With Its
Natural Substrate 1-H-3-Hydroxy-4-Oxoquinaldine
pdb|2WJ4|C Chain C, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Anaerobically Complexed With Its
Natural Substrate 1-H-3-Hydroxy-4-Oxoquinaldine
pdb|2WJ4|D Chain D, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Anaerobically Complexed With Its
Natural Substrate 1-H-3-Hydroxy-4-Oxoquinaldine
pdb|2WJ6|A Chain A, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Complexed With Its Natural
Product N-Acetylanthranilate
pdb|2WJ6|B Chain B, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Complexed With Its Natural
Product N-Acetylanthranilate
pdb|2WJ6|C Chain C, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Complexed With Its Natural
Product N-Acetylanthranilate
pdb|2WJ6|D Chain D, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a Complexed With Its Natural
Product N-Acetylanthranilate
Length = 276
Score = 32.3 bits (72), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 258 QDHLRFRQHLANEMAHYAADCWDAE---IECSYG 288
D R R HL EMA Y DCW IE +YG
Sbjct: 164 HDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYG 197
>pdb|2WM2|A Chain A, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a In Complex With Chloride
pdb|2WM2|B Chain B, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a In Complex With Chloride
pdb|2WM2|C Chain C, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a In Complex With Chloride
pdb|2WM2|D Chain D, Crystal Structure Of The Cofactor-Devoid 1-H-3-Hydroxy-4-
Oxoquinaldine 2,4-Dioxygenase (Hod) From Arthrobacter
Nitroguajacolicus Ru61a In Complex With Chloride
Length = 279
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 258 QDHLRFRQHLANEMAHYAADCWDAE---IECSYG 288
D R R HL EMA Y DCW IE +YG
Sbjct: 167 HDEKRVRHHLLEEMADYGYDCWGRSGRVIEDAYG 200
>pdb|2QEN|A Chain A, The Walker-type Atpase Paby2304 Of Pyrococcus Abyssi
Length = 350
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 32/128 (25%), Positives = 49/128 (38%), Gaps = 28/128 (21%)
Query: 110 YPFNLMFQTS-VGPSGLTAAYVRPETAPGIFVNFKDLYYNNGNKLPFAAAQIGQAFRNEI 168
YP L+ VG S L A++ PGI ++ ++LY G+
Sbjct: 31 YPLTLLLGIRRVGKSSLLRAFL--NERPGILIDCRELYAERGHI---------------- 72
Query: 169 SPRQGFSRVREFTLAEIEHFVDPKDKSHPKFSEVKNLEFLMF-PREEQMSAQSAKKIRLG 227
RE + E++ + P K KF NL+FL PR+ + + LG
Sbjct: 73 --------TREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLG 124
Query: 228 EAVSRGIV 235
E + IV
Sbjct: 125 EELGEFIV 132
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
0.320 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,944,858
Number of Sequences: 62578
Number of extensions: 357133
Number of successful extensions: 976
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 959
Number of HSP's gapped (non-prelim): 12
length of query: 310
length of database: 14,973,337
effective HSP length: 99
effective length of query: 211
effective length of database: 8,778,115
effective search space: 1852182265
effective search space used: 1852182265
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)