254780757

glycyl-tRNA synthetase subunit alpha

GeneID in NCBI database:	8209762	Locus tag:	CLIBASIA_03220
Protein GI in NCBI database:	254780757	Protein Accession:	YP_003065170.1
Gene range:	-(509284, 510207)	Protein Length:	307aa
Gene description:	glycyl-tRNA synthetase subunit alpha
COG prediction:	none
KEGG prediction:	glyQ; glycyl-tRNA synthetase subunit alpha (EC:6.1.1.14); K01878 glycyl-tRNA synthetase alpha chain [EC:6.1.1.14]
SEED prediction:	Glycyl-tRNA synthetase alpha chain (EC 6.1.1.14)
Pathway involved in KEGG:	Aminoacyl-tRNA biosynthesis [PATH:las00970]
Subsystem involved in SEED:	tRNA aminoacylation, Gly
sequence	sequence profile

Prediction of Local Sequence Properties

Source	Summary	Result

	scaler
NCBI Database	sequence
PSIPRED	secondary structure
SSPRO	secondary structure
DISEMBL	coil and loop
DISEMBL	flexible loop
SEG	low complexity
DISOPRED	disordered
DISEMBL	missing residues
DISPRO	disordered
TMHMM	none TM-Helix
TOPPRED	none TM-Helix
HMMTOP	none TM-Helix
MEMSAT	none TM-Helix
MEMSAT_SVM	none TM-Helix
PHOBIUS	none TM-Helix
SignalP_HMM	no
SignalP_NN	no
COILS	coiled coil
70% MSA	conservation map
90% MSA	conservation map

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------

MAPIHNKKNDLSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMTPNGGH

ccccccccccccHHHHHHHHHHHHHHcccEEEEccccccccccccHHHHHHHHcccccccEEccccccccccccccccHHHHHEEEEEEEEccccccHHHHHHHHHHHHcccHHHccEEEEEcccccccccccccccEEEEcccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcccccEEEEEEcccccccccEEEEEEccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHccccccc

ccccccccccHHHHHHHHHHHHHHHHcccEEEEccccccccccccHHHHHHHcccccccEEEEccccccccccccccccccccccEEEEEEccccHHHHHHHHHHHHHHccccccccEEEEEcccccccccccccEEEEEEcccEEcEEEEEEEcccccccccccEEcHHHHHHHHHHcccccEEEEEEcccccccEEEccccccccEEEcEEccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHcccccc

mapihnkkndlsFQNIILTLTQYWAQqgctilqpydmevgagtfhpsttlralgplswkaayvqpsrrpldgryaenpnrlqhYYQFQViikpnplnlqNLYIESLkavgidplihdvrfvednwesptlgawglgwecwcdgmeisqfTYFQQvcgiecspisgeiTYGLERLAMYVQNVNSVYDIVFNAIegqnvlygdifaqseQEYSRynfeyanpeilhnhfiDSEKECLDLLkkgipnehhrhhlcvfpaydqcIKASHIFNLldargvistTERQRYILRIRSLAKACGeaflmtpnggh

mapihnkkndlsFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACgeaflmtpnggh

*************QNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMTP****

*****NKKNDLSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMT*****

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

Original result of PSI-BLAST first 2 iterations

Identity	Alignment graph	Length	Definition	Round	E-value
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
315121920		308	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi	1	1e-168
222085062		319	glycyl-tRNA synthetase [Agrobacterium radiobacter K84]	1	1e-140
307309350		320	glycyl-tRNA synthetase, alpha subunit [Sinorhizobium me	1	1e-139
15964604		311	glycyl-tRNA synthetase subunit alpha [Sinorhizobium mel	1	1e-139
227821042		320	glycyl-tRNA synthetase subunit alpha [Sinorhizobium fre	1	1e-139
150395688		320	glycyl-tRNA synthetase subunit alpha [Sinorhizobium med	1	1e-139
325292021		320	glycyl-tRNA synthetase alpha chain [Agrobacterium sp. H	1	1e-139
159184400		310	glycyl-tRNA synthetase subunit alpha [Agrobacterium tum	1	1e-138
86356527		318	glycyl-tRNA synthetase subunit alpha [Rhizobium etli CF	1	1e-138
218682936		318	glycyl-tRNA synthetase subunit alpha [Rhizobium etli CI	1	1e-138

>gi\|315121920\|ref\|YP_004062409.1\| glycyl-tRNA synthetase subunit alpha [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 308	Back alignment and organism information

 Score =  593 bits (1530), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 277/307 (90%), Positives = 292/307 (95%)

Query: 1   MAPIHNKKNDLSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKA 60
           MAPIH+KKN  SFQNI+L LT+YWA+QGCTILQPYDMEVGAGTFHPSTTLRALGPL WKA
Sbjct: 1   MAPIHDKKNKTSFQNIVLILTEYWAKQGCTILQPYDMEVGAGTFHPSTTLRALGPLPWKA 60

Query: 61  AYVQPSRRPLDGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRF 120
           AYVQPSRRPLDGRYA+NPNRLQHYYQFQVIIKPNPL+LQ LYIESL+AVGIDPL+HD+RF
Sbjct: 61  AYVQPSRRPLDGRYAQNPNRLQHYYQFQVIIKPNPLDLQKLYIESLQAVGIDPLVHDIRF 120

Query: 121 VEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQN 180
           VEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQN
Sbjct: 121 VEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQN 180

Query: 181 VNSVYDIVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKK 240
           VNSV+DIVFN IEG+NVLYGDIFAQSEQEYSRYNFEYAN  ILHNHFID EKEC  LL+ 
Sbjct: 181 VNSVFDIVFNTIEGKNVLYGDIFAQSEQEYSRYNFEYANTNILHNHFIDHEKECQKLLEA 240

Query: 241 GIPNEHHRHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFL 300
           G PN+HH HHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFL
Sbjct: 241 GAPNKHHNHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFL 300

Query: 301 MTPNGGH 307
           MT +GG+
Sbjct: 301 MTSSGGY 307

Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

>gi\|222085062\|ref\|YP_002543592.1\| glycyl-tRNA synthetase [Agrobacterium radiobacter K84] Length = 319	Back alignment and organism information

>gi\|307309350\|ref\|ZP_07589013.1\| glycyl-tRNA synthetase, alpha subunit [Sinorhizobium meliloti BL225C] Length = 320	Back alignment and organism information

>gi\|15964604\|ref\|NP_384957.1\| glycyl-tRNA synthetase subunit alpha [Sinorhizobium meliloti 1021] Length = 311	Back alignment and organism information

>gi\|227821042\|ref\|YP_002825012.1\| glycyl-tRNA synthetase subunit alpha [Sinorhizobium fredii NGR234] Length = 320	Back alignment and organism information

>gi\|150395688\|ref\|YP_001326155.1\| glycyl-tRNA synthetase subunit alpha [Sinorhizobium medicae WSM419] Length = 320	Back alignment and organism information

>gi\|325292021\|ref\|YP_004277885.1\| glycyl-tRNA synthetase alpha chain [Agrobacterium sp. H13-3] Length = 320	Back alignment and organism information

>gi\|159184400\|ref\|NP_353661.2\| glycyl-tRNA synthetase subunit alpha [Agrobacterium tumefaciens str. C58] Length = 310	Back alignment and organism information

>gi\|86356527\|ref\|YP_468419.1\| glycyl-tRNA synthetase subunit alpha [Rhizobium etli CFN 42] Length = 318	Back alignment and organism information

>gi\|218682936\|ref\|ZP_03530537.1\| glycyl-tRNA synthetase subunit alpha [Rhizobium etli CIAT 894] Length = 318	Back alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

Identity	Alignment graph	Length	Definition	E-value
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
PRK09348		283	PRK09348, glyQ, glycyl-tRNA synthetase subunit alpha; V	1e-173
pfam02091		284	pfam02091, tRNA-synt_2e, Glycyl-tRNA synthetase alpha s	1e-136
cd00733		279	cd00733, GlyRS_alpha_core, Class II Glycyl-tRNA synthet	1e-134
PRK14908		1000	PRK14908, PRK14908, glycyl-tRNA synthetase; Provisional	1e-131
TIGR00388		293	TIGR00388, glyQ, glycyl-tRNA synthetase, tetrameric typ	1e-128
COG0752		298	COG0752, GlyQ, Glycyl-tRNA synthetase, alpha subunit [T	1e-147
cd00768		211	cd00768, class_II_aaRS-like_core, Class II tRNA amino-a	7e-08

>gnl\|CDD\|181790 PRK09348, glyQ, glycyl-tRNA synthetase subunit alpha; Validated	Back alignment and domain information

>gnl\|CDD\|111033 pfam02091, tRNA-synt_2e, Glycyl-tRNA synthetase alpha subunit	Back alignment and domain information

>gnl\|CDD\|29812 cd00733, GlyRS_alpha_core, Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain	Back alignment and domain information

>gnl\|CDD\|184901 PRK14908, PRK14908, glycyl-tRNA synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|129483 TIGR00388, glyQ, glycyl-tRNA synthetase, tetrameric type, alpha subunit	Back alignment and domain information

>gnl\|CDD\|31095 COG0752, GlyQ, Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|29813 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl synthetase-like catalytic core domain	Back alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

Identity	Alignment graph	Length	Definition	Probability
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
PRK09348		291	glyQ glycyl-tRNA synthetase subunit alpha; Validated	100.0
cd00733		279	GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS	100.0
pfam02091		284	tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit.	100.0
COG0752		298	GlyQ Glycyl-tRNA synthetase, alpha subunit [Translation	100.0
TIGR00388		295	glyQ glycyl-tRNA synthetase, alpha subunit; InterPro: I	100.0
PRK13902		898	alaS lanyl-tRNA synthetase; Provisional	98.14
PRK01584		593	alanyl-tRNA synthetase; Provisional	97.77
PRK00252		864	alaS alanyl-tRNA synthetase; Reviewed	97.48
COG0013		879	AlaS Alanyl-tRNA synthetase [Translation, ribosomal str	96.96
cd00673		232	AlaRS_core Alanyl-tRNA synthetase (AlaRS) class II core	96.65
cd00768		211	class_II_aaRS-like_core Class II tRNA amino-acyl synthe	97.15
PRK10748		238	flavin mononucleotide phosphatase; Provisional	94.39
PRK09449		225	nucleotidase; Provisional	91.34

>PRK09348 glyQ glycyl-tRNA synthetase subunit alpha; Validated	Back alignment and domain information

>cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain	Back alignment and domain information

>pfam02091 tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit	Back alignment and domain information

>COG0752 GlyQ Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR00388 glyQ glycyl-tRNA synthetase, alpha subunit; InterPro: IPR002310 The aminoacyl-tRNA synthetases (6	Back alignment and domain information

>PRK13902 alaS lanyl-tRNA synthetase; Provisional	Back alignment and domain information

>PRK01584 alanyl-tRNA synthetase; Provisional	Back alignment and domain information

>PRK00252 alaS alanyl-tRNA synthetase; Reviewed	Back alignment and domain information

>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd00673 AlaRS_core Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain	Back alignment and domain information

>cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain	Back alignment and domain information

>PRK10748 flavin mononucleotide phosphatase; Provisional	Back alignment and domain information

>PRK09449 nucleotidase; Provisional	Back alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

Original result of PSI-BLAST

Identity	Alignment graph	Length	Definition	E-value
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
1j5w_A		298	Crystal Structure Of Glycyl-Trna Synthetase Alpha C	1e-138
3rf1_A		311	The Crystal Structure Of Glycyl-Trna Synthetase Sub	1e-138

>gi|22218825|pdb|1J5W|A Chain A, Crystal Structure Of Glycyl-Trna Synthetase Alpha Chain (Tm0216) From Thermotoga Maritima At 1.95 A Resolution Length = 298

Back alignment and structure

 Score =  496 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 160/293 (54%), Positives = 204/293 (69%), Gaps = 14/293 (4%)

Query: 12  SFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLD 71
             Q++I  L  +WA +GC + QPYD EVGAGTFHP+T   +L    WK AYVQPSRRP D
Sbjct: 14  YLQDVIXKLNDFWASKGCLLEQPYDXEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPTD 73

Query: 72  GRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLG 131
           GRY ENPNRLQ Y+Q+QVIIKP+P N Q LY+ESL+ +GI+   HD+RFVEDNWESPTLG
Sbjct: 74  GRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTLG 133

Query: 132 AWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFNA 191
           AWG+GWE W DG EI+QFTYFQQ+ GI    I  EITYGLER+A Y+Q V++VY++ +N 
Sbjct: 134 AWGVGWEVWLDGXEITQFTYFQQIGGISLKDIPLEITYGLERIAXYLQGVDNVYEVQWN- 192

Query: 192 IEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHHL 251
              +NV YGD+F ++E+E+S +NFE AN  +L  HF + EKE   L++K +         
Sbjct: 193 ---ENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNL--------- 240

Query: 252 CVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMTPN 304
              PAYD  +K SH FNLLDARG IS ++RQ Y+ RI++ A+     FL    
Sbjct: 241 -YLPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAXARKAARVFLEVQA 292

PyMOL of 1j5w

>gi|329666299|pdb|3RF1|A Chain A, The Crystal Structure Of Glycyl-Trna Synthetase Subunit Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc 11168 Length = 311

Back alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

Identity	Alignment graph	Length	Definition	E-value
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
1j5w_A		298	Glycyl-tRNA synthetase alpha chain; structural genomics	1e-148
2ztg_A		739	Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthet	3e-05

>1j5w_A Glycyl-tRNA synthetase alpha chain; structural genomics, TM0216, JCSG, PSI, protein structure initiative; 1.95A {Thermotoga maritima} SCOP: d.104.1.1 Length = 298	Back alignment and structure

 Score =  519 bits (1338), Expect = e-148
 Identities = 163/292 (55%), Positives = 210/292 (71%), Gaps = 14/292 (4%)

Query: 11  LSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPL 70
           +  Q++I+ L  +WA +GC + QPYDMEVGAGTFHP+T   +L    WK AYVQPSRRP 
Sbjct: 13  MYLQDVIMKLNDFWASKGCLLEQPYDMEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPT 72

Query: 71  DGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTL 130
           DGRY ENPNRLQ Y+Q+QVIIKP+P N Q LY+ESL+ +GI+   HD+RFVEDNWESPTL
Sbjct: 73  DGRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTL 132

Query: 131 GAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFN 190
           GAWG+GWE W DGMEI+QFTYFQQ+ GI    I  EITYGLER+AMY+Q V++VY++ +N
Sbjct: 133 GAWGVGWEVWLDGMEITQFTYFQQIGGISLKDIPLEITYGLERIAMYLQGVDNVYEVQWN 192

Query: 191 AIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHH 250
               +NV YGD+F ++E+E+S +NFE AN  +L  HF + EKE   L++K +        
Sbjct: 193 ----ENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLY------- 241

Query: 251 LCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMT 302
               PAYD  +K SH FNLLDARG IS ++RQ Y+ RI+++A+     FL  
Sbjct: 242 ---LPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAMARKAARVFLEV 290

PyMOL of 1j5w

>2ztg_A Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthetase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: A5A; 2.20A {Archaeoglobus fulgidus} Length = 739	Back alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

Identity	Alignment graph	Length	Definition	Probability
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
1j5w_A		298	Glycyl-tRNA synthetase alpha chain; structural genomics	100.0
2ztg_A		739	Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthet	98.84
2zze_A		752	Alanyl-tRNA synthetase; ligase, hydrolase; HET: MLY; 2.	98.56
1yfs_A		465	Alanyl-tRNA synthetase; alpha-beta fold, helix-loop-hel	98.25
3hy0_A		441	Alanyl-tRNA synthetase; aminoacyl-tRNA synthetase, liga	98.13
3dsq_A		288	Pyrrolysyl-tRNA synthetase; homodimer, aminoacyl-tRNA s	94.71
2zin_A		291	Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthetase,	93.49
3ib6_A		189	Uncharacterized protein; structural genomics, unknown f	93.28
3l4g_A		508	Phenylalanyl-tRNA synthetase alpha chain; aminoacylatio	91.24
2du7_A		549	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase	90.58

>1j5w_A Glycyl-tRNA synthetase alpha chain; structural genomics, TM0216, JCSG, PSI, protein structure initiative; 1.95A {Thermotoga maritima} SCOP: d.104.1.1	Back alignment and structure

Probab=100.00  E-value=0  Score=1221.61  Aligned_cols=290  Identities=57%  Similarity=1.021  Sum_probs=284.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCCE
Q ss_conf             43356777799999999999986695896116754333224857898744834401676415578876554667750011
Q gi|254780757|r    4 IHNKKNDLSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDGRYAENPNRLQH   83 (307)
Q Consensus         4 ~~~~~~~~~fq~ii~~L~~fW~~~GC~i~qpyd~e~GAgT~hp~T~lr~lg~~pw~~aYvqPsrRP~DgRYGeNPNRlq~   83 (307)
                      +....+.|+||+||++||+||+++||+|+||||+|||||||||+|||||||||||++|||||||||+|||||+|||||||
T Consensus         6 ~~~~~~~m~fq~~i~~L~~fW~~~GC~i~qpyd~evGAgT~~P~T~lr~lgp~pw~~aYvqPsrRP~DgRYGeNPNRLq~   85 (298)
T 1j5w_A            6 IHHHHHHMYLQDVIMKLNDFWASKGCLLEQPYDMEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPTDGRYGENPNRLQR   85 (298)
T ss_dssp             -------CCHHHHHHHHHHHHHHTTCEECCCCSSCCSSGGGSHHHHTGGGCSSCEEEEEEEEEECCC-----CCTTCCSE
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCHHCE
T ss_conf             33210322299999999999987796887675542464668889998631987632664246779998876789323110


Q ss_pred             EEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCHHHHCCCCEEEEECCEEEHHHHHHHHHCCCCCCCC
Q ss_conf             44445575798335899999999981999621717988328887001101232176887874147778998668257751
Q gi|254780757|r   84 YYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPI  163 (307)
Q Consensus        84 y~QfQVilKPsp~niq~lYl~SL~~iGid~~~hDIrFveDnWEsPtLGAwGlGWEvwldGMEItQFTYFQQvGGi~c~pv  163 (307)
                      ||||||||||||+|+|+|||+||++||||+++||||||||||||||||||||||||||||||||||||||||||++|+||
T Consensus        86 y~QfQVilKPsp~n~q~lYL~SL~~igid~~~hDIrFveDnWEsPtLGAwGlGWEVwldGMEItQFTYFQQvGGi~c~pv  165 (298)
T 1j5w_A           86 YFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTLGAWGVGWEVWLDGMEITQFTYFQQIGGISLKDI  165 (298)
T ss_dssp             EEEEEEEEESCCSSHHHHHHHHHHHTTCCTTTSCEEEEEECCEEGGGTEEEEEEEEEETTEEEEEEEEEEEBTTBCCSSC
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCEEEEEEEEECCEEEEEEEEEEEECCEECCCC
T ss_conf             03458997789466899999999983999202144786227778761211200599988768752440311277533442


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             45678789999999869982113320688878831106244746997776350179899999999999999999850066
Q gi|254780757|r  164 SGEITYGLERLAMYVQNVNSVYDIVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIP  243 (307)
Q Consensus       164 ~~EiTYGLERiaMylQ~vdnvyDl~wn~~~~~~vtYGdif~q~E~E~S~YNFE~Ad~~~L~~~F~~yE~Ea~rLle~~LP  243 (307)
                      ++||||||||||||||+|||||||+||    +++||||||+|+|+|||+||||+||+++|+++|++||+||++||+++||
T Consensus       166 ~~EiTYGLERiaMylQ~vdnv~Dl~w~----~~vtYGDif~q~E~E~S~YNFe~ad~~~L~~~F~~~E~Ea~rLle~~L~  241 (298)
T 1j5w_A          166 PLEITYGLERIAMYLQGVDNVYEVQWN----ENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLY  241 (298)
T ss_dssp             CEEEEEEHHHHHHHHHTCSSGGGCEEE----TTEEHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHTTCH
T ss_pred             CHHHHHHHHHHHHHHHCCCHHHCCCCC----CCCCHHHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             201002499999998487335030057----9974327753558999885535339999999999999999999866999


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CC
Q ss_conf             53233553013828999999999878883875017889999999999999999999854516-89
Q gi|254780757|r  244 NEHHRHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMTPNG-GH  307 (307)
Q Consensus       244 ~~~~~~~~lvlPAYD~~LKaSH~FNLLDARGaISVTERq~YI~RIR~Lak~~A~ayl~~re~-g~  307 (307)
                                +||||+||||||+||||||||||||||||+||+|||+|||+||++|+++|+. |+
T Consensus       242 ----------lPAYD~~LKaSH~FNLLDARGaISVtER~~YI~RVR~LAk~~A~~y~e~r~~lgf  296 (298)
T 1j5w_A          242 ----------LPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAMARKAARVFLEVQANENS  296 (298)
T ss_dssp             ----------HHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC---
T ss_pred             ----------CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             ----------6669999999888888763478758999999999999999999999998875599

PyMOL of 1j5w

>2ztg_A Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthetase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: A5A; 2.20A {Archaeoglobus fulgidus}	Back alignment and structure

>2zze_A Alanyl-tRNA synthetase; ligase, hydrolase; HET: MLY; 2.16A {Pyrococcus horikoshii} PDB: 2zzf_A 2zzg_A*	Back alignment and structure

>1yfs_A Alanyl-tRNA synthetase; alpha-beta fold, helix-loop-helix motif, amino acid binding, ligase; 2.08A {Aquifex aeolicus} SCOP: a.203.1.1 d.104.1.1 PDB: 1yfr_A* 1riq_A 1yft_A 1ygb_A 3htz_A	Back alignment and structure

>3hy0_A Alanyl-tRNA synthetase; aminoacyl-tRNA synthetase, ligase, protein biosynthesis, nucleotide-binding, amino acid-binding, acetylation; HET: G5A EPE; 1.90A {Escherichia coli} PDB: 3hxz_A* 3hy1_A* 3hxv_A* 3hxu_A* 3hxw_A* 3hxx_A* 3hxy_A*	Back alignment and structure

>3dsq_A Pyrrolysyl-tRNA synthetase; homodimer, aminoacyl-tRNA synthetase, ligase; 2.10A {Desulfitobacterium hafniense} PDB: 2znj_A 2zni_A	Back alignment and structure

>2zin_A Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthetase, pyrrolysine, ATP analogue, non-natural amino acid, unnatural amino acid, ATP-binding; HET: ANP LBY; 1.79A {Methanosarcina mazei} PDB: 2e3c_A* 2zcd_A* 2zce_A* 2zio_A* 2q7e_A* 2q7g_A* 2q7h_A* 2zim_A*	Back alignment and structure

>3ib6_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein structure initiative; 2.20A {Listeria monocytogenes CLIP81459}	Back alignment and structure

>3l4g_A Phenylalanyl-tRNA synthetase alpha chain; aminoacylation, tRNA-binding, DNA-binding domain, four-helix acetylation, aminoacyl-tRNA synthetase; HET: PHE; 3.30A {Homo sapiens}	Back alignment and structure

>2du7_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase, structural genomics, NPPSFA; 3.60A {Methanocaldococcus jannaschii}	Back alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

Identity	Alignment graph	Length	Definition	E-value
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
d1j5wa_		281	d.104.1.1 (A:) Glycyl-tRNA synthetase (GlyRS) alpha cha	1e-139

>d1j5wa_ d.104.1.1 (A:) Glycyl-tRNA synthetase (GlyRS) alpha chain {Thermotoga maritima [TaxId: 2336]} Length = 281	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Class II aaRS and biotin synthetases
superfamily: Class II aaRS and biotin synthetases
family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
domain: Glycyl-tRNA synthetase (GlyRS) alpha chain
species: Thermotoga maritima [TaxId: 2336]

 Score =  488 bits (1258), Expect = e-139
 Identities = 163/292 (55%), Positives = 210/292 (71%), Gaps = 14/292 (4%)

Query: 11  LSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPL 70
           +  Q++I+ L  +WA +GC + QPYDMEVGAGTFHP+T   +L    WK AYVQPSRRP 
Sbjct: 1   MYLQDVIMKLNDFWASKGCLLEQPYDMEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPT 60

Query: 71  DGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTL 130
           DGRY ENPNRLQ Y+Q+QVIIKP+P N Q LY+ESL+ +GI+   HD+RFVEDNWESPTL
Sbjct: 61  DGRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTL 120

Query: 131 GAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFN 190
           GAWG+GWE W DGMEI+QFTYFQQ+ GI    I  EITYGLER+AMY+Q V++VY++ +N
Sbjct: 121 GAWGVGWEVWLDGMEITQFTYFQQIGGISLKDIPLEITYGLERIAMYLQGVDNVYEVQWN 180

Query: 191 AIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHH 250
               +NV YGD+F ++E+E+S +NFE AN  +L  HF + EKE   L++K +        
Sbjct: 181 ----ENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLY------- 229

Query: 251 LCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMT 302
               PAYD  +K SH FNLLDARG IS ++RQ Y+ RI+++A+     FL  
Sbjct: 230 ---LPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAMARKAARVFLEV 278

PyMOL of d1j5wa_

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

Identity	Alignment graph	Length	Definition	Probability
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
d1j5wa_		281	Glycyl-tRNA synthetase (GlyRS) alpha chain {Thermotoga	100.0
d1riqa2		236	Alanyl-tRNA synthetase (AlaRS) {Aquifex aeolicus [TaxId	98.02

>d1j5wa_ d.104.1.1 (A:) Glycyl-tRNA synthetase (GlyRS) alpha chain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Class II aaRS and biotin synthetases
superfamily: Class II aaRS and biotin synthetases
family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
domain: Glycyl-tRNA synthetase (GlyRS) alpha chain
species: Thermotoga maritima [TaxId: 2336]

Probab=100.00  E-value=0  Score=1223.22  Aligned_cols=281  Identities=58%  Similarity=1.037  Sum_probs=278.6

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEE
Q ss_conf             77999999999999866958961167543332248578987448344016764155788765546677500114444557
Q gi|254780757|r   11 LSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDGRYAENPNRLQHYYQFQVI   90 (307)
Q Consensus        11 ~~fq~ii~~L~~fW~~~GC~i~qpyd~e~GAgT~hp~T~lr~lg~~pw~~aYvqPsrRP~DgRYGeNPNRlq~y~QfQVi   90 (307)
                      |+|||||++||+||+++||+|+||||+|||||||||+||||+||||||++|||||||||+|||||+||||||||||||||
T Consensus         1 m~fq~~i~~L~~~W~~~gC~i~qpyd~evGAgT~~p~T~lr~lgp~pw~~ayvqpsrRP~DgRYg~NPNRlq~y~QfQVi   80 (281)
T d1j5wa_           1 MYLQDVIMKLNDFWASKGCLLEQPYDMEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPTDGRYGENPNRLQRYFQYQVI   80 (281)
T ss_dssp             CCHHHHHHHHHHHHHHTTCEECCCCSSCCSSGGGSHHHHTGGGCSSCEEEEEEEEEECCC-----CCTTCCSEEEEEEEE
T ss_pred             CCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHEEEE
T ss_conf             96899999999999878978977765544646687588874049987532343556688654335892044345530235


Q ss_pred             ECCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCHHHHCCCCEEEEECCEEEHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf             57983358999999999819996217179883288870011012321768878741477789986682577514567878
Q gi|254780757|r   91 IKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYG  170 (307)
Q Consensus        91 lKPsp~niq~lYl~SL~~iGid~~~hDIrFveDnWEsPtLGAwGlGWEvwldGMEItQFTYFQQvGGi~c~pv~~EiTYG  170 (307)
                      |||||+|+|+|||+||++||||+++||||||||||||||||||||||||||||||||||||||||||++|+||++|||||
T Consensus        81 ~KPsp~n~q~lyL~SL~~igid~~~hDIrfvEDnWEsPtlGAwGlGWEVwldGMEItQFTYFQQvGg~~c~pv~~EiTYG  160 (281)
T d1j5wa_          81 IKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTLGAWGVGWEVWLDGMEITQFTYFQQIGGISLKDIPLEITYG  160 (281)
T ss_dssp             EESCCSSHHHHHHHHHHHTTCCTTTSCEEEEEECCEEGGGTEEEEEEEEEETTEEEEEEEEEEEBTTBCCSSCCEEEEEE
T ss_pred             ECCCCCCHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCEEEEEEEEECCEEEEEEEHHHHHCCCCCCCCCHHHHHH
T ss_conf             05894128999999999819993214257873167687602102224788767366532163563683256530554432


Q ss_pred             HHHHHHHHCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             99999998699821133206888788311062447469977763501798999999999999999998500665323355
Q gi|254780757|r  171 LERLAMYVQNVNSVYDIVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHH  250 (307)
Q Consensus       171 LERiaMylQ~vdnvyDl~wn~~~~~~vtYGdif~q~E~E~S~YNFE~Ad~~~L~~~F~~yE~Ea~rLle~~LP~~~~~~~  250 (307)
                      |||||||||+|||||||.||    +++||||||+|+|+|||+||||+||+++|+++|++||+||++|++++||       
T Consensus       161 LERiaMylQ~vd~v~Dl~wn----~~vtYgDvf~q~E~E~S~YNFE~Ad~~~L~~~F~~yE~Ea~~Lle~~L~-------  229 (281)
T d1j5wa_         161 LERIAMYLQGVDNVYEVQWN----ENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLY-------  229 (281)
T ss_dssp             HHHHHHHHHTCSSGGGCEEE----TTEEHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHTTCH-------
T ss_pred             HHHHHHHHHCCCHHEEEECC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-------
T ss_conf             89999998486404032224----8944679887769999998698731999999999999999999865998-------


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             3013828999999999878883875017889999999999999999999854516
Q gi|254780757|r  251 LCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFLMTPNG  305 (307)
Q Consensus       251 ~lvlPAYD~~LKaSH~FNLLDARGaISVTERq~YI~RIR~Lak~~A~ayl~~re~  305 (307)
                         +||||+||||||+||||||||||||||||+||+|||+|||+||++|+++|+.
T Consensus       230 ---lPAYD~~LKaSH~FNLLDARGaISVTERa~YI~RIR~LAk~~a~~yle~r~n  281 (281)
T d1j5wa_         230 ---LPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAMARKAARVFLEVQAN  281 (281)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             ---CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             ---5279999998878764611688548998999999999999999999986459

PyMOL of d1j5wa_

>d1riqa2 d.104.1.1 (A:1-236) Alanyl-tRNA synthetase (AlaRS) {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

Identity	Alignment graph	Length	Definition	E-value
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus L
1j5w_A_1-199		199	(A:1-199) Glycyl-tRNA synthetase alpha chain; stru	1e-100
1j5w_A_200-298		99	(A:200-298) Glycyl-tRNA synthetase alpha chain; st	2e-35

>1j5w_A (A:1-199) Glycyl-tRNA synthetase alpha chain; structural genomics, TM0216, JCSG, PSI, protein structure initiative; 1.95A {Thermotoga maritima}Length = 199	Back alignment and structure

 Score =  357 bits (919), Expect = e-100
 Identities = 120/198 (60%), Positives = 148/198 (74%), Gaps = 4/198 (2%)

Query: 4   IHNKKNDLSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYV 63
           IH+  +    Q++I  L  +WA +GC + QPYD EVGAGTFHP+T   +L    WK AYV
Sbjct: 6   IHHHHHHXYLQDVIXKLNDFWASKGCLLEQPYDXEVGAGTFHPATFFGSLRKGPWKVAYV 65

Query: 64  QPSRRPLDGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVED 123
           QPSRRP DGRY ENPNRLQ Y+Q+QVIIKP+P N Q LY+ESL+ +GI+   HD+RFVED
Sbjct: 66  QPSRRPTDGRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVED 125

Query: 124 NWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNS 183
           NWESPTLGAWG+GWE W DG EI+QFTYFQQ+ GI    I  EITYGLER+A Y+Q V++
Sbjct: 126 NWESPTLGAWGVGWEVWLDGXEITQFTYFQQIGGISLKDIPLEITYGLERIAXYLQGVDN 185

Query: 184 VYDIVFNAIEGQNVLYGD 201
           VY++ +N    +NV YGD
Sbjct: 186 VYEVQWN----ENVKYGD 199

PyMOL of 1j5w

>1j5w_A (A:200-298) Glycyl-tRNA synthetase alpha chain; structural genomics, TM0216, JCSG, PSI, protein structure initiative; 1.95A {Thermotoga maritima}Length = 99	Back alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

Identity	Alignment graph	Length	Definition	Probability
Target		307	glycyl-tRNA synthetase subunit alpha [Candidatus Liberi
1j5w_A_1-199		199	Glycyl-tRNA synthetase alpha chain; structural gen	100.0
2ztg_A_1-260		260	Alanyl-tRNA synthetase; class-II aminoacyl-tRNA sy	98.01
2zze_A_1-266		266	Alanyl-tRNA synthetase; ligase, hydrolase; HET: ML	97.97
1c0a_A_129-271_422-557		279	Aspartyl tRNA synthetase; protein-RNA complex; HET	97.25
1yfs_A_1-237		237	Alanyl-tRNA synthetase; alpha-beta fold, helix-loo	96.93
3hy0_A_1-252		252	Alanyl-tRNA synthetase; aminoacyl-tRNA synthetase,	96.69
1l0w_A_135-278_415-546		276	Aspartyl-tRNA synthetase; space-grown crystal, dim	95.69
1j5w_A_200-298		99	Glycyl-tRNA synthetase alpha chain; structural gen	100.0

>1j5w_A (A:1-199) Glycyl-tRNA synthetase alpha chain; structural genomics, TM0216, JCSG, PSI, protein structure initiative; 1.95A {Thermotoga maritima}	Back alignment and structure

Probab=100.00  E-value=0  Score=856.45  Aligned_cols=195  Identities=62%  Similarity=1.127  Sum_probs=191.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             64335677779999999999998669589611675433322485789874483440167641557887655466775001
Q gi|254780757|r    3 PIHNKKNDLSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDGRYAENPNRLQ   82 (307)
Q Consensus         3 ~~~~~~~~~~fq~ii~~L~~fW~~~GC~i~qpyd~e~GAgT~hp~T~lr~lg~~pw~~aYvqPsrRP~DgRYGeNPNRlq   82 (307)
                      .+..++++++||+||++||+||+++||+|+||||+|||||||||+|||||||||||++|||||||||+||||||||||||
T Consensus         5 ~~~~~~~~~~fq~~I~~Lq~fW~~~GC~i~qpyd~evGAGT~hpaTflralgpepw~~aYVqPsrRP~DgRYGeNPNRLq   84 (199)
T 1j5w_A            5 KIHHHHHHXYLQDVIXKLNDFWASKGCLLEQPYDXEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPTDGRYGENPNRLQ   84 (199)
T ss_dssp             --------CCHHHHHHHHHHHHHHTTCEECCCCSSCCSSGGGSHHHHTGGGCSSCEEEEEEEEEECCC-----CCTTCCS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCHHC
T ss_conf             23321021329999999999997779688777654336465888999864198763255424677999887678930320


Q ss_pred             EEEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCHHHHCCCCEEEEECCEEEHHHHHHHHHCCCCCCC
Q ss_conf             14444557579833589999999998199962171798832888700110123217688787414777899866825775
Q gi|254780757|r   83 HYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSP  162 (307)
Q Consensus        83 ~y~QfQVilKPsp~niq~lYl~SL~~iGid~~~hDIrFveDnWEsPtLGAwGlGWEvwldGMEItQFTYFQQvGGi~c~p  162 (307)
                      |||||||||||||+|||+|||+||++||||+++|||||||||||||||||||||||||||||||||||||||||||+|+|
T Consensus        85 ~yyQfQViiKPsP~niq~lYL~SL~~lGid~~~hDIRFvEDnWEsPtLGAwGlGWEvwldGMEitQfTYFQqvGgi~~~p  164 (199)
T 1j5w_A           85 RYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTLGAWGVGWEVWLDGXEITQFTYFQQIGGISLKD  164 (199)
T ss_dssp             EEEEEEEEEESCCSSHHHHHHHHHHHTTCCTTTSCEEEEEECCEEGGGTEEEEEEEEEETTEEEEEEEEEEEBTTBCCSS
T ss_pred             EEEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCEEEEEEEEECCEEEEEEEEEEEECCEECCC
T ss_conf             01245789778947689999999998099910214478622777877011120059998876875344031027743344


Q ss_pred             CHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCH
Q ss_conf             145678789999999869982113320688878831106
Q gi|254780757|r  163 ISGEITYGLERLAMYVQNVNSVYDIVFNAIEGQNVLYGD  201 (307)
Q Consensus       163 v~~EiTYGLERiaMylQ~vdnvyDl~wn~~~~~~vtYGd  201 (307)
                      |++||||||||||||||+|||||||.||    +++||||
T Consensus       165 v~~EiTYGLERiamylQ~vd~v~dl~w~----~~~tYgd  199 (199)
T 1j5w_A          165 IPLEITYGLERIAXYLQGVDNVYEVQWN----ENVKYGD  199 (199)
T ss_dssp             CCEEEEEEHHHHHHHHHTCSSGGGCEEE----TTEEHHH
T ss_pred             CCHHHHHHHHHHHHHHHCCCHHHCCCCC----CCCCHHH
T ss_conf             2200001499999998387246222167----9974669

PyMOL of 1j5w

>2ztg_A (A:1-260) Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthetase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: A5A; 2.20A {Archaeoglobus fulgidus}	Back alignment and structure

>2zze_A (A:1-266) Alanyl-tRNA synthetase; ligase, hydrolase; HET: MLY; 2.16A {Pyrococcus horikoshii} PDB: 2zzf_A 2zzg_A*	Back alignment and structure

>1c0a_A (A:129-271,A:422-557) Aspartyl tRNA synthetase; protein-RNA complex; HET: 4SU H2U QUO G7M 5MU PSU AMP AMO; 2.40A {Escherichia coli}	Back alignment and structure

>1yfs_A (A:1-237) Alanyl-tRNA synthetase; alpha-beta fold, helix-loop-helix motif, amino acid binding, ligase; 2.08A {Aquifex aeolicus}	Back alignment and structure

>3hy0_A (A:1-252) Alanyl-tRNA synthetase; aminoacyl-tRNA synthetase, ligase, protein biosynthesis, nucleotide-binding, amino acid-binding, acetylation; HET: G5A EPE; 1.90A {Escherichia coli} PDB: 3hxz_A* 3hy1_A* 3hxv_A* 3hxu_A* 3hxw_A* 3hxx_A* 3hxy_A*	Back alignment and structure

>1l0w_A (A:135-278,A:415-546) Aspartyl-tRNA synthetase; space-grown crystal, dimeric enzyme, flexible domains, ligase; 2.01A {Thermus thermophilus}	Back alignment and structure

>1j5w_A (A:200-298) Glycyl-tRNA synthetase alpha chain; structural genomics, TM0216, JCSG, PSI, protein structure initiative; 1.95A {Thermotoga maritima}	Back alignment and structure

Protein GIs
254780773	254780772
254780771	254780770
255764481	254780768
254780767	254780766
254780765	254780764
peg_472	peg_473
254780763	254780762
peg_476	peg_477
254780761	254780760
254780759	254780758
254780757	255764482
254780755	254780754
254780753	254780752
254780751	254780750
254780749	254780748
254780747	peg_493
254780746	254780745
254780744	254780743
254780742	254780741
254780740	254780739
255764483	254780737
254780736	254780735
254780734	254780733
254780732	peg_509
255764484	254780730
254780729	254780728
254780727	255764485
254780725	254780724
254780723	254780722
254780721	254780720
254780719	254780718
peg_523	254780717
254780716	254780715
254780714	254780713
254780712	254780711
254780710	peg_532
254780709	254780708
254780707	255764486
254780705	254780704
254780703	255764487
254780701	peg_542
254780700	254780699
254780698	254780697
254780696	254780695
254780694	254780693
254780692	254780691
254780690	254780689
254780688	254780687
255764488	254780685
254780684	254780683
254780682	255764489
254780680	peg_563
254780679	254780678
254780677	254780676
254780675	254780674
peg_568	254780673
255764490	254780671
254780670	254780669
peg_574	254780668
254780667	254780666
255764491	peg_577
254780664	254780663
254780662	254780661
peg_582	254780660
254780659	254780658
254780657	255764492
254780655	254780654
254780653	254780652
254780651	254780650
peg_593	254780649
254780648	254780647
254780646	peg_598
254780645	254780644
255764493	254780642
254780641	254780640
peg_603	254780639
254780638	255764494
254780636	254780635
254780634	254780633
254780632	254780631
peg_612	254780630
254780629	254780628
254780627	254780626
254780625	254780624
254780623	254780622
254780621	254780620
254780619	254780618
254780617	254780616
254780615	254780614
254780613	254780612
254780611	254780610
peg_634	255764495
254780608	254780607
254780606	254780605
254780604	254780603
254780602	254780601
254780600	255764496
254780598	255764497
254780596	254780595
254780594	254780593
254780592	254780591
254780590	254780589
254780588	255764498
peg_658	254780586
254780585	254780584
254780583	254780582
254780581	255764499
254780579	254780578
254780577	254780576
254780575	255764500
peg_671	254780573
254780572	254780571
254780570	254780569
254780568	254780567
254780565	254780564
254780563	254780562
peg_683	254780561
255764501	254780559
254780558	254780557
254780556	254780555
peg_691	254780554
254780553	254780552
254780551	255764502
254780549	254780548
254780547	254780546
254780545	254780544
254780543	254780542
255764503	254780540
254780539	254780538
254780537	254780536
254780535	254780534
254780533	254780532
254780531	254780530
254780529	254780528
254780527	254780526
254780525	254780524
254780523	254780522
254780521	254780520
254780519	254780518
255764504	254780516
254780515	254780514
254780513	254780512
254780511	254780510
254780509	254780508
254780507	254780506
254780505	254780504
254780503	254780502
254780501	254780500
254780499	254780498
254780497	254780496
254780495	254780494
254780493	254780830
254780831	254780832
254780833	peg_753
peg_754	254780834
255764505	254780836
254780837	peg_759
254780838	254780839
254780840	254780841
254780842	254780843
254780844	254780845
254780846	254780847
254780848	254780849
254780850	254780851
254780852	254780853
254780854	254780855
254780856	254780857
254780858	254780859
254780860	254780861
254780862	254780863
254780864	254780865
254780866	254780867
254780868	254780869
peg_786	254780870
peg_788	peg_789
254780871	254780872
254780873	254780874
254780875	254780876
254780877	254780878
254780879	254780880
254780881	254780882
254780883	255764506
254780885	254780886
254780887	254780888
peg_804	254780889
254780890	254780891
254780892	254780893
254780894	254780895
254780896	peg_813
254780897	254780898
peg_816	peg_817
peg_818	254780899
254780900	254780901
254780902	254780903
254780904	254780905
254780906	254780907
254780908	254780909
255764507	254780911
254780912	254780913
254780914	peg_834
254780915	254780916
254780917	254780918
254780919	254780920
254780921	254780922
254780923	254780924
254780925	254780926
254780927	254780928
254780929	254780930
254780931	peg_851
peg_852	254780932
254780933	254780934
254780935	254780936
254780937	254780938
254780939	254780940
254780941	254780942
254780943	254780944
254780945	254780946
254780947	peg_869
254780948	254780949
255764508	peg_873
peg_874	254780951
254780952	254780953
254780954	254780955
peg_880	254780956
254780957	254780958
254780959	peg_885
254780960	peg_887
peg_888	peg_889
254780961	254780962
254780963	254780964
254780965	254780966
254780967	254780968
254780969	254780970
254780971	254780972
254780973	254780974
254780975	peg_905
254780976	254780977
254780978	254780979
254780980	peg_911
peg_912	254780981
peg_913	254780982
254780983	peg_916
254780984	254780985
254780986	254780987
254780988	254780989
254780990	254780991
254780992	254780993
254780994	254780995
254780996	254780997
254780998	254780999
peg_930	peg_931
254781000	254781001
254781002	254781003
254781004	peg_937
254781005	254781006
254781007	254781008
peg_942	254781009
254781010	peg_945
254781011	254781012
254781013	254781014
peg_950	254781015
254781016	254781017
254781018	254781019
254781020	255764509
254781022	254781023
254781024	254781025
peg_961	254781026
254781027	254781028
254781029	254781030
254781031	254781032
254781033	254781034
255764510	254781036
254781037	254781038
254781039	254781040
254781041	254781042
254781043	254781044
254781045	254781046
254781047	254781048
254781049	254781050
254781051	254781052
254781053	254781054
254781055	254781056
254781057	254781058
peg_993	254781059
254781060	254781061
254781062	254781063
254781064	254781065
254781066	254781067
254781068	254781069
254781070	254781071
254781072	254781073
254781074	254781075
254781076	254781077
254781078	254781079
254781080	254781081
254781082	254781083
254781084	254781085
254781086	254781087
254781088	254781089
254781090	254781091
254781092	254781093
254781094	254781095
254781096	254781097
254781098	254781099
254781100	254781101
254781102	254781103
254781104	255764511
254781106	254781107
254781108	254781109
254781110	peg_1044
254781111	254781112
254781113	254781114
254781115	255764512
255764513	254781118
254781119	254781120
254781121	254781122
254781123	254781124
254781125	peg_1058
254781126	254781127
254781128	254781129
254781130	254781131
peg_1064	254781132
254781133	254781134
254781135	254781136
254781137	254781138
254781139	254781140
peg_1073	peg_1074
254781141	254781142
254781143	254781144
254781145	peg_1078
peg_1079	peg_1080
254781146	254781147
peg_1083	254781148
254781149	peg_1086
peg_1087	254781150
254781151	254781152
peg_1090	254781153
254781154	254781155
254781156	254781157
254781158	254781159
peg_1096	254781160
254781161	254781162
254781163	peg_1101
254781164	254781165
254781166	254781167
254781168	254781169
peg_1107	254781170
254781171	254781172
255764514	254781174
254781175	254781176
254781177	254781178
254781179	254781180
254781181	peg_1120
254781182	254781183
peg_1123	254781184
254781185	254781186
254781187	254781188
peg_1128	254781189
254781190	254781191
254781192	254781193
254781194	255764515
254781196	254781197
254781198	254781199
peg_1140	255764516
peg_1142	255764517
254781202	254781203
254781204	254781205
254781206	254781207
254781208	254781209
254781210	254781211
254781212	254781213
254781214	254781215
254781216	254781217
254781218	254781219
254781220	254781221
254781222	254781223
254781224	254781225
254781226	254781227
254781228	254780122
254780123	254780124
254780125	254780126
254780127	254780128
254780129	254780130
254780131	254780132
254780133	254780134
254780135	254780136
peg_15	254780137
254780138	254780139
254780140	254780141
peg_21	254780142
254780143	254780144
254780145	peg_26
254780146	254780147
254780148	254780149
254780150	254780151
peg_33	peg_34
254780152	peg_36
254780153	254780154
254780155	254780156
254780157	254780158
peg_42	254780159
254780160	254780161
254780162	254780163
254780164	254780165
254780166	254780167
254780168	254780169
peg_54	254780170
254780171	254780172
254780173	254780174
peg_60	254780175
254780176	254780177
254780178	254780179
254780180	254780181
254780182	254780183
254780184	254780185
254780186	254780187
254780188	peg_74
peg_75	254780189
254780190	254780191
255764460	peg_80
254780193	peg_82
254780194	254780195
254780196	254780197
254780198	254780199
254780200	254780201
254780202	peg_91
254780203	254780204
254780205	254780206
254780207	254780208
peg_97	peg_98
254780209	254780210
254780211	254780212
254780213	254780214
254780215	255764461
254780217	254780218
254780219	254780220
peg_109	254780221
254780222	254780223
254780224	254780225
254780226	peg_116
254780227	254780228
254780229	254780230
254780231	254780232
254780233	254780234
254780235	254780236
254780237	peg_128
254780238	254780239
254780240	254780241
254780242	254780243
254780244	254780245
254780246	254780247
254780248	254780249
254780250	254780251
254780252	254780253
254780254	254780255
254780256	254780257
254780258	254780259
254780260	254780261
254780262	254780263
254780264	254780265
254780266	254780267
254780268	254780269
254780270	254780271
254780272	254780273
254780274	peg_166
254780275	254780276
254780277	254780278
254780279	254780280
254780281	254780282
254780283	254780284
254780285	254780286
254780287	254780288
254780289	254780290
254780291	254780292
254780293	peg_186
254780294	254780295
255764462	254780297
peg_191	254780298
254780299	254780300
254780301	254780302
254780303	254780304
254780305	254780306
254780307	254780308
254780309	254780310
peg_204	254780311
254780312	254780313
254780314	254780315
254780316	254780317
254780318	254780319
254780320	254780321
254780322	254780323
peg_218	254780324
254780325	254780326
254780327	254780328
peg_224	254780329
254780330	peg_227
254780331	254780332
254780333	254780334
peg_232	254780335
peg_233	254780336
254780337	254780338
peg_237	254780339
254780340	254780341
254780342	254780343
254780344	254780345
254780346	254780347
254780348	peg_248
254780349	254780350
254780351	peg_252
255764463	peg_254
254780353	254780354
254780355	254780356
254780357	255764464
254780359	254780360
254780361	255764465
254780363	254780364
254780365	255764466
254780367	254780368
254780369	254780370
254780371	254780372
254780373	254780374
254780375	254780376
254780377	254780378
254780379	254780380
254780381	254780382
254780383	254780384
255764467	254780386
254780387	254780388
254780389	254780390
254780391	254780392
255764468	255764469
254780395	peg_298
254780396	254780397
254780398	254780399
254780400	254780401
254780402	254780403
254780404	254780405
254780406	254780407
254780408	254780409
254780410	254780411
254780412	254780413
254780414	255764470
254780416	254780417
254780418	254780419
254780420	254780421
255764471	254780423
254780424	254780425
254780426	peg_330
254780427	255764472
254780429	254780430
254780431	254780432
255764473	254780434
254780435	254780436
254780437	254780438
254780439	254780440
255764474	254780442
254780443	peg_348
peg_349	254780444
254780445	254780446
254780447	254780448
254780449	254780450
254780451	254780452
254780453	254780454
peg_360	254780455
254780456	peg_363
254780457	254780458
254780459	254780460
254780461	254780462
254780463	254780464
254780465	254780466
peg_374	254780467
254780468	254780469
254780470	254780471
254780472	254780473
254780474	254780475
254780476	254780477
254780478	254780479
254780480	254780481
254780482	254780483
254780484	peg_393
peg_394	254780485
254780486	254780487
254780488	254780489
254780490	254780491
254780492	254780829
254780828	254780827
254780826	255764475
255764476	254780824
254780823	peg_409
peg_410	254780822
254780821	254780820
peg_414	255764477
254780818	254780817
254780816	254780815
254780814	254780813
254780812	254780811
peg_423	254780810
254780809	254780808
254780807	254780806
254780805	254780804
254780803	254780802
254780801	254780800
254780799	254780798
254780797	254780796
254780795	254780794
254780793	255764478
254780791	254780790
254780789	254780788
254780787	254780786
254780785	254780784
254780783	254780782
255764479	254780781
254780780	peg_455
255764480	254780779
254780778	254780777
254780776	254780775
254780774

254780757

glycyl-tRNA synthetase subunit alpha

Prediction of Local Sequence Properties

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

Conserved Domains in CDD DatabaseDetected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

Conserved Domains in CDD Database Detected by HHsearch

Homologous Structures in PDB DatabaseDetected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Homologous Structures in PDB70 Database Detected by HHsearch

Homologous Domains in SCOP and MMDB DatabaseDetected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Homologous Domains in MMDB70 Database Detected by HHsearch

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch