Psyllid ID: psy5542

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80------
Protein Sequence
MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGAV
Secondary Structure (PSIPRED)
ccHHHHHcccccccHHHHHHcccccccccccccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcccccHHHHHHHccHcccccccHHcHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEccccc
Coil and Loop (DISEMBL)
mvadmklshkALPLLLYQFTSKFrdelrpkfglmrSREFLMKDLYAFtasevdandvynLVGKCYDDVFNTLGIKYRKVIVRHGAV
Flexible Loop (DISEMBL)
mvadmklshkalPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGAV
Low Complexity Region (SEG)
MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGAV
Disordered region (IsUnstruct)
*********KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVR****
Disordered Region (DISOPRED)
*VADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGA*
Disordered Region (DISEMBL)
MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGAV
Disordered Region (DISPRO)
MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHG**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGAV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	86	2.2.26 [Sep-21-2011]
B8DG08	568	Proline--tRNA ligase OS=L	yes	N/A	1.0	0.151	0.465	8e-19
Q8Y7G2	568	Proline--tRNA ligase OS=L	yes	N/A	1.0	0.151	0.465	8e-19
Q720A3	568	Proline--tRNA ligase OS=L	yes	N/A	1.0	0.151	0.465	8e-19
C1L2M5	568	Proline--tRNA ligase OS=L	yes	N/A	1.0	0.151	0.465	9e-19
Q04F81	570	Proline--tRNA ligase OS=O	yes	N/A	1.0	0.150	0.453	1e-18
B9IVA8	566	Proline--tRNA ligase OS=B	yes	N/A	1.0	0.151	0.488	1e-18
B7HLF2	566	Proline--tRNA ligase OS=B	yes	N/A	1.0	0.151	0.488	1e-18
Q732Q0	566	Proline--tRNA ligase 1 OS	yes	N/A	1.0	0.151	0.488	1e-18
C1EP43	566	Proline--tRNA ligase OS=B	yes	N/A	1.0	0.151	0.488	1e-18
B7JJ97	566	Proline--tRNA ligase OS=B	yes	N/A	1.0	0.151	0.488	1e-18

>sp|B8DG08|SYP_LISMH Proline--tRNA ligase OS=Listeria monocytogenes serotype 4a (strain HCC23) GN=proS PE=3 SV=1

 Score = 92.4 bits (228), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 40/86 (46%), Positives = 60/86 (69%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL LYQ  +KFRDE RP+FGL+R REF+MKD Y+F A+    ++VYNL
Sbjct: 117 LLRDEVKSYKRLPLTLYQIQTKFRDEKRPRFGLLRGREFIMKDAYSFHATSESLDEVYNL 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + + Y ++F   G+++R VI   G++
Sbjct: 177 MHQAYSNIFTRCGLEFRSVIADSGSI 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.
Listeria monocytogenes serotype 4a (strain HCC23) (taxid: 552536)
EC: 6EC: .EC: 1EC: .EC: 1EC: .EC: 1EC: 5

>sp|Q8Y7G2|SYP_LISMO Proline--tRNA ligase OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) GN=proS PE=3 SV=1

 Score = 92.0 bits (227), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 40/86 (46%), Positives = 60/86 (69%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL LYQ  +KFRDE RP+FGL+R REF+MKD Y+F A+    ++VYNL
Sbjct: 117 LLRDEVKSYKRLPLTLYQIQTKFRDEKRPRFGLLRGREFIMKDAYSFHATSESLDEVYNL 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + + Y ++F   G+++R VI   G++
Sbjct: 177 MHQAYSNIFTRCGLEFRSVIADSGSI 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (taxid: 169963)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|Q720A3|SYP_LISMF Proline--tRNA ligase OS=Listeria monocytogenes serotype 4b (strain F2365) GN=proS PE=3 SV=1

 Score = 92.0 bits (227), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 40/86 (46%), Positives = 60/86 (69%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL LYQ  +KFRDE RP+FGL+R REF+MKD Y+F A+    ++VYNL
Sbjct: 117 LLRDEVKSYKRLPLTLYQIQTKFRDEKRPRFGLLRGREFIMKDAYSFHATSESLDEVYNL 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + + Y ++F   G+++R VI   G++
Sbjct: 177 MHQAYSNIFTRCGLEFRSVIADSGSI 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Listeria monocytogenes serotype 4b (strain F2365) (taxid: 265669)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|C1L2M5|SYP_LISMC Proline--tRNA ligase OS=Listeria monocytogenes serotype 4b (strain CLIP80459) GN=proS PE=3 SV=1

 Score = 92.0 bits (227), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 40/86 (46%), Positives = 60/86 (69%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL LYQ  +KFRDE RP+FGL+R REF+MKD Y+F A+    ++VYNL
Sbjct: 117 LLRDEVKSYKRLPLTLYQIQTKFRDEKRPRFGLLRGREFIMKDAYSFHATSESLDEVYNL 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + + Y ++F   G+++R VI   G++
Sbjct: 177 MHQAYSNIFTRCGLEFRSVIADSGSI 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Listeria monocytogenes serotype 4b (strain Clip81459) (taxid: 568819)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|Q04F81|SYP_OENOB Proline--tRNA ligase OS=Oenococcus oeni (strain ATCC BAA-331 / PSU-1) GN=proS PE=3 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 39/86 (45%), Positives = 61/86 (70%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +++D   S+K LPL+LYQ   KFRDELRPK GL+R REF+MKD Y+F++ +   +D Y+L
Sbjct: 117 IISDEIKSYKKLPLILYQIQQKFRDELRPKNGLLRGREFIMKDAYSFSSDQKGLDDAYDL 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           +   Y  +F+ +G+ YR++I   G++
Sbjct: 177 IESAYKRIFDRVGLDYREIIADSGSM 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Oenococcus oeni (strain ATCC BAA-331 / PSU-1) (taxid: 203123)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|B9IVA8|SYP_BACCQ Proline--tRNA ligase OS=Bacillus cereus (strain Q1) GN=proS PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/86 (48%), Positives = 59/86 (68%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V D   S+K LPL LYQ  +KFRDE RP+FGL+R REFLMKD Y+F A++   ++VY+ 
Sbjct: 117 LVRDEVKSYKKLPLTLYQIQTKFRDEQRPRFGLLRGREFLMKDAYSFHATQESLDEVYDR 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + K Y ++F   G+ +R VI   GA+
Sbjct: 177 LYKAYSNIFARCGLNFRAVIADSGAM 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Bacillus cereus (strain Q1) (taxid: 361100)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|B7HLF2|SYP_BACC7 Proline--tRNA ligase OS=Bacillus cereus (strain AH187) GN=proS PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/86 (48%), Positives = 59/86 (68%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V D   S+K LPL LYQ  +KFRDE RP+FGL+R REFLMKD Y+F A++   ++VY+ 
Sbjct: 117 LVRDEVKSYKKLPLTLYQIQTKFRDEQRPRFGLLRGREFLMKDAYSFHATQESLDEVYDR 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + K Y ++F   G+ +R VI   GA+
Sbjct: 177 LYKAYSNIFARCGLNFRAVIADSGAM 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Bacillus cereus (strain AH187) (taxid: 405534)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|Q732Q0|SYP1_BACC1 Proline--tRNA ligase 1 OS=Bacillus cereus (strain ATCC 10987) GN=proS1 PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/86 (48%), Positives = 59/86 (68%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V D   S+K LPL LYQ  +KFRDE RP+FGL+R REFLMKD Y+F A++   ++VY+ 
Sbjct: 117 LVRDEVKSYKKLPLTLYQIQTKFRDEQRPRFGLLRGREFLMKDAYSFHATQESLDEVYDR 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + K Y ++F   G+ +R VI   GA+
Sbjct: 177 LYKAYSNIFARCGLNFRAVIADSGAM 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Bacillus cereus (strain ATCC 10987) (taxid: 222523)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|C1EP43|SYP_BACC3 Proline--tRNA ligase OS=Bacillus cereus (strain 03BB102) GN=proS PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/86 (48%), Positives = 59/86 (68%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V D   S+K LPL LYQ  +KFRDE RP+FGL+R REFLMKD Y+F A++   ++VY+ 
Sbjct: 117 LVRDEVKSYKKLPLTLYQIQTKFRDEQRPRFGLLRGREFLMKDAYSFHATQESLDEVYDR 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + K Y ++F   G+ +R VI   GA+
Sbjct: 177 LYKAYSNIFARCGLNFRAVIADSGAM 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Bacillus cereus (strain 03BB102) (taxid: 572264)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

>sp|B7JJ97|SYP_BACC0 Proline--tRNA ligase OS=Bacillus cereus (strain AH820) GN=proS PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/86 (48%), Positives = 59/86 (68%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V D   S+K LPL LYQ  +KFRDE RP+FGL+R REFLMKD Y+F A++   ++VY+ 
Sbjct: 117 LVRDEVKSYKKLPLTLYQIQTKFRDEQRPRFGLLRGREFLMKDAYSFHATQESLDEVYDR 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + K Y ++F   G+ +R VI   GA+
Sbjct: 177 LYKAYSNIFARCGLNFRAVIADSGAM 202

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.

Bacillus cereus (strain AH820) (taxid: 405535)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	86
402854677	475	PREDICTED: probable proline--tRNA ligase	1.0	0.181	0.523	2e-18
383417329	475	putative prolyl-tRNA synthetase, mitocho	1.0	0.181	0.523	2e-18
380791433	372	putative prolyl-tRNA synthetase, mitocho	1.0	0.231	0.523	2e-18
355558037	475	hypothetical protein EGK_00802 [Macaca m	1.0	0.181	0.523	2e-18
109005002	475	PREDICTED: probable prolyl-tRNA syntheta	1.0	0.181	0.523	2e-18
227524393	569	prolyl-tRNA synthetase [Lactobacillus hi	1.0	0.151	0.488	6e-18
149909734	573	prolyl-tRNA synthetase [Moritella sp. PE	0.918	0.137	0.518	7e-18
330839271	568	Prolyl-tRNA synthetase [Selenomonas sput	1.0	0.151	0.511	8e-18
260886940	543	proline--tRNA ligase [Selenomonas sputig	1.0	0.158	0.511	8e-18
227510249	569	prolyl-tRNA synthetase [Lactobacillus br	1.0	0.151	0.488	8e-18

>gi|402854677|ref|XP_003891987.1| PREDICTED: probable proline--tRNA ligase, mitochondrial [Papio anubis]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/86 (52%), Positives = 57/86 (66%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           + A  KLS+K LP LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   YNL
Sbjct: 166 IAAQKKLSYKQLPFLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAAQQTYNL 225

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           V   Y  +FN LG+++ KV    G++
Sbjct: 226 VCDAYCSLFNRLGLRFVKVQADVGSI 251

Source: Papio anubis

Species: Papio anubis

Genus: Papio

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|383417329|gb|AFH31878.1| putative prolyl-tRNA synthetase, mitochondrial precursor [Macaca mulatta]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/86 (52%), Positives = 57/86 (66%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           + A  KLS+K LP LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   YNL
Sbjct: 166 IAAQKKLSYKQLPFLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAAQQTYNL 225

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           V   Y  +FN LG+++ KV    G++
Sbjct: 226 VCDAYCSLFNRLGLRFVKVQADVGSI 251

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|380791433|gb|AFE67592.1| putative prolyl-tRNA synthetase, mitochondrial precursor, partial [Macaca mulatta]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/86 (52%), Positives = 57/86 (66%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           + A  KLS+K LP LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   YNL
Sbjct: 166 IAAQKKLSYKQLPFLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAAQQTYNL 225

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           V   Y  +FN LG+++ KV    G++
Sbjct: 226 VCDAYCSLFNRLGLRFVKVQADVGSI 251

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|355558037|gb|EHH14817.1| hypothetical protein EGK_00802 [Macaca mulatta] gi|355745310|gb|EHH49935.1| hypothetical protein EGM_00680 [Macaca fascicularis]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/86 (52%), Positives = 57/86 (66%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           + A  KLS+K LP LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   YNL
Sbjct: 166 IAAQKKLSYKQLPFLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAAQQTYNL 225

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           V   Y  +FN LG+++ KV    G++
Sbjct: 226 VCDAYCSLFNRLGLRFVKVQADVGSI 251

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|109005002|ref|XP_001114166.1| PREDICTED: probable prolyl-tRNA synthetase, mitochondrial-like [Macaca mulatta]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/86 (52%), Positives = 57/86 (66%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           + A  KLS+K LP LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   YNL
Sbjct: 166 IAAQKKLSYKQLPFLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAAQQTYNL 225

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           V   Y  +FN LG+++ KV    G++
Sbjct: 226 VCDAYCSLFNRLGLRFVKVQADVGSI 251

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|227524393|ref|ZP_03954442.1| prolyl-tRNA synthetase [Lactobacillus hilgardii ATCC 8290] gi|227088624|gb|EEI23936.1| prolyl-tRNA synthetase [Lactobacillus hilgardii ATCC 8290]

 Score = 94.7 bits (234), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 42/86 (48%), Positives = 62/86 (72%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL+LYQ  +K+RDE RP++GL+RSREF+MKD Y+F A+E D +D Y  
Sbjct: 117 LIRDSIKSYKQLPLILYQIQNKYRDEDRPRYGLLRSREFIMKDAYSFAANEADLDDAYRA 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + K Y  +F+ +G+KYR +I   GA+
Sbjct: 177 MEKAYRTIFDRIGLKYRVIIGDGGAM 202

Source: Lactobacillus hilgardii ATCC 8290

Species: Lactobacillus hilgardii

Genus: Lactobacillus

Family: Lactobacillaceae

Order: Lactobacillales

Class: Bacilli

Phylum: Firmicutes

Superkingdom: Bacteria

>gi|149909734|ref|ZP_01898386.1| prolyl-tRNA synthetase [Moritella sp. PE36] gi|149807248|gb|EDM67203.1| prolyl-tRNA synthetase [Moritella sp. PE36]

 Score = 94.7 bits (234), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 41/79 (51%), Positives = 57/79 (72%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDD 67
           S+K LPL LYQ  +KFRDE+RP+FG+MRSREFLMKD Y+F  S+   ND YN +   Y +
Sbjct: 124 SYKQLPLTLYQIQTKFRDEVRPRFGVMRSREFLMKDAYSFHISDECLNDTYNKMHTAYCN 183

Query: 68  VFNTLGIKYRKVIVRHGAV 86
           +F  +G++YR V+   G++
Sbjct: 184 IFERIGLEYRPVLADTGSI 202

Source: Moritella sp. PE36

Species: Moritella sp. PE36

Genus: Moritella

Family: Moritellaceae

Order: Alteromonadales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|330839271|ref|YP_004413851.1| Prolyl-tRNA synthetase [Selenomonas sputigena ATCC 35185] gi|329747035|gb|AEC00392.1| Prolyl-tRNA synthetase [Selenomonas sputigena ATCC 35185]

 Score = 94.4 bits (233), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 44/86 (51%), Positives = 58/86 (67%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V D   S+K LPLLLYQ  +K+RDE+RP+FGLMRSREF+MKDLY+F   E  A+  Y  
Sbjct: 117 LVRDEVRSYKQLPLLLYQIQNKYRDEIRPRFGLMRSREFIMKDLYSFDKDEAGADISYKK 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           +   Y +VF   G+K+R V    GA+
Sbjct: 177 MYDAYTNVFTRCGLKFRPVEADAGAI 202

Source: Selenomonas sputigena ATCC 35185

Species: Selenomonas sputigena

Genus: Selenomonas

Family: Veillonellaceae

Order: Selenomonadales

Class: Negativicutes

Phylum: Firmicutes

Superkingdom: Bacteria

>gi|260886940|ref|ZP_05898203.1| proline--tRNA ligase [Selenomonas sputigena ATCC 35185] gi|260863002|gb|EEX77502.1| proline--tRNA ligase [Selenomonas sputigena ATCC 35185]

 Score = 94.4 bits (233), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 44/86 (51%), Positives = 58/86 (67%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V D   S+K LPLLLYQ  +K+RDE+RP+FGLMRSREF+MKDLY+F   E  A+  Y  
Sbjct: 92  LVRDEVRSYKQLPLLLYQIQNKYRDEIRPRFGLMRSREFIMKDLYSFDKDEAGADISYKK 151

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           +   Y +VF   G+K+R V    GA+
Sbjct: 152 MYDAYTNVFTRCGLKFRPVEADAGAI 177

Source: Selenomonas sputigena ATCC 35185

Species: Selenomonas sputigena

Genus: Selenomonas

Family: Veillonellaceae

Order: Selenomonadales

Class: Negativicutes

Phylum: Firmicutes

Superkingdom: Bacteria

>gi|227510249|ref|ZP_03940298.1| prolyl-tRNA synthetase [Lactobacillus brevis subsp. gravesensis ATCC 27305] gi|227189901|gb|EEI69968.1| prolyl-tRNA synthetase [Lactobacillus brevis subsp. gravesensis ATCC 27305]

 Score = 94.4 bits (233), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 42/86 (48%), Positives = 62/86 (72%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL+LYQ  +K+RDE RP++GL+RSREF+MKD Y+F A+E D +D Y  
Sbjct: 117 LIRDSIKSYKQLPLVLYQIQNKYRDEDRPRYGLLRSREFIMKDAYSFAANEADLDDAYRA 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + K Y  +F+ +G+KYR +I   GA+
Sbjct: 177 MEKAYRTIFDRIGLKYRVIIGDGGAM 202

Source: Lactobacillus brevis subsp. gravesensis ATCC 27305

Species: Lactobacillus brevis

Genus: Lactobacillus

Family: Lactobacillaceae

Order: Lactobacillales

Class: Bacilli

Phylum: Firmicutes

Superkingdom: Bacteria

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	86
TIGR_CMR|BA_3957	566	BA_3957 "prolyl-tRNA synthetas	1.0	0.151	0.488	4.7e-17
RGD|1305345	475	Pars2 "prolyl-tRNA synthetase	1.0	0.181	0.488	8.6e-17
UNIPROTKB|Q5M7W7	475	Pars2 "Probable proline--tRNA	1.0	0.181	0.488	8.6e-17
UNIPROTKB|Q7L3T8	475	PARS2 "Probable proline--tRNA	1.0	0.181	0.5	1.1e-16
MGI|MGI:2386296	475	Pars2 "prolyl-tRNA synthetase	1.0	0.181	0.488	1.4e-16
UNIPROTKB|F1MHD4	475	PARS2 "Uncharacterized protein	1.0	0.181	0.517	1.8e-16
UNIPROTKB|E1BZP0	470	PARS2 "Uncharacterized protein	1.0	0.182	0.488	1e-15
UNIPROTKB|F1S781	472	PARS2 "Uncharacterized protein	1.0	0.182	0.494	1e-15
TIGR_CMR|CHY_1775	569	CHY_1775 "prolyl-tRNA syntheta	0.918	0.138	0.506	2.6e-15
TIGR_CMR|CBU_0081	566	CBU_0081 "prolyl-tRNA syntheta	0.988	0.150	0.465	6.9e-15

TIGR_CMR|BA_3957 BA_3957 "prolyl-tRNA synthetase" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 218 (81.8 bits), Expect = 4.7e-17, P = 4.7e-17
 Identities = 42/86 (48%), Positives = 59/86 (68%)

Query:     1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
             +V D   S+K LPL LYQ  +KFRDE RP+FGL+R REFLMKD Y+F A++   ++VY+ 
Sbjct:   117 LVRDEVKSYKKLPLTLYQIQTKFRDEQRPRFGLLRGREFLMKDAYSFHATQESLDEVYDR 176

Query:    61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             + K Y ++F   G+ +R VI   GA+
Sbjct:   177 LYKAYSNIFARCGLNFRAVIADSGAM 202

GO:0004827 "proline-tRNA ligase activity" evidence=ISS

GO:0006433 "prolyl-tRNA aminoacylation" evidence=ISS

RGD|1305345 Pars2 "prolyl-tRNA synthetase 2, mitochondrial (putative)" [Rattus norvegicus (taxid:10116)]

 Score = 214 (80.4 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 42/86 (48%), Positives = 58/86 (67%)

Query:     1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
             + +  KLS+K LPLLLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A + Y+L
Sbjct:   166 VASQKKLSYKQLPLLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSSEAAQETYSL 225

Query:    61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             V   Y  +F+ LG+++ K     G++
Sbjct:   226 VCDAYCRLFDRLGLRWMKARADVGSI 251

GO:0004827 "proline-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005759 "mitochondrial matrix" evidence=IEA

GO:0006433 "prolyl-tRNA aminoacylation" evidence=IEA

UNIPROTKB|Q5M7W7 Pars2 "Probable proline--tRNA ligase, mitochondrial" [Rattus norvegicus (taxid:10116)]

 Score = 214 (80.4 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 42/86 (48%), Positives = 58/86 (67%)

Query:     1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
             + +  KLS+K LPLLLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A + Y+L
Sbjct:   166 VASQKKLSYKQLPLLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSSEAAQETYSL 225

Query:    61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             V   Y  +F+ LG+++ K     G++
Sbjct:   226 VCDAYCRLFDRLGLRWMKARADVGSI 251

GO:0006433 "prolyl-tRNA aminoacylation" evidence=IEA

UNIPROTKB|Q7L3T8 PARS2 "Probable proline--tRNA ligase, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 213 (80.0 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 43/86 (50%), Positives = 55/86 (63%)

Query:     1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
             + +  KLS+K LP LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   Y+L
Sbjct:   166 IASQKKLSYKQLPFLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAAQQTYSL 225

Query:    61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             V   Y  +FN LG+ + KV    G +
Sbjct:   226 VCDAYCSLFNKLGLPFVKVQADVGTI 251

GO:0006433 "prolyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004827 "proline-tRNA ligase activity" evidence=IEA

GO:0005759 "mitochondrial matrix" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

MGI|MGI:2386296 Pars2 "prolyl-tRNA synthetase (mitochondrial)(putative)" [Mus musculus (taxid:10090)]

 Score = 212 (79.7 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 42/86 (48%), Positives = 57/86 (66%)

Query:     1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
             + +  KLS+K LPLLLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A + Y L
Sbjct:   166 VASQKKLSYKQLPLLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSSEAAQETYGL 225

Query:    61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             V   Y  +F+ LG+++ K     G++
Sbjct:   226 VCDAYCRLFDRLGLQWMKARADVGSI 251

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004812 "aminoacyl-tRNA ligase activity" evidence=IEA

GO:0004827 "proline-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006412 "translation" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=IEA

GO:0006433 "prolyl-tRNA aminoacylation" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

UNIPROTKB|F1MHD4 PARS2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 211 (79.3 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 45/87 (51%), Positives = 57/87 (65%)

Query:     1 MVADMK-LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYN 59
             +VA  K LS+K LP LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   Y+
Sbjct:   165 LVASQKTLSYKQLPFLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAAQLTYS 224

Query:    60 LVGKCYDDVFNTLGIKYRKVIVRHGAV 86
             LV   Y  +FN LG++  KV    G++
Sbjct:   225 LVCDAYSSLFNRLGLRCIKVQADVGSI 251

GO:0005739 "mitochondrion" evidence=IEA

GO:0006433 "prolyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004827 "proline-tRNA ligase activity" evidence=IEA

UNIPROTKB|E1BZP0 PARS2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 204 (76.9 bits), Expect = 1.0e-15, P = 1.0e-15
 Identities = 42/86 (48%), Positives = 54/86 (62%)

Query:     1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
             + A   LS++ LPL LYQ T KFRDE +P+FGL+RSREF MKD+Y F ASE  A   Y L
Sbjct:   161 VAAHSNLSYRQLPLRLYQVTRKFRDEPKPRFGLLRSREFYMKDMYTFDASEEAARHTYEL 220

Query:    61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             V   Y  +F  LG++  +V    G +
Sbjct:   221 VCTAYRSLFKRLGLRCVQVRAATGTI 246

GO:0006433 "prolyl-tRNA aminoacylation" evidence=IEA

GO:0004827 "proline-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

UNIPROTKB|F1S781 PARS2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 204 (76.9 bits), Expect = 1.0e-15, P = 1.0e-15
 Identities = 43/87 (49%), Positives = 58/87 (66%)

Query:     1 MVADMK-LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYN 59
             +VA  K LS+K LP+LLYQ T KFRDE RP+FGL+R REF MKD+Y F +S   A   Y+
Sbjct:   162 LVASQKTLSYKQLPVLLYQVTRKFRDEPRPRFGLLRGREFYMKDMYTFDSSPEAARRTYS 221

Query:    60 LVGKCYDDVFNTLGIKYRKVIVRHGAV 86
             LV   Y  +F+ LG++  +V    G++
Sbjct:   222 LVCDAYGSLFDRLGLQCLQVQADVGSI 248

GO:0005739 "mitochondrion" evidence=IEA

GO:0006433 "prolyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004827 "proline-tRNA ligase activity" evidence=IEA

TIGR_CMR|CHY_1775 CHY_1775 "prolyl-tRNA synthetase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 202 (76.2 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 40/79 (50%), Positives = 52/79 (65%)

Query:     8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDD 67
             S+K LPLLLYQ  +K+RDE RP+FGLMR REF+MKDLY+F   E      Y  + + Y +
Sbjct:   124 SYKELPLLLYQIQNKYRDEKRPRFGLMRGREFIMKDLYSFDRDEEGLEISYRKMYEAYTN 183

Query:    68 VFNTLGIKYRKVIVRHGAV 86
             VF   G+K+R V    GA+
Sbjct:   184 VFTRCGLKFRAVEADAGAI 202

GO:0004827 "proline-tRNA ligase activity" evidence=ISS

GO:0006433 "prolyl-tRNA aminoacylation" evidence=ISS

TIGR_CMR|CBU_0081 CBU_0081 "prolyl-tRNA synthetase" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 198 (74.8 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 40/86 (46%), Positives = 54/86 (62%)

Query:     2 VADMKL-SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
             +A  +L S+K LPL  YQ  +KFRDE+RP+FG+MRSREFLMKD Y+F   E      Y  
Sbjct:   119 IARQELKSYKQLPLNFYQIQTKFRDEIRPRFGVMRSREFLMKDAYSFDLDEKGMQAAYEK 178

Query:    61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             +   Y  +F  LG+ +R V+   GA+
Sbjct:   179 MFDAYRRIFTRLGLNFRAVLADTGAI 204

GO:0004827 "proline-tRNA ligase activity" evidence=ISS

GO:0006433 "prolyl-tRNA aminoacylation" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8CFI5	SYPM_MOUSE	6, ., 1, ., 1, ., 1, 5	0.5185	0.9418	0.1705	yes	N/A
A8FDC1	SYP_BACP2	6, ., 1, ., 1, ., 1, 5	0.5189	0.9186	0.1398	yes	N/A
Q5M7W7	SYPM_RAT	6, ., 1, ., 1, ., 1, 5	0.5185	0.9418	0.1705	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.1.1	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	86
cd00779	255	cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (	2e-32
PRK09194	565	PRK09194, PRK09194, prolyl-tRNA synthetase; Provis	1e-26
TIGR00409	568	TIGR00409, proS_fam_II, prolyl-tRNA synthetase, fa	4e-26
COG0442	500	COG0442, ProS, Prolyl-tRNA synthetase [Translation	1e-25
PRK12325	439	PRK12325, PRK12325, prolyl-tRNA synthetase; Provis	2e-23
pfam00587	171	pfam00587, tRNA-synt_2b, tRNA synthetase class II	2e-20
cd00772	264	cd00772, ProRS_core, Prolyl-tRNA synthetase (ProRS	2e-12
cd00670	235	cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro	1e-10
cd00768	211	cd00768, class_II_aaRS-like_core, Class II tRNA am	3e-07
cd00778	261	cd00778, ProRS_core_arch_euk, Prolyl-tRNA syntheta	7e-07
TIGR00408	472	TIGR00408, proS_fam_I, prolyl-tRNA synthetase, fam	2e-06
TIGR00418	563	TIGR00418, thrS, threonyl-tRNA synthetase	9e-06
PRK08661	477	PRK08661, PRK08661, prolyl-tRNA synthetase; Provis	2e-05
COG0441	589	COG0441, ThrS, Threonyl-tRNA synthetase [Translati	2e-05
PRK03991	613	PRK03991, PRK03991, threonyl-tRNA synthetase; Vali	2e-04
TIGR00389	551	TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, d	2e-04
cd00771	298	cd00771, ThrRS_core, Threonyl-tRNA synthetase (Thr	0.003

>gnl|CDD|238402 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain

 Score =  112 bits (282), Expect = 2e-32
 Identities = 41/85 (48%), Positives = 54/85 (63%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +VA+   S+K LPL LYQ  +KFRDE+RP+FGLMR REFLMKD Y+F   E    + Y  
Sbjct: 101 LVANEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEETYEK 160

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGA 85
           + + Y  +F  LG+ + KV    GA
Sbjct: 161 MYQAYSRIFKRLGLPFVKVEADSGA 185

ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes. Length = 255

>gnl|CDD|236405 PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional

 Score =  100 bits (252), Expect = 1e-26
 Identities = 38/80 (47%), Positives = 55/80 (68%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +V +   S+K LPL LYQ  +KFRDE+RP+FGLMR REF+MKD Y+F A E   ++ Y+ 
Sbjct: 117 LVRNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHADEESLDETYDA 176

Query: 61  VGKCYDDVFNTLGIKYRKVI 80
           + + Y  +F+ LG+ +R V 
Sbjct: 177 MYQAYSRIFDRLGLDFRAVE 196

Length = 565

>gnl|CDD|232962 TIGR00409, proS_fam_II, prolyl-tRNA synthetase, family II

 Score = 99.1 bits (247), Expect = 4e-26
 Identities = 38/86 (44%), Positives = 56/86 (65%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +  +   S+K LPL LYQ  +KFRDE+RP+FGLMR REF+MKD Y+F + E   +  Y  
Sbjct: 117 LARNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHSDEESLDATYQK 176

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
           + + Y ++F+ LG+ +R V    GA+
Sbjct: 177 MYQAYSNIFSRLGLDFRPVQADSGAI 202

Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi [Protein synthesis, tRNA aminoacylation]. Length = 568

>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 97.7 bits (244), Expect = 1e-25
 Identities = 39/80 (48%), Positives = 48/80 (60%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           M      S+K LPL LYQ  SKFRDE RP+FGL+R REFLMKD Y+F A E DA + Y  
Sbjct: 117 MFRKWIRSYKDLPLKLYQIQSKFRDEKRPRFGLLRGREFLMKDAYSFHADEEDAEETYEK 176

Query: 61  VGKCYDDVFNTLGIKYRKVI 80
           +   Y  +F  L + +  V 
Sbjct: 177 MLDAYSRIFLRLPLIFGPVP 196

Length = 500

>gnl|CDD|237059 PRK12325, PRK12325, prolyl-tRNA synthetase; Provisional

 Score = 91.5 bits (228), Expect = 2e-23
 Identities = 36/68 (52%), Positives = 43/68 (63%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDD 67
           S+K LPL LY    KFRDE+RP+FG+MR REFLMKD Y+F   E  A   YN +   Y  
Sbjct: 124 SYKDLPLNLYHIQWKFRDEIRPRFGVMRGREFLMKDAYSFDLDEEGARHSYNRMFVAYLR 183

Query: 68  VFNTLGIK 75
            F  LG+K
Sbjct: 184 TFARLGLK 191

Length = 439

>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G, H, P, S and T)

 Score = 79.6 bits (197), Expect = 2e-20
 Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +  +  LS++ LPL LYQ    FR E RP+ GL R REF   D   F   E  + +    
Sbjct: 70  LFKNEILSYRELPLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIFGTPE-QSEEELEE 128

Query: 61  VGKCYDDVFNTLGIKYRKVI 80
           + K  +++   LG+ YR V+
Sbjct: 129 LLKLAEEILQDLGLPYRVVL 148

Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. Length = 171

>gnl|CDD|238395 cd00772, ProRS_core, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain

 Score = 60.1 bits (145), Expect = 2e-12
 Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 1/86 (1%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           + A    S K LP  L Q  +KFRDE+RP+FG +R+REF+MKD ++  A   +A++ +  
Sbjct: 107 IAAKFIKSWKDLPQHLNQIGNKFRDEIRPRFGFLRAREFIMKDGHSAHADAEEADEEFLN 166

Query: 61  VGKCYDDVFNTLG-IKYRKVIVRHGA 85
           +   Y ++   L  I + +     GA
Sbjct: 167 MLSAYAEIARDLAAIDFIEGEADEGA 192

ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. Length = 264

>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain

 Score = 54.7 bits (132), Expect = 1e-10
 Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 6   KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCY 65
            LS++ALPL L Q    FR E   + GLMR REF   +   F   E +A +      +  
Sbjct: 81  ILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVFGEPE-EAEEERREWLELA 139

Query: 66  DDVFNTLGIKYRKVIV 81
           +++   LG+  R V+ 
Sbjct: 140 EEIARELGLPVRVVVA 155

This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. Length = 235

>gnl|CDD|238391 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl synthetase-like catalytic core domain

 Score = 45.2 bits (107), Expect = 3e-07
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 10  KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVF 69
           + LPL L +    FR+E     GL R REF   +   F     +A++   L+    +++ 
Sbjct: 72  RKLPLRLAEIGPAFRNEGGR-RGLRRVREFTQLEGEVFGEDGEEASEFEELIEL-TEELL 129

Query: 70  NTLGIKYRKVIV 81
             LGIK   V V
Sbjct: 130 RALGIKLDIVFV 141

Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ. Length = 211

>gnl|CDD|238401 cd00778, ProRS_core_arch_euk, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain

 Score = 44.5 bits (106), Expect = 7e-07
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDD 67
           S++ LPL + Q+ + FR E +     +R+REFL ++ +   A+E +A +    +   Y +
Sbjct: 114 SYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDLYKE 173

Query: 68  VFNT-LGIKY 76
            +   L I  
Sbjct: 174 FYEDLLAIPV 183

ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria. Length = 261

>gnl|CDD|232961 TIGR00408, proS_fam_I, prolyl-tRNA synthetase, family I

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           M      S+  LPL + Q+ + FR E +     +R+REF  ++ +   A+  +A +    
Sbjct: 113 MFKKWVKSYTDLPLKINQWVNVFRYETKHTRPFLRTREFTWQEAHTAHATAEEAEEQVLR 172

Query: 61  VGKCYDDVF-NTLGIKY 76
               Y +   N+L I Y
Sbjct: 173 ALDIYKEFIENSLAIPY 189

Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae [Protein synthesis, tRNA aminoacylation]. Length = 472

>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase

 Score = 41.5 bits (98), Expect = 9e-06
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYN 59
           +      S++ LPL + +     R E   +  GLMR R F   D + F   +    +  N
Sbjct: 270 IFKSSLRSYRDLPLRIAELGYSHRYEQSGELHGLMRVRGFTQDDAHIFCTEDQIKEEFKN 329

Query: 60  LVGKCYDDVFNTLGIKYRKV 79
                   V++  G  + K 
Sbjct: 330 QFRLIQ-KVYSDFGFSFDKY 348

This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether. [Protein synthesis, tRNA aminoacylation]. Length = 563

>gnl|CDD|236327 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional

 Score = 40.5 bits (96), Expect = 2e-05
 Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFL 40
           S++ LPLL  Q+ +  R E + +   +R+REFL
Sbjct: 126 SYRDLPLLYNQWVNVVRWETKTRP-FLRTREFL 157

Length = 477

>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYN 59
           +      S++ LPL L +F   +R E      GLMR R F   D + F   +   ++   
Sbjct: 289 IFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAHIFCTPDQIKDEFKG 348

Query: 60  LVGKCYDDVFNTLGIKYRKVIVR 82
           ++     +V+   G    +V + 
Sbjct: 349 ILELIL-EVYKDFGFTDYEVKLS 370

Length = 589

>gnl|CDD|235190 PRK03991, PRK03991, threonyl-tRNA synthetase; Validated

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 1   MVADMKLSHKALPLLLYQFTSK-FRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDV- 57
           M+ DM +S+K LPL +Y+ ++  FR E R +  GL R R F M D++        A +  
Sbjct: 296 MLKDMTISYKNLPLKMYELSTYSFRLEQRGELVGLKRLRAFTMPDMHTLCKDMEQAMEEF 355

Query: 58  YNLVGKCYDDVFNTLGIKYRKVIVR 82
                    +    LG  Y +V +R
Sbjct: 356 EKQYEMIL-ETGEDLGRDY-EVAIR 378

Length = 613

>gnl|CDD|232951 TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, dimeric type

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 15/50 (30%), Positives = 24/50 (48%)

Query: 12  LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61
           LP  + Q    FR+E+ P+ GL R REF   ++  F      ++  +  V
Sbjct: 182 LPFGVAQIGKSFRNEISPRNGLFRVREFEQAEIEFFVHPLDKSHPKFEEV 231

This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases [Protein synthesis, tRNA aminoacylation]. Length = 551

>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain

 Score = 34.4 bits (80), Expect = 0.003
 Identities = 22/83 (26%), Positives = 32/83 (38%), Gaps = 9/83 (10%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTA-----SEVDA 54
           +      S++ LPL L +F +  R E      GL R R F   D + F        E+  
Sbjct: 99  IFKSKPRSYRDLPLRLAEFGTVHRYEQSGALHGLTRVRGFTQDDAHIFCTPDQIKEEI-- 156

Query: 55  NDVYNLVGKCYDDVFNTLGIKYR 77
             V +L+ + Y D F     K  
Sbjct: 157 KGVLDLIKEVYSD-FGFFDYKVE 178

ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. Length = 298

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	86
COG0442	500	ProS Prolyl-tRNA synthetase [Translation, ribosoma	99.96
KOG2324|consensus	457		99.95
cd00772	264	ProRS_core Prolyl-tRNA synthetase (ProRS) class II	99.94
PRK12325	439	prolyl-tRNA synthetase; Provisional	99.94
cd00779	255	ProRS_core_prok Prolyl-tRNA synthetase (ProRS) cla	99.94
cd00778	261	ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS)	99.93
TIGR00409	568	proS_fam_II prolyl-tRNA synthetase, family II. Pro	99.93
PRK09194	565	prolyl-tRNA synthetase; Provisional	99.93
PF00587	173	tRNA-synt_2b: tRNA synthetase class II core domain	99.93
cd00770	297	SerRS_core Seryl-tRNA synthetase (SerRS) class II	99.92
PRK05431	425	seryl-tRNA synthetase; Provisional	99.92
TIGR00414	418	serS seryl-tRNA synthetase. This model represents	99.91
PRK03991	613	threonyl-tRNA synthetase; Validated	99.91
PRK08661	477	prolyl-tRNA synthetase; Provisional	99.89
TIGR00408	472	proS_fam_I prolyl-tRNA synthetase, family I. Proly	99.89
PLN02837	614	threonine-tRNA ligase	99.89
PLN02678	448	seryl-tRNA synthetase	99.87
PLN02320	502	seryl-tRNA synthetase	99.87
cd00771	298	ThrRS_core Threonyl-tRNA synthetase (ThrRS) class	99.84
PRK14799	545	thrS threonyl-tRNA synthetase; Provisional	99.83
PLN02908	686	threonyl-tRNA synthetase	99.83
TIGR00418	563	thrS threonyl-tRNA synthetase. This model represen	99.83
PRK12444	639	threonyl-tRNA synthetase; Reviewed	99.82
cd00670	235	Gly_His_Pro_Ser_Thr_tRS_core Gly_His_Pro_Ser_Thr_t	99.81
PRK04173	456	glycyl-tRNA synthetase; Provisional	99.81
PRK00960	517	seryl-tRNA synthetase; Provisional	99.8
COG0172	429	SerS Seryl-tRNA synthetase [Translation, ribosomal	99.78
cd00774	254	GlyRS-like_core Glycyl-tRNA synthetase (GlyRS)-lik	99.76
TIGR00415	520	serS_MJ seryl-tRNA synthetase, Methanococcus janna	99.76
PRK12305	575	thrS threonyl-tRNA synthetase; Reviewed	99.76
COG0441	589	ThrS Threonyl-tRNA synthetase [Translation, riboso	99.75
KOG4163|consensus	551		99.71
PRK00413	638	thrS threonyl-tRNA synthetase; Reviewed	99.68
KOG2509|consensus	455		99.66
KOG1637|consensus	560		99.6
PRK14894	539	glycyl-tRNA synthetase; Provisional	99.32
TIGR00389	551	glyS_dimeric glycyl-tRNA synthetase, dimeric type.	99.32
PLN02734	684	glycyl-tRNA synthetase	99.29
CHL00201	430	syh histidine-tRNA synthetase; Provisional	99.24
COG0423	558	GRS1 Glycyl-tRNA synthetase (class II) [Translatio	99.22
COG0124	429	HisS Histidyl-tRNA synthetase [Translation, riboso	99.17
TIGR00442	397	hisS histidyl-tRNA synthetase. This model finds a	99.01
cd00773	261	HisRS-like_core Class II Histidinyl-tRNA synthetas	98.95
KOG2298|consensus	599		98.9
PRK00037	412	hisS histidyl-tRNA synthetase; Reviewed	98.87
PLN02530	487	histidine-tRNA ligase	98.86
cd00768	211	class_II_aaRS-like_core Class II tRNA amino-acyl s	98.83
PRK12420	423	histidyl-tRNA synthetase; Provisional	98.75
TIGR00443	314	hisZ_biosyn_reg ATP phosphoribosyltransferase, reg	98.71
PRK12292	391	hisZ ATP phosphoribosyltransferase regulatory subu	98.61
PRK12421	392	ATP phosphoribosyltransferase regulatory subunit;	98.45
PRK09537	417	pylS pyrolysyl-tRNA synthetase; Reviewed	98.42
PLN02972	763	Histidyl-tRNA synthetase	98.42
TIGR02367	453	PylS pyrrolysyl-tRNA synthetase. PylS is the archa	98.19
PF13393	311	tRNA-synt_His: Histidyl-tRNA synthetase; PDB: 3HRI	98.07
PRK12295	373	hisZ ATP phosphoribosyltransferase regulatory subu	98.06
PRK12293	281	hisZ ATP phosphoribosyltransferase regulatory subu	97.89
PRK07080	317	hypothetical protein; Validated	97.84
cd00669	269	Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase cl	97.66
PTZ00326	494	phenylalanyl-tRNA synthetase alpha chain; Provisio	97.62
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	97.38
PRK09350	306	poxB regulator PoxA; Provisional	97.37
TIGR00462	304	genX lysyl-tRNA synthetase-like protein GenX. Many	97.29
TIGR00459	583	aspS_bact aspartyl-tRNA synthetase, bacterial type	97.27
cd00777	280	AspRS_core Asp tRNA synthetase (aspRS) class II co	97.26
PLN02903	652	aminoacyl-tRNA ligase	97.23
KOG1936|consensus	518		97.2
PF00152	335	tRNA-synt_2: tRNA synthetases class II (D, K and N	97.18
cd00775	329	LysRS_core Lys_tRNA synthetase (LysRS) class II co	97.15
COG0173	585	AspS Aspartyl-tRNA synthetase [Translation, riboso	97.09
PRK00484	491	lysS lysyl-tRNA synthetase; Reviewed	97.04
PRK12820	706	bifunctional aspartyl-tRNA synthetase/aspartyl/glu	97.04
PRK00476	588	aspS aspartyl-tRNA synthetase; Validated	97.0
PRK06462	335	asparagine synthetase A; Reviewed	96.99
PRK12445	505	lysyl-tRNA synthetase; Reviewed	96.84
cd00776	322	AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class	96.83
KOG2411|consensus	628		96.77
PTZ00385	659	lysyl-tRNA synthetase; Provisional	96.77
PF01409	247	tRNA-synt_2d: tRNA synthetases class II core domai	96.75
PLN02502	553	lysyl-tRNA synthetase	96.75
PRK05159	437	aspC aspartyl-tRNA synthetase; Provisional	96.62
PTZ00417	585	lysine-tRNA ligase; Provisional	96.62
TIGR00499	496	lysS_bact lysyl-tRNA synthetase, eukaryotic and no	96.61
TIGR00458	428	aspS_arch aspartyl-tRNA synthetase, archaeal type.	96.44
PRK03932	450	asnC asparaginyl-tRNA synthetase; Validated	96.36
COG2269	322	Truncated, possibly inactive, lysyl-tRNA synthetas	96.19
PRK02983	1094	lysS lysyl-tRNA synthetase; Provisional	96.16
PLN02850	530	aspartate-tRNA ligase	95.99
TIGR00457	453	asnS asparaginyl-tRNA synthetase. In a multiple se	95.93
PTZ00401	550	aspartyl-tRNA synthetase; Provisional	95.67
PLN02532	633	asparagine-tRNA synthetase	95.63
TIGR00470	533	sepS O-phosphoseryl-tRNA(Cys) synthetase. This fam	95.62
PTZ00425	586	asparagine-tRNA ligase; Provisional	95.3
PLN02221	572	asparaginyl-tRNA synthetase	95.28
COG3705	390	HisZ ATP phosphoribosyltransferase involved in his	95.14
cd00496	218	PheRS_alpha_core Phenylalanyl-tRNA synthetase (Phe	95.02
PLN02603	565	asparaginyl-tRNA synthetase	94.81
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	94.68
COG0017	435	AsnS Aspartyl/asparaginyl-tRNA synthetases [Transl	94.57
TIGR00468	294	pheS phenylalanyl-tRNA synthetase, alpha subunit.	94.37
PRK00488	339	pheS phenylalanyl-tRNA synthetase subunit alpha; V	94.03
COG0016	335	PheS Phenylalanyl-tRNA synthetase alpha subunit [T	91.42
KOG2784|consensus	483		90.17
COG2024	536	Phenylalanyl-tRNA synthetase alpha subunit (archae	87.07
PRK12294	272	hisZ ATP phosphoribosyltransferase regulatory subu	86.2
COG1190	502	LysU Lysyl-tRNA synthetase (class II) [Translation	85.59
PRK09616	552	pheT phenylalanyl-tRNA synthetase subunit beta; Re	80.92

>COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=2e-29  Score=192.16  Aligned_cols=86  Identities=47%  Similarity=0.739  Sum_probs=83.6

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      |+++||.||||||+++|||+++||+|.||++||+|.|||+|+|+|+||.+.++|+++|.++.++|.+||.++|+.+..+.
T Consensus       117 ~~~~~i~SYkdLPl~lYQi~~kfRdE~rpr~gllR~REF~mkdaySfh~~~e~a~~~y~~~~~~Y~~if~~i~l~~~~~~  196 (500)
T COG0442         117 MFRKWIRSYKDLPLKLYQIQSKFRDEKRPRFGLLRGREFLMKDAYSFHADEEDAEETYEKMLDAYSRIFLRLPLIFGPVP  196 (500)
T ss_pred             HHHHHhhhhhhCCcceeeeeeEEeccccCCCCccchheeeecccccccCCHHHHHHHHHHHHHHHHHHHHhCCceEEeec
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy5542          81 VRHGAV   86 (86)
Q Consensus        81 ~~~g~~   86 (86)
                      +++|.+
T Consensus       197 ad~g~~  202 (500)
T COG0442         197 ADEGFI  202 (500)
T ss_pred             ccCCCC
Confidence            999864

>KOG2324|consensus

Probab=99.95  E-value=6e-29  Score=183.30  Aligned_cols=82  Identities=50%  Similarity=0.931  Sum_probs=79.6

Q ss_pred             ccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Q psy5542           5 MKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHG   84 (86)
Q Consensus         5 ~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g   84 (86)
                      ..+||+|||+++||++++||||.+|++||+|.|||.|+|+|+|+.+++.|.++|+.+.++|.++|+.||+||+.|.|++|
T Consensus       127 ~~lsykqlPi~vYQigrKfRDElrpRfGLlRgREFlMKDmYsFd~~~etA~qTy~~v~~aY~~iFkqL~~pfVkv~AdsG  206 (457)
T KOG2324|consen  127 IPLSYKQLPIRVYQIGRKFRDELRPRFGLLRGREFLMKDMYSFDSDEETAQQTYQLVDQAYDRIFKQLGLPFVKVWADSG  206 (457)
T ss_pred             CccccccCcEEeeeechhhhhccCccccchhhHHHHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHcCCCeEEEeeccc
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q psy5542          85 AV   86 (86)
Q Consensus        85 ~~   86 (86)
                      +|
T Consensus       207 ~i  208 (457)
T KOG2324|consen  207 DI  208 (457)
T ss_pred             cc
Confidence            86

>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain

Probab=99.94  E-value=2.9e-27  Score=168.21  Aligned_cols=86  Identities=35%  Similarity=0.545  Sum_probs=82.0

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcC-CcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLG-IKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lg-i~~~~~   79 (86)
                      |+++++.||++||+++||+++|||+|++|+.||+|+|||+|+|+|+||.+.+++++++..++++|.+++++|| +||+++
T Consensus       107 ~~~~~i~s~~~LPlrl~~~~~~fR~E~r~~~Gl~R~reF~~~e~~~~~~~~e~a~~e~~~~~~~~~~i~~~l~~lp~~~~  186 (264)
T cd00772         107 IAAKFIKSWKDLPQHLNQIGNKFRDEIRPRFGFLRAREFIMKDGHSAHADAEEADEEFLNMLSAYAEIARDLAAIDFIEG  186 (264)
T ss_pred             HHHhhhhhhhccCeeEEEEeCeEeCcCCCCCCcceeeEEEEeeeEEecCCHHHHHHHHHHHHHHHHHHHHhcCCccEEEE
Confidence            4688999999999999999999999999989999999999999999988888999999999999999999999 999999


Q ss_pred             EecCCCC
Q psy5542          80 IVRHGAV   86 (86)
Q Consensus        80 ~~~~g~~   86 (86)
                      .+++|++
T Consensus       187 ~~~~~d~  193 (264)
T cd00772         187 EADEGAK  193 (264)
T ss_pred             EcCCCcc
Confidence            9999983

ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.

>PRK12325 prolyl-tRNA synthetase; Provisional

Probab=99.94  E-value=5.7e-27  Score=176.27  Aligned_cols=86  Identities=43%  Similarity=0.677  Sum_probs=81.7

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      |+++++.|||+||+++||++++||+|.+|+.||+|+|||+|+|+|+||.+.+++.+++.+++++|.++|+.||++++.+.
T Consensus       117 ~~~~~~~syrdLPlrl~q~~~~fR~E~~~~~GL~R~reF~~~D~h~f~~~~~~a~~~~~~~~~~~~~i~~~lgl~~~~v~  196 (439)
T PRK12325        117 IFRSYVKSYKDLPLNLYHIQWKFRDEIRPRFGVMRGREFLMKDAYSFDLDEEGARHSYNRMFVAYLRTFARLGLKAIPMR  196 (439)
T ss_pred             HHHHHhhhchhhchHheEecCEecCCCCCCCCccccceEeEeccEEEeCCHHHHHHHHHHHHHHHHHHHHHcCCceEEEE
Confidence            47889999999999999999999999999889999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy5542          81 VRHGAV   86 (86)
Q Consensus        81 ~~~g~~   86 (86)
                      +++|.|
T Consensus       197 ~~~~~~  202 (439)
T PRK12325        197 ADTGPI  202 (439)
T ss_pred             EccCCC
Confidence            988863

>cd00779 ProRS_core_prok Prolyl-tRNA synthetase (ProRS) class II core catalytic domain

Probab=99.94  E-value=8.1e-27  Score=164.94  Aligned_cols=86  Identities=48%  Similarity=0.822  Sum_probs=81.9

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      ++++++.||++||+++||+++|||+|++|+.||+|+|||+|.|+|+||.++++++++++++++++.++|++|||||+++.
T Consensus       101 ~~~~~i~s~~~LPlr~~~~~~~FR~E~~~~~Gl~R~reF~q~e~~~~~~~~~~a~~~~~~i~~~~~~il~~Lgl~~~~~~  180 (255)
T cd00779         101 LVANEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEETYEKMYQAYSRIFKRLGLPFVKVE  180 (255)
T ss_pred             HHHhccccHhhCCHHHHhCcceecCCCCCCCceeeeeeEeHhhheeccCCHHHHHHHHHHHHHHHHHHHHHcCCcEEEEE
Confidence            46789999999999999999999999999999999999999999999999888999999999999999999999999999


Q ss_pred             ecCCCC
Q psy5542          81 VRHGAV   86 (86)
Q Consensus        81 ~~~g~~   86 (86)
                      +++|+|
T Consensus       181 ~~~~~~  186 (255)
T cd00779         181 ADSGAI  186 (255)
T ss_pred             ecCCCC
Confidence            999876

ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.

>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain

Probab=99.93  E-value=8.7e-27  Score=165.24  Aligned_cols=86  Identities=24%  Similarity=0.280  Sum_probs=80.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc-CCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL-GIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l-gi~~~~~   79 (86)
                      ++++++.|||+||+++||+++|||+|.+++.||+|+|||+|+|+|+++.+++++.+++++++++|++||++| ||||+.+
T Consensus       107 ~~~~~i~s~r~LPlr~~~~~~~fR~E~~~~~Gl~R~reF~~~d~h~~~~~~e~~~~~~~~~~~~~~~i~~~llgl~~~~~  186 (261)
T cd00778         107 MFSKWIRSYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDLYKEFYEDLLAIPVVKG  186 (261)
T ss_pred             HHHhhccchhhcCHHHHhhhhhccCCCCCCCceeEeeeeeeeceeeccCCHHHHHHHHHHHHHHHHHHHHHhCCCeEEEe
Confidence            468899999999999999999999999999999999999999999877778899999999999999999998 9999999


Q ss_pred             EecCCCC
Q psy5542          80 IVRHGAV   86 (86)
Q Consensus        80 ~~~~g~~   86 (86)
                      ..+++++
T Consensus       187 ~~~~~d~  193 (261)
T cd00778         187 RKTEWEK  193 (261)
T ss_pred             cCCcccc
Confidence            9887663

ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.

>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II

Probab=99.93  E-value=2.6e-26  Score=177.41  Aligned_cols=86  Identities=44%  Similarity=0.820  Sum_probs=82.5

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      ++++++.|||+||+++||+++|||+|.+|+.||+|+|||+|.|+|+||.+++++++++..+.++|.++|++|||||+++.
T Consensus       117 ~~~~~i~syr~LPlrlyqi~~~fR~E~rpr~Gl~R~REF~~~d~~~f~~~~~~a~~e~~~~~~~y~~if~~LgL~~~~v~  196 (568)
T TIGR00409       117 LARNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHSDEESLDATYQKMYQAYSNIFSRLGLDFRPVQ  196 (568)
T ss_pred             HHHHHHhhccccCeEEEEeeCEeeCCCCCCCCccccccEEEEEEEEEeCChHHHHHHHHHHHHHHHHHHHHhCCcceEEE
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy5542          81 VRHGAV   86 (86)
Q Consensus        81 ~~~g~~   86 (86)
                      +++|+|
T Consensus       197 ~~~g~~  202 (568)
T TIGR00409       197 ADSGAI  202 (568)
T ss_pred             eccccC
Confidence            999986

Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.

>PRK09194 prolyl-tRNA synthetase; Provisional

Probab=99.93  E-value=2.9e-26  Score=176.64  Aligned_cols=86  Identities=47%  Similarity=0.852  Sum_probs=82.7

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      |+++++.||++||+++||++++||+|++|+.||+|+|||+|.|+|+||.+++++++++.+++++|.++|++|||||+++.
T Consensus       117 ~~~~~~~s~~~LP~r~yqi~~~fR~E~rp~~Gl~R~reF~q~d~~~f~~~~~~a~~~~~~~~~~~~~i~~~lgl~~~~~~  196 (565)
T PRK09194        117 LVRNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHADEESLDETYDAMYQAYSRIFDRLGLDFRAVE  196 (565)
T ss_pred             HHHhhhhhcccCCeEEEEeeCCccCCCCCCCcccccccEEEeeEEEEcCChHHHHHHHHHHHHHHHHHHHHhCCccEEEE
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy5542          81 VRHGAV   86 (86)
Q Consensus        81 ~~~g~~   86 (86)
                      +++|+|
T Consensus       197 ~~~g~~  202 (565)
T PRK09194        197 ADSGAI  202 (565)
T ss_pred             cccccC
Confidence            999986

>PF00587 tRNA-synt_2b: tRNA synthetase class II core domain (G, H, P, S and T) This Prosite entry contains all class II enzymes

Probab=99.93  E-value=8.6e-26  Score=150.84  Aligned_cols=84  Identities=32%  Similarity=0.593  Sum_probs=78.3

Q ss_pred             cccccCC-cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC-cEEEE
Q psy5542           2 VADMKLS-HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI-KYRKV   79 (86)
Q Consensus         2 ~~~~i~S-yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi-~~~~~   79 (86)
                      +++.+.| |++||++++|+|+|||+|+++..|+.|+|||+|.|+|+||++ +++.++++++++.+.++++.||| +|+++
T Consensus        71 ~~~~~~~~~~~LP~~~~~~g~~fR~E~~~~~gl~R~reF~~~e~~~f~~~-~~~~~~~~~~~~~~~~i~~~lgl~~~~~~  149 (173)
T PF00587_consen   71 FKNEIRSSYRDLPLKLYQIGTCFRNEARPTRGLFRLREFTMDEMHIFCTP-EQSEEEFEELLELYKEILEKLGLEPYRIV  149 (173)
T ss_dssp             HHHHEEBHGGGSSEEEEEEEEEEBSSSSSBSTTTS-SEEEEEEEEEEESS-HHHHHHHHHHHHHHHHHHHHTTSGCEEEE
T ss_pred             ecceeeeccccCCeEEeecccccccccccccccceeeEeeeeceEEEeCC-cccHHHHHHHHHHHHHHHHHcCCceEEEE
Confidence            5677888 999999999999999999988889999999999999999998 77888999999999999999999 99999


Q ss_pred             EecCCCC
Q psy5542          80 IVRHGAV   86 (86)
Q Consensus        80 ~~~~g~~   86 (86)
                      .+++|++
T Consensus       150 ~~~~~~~  156 (173)
T PF00587_consen  150 LSSSGEL  156 (173)
T ss_dssp             EEETCTS
T ss_pred             EcCCCcc
Confidence            9999875

seryl tRNA synthetase structure; InterPro: IPR002314 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain includes the glycine, histidine, proline, threonine and serine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3UH0_A 3UGT_C 3UGQ_A 1B76_B 1GGM_B 1ATI_A 1ADY_C 1ADJ_C 2I4O_A 2I4M_B ....

>cd00770 SerRS_core Seryl-tRNA synthetase (SerRS) class II core catalytic domain

Probab=99.92  E-value=8.5e-26  Score=162.85  Aligned_cols=85  Identities=24%  Similarity=0.398  Sum_probs=79.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC----CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~----~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      |+++++.||++||++++|+++|||+|++|+    .||+|+|||+|+|+|+||++ +++++++.++++.+.+++++||||+
T Consensus       119 l~~~~~~s~~~LPlr~~~~~~~fR~E~~~~g~~~~GL~R~reF~~~e~~~f~~~-e~~~~~~~~~l~~~~~i~~~lgl~~  197 (297)
T cd00770         119 LHRDEILEEEELPLKYAGYSPCFRKEAGSAGRDTRGLFRVHQFEKVEQFVFTKP-EESWEELEELISNAEEILQELGLPY  197 (297)
T ss_pred             HHhcccCCHhhCCchheecChhHhCccccCCCCCCCceEEEeeeeeeEEEEECc-hHHHHHHHHHHHHHHHHHHHcCCcE
Confidence            478899999999999999999999999975    59999999999999999998 6778899999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +.+.+++|+|
T Consensus       198 ~~~~~~~~dl  207 (297)
T cd00770         198 RVVNICTGDL  207 (297)
T ss_pred             EEEEccCccc
Confidence            9999999975

SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. SerRS synthetase is a homodimer.

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=99.92  E-value=1.4e-25  Score=168.53  Aligned_cols=85  Identities=25%  Similarity=0.405  Sum_probs=79.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      |++++++||++||++++|+++|||+|+++    +.||+|+|||+|+|+|+||++ +++.+++++++++++++|+.|||||
T Consensus       238 l~~~~~~s~~dLPlr~~~~s~~fR~Eag~~g~~~~GL~Rv~qF~k~E~~~f~~~-e~s~~~~~~~l~~~~~i~~~Lglpy  316 (425)
T PRK05431        238 LHRDEILDEEELPLKYTAYSPCFRSEAGSAGRDTRGLIRVHQFDKVELVKFTKP-EDSYAELEELTANAEEILQKLELPY  316 (425)
T ss_pred             HHhcccCCHHhCCeeEEEEcCEecCCCCcCCCCCCceeeeeeeeeeeEEEEECH-HHHHHHHHHHHHHHHHHHHHcCCcE
Confidence            57899999999999999999999999976    359999999999999999997 6778899999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +++.+++|+|
T Consensus       317 r~v~~~s~dl  326 (425)
T PRK05431        317 RVVLLCTGDL  326 (425)
T ss_pred             EEEEcCCccc
Confidence            9999999986

>TIGR00414 serS seryl-tRNA synthetase

Probab=99.91  E-value=6e-25  Score=164.82  Aligned_cols=85  Identities=20%  Similarity=0.327  Sum_probs=78.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC----CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~----~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      |++++++||++||++++|+++|||+|++|.    .||+|+|||+|+|+|+||++ +++.++++++++.+.++|+.|||||
T Consensus       240 ~~~~~i~s~~~LPlr~~~~s~~FR~E~g~~G~~t~GL~Rv~qF~k~E~~~f~~~-e~s~~~~~~~~~~~~~i~~~Lglp~  318 (418)
T TIGR00414       240 LHRNEILEEEELPIKYTAHSPCFRSEAGSYGKDTKGLIRVHQFNKVELVKFCKP-EESAEELEEMTSDAEQILQELELPY  318 (418)
T ss_pred             HHhCcCCChHhCCeeEEEEcccccCCCCccCCCCCccccccceeeeeEEEEcCH-HHHHHHHHHHHHHHHHHHHHcCCce
Confidence            578999999999999999999999999764    39999999999999999997 4566799999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +++.+++|+|
T Consensus       319 r~v~~~t~dl  328 (418)
T TIGR00414       319 RVVNLCSGDL  328 (418)
T ss_pred             EEEecCcccc
Confidence            9999999986

This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.

>PRK03991 threonyl-tRNA synthetase; Validated

Probab=99.91  E-value=1.1e-24  Score=169.54  Aligned_cols=84  Identities=30%  Similarity=0.415  Sum_probs=79.1

Q ss_pred             CcccccCCcCCcchhhheeec-eeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTS-KFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRK   78 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~-~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~   78 (86)
                      ||+++++|||+||++++|+++ |||+|++|+. ||+|+|||+|+|+|+||++.+++.+++..+++++.++++.||++|++
T Consensus       296 ~~~~~~~SyrdLPlr~~e~~~~~fR~E~~g~l~GL~RvReF~~~D~h~f~~~~eqa~~e~~~~l~~~~~i~~~lGl~~~~  375 (613)
T PRK03991        296 MLKDMTISYKNLPLKMYELSTYSFRLEQRGELVGLKRLRAFTMPDMHTLCKDMEQAMEEFEKQYEMILETGEDLGRDYEV  375 (613)
T ss_pred             HHhCCcCchhhCChhhheecchheeCCCCCCCcCcccccceEeeeEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCCeEE
Confidence            578999999999999999999 9999999975 99999999999999999987888999999999999999999999999


Q ss_pred             EEecCC
Q psy5542          79 VIVRHG   84 (86)
Q Consensus        79 ~~~~~g   84 (86)
                      +..+++
T Consensus       376 ~~~~t~  381 (613)
T PRK03991        376 AIRFTE  381 (613)
T ss_pred             EecCHH
Confidence            887664

>PRK08661 prolyl-tRNA synthetase; Provisional

Probab=99.89  E-value=8.7e-24  Score=160.54  Aligned_cols=82  Identities=26%  Similarity=0.267  Sum_probs=76.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHH-HHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVF-NTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~-~~lgi~~~~~   79 (86)
                      ++++++.|||+||+++||+++|||+|.+ ..||+|+|||+|+|+|+||.+++++.+++.+++++|.+++ +.||||++.+
T Consensus       119 ~~~~~i~SyrdLPlrl~q~~~vfR~E~~-~rgl~R~rEF~~~E~h~~~~~~eea~~e~~~~l~~y~~i~~~~Lglp~~~~  197 (477)
T PRK08661        119 MYKKWIQSYRDLPLLYNQWVNVVRWETK-TRPFLRTREFLWQEGHTAHATEEEAEEETLEMLEIYKEFFEDYLAIPVIIG  197 (477)
T ss_pred             HHHhhhcchhhcCHHHhcccceeeCCCC-CCCcceeeeEEEcceeeeeCCHHHHHHHHHHHHHHHHHHHHHhcCCeEEEE
Confidence            4789999999999999999999999998 4599999999999999998889999999999999999999 8899999988


Q ss_pred             EecC
Q psy5542          80 IVRH   83 (86)
Q Consensus        80 ~~~~   83 (86)
                      ..+.
T Consensus       198 ~~~~  201 (477)
T PRK08661        198 KKTE  201 (477)
T ss_pred             ecCh
Confidence            7664

>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I

Probab=99.89  E-value=5.8e-24  Score=161.37  Aligned_cols=83  Identities=23%  Similarity=0.267  Sum_probs=77.6

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH-HcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN-TLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~-~lgi~~~~~   79 (86)
                      ||++++.|||+||+++||+++|||+|.+++.||+|+|||+|+|+|+++.+.+++.+++..++++|.++|+ .||||++.+
T Consensus       113 ~~~~~i~S~rdLPlr~~q~~~vfR~E~~~~~gl~R~rEF~~~e~h~~~~~~e~a~~e~~~~l~~y~~i~~~~lglp~~~~  192 (472)
T TIGR00408       113 MFKKWVKSYTDLPLKINQWVNVFRYETKHTRPFLRTREFTWQEAHTAHATAEEAEEQVLRALDIYKEFIENSLAIPYFVG  192 (472)
T ss_pred             HHhccccChhhcCHHHhheeeeecCCCCCCCCcceeeeeehhhhhhhhCCHHHHHHHHHHHHHHHHHHHHhccCCeEEEE
Confidence            5789999999999999999999999999888999999999999998777789999999999999999998 899999988


Q ss_pred             EecC
Q psy5542          80 IVRH   83 (86)
Q Consensus        80 ~~~~   83 (86)
                      ..+.
T Consensus       193 ~~~~  196 (472)
T TIGR00408       193 RKPE  196 (472)
T ss_pred             ecCc
Confidence            7654

Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.

>PLN02837 threonine-tRNA ligase

Probab=99.89  E-value=1.4e-23  Score=163.29  Aligned_cols=84  Identities=19%  Similarity=0.272  Sum_probs=77.5

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ||+++++|||+||++++|+++|||+|++|.. ||+|+|||+|+|+|+||++ +++++++..+++.+.++++.||+|++.+
T Consensus       317 ~~~~~~~SyrdLPlr~~~~~~~~R~E~~g~~~GL~RvreF~~~e~h~f~~~-~q~~~e~~~~l~~~~~~~~~lg~~~~~~  395 (614)
T PLN02837        317 VYKRKLHSYRDLPIRVAELGTVYRYELSGSLHGLFRVRGFTQDDAHIFCLE-DQIKDEIRGVLDLTEEILKQFGFSKYEI  395 (614)
T ss_pred             HHhCccCChhHCCHhhEeecccccCCCCCCCcCcccccceEECeEEEEeCH-HHHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence            5789999999999999999999999998754 9999999999999999997 4578899999999999999999999998


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      .++++.
T Consensus       396 ~~~t~~  401 (614)
T PLN02837        396 NLSTRP  401 (614)
T ss_pred             EecCCc
Confidence            888763

>PLN02678 seryl-tRNA synthetase

Probab=99.87  E-value=1.5e-22  Score=153.23  Aligned_cols=86  Identities=22%  Similarity=0.392  Sum_probs=78.9

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      +++++++||++||++++++++|||.|+++    ..||+|+|||+|+|++.||.+++ ++.++++++++.++.||+.||||
T Consensus       243 ~h~~~~~s~~eLPlr~~~~s~cfR~Eags~G~~~~GL~RvhqF~KvE~f~~~~pe~~~s~~~~e~~l~~~~~i~~~L~lp  322 (448)
T PLN02678        243 YHRGDWIDPKELPIRYAGYSTCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNGNESWEMHEEMLKNSEDFYQSLGIP  322 (448)
T ss_pred             HHhcccCCHHhCCceeEEeccccccccccCCCcCCcceEEEEEEEEEEEEEECCCchhHHHHHHHHHHHHHHHHHHcCCC
Confidence            46789999999999999999999999973    34999999999999999999864 36779999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy5542          76 YRKVIVRHGAV   86 (86)
Q Consensus        76 ~~~~~~~~g~~   86 (86)
                      |+++.+|+|||
T Consensus       323 yrvv~~~sgdl  333 (448)
T PLN02678        323 YQVVSIVSGAL  333 (448)
T ss_pred             eEEEeeccccc
Confidence            99999999997

>PLN02320 seryl-tRNA synthetase

Probab=99.87  E-value=4.4e-22  Score=152.09  Aligned_cols=85  Identities=21%  Similarity=0.377  Sum_probs=78.2

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCC--CC--CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELR--PK--FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~--~~--~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      ++.++++||++||++++.+++|||.|++  |+  .||+|+|||+++|+|+||.+ ++++++++++++..+++|+.|||||
T Consensus       301 ~~~~~ils~~dLPlRy~~~s~cFR~EAgs~G~d~rGL~RvhQF~KvE~~if~~p-eqs~~e~e~ll~~~e~i~~~LgLpy  379 (502)
T PLN02320        301 IHMDSILLESALPLKYVAFSHCFRTEAGAAGAATRGLYRVHQFSKVEMFVICRP-EESESFHEELIQIEEDLFTSLGLHF  379 (502)
T ss_pred             cccccccCHhhCCceeEEeccccccccccCCCcCCCceeeeeeecccEEEEECH-HHHHHHHHHHHHHHHHHHHHcCCCe
Confidence            3568899999999999999999999998  42  39999999999999999997 5567799999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +++..++|||
T Consensus       380 rvv~l~tgDL  389 (502)
T PLN02320        380 KTLDMATADL  389 (502)
T ss_pred             EEEEecCCcc
Confidence            9999999997

>cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain

Probab=99.84  E-value=3e-21  Score=139.08  Aligned_cols=84  Identities=24%  Similarity=0.265  Sum_probs=75.1

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ++++++.||++||+|++++++|||+|+++. .||+|+|||+|.|+|+||++ +++++++.++++++.++++.||++...+
T Consensus        99 ~~~~~~~s~~~LPlr~~~~g~vfR~E~~~~~~Gl~R~reF~q~e~~i~~~~-e~~~~e~~e~l~~~~~~l~~lgl~~~~i  177 (298)
T cd00771          99 IFKSKPRSYRDLPLRLAEFGTVHRYEQSGALHGLTRVRGFTQDDAHIFCTP-DQIKEEIKGVLDLIKEVYSDFGFFDYKV  177 (298)
T ss_pred             HHHhhccchhhCCeEEEEecCcccCCCCCCCCCccccccEEECCEEEEeCC-cchHHHHHHHHHHHHHHHHHcCCCcEEE
Confidence            467889999999999999999999998874 59999999999999999997 5667788999999999999999998888


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      ..++++
T Consensus       178 ~l~~~~  183 (298)
T cd00771         178 ELSTRP  183 (298)
T ss_pred             EEEcCh
Confidence            777653

ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.

>PRK14799 thrS threonyl-tRNA synthetase; Provisional

Probab=99.83  E-value=1.2e-20  Score=145.59  Aligned_cols=79  Identities=19%  Similarity=0.325  Sum_probs=70.6

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc---E
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK---Y   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~---~   76 (86)
                      ||+++++|||+||++++|+++|||+|.+++. ||+|+|||+|+|+|+||++ +++.+++.++++++.++|+.||++   +
T Consensus       237 ~~~~~~~SyrdLPlR~~e~g~vfR~E~sg~l~GL~RvReF~Q~DaHif~~~-~q~~~E~~~~l~~i~~vy~~fG~~~~~~  315 (545)
T PRK14799        237 IYKSKPRTYRDLPIRFSEFGHVYRWEKKGELYGLLRVRGFVQDDGHIFLRE-DQLREEIKMLISKTVEVWHKFGFKDDDI  315 (545)
T ss_pred             HHhccccChhhCCHhhEEecceecCCCCCCccccccceeEEEcccEEEeCH-HHHHHHHHHHHHHHHHHHHHhCCCcccE
Confidence            5789999999999999999999999999876 9999999999999999996 566567889999999999999996   5


Q ss_pred             EEEE
Q psy5542          77 RKVI   80 (86)
Q Consensus        77 ~~~~   80 (86)
                      ....
T Consensus       316 ~i~l  319 (545)
T PRK14799        316 KPYL  319 (545)
T ss_pred             EEEE
Confidence            5443

>PLN02908 threonyl-tRNA synthetase

Probab=99.83  E-value=1.3e-20  Score=148.19  Aligned_cols=81  Identities=30%  Similarity=0.370  Sum_probs=73.6

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ||++++.|||+||++++++++|||+|.+|.. ||+|+|||+|+|+|+||++ +++.+++.++++.+.++|+.||++|+..
T Consensus       390 ~~~~~~~s~r~LPlr~~~~g~~fR~E~~~~l~Gl~RvReF~q~d~~if~~~-~q~~~e~~~~l~~~~~v~~~lG~~~~~~  468 (686)
T PLN02908        390 MFAHRVRSYRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCRE-DQIKDEVKGVLDFLDYVYEVFGFTYELK  468 (686)
T ss_pred             HHhccccChhhCCHhHEEeeccccCCCCcCCcCccccccEEEeeEEEEcCH-HHHHHHHHHHHHHHHHHHHHCCCcEEEE
Confidence            5788999999999999999999999999865 9999999999999999996 5667788999999999999999998876


Q ss_pred             Eec
Q psy5542          80 IVR   82 (86)
Q Consensus        80 ~~~   82 (86)
                      ..+
T Consensus       469 ls~  471 (686)
T PLN02908        469 LST  471 (686)
T ss_pred             EeC
Confidence            544

>TIGR00418 thrS threonyl-tRNA synthetase

Probab=99.83  E-value=1.3e-20  Score=144.62  Aligned_cols=84  Identities=21%  Similarity=0.305  Sum_probs=77.1

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +|+++++||++||+++|+++++||+|++|+ .||+|+|||+|.|+|+||. .+++++++.++++++.++++.||+++..+
T Consensus       270 ~~~~~~~s~~~lP~rl~~~g~~fR~E~~g~~~Gl~R~reF~q~~~~~~~~-~~~~~~e~~~~i~~~~~~~~~lgl~~~~~  348 (563)
T TIGR00418       270 IFKSSLRSYRDLPLRIAELGYSHRYEQSGELHGLMRVRGFTQDDAHIFCT-EDQIKEEFKNQFRLIQKVYSDFGFSFDKY  348 (563)
T ss_pred             HHhCcCCChHHCCceeeEeccccCCCCCcCCcCcccccceEEeeeEEEcC-HHHHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence            367889999999999999999999999985 5999999999999999999 67888899999999999999999998888


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      .+++|+
T Consensus       349 ~l~~~~  354 (563)
T TIGR00418       349 ELSTRD  354 (563)
T ss_pred             EEeCCC
Confidence            888764

This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..

>PRK12444 threonyl-tRNA synthetase; Reviewed

Probab=99.82  E-value=1.3e-20  Score=146.88  Aligned_cols=78  Identities=27%  Similarity=0.404  Sum_probs=70.9

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +|++++.||++||+++||+++|||+|.+|. .||+|+|||+|+|+|+||+++ ++++++..+++++.++|+.||++|+..
T Consensus       343 ~~~~~~~sy~~LP~r~~~~g~~fR~E~~~~~~Gl~R~reF~q~d~~~f~~~~-~~~~e~~~~~~~~~~i~~~lgl~~~~~  421 (639)
T PRK12444        343 MFKNKLHSYRELPIRMCEFGQVHRHEFSGALNGLLRVRTFCQDDAHLFVTPD-QIEDEIKSVMAQIDYVYKTFGFEYEVE  421 (639)
T ss_pred             HHhCcccChhhCCceeEEeccccCCCCCcCCcCcceeeeeEEccEEEECCHH-HHHHHHHHHHHHHHHHHHHcCCcEEEE
Confidence            468899999999999999999999998874 599999999999999999964 578889999999999999999998753

>cd00670 Gly_His_Pro_Ser_Thr_tRS_core Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain

Probab=99.81  E-value=3.7e-20  Score=127.42  Aligned_cols=84  Identities=30%  Similarity=0.367  Sum_probs=75.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      ++++++.||++||++++|+++|||+|.++..|+.|+|||+|.|+|+||.++ ++.+...++++.+.++++.||+++.++.
T Consensus        76 ~~~~~~~~~~~lP~r~~~~g~~fR~E~~~~~gl~R~reF~q~e~~~~~~~~-~~~~~~~e~~~~~~~~l~~lgl~~~i~~  154 (235)
T cd00670          76 IFSGEILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVFGEPE-EAEEERREWLELAEEIARELGLPVRVVV  154 (235)
T ss_pred             HHhccCccchhcCeeeeeecccccCCCCCCCCChhheeeeeceEEEEcCHH-HHHHHHHHHHHHHHHHHHHcCCcEEEEE
Confidence            357788999999999999999999999888789999999999999999975 5566789999999999999999999988


Q ss_pred             ecCCC
Q psy5542          81 VRHGA   85 (86)
Q Consensus        81 ~~~g~   85 (86)
                      ++.++
T Consensus       155 ~~~~~  159 (235)
T cd00670         155 ADDPF  159 (235)
T ss_pred             ccChh
Confidence            87764

This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.

>PRK04173 glycyl-tRNA synthetase; Provisional

Probab=99.81  E-value=1.3e-20  Score=142.79  Aligned_cols=73  Identities=23%  Similarity=0.350  Sum_probs=68.1

Q ss_pred             cccccCCcC-CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           2 VADMKLSHK-ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         2 ~~~~i~Syr-~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      |++++.||| +||++++|+++|||+|.+|..||+|+|||+|+|+|+||++ +++.+++..+++.+..++..||++
T Consensus       174 f~~~~~syr~dLPlr~aq~g~~~RnE~s~~~gL~RvReF~q~e~hiF~~p-eq~~~e~~~~l~~~~~~l~~lG~~  247 (456)
T PRK04173        174 FKNVLRTARKKLPFGIAQIGKSFRNEITPRNFIFRTREFEQMELEFFVKP-GTDNEWFAYWIELRKNWLLDLGID  247 (456)
T ss_pred             HHHHHHhccccCCeeeeEEchhHhCccCCCCCceeeceeeeeEEEEEECc-ChHHHHHHHHHHHHHHHHHHcCCC
Confidence            678889999 9999999999999999999779999999999999999997 456778899999999999999997

>PRK00960 seryl-tRNA synthetase; Provisional

Probab=99.80  E-value=9.2e-20  Score=139.88  Aligned_cols=79  Identities=16%  Similarity=0.213  Sum_probs=70.5

Q ss_pred             CcccccCCcCCcchhhhe-eeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEE
Q psy5542           1 MVADMKLSHKALPLLLYQ-FTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRK   78 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q-~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~   78 (86)
                      ||+++++||++||+++++ .++|||+|.++..||+|+|||+|.|+|.||++ +++.+++.++++....+++.|||| ++.
T Consensus       323 ~~~~~ils~rdLPLrl~e~sG~cFR~EsGs~~GL~RV~eF~kvE~h~f~tp-Eqs~ee~e~ll~~~e~i~~~LgLp~~r~  401 (517)
T PRK00960        323 FFQGETVDVDELPIKFFDRSGWTYRWEGGGAHGLERVNEFHRIEIVWLGTP-EQVEEIRDELLKYAHILAEKLDLEYWRE  401 (517)
T ss_pred             HHhCCcCChhhCCHHHhhccCCceeCCCCCCCCCcccceeEEEEEEEEeCH-HHHHHHHHHHHHHHHHHHHHcCCCceEE
Confidence            478899999999999999 55999999666669999999999999999996 566778899999999999999999 776


Q ss_pred             EE
Q psy5542          79 VI   80 (86)
Q Consensus        79 ~~   80 (86)
                      +.
T Consensus       402 v~  403 (517)
T PRK00960        402 VG  403 (517)
T ss_pred             ec
Confidence            66

>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.78  E-value=5e-19  Score=133.24  Aligned_cols=85  Identities=24%  Similarity=0.353  Sum_probs=79.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      |++++|++-.+||++++.+++|||.|+++    +.||+|+|||.+.|+..||.++++ .++++++....+++++.|+|||
T Consensus       241 l~~~Eil~~~~LP~k~~~~S~cFR~EAGs~GrdtrGliRvHQF~KVE~v~~~~Pe~S-~~~~E~m~~~ae~il~~LeLPy  319 (429)
T COG0172         241 LHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVHQFDKVELVVITKPEES-EEELEEMLGNAEEVLQELELPY  319 (429)
T ss_pred             hhcccccccccCCeeeEEEChhhhcccccccccccceeeeeeeeeEEEEEEeCcchh-HHHHHHHHHHHHHHHHHhCCCc
Confidence            57899999999999999999999999988    559999999999999999998666 4578999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +++..|||||
T Consensus       320 Rvv~lctGDl  329 (429)
T COG0172         320 RVVNLCTGDL  329 (429)
T ss_pred             eEeeeccCCc
Confidence            9999999997

>cd00774 GlyRS-like_core Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain

Probab=99.76  E-value=2.2e-19  Score=127.01  Aligned_cols=71  Identities=21%  Similarity=0.359  Sum_probs=63.6

Q ss_pred             cccCCc-CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           4 DMKLSH-KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         4 ~~i~Sy-r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      +...|+ ++||++++|+++|||+|.+|+.||+|+|||+|.|+|+||+++ ++.+++..+.+.+.++++++|++
T Consensus        97 ~~~~~~~~~lP~~~~qig~~fR~E~~~~~gl~R~ReF~q~d~~~f~~~~-~~~e~~~~v~~~~~~~l~~~G~~  168 (254)
T cd00774          97 NLLEFNRRKLPFGVAQIGKSFRNEISPRNGLFRVREFTQAEIEFFVDPE-KSHPWFDYWADQRLKWLPKFAQS  168 (254)
T ss_pred             HHHHHhCCCCCchhhhhchhhccccCcccceeeeccchhhheeeeECCC-CchHHHHHHHHHHHHHHHHcCCC
Confidence            334455 599999999999999999999999999999999999999865 66779999999999999999974

GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains only sequences from the GlyRS form which homodimerizes. The heterotetramer glyQ is in a different family of class II aaRS. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the N-terminus of the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). Pol gamma b stimulates processive DNA synthesis and is functional as a homodimer, which can associate with the catalytic subunit Pol gamma alpha to form a heterotrimer. Despite significant both structural and sequence similarity with Gly

>TIGR00415 serS_MJ seryl-tRNA synthetase, Methanococcus jannaschii family

Probab=99.76  E-value=1.6e-18  Score=132.71  Aligned_cols=81  Identities=14%  Similarity=0.200  Sum_probs=73.9

Q ss_pred             CcccccCCcCCcchhhheee-ceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFT-SKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~-~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      |++++++|+++||++++|++ +|||+|.++..||+|++||.|.|+|.++++ +++.+..+++++.+..+++.|||||+++
T Consensus       323 ~~a~~Ils~~dLPlk~~~~s~~CFR~EaGstrGL~RvhEF~kvE~v~~~tp-Eea~e~~e~mle~~~~~l~~L~Lpyrv~  401 (520)
T TIGR00415       323 FFEGEVIDAEDKPIKFFDRSGWTYRWEAGGAKGLDRVHEFLRVECVWIAEP-EETEEIRDKTLELAEDAADELDLEWWTE  401 (520)
T ss_pred             HHhccccChhhCCeeEEEEecCeEeCCCCCCCCCceeeEEEEEEEEEEeCH-HHHHHHHHHHHHHHHHHHHHcCCCeEEe
Confidence            57899999999999999955 799999988899999999999999998775 5667788999999999999999999999


Q ss_pred             Eec
Q psy5542          80 IVR   82 (86)
Q Consensus        80 ~~~   82 (86)
                      .|+
T Consensus       402 ~ad  404 (520)
T TIGR00415       402 VGD  404 (520)
T ss_pred             ecC
Confidence            766

The seryl-tRNA synthetases from a few of the Archaea, represented by this model, are very different from the set of mutually more closely related seryl-tRNA synthetases from Eubacteria, Eukaryotes, and other Archaea. Although distantly homologous, the present set differs enough not to be recognized by the pfam model tRNA-synt_2b that recognizes the remainder of seryl-tRNA synthetases among oither class II amino-acyl tRNA synthetases.

>PRK12305 thrS threonyl-tRNA synthetase; Reviewed

Probab=99.76  E-value=1.1e-18  Score=134.39  Aligned_cols=84  Identities=23%  Similarity=0.253  Sum_probs=72.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +++++..||++||++++++++|||+|.++. .|+.|+|||+|.|+|+||.++ ++.+++.++++++.++++.||++...+
T Consensus       276 ~~~~~~~s~~~lP~r~~~~g~~fR~E~~~~~~Gl~R~reF~q~~~~if~~~~-~~~~e~~e~i~l~~~~~~~lgl~~~~i  354 (575)
T PRK12305        276 IYKSRLRSYRDLPLRLAEFGTVYRYEKSGVLHGLTRVRGFTQDDAHIFCTPD-QIEDEILKVLDFVLELLKDFGFKDYYL  354 (575)
T ss_pred             HHhcccCChhhCCHhhEEecccccCCCCCCCcCcccccCeEEcceEEEeCHH-HHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence            367788899999999999999999998754 599999999999999999854 445577999999999999999997667


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      ..++++
T Consensus       355 ~l~~r~  360 (575)
T PRK12305        355 ELSTRE  360 (575)
T ss_pred             EEeCCC
Confidence            777764

>COG0441 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.75  E-value=1.5e-18  Score=134.74  Aligned_cols=82  Identities=24%  Similarity=0.314  Sum_probs=73.4

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ||++..+|||+||+++++.+.|||+|++|.. ||.|+|.|+|+|+|+||+ .+++.+++..+++....+++.+|++...+
T Consensus       289 ifk~~~~SYR~LP~r~~E~g~v~R~E~SGal~GL~RvR~ftqdDaHifc~-~dQi~~E~~~~~~~i~~v~~~fg~~~y~~  367 (589)
T COG0441         289 IFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAHIFCT-PDQIKDEFKGILELILEVYKDFGFTDYEV  367 (589)
T ss_pred             HHhcCCcceeccchhhhhcceeecccCcchhhccccccceeecccceecc-HHHHHHHHHHHHHHHHHHHHhcCCceEEE
Confidence            4788999999999999999999999999998 999999999999999999 67777788999999999999999984444


Q ss_pred             EecC
Q psy5542          80 IVRH   83 (86)
Q Consensus        80 ~~~~   83 (86)
                      ..++
T Consensus       368 ~ls~  371 (589)
T COG0441         368 KLST  371 (589)
T ss_pred             EEec
Confidence            4443

>KOG4163|consensus

Probab=99.71  E-value=2e-18  Score=130.01  Aligned_cols=79  Identities=28%  Similarity=0.318  Sum_probs=73.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHH-cCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNT-LGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~-lgi~~~~~   79 (86)
                      +|+.||+||||||++|+||+++-|.|-+....++|.|||+|+|+|+-+.+.++|+++..+++++|..++.. |.+|++.-
T Consensus       173 ~yakWi~ShRDLPlkLNQW~nVvRWEfk~p~PFlRtrEFLWQEGHTAfat~~eA~eEvlqiLdlYa~vy~ellAiPVvkG  252 (551)
T KOG4163|consen  173 YYAKWIQSHRDLPLKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHTAFATPEEAEEEVLQILDLYARVYEELLAIPVVKG  252 (551)
T ss_pred             HHHHHHHhhccCchhhhhhhhheeeeccCCCcchhhhHHHHhcCcchhCCHhHHHHHHHHHHHHHHHHHHhhhccccccC
Confidence            47899999999999999999999999997778999999999999999999999999999999999999997 78898753

>PRK00413 thrS threonyl-tRNA synthetase; Reviewed

Probab=99.68  E-value=8.3e-17  Score=125.09  Aligned_cols=82  Identities=27%  Similarity=0.300  Sum_probs=68.9

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +++++..||++||+|+|++++|||+|.++. .||.|+|||+|.|+|+||.+++ +.+++.++++++.++|+.||++-..+
T Consensus       340 ~~~~~~~s~~~lP~r~~~~g~~fR~E~~~~~~Gl~R~reF~q~~~~~~g~~~~-~~~e~~eii~l~~~~~~~lg~~~~~i  418 (638)
T PRK00413        340 IYKQGLRSYRDLPLRLAEFGTVHRYEPSGALHGLMRVRGFTQDDAHIFCTPEQ-IEEEVKKVIDLILDVYKDFGFEDYEV  418 (638)
T ss_pred             HHhCcCCChhhCCceeeeccCeecCCCCCCCcCcceeeeeEEeeEEEEcCHHH-HHHHHHHHHHHHHHHHHHcCCceEEE
Confidence            356788999999999999999999997765 4999999999999999998644 44466999999999999999964444


Q ss_pred             EecC
Q psy5542          80 IVRH   83 (86)
Q Consensus        80 ~~~~   83 (86)
                      ..++
T Consensus       419 ~l~~  422 (638)
T PRK00413        419 KLST  422 (638)
T ss_pred             EEec
Confidence            4444

>KOG2509|consensus

Probab=99.66  E-value=1.1e-16  Score=120.28  Aligned_cols=84  Identities=21%  Similarity=0.342  Sum_probs=76.2

Q ss_pred             cccccCCcCCcchhhheeeceeecCCCCCC----CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542           2 VADMKLSHKALPLLLYQFTSKFRDELRPKF----GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR   77 (86)
Q Consensus         2 ~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~----Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~   77 (86)
                      ++++...-.+||+++..+++|||.|.++.+    ||+|+|||++.|+...|.++++. +.+++|++.-+++|+.|||||+
T Consensus       255 ~~~e~~~~~~lPiK~vg~S~CfR~EaGs~G~d~~GlyRVHqF~KVE~Fvit~Pe~S~-~~~eEmi~~~eef~qsLgip~r  333 (455)
T KOG2509|consen  255 HRDEWLEEDQLPIKYVGVSRCFRAEAGSHGKDTKGLYRVHQFEKVEQFVITGPEDSW-EMLEEMINNQEEFYQSLGLPYR  333 (455)
T ss_pred             hcccccccccCceeeeehhHHHHHHhhhcccccccceeeeeeeeeEEEEecCcchhH-HHHHHHHHHHHHHHHHhCCcee
Confidence            567778889999999999999999985543    99999999999999999998764 4889999999999999999999


Q ss_pred             EEEecCCCC
Q psy5542          78 KVIVRHGAV   86 (86)
Q Consensus        78 ~~~~~~g~~   86 (86)
                      ++...+|++
T Consensus       334 vl~m~S~eL  342 (455)
T KOG2509|consen  334 VLNMPSGEL  342 (455)
T ss_pred             EecCCchhh
Confidence            999999875

>KOG1637|consensus

Probab=99.60  E-value=1.5e-15  Score=115.34  Aligned_cols=80  Identities=24%  Similarity=0.337  Sum_probs=72.2

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ||+...+|||+||+++..++.++|||.+|.+ ||.|+|.|.|+|+|+||++ ++..+++.-.++.++.+|.-+|..+...
T Consensus       261 mf~~r~rS~reLPlR~aDFg~LHRnE~SGaLsGLTRvRrFqQDDaHIFCt~-~Qi~~Eik~~l~fl~~vY~~fgf~f~l~  339 (560)
T KOG1637|consen  261 MFAHRDRSYRELPLRFADFGVLHRNEASGALSGLTRVRRFQQDDAHIFCTP-DQVKEEIKGCLDFLDYVYGVFGFTFKLN  339 (560)
T ss_pred             ccccCCccHhhCCccccCcceeeeccccccccccceeeeecccCceEEecC-ccHHHHHHHHHHHHHHHHHhccccceeE
Confidence            6889999999999999999999999999998 9999999999999999997 5667788999999999999888777654


Q ss_pred             Ee
Q psy5542          80 IV   81 (86)
Q Consensus        80 ~~   81 (86)
                      ..
T Consensus       340 lS  341 (560)
T KOG1637|consen  340 LS  341 (560)
T ss_pred             ec
Confidence            43

>PRK14894 glycyl-tRNA synthetase; Provisional

Probab=99.32  E-value=2e-12  Score=99.42  Aligned_cols=67  Identities=24%  Similarity=0.318  Sum_probs=60.8

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      +-+.||+.++|+|.+||||.+|+.||+|+|||+|.|+-.|+.+.+ +.+++...++.....+.++||+
T Consensus       160 ~~~klPFgiaQIGk~FRNEIsPr~~l~R~REF~q~EiE~Fv~P~~-~~~~~~y~~~~~~~fl~~iGi~  226 (539)
T PRK14894        160 SARKLPFGIAQVGKAFRNEINPRNFLFRVREFEQMEIEYFVMPGT-DEEWHQRWLEARLAWWEQIGIP  226 (539)
T ss_pred             cCCCCCeeEEeeeccccCccCCCCceeecccchhheEEEEeCCCc-hHHHHHHHHHHHHHHHHHhCCC
Confidence            446999999999999999999999999999999999999999854 4668888888888999999996

>TIGR00389 glyS_dimeric glycyl-tRNA synthetase, dimeric type

Probab=99.32  E-value=8.2e-13  Score=102.41  Aligned_cols=45  Identities=31%  Similarity=0.500  Sum_probs=42.0

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChH
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEV   52 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~   52 (86)
                      +-..||+.++|||.+||||.+|+.||+|+|||+|.|+..||.+++
T Consensus       178 ~~~klPfgiaQiGk~fRNEIsPr~~l~R~REF~q~EiE~F~~p~~  222 (551)
T TIGR00389       178 FRRKLPFGVAQIGKSFRNEISPRNGLFRVREFEQAEIEFFVHPLD  222 (551)
T ss_pred             cCCCCCeeehhhhHhhhcccCcccceEEeehhhhchhheecCccc
Confidence            345999999999999999999999999999999999999999853

This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases.

>PLN02734 glycyl-tRNA synthetase

Probab=99.29  E-value=1.9e-12  Score=102.19  Aligned_cols=66  Identities=29%  Similarity=0.453  Sum_probs=56.7

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHh------------------------------------
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVD------------------------------------   53 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~------------------------------------   53 (86)
                      ..||+..+|||..||||.+|+.||+|+|||+|.|+-.|+.+++.                                    
T Consensus       272 ~klPF~~AQIGk~FRNEIsPR~gl~R~REF~qaEiE~Fv~P~~k~h~~f~~v~~~~l~l~~~~~q~~~~~~~~~t~~eAv  351 (684)
T PLN02734        272 GKLPFAAAQIGQAFRNEISPRQGLLRVREFTLAEIEHFVDPEDKSHPKFSEVADLEFLLFPREEQLGGQKAKPMRLGEAV  351 (684)
T ss_pred             CCCCeeeeeccHhhhcccCcccceeeechhhhhhhheecCcccccccchhhhhhhhhhcccHhhhhccCCcccccHHHHH
Confidence            48999999999999999999999999999999999999998632                                    


Q ss_pred             -----HHHHHHHHHHHHHHHHHHcCCc
Q psy5542          54 -----ANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        54 -----~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                           +++++...+.-....+.++||+
T Consensus       352 ~~gii~ne~l~Y~~~r~~~fl~~iGi~  378 (684)
T PLN02734        352 SKGIVNNETLGYFIGRTYLFLTKLGID  378 (684)
T ss_pred             HcCccchHHHHHHHHHHHHHHHHcCCC
Confidence                 1346677777777778888885

>CHL00201 syh histidine-tRNA synthetase; Provisional

Probab=99.24  E-value=1.6e-11  Score=92.46  Aligned_cols=72  Identities=25%  Similarity=0.245  Sum_probs=61.1

Q ss_pred             cCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecC
Q psy5542           6 KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRH   83 (86)
Q Consensus         6 i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~   83 (86)
                      ..|++++|+|+|++++|||+| +|..|  |.|||+|.+++.|+.+...++   .+++.+..++++.||++ +.....+.
T Consensus        95 ~~~~~~~p~R~~y~g~vfR~e-~~q~G--R~Ref~Q~g~EiiG~~~~~aD---~Evi~l~~~~l~~lGl~~~~i~l~~~  167 (430)
T CHL00201         95 KMDYHSNLQRLWYSGPMFRYE-RPQSG--RQRQFHQLGIEFIGSIDARAD---TEVIHLAMQIFNELQVKNLILDINSI  167 (430)
T ss_pred             cccccCCCeEEEEEcceecCC-CCcCC--ccceeEEeceEEECCCChhhH---HHHHHHHHHHHHHcCCCceEEEECCC
Confidence            346788999999999999999 55567  999999999999999888887   77899999999999996 55544443

>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]

Probab=99.22  E-value=9.5e-12  Score=95.78  Aligned_cols=44  Identities=34%  Similarity=0.604  Sum_probs=42.0

Q ss_pred             cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChH
Q psy5542           9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEV   52 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~   52 (86)
                      -+.||+.++|||..||||.+|+.||+|+|||+|.|+-.|+.+++
T Consensus       183 r~klPFgiaQIGKsfRNEISPr~gl~R~REF~QaEiE~Fv~P~~  226 (558)
T COG0423         183 RNKLPFGIAQIGKSFRNEISPRNGLFRTREFEQAEIEFFVDPEE  226 (558)
T ss_pred             ccCCCeEEEeechhhccccCcccceeehhhhhhhheeeEECCCc
Confidence            45899999999999999999999999999999999999999877

>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.17  E-value=4.5e-11  Score=90.57  Aligned_cols=68  Identities=32%  Similarity=0.460  Sum_probs=60.2

Q ss_pred             CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecCC
Q psy5542          11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRHG   84 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~g   84 (86)
                      .+|+|+|.++++||+| +|+.|  |.|||.|.++.+|..+...++   .+++.+..+++++|||. |....-+.|
T Consensus        99 ~~p~k~yy~g~vfRyE-rPQ~G--R~RqF~Q~g~E~iG~~~~~~D---AEvi~l~~~~l~~lGi~~~~l~iN~~g  167 (429)
T COG0124          99 PKPLKLYYFGPVFRYE-RPQKG--RYRQFYQFGVEVIGSDSPDAD---AEVIALAVEILEALGIGGFTLEINSRG  167 (429)
T ss_pred             cCCeeEEEecceecCC-CCCCC--CceeeEEcCeEEeCCCCcccC---HHHHHHHHHHHHHcCCCcEEEEEcCcc
Confidence            3899999999999999 88889  999999999999999888888   77999999999999997 655555444

>TIGR00442 hisS histidyl-tRNA synthetase

Probab=99.01  E-value=1.1e-09  Score=81.17  Aligned_cols=70  Identities=23%  Similarity=0.243  Sum_probs=57.6

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecC
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRH   83 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~   83 (86)
                      +++++|+|+|++++|||+|.. ..|  |.|||+|.++++|+.+...++   .+++.++.++++.||++ +.....+.
T Consensus        92 ~~~~~p~r~~y~g~vfR~e~~-~~g--r~ref~Q~g~eiig~~~~~~d---~E~i~l~~e~l~~lg~~~~~i~i~~~  162 (397)
T TIGR00442        92 LLLPKPFKLYYIGPMFRYERP-QKG--RYRQFHQFGVEVIGSDSPLAD---AEIIALAAEILKELGIKDFTLEINSL  162 (397)
T ss_pred             cccCCCeEEEEEcCeecCCCC-CCC--cccceEEcCeeeeCCCCHHHH---HHHHHHHHHHHHHcCCCceEEEecCc
Confidence            357899999999999999954 345  999999999999999866665   57899999999999997 55554443

This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff.

>cd00773 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain

Probab=98.95  E-value=2.1e-09  Score=75.91  Aligned_cols=62  Identities=29%  Similarity=0.302  Sum_probs=53.7

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR   77 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~   77 (86)
                      +++|+|+|++++|||+|.++ .|  |.|||+|.+++.|+.+...++   .+++.+..++++.||++-.
T Consensus        79 ~~~p~k~~y~g~vfR~e~~~-~g--~~re~~Q~g~Eiig~~~~~~d---aE~i~l~~~~l~~lg~~~~  140 (261)
T cd00773          79 LPLPLKLYYIGPVFRYERPQ-KG--RYREFYQVGVEIIGSDSPLAD---AEVIALAVEILEALGLKDF  140 (261)
T ss_pred             CCCCeEEEEEcCEEecCCCC-CC--CccceEEeceeeeCCCChHHH---HHHHHHHHHHHHHcCCCce
Confidence            57999999999999999655 44  999999999999999766665   7799999999999998633

HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.

>KOG2298|consensus

Probab=98.90  E-value=2.9e-10  Score=87.10  Aligned_cols=55  Identities=31%  Similarity=0.578  Sum_probs=46.8

Q ss_pred             cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542           9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK   63 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~   63 (86)
                      -+.||+.-+|||..||||.+|+.||+|+|||+|.|+++|+.+......-|..+.+
T Consensus       205 ~~KlPFA~AqiG~~fRNEISpRsGLlRvrEF~maEIEHFvdP~~K~h~kF~~V~~  259 (599)
T KOG2298|consen  205 QGKLPFASAQIGKSFRNEISPRSGLLRVREFTMAEIEHFVDPLLKSHPKFSLVAA  259 (599)
T ss_pred             CCCCcchHHHhchHhhhccCcccCceeEEEeehHHhhccCCCCCCCChhhhhhhh
Confidence            4689999999999999999999999999999999999999987654444444443

>PRK00037 hisS histidyl-tRNA synthetase; Reviewed

Probab=98.87  E-value=3.5e-09  Score=78.68  Aligned_cols=61  Identities=28%  Similarity=0.303  Sum_probs=52.4

Q ss_pred             cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEE
Q psy5542          12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRK   78 (86)
Q Consensus        12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~   78 (86)
                      +|+|+|+++++||+|.. ..|  |.|||+|.++++|+.+...++   .+++.++.++++.||++...
T Consensus        97 ~p~r~~~~g~vfR~e~~-~~g--r~ref~Q~g~ei~g~~~~~~d---~E~i~~~~~~l~~lg~~~~~  157 (412)
T PRK00037         97 QPFKLYYIGPMFRYERP-QKG--RYRQFHQFGVEVIGSDSPLAD---AEVIALAADILKALGLKGLK  157 (412)
T ss_pred             CCeEEEEEcCccccCCC-CCC--cccceEEcCeeeeCCCCcchh---HHHHHHHHHHHHHcCCCcee
Confidence            99999999999999954 445  999999999999999866666   55888999999999997443

>PLN02530 histidine-tRNA ligase

Probab=98.86  E-value=3.5e-09  Score=80.99  Aligned_cols=59  Identities=25%  Similarity=0.344  Sum_probs=53.1

Q ss_pred             CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      .+|+|+|++++|||+| ++..|  |.|||+|.++..|+.+...++   .+++.+..++++.||++
T Consensus       162 ~~P~r~~y~g~vfR~e-~~q~g--r~REf~Q~giEiiG~~~~~aD---aEvi~l~~~~l~~lgl~  220 (487)
T PLN02530        162 SLPLKWFAIGQCWRYE-RMTRG--RRREHYQWNMDIIGVPGVEAE---AELLAAIVTFFKRVGIT  220 (487)
T ss_pred             CCCeEEEEEcCEEcCc-CCCCC--CccceEEcCeeEeCCCCcchh---HHHHHHHHHHHHHcCCC
Confidence            6899999999999999 56677  999999999999999877677   67889999999999995

>cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain

Probab=98.83  E-value=1.5e-08  Score=67.76  Aligned_cols=68  Identities=28%  Similarity=0.367  Sum_probs=55.8

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC--cEEEE
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI--KYRKV   79 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi--~~~~~   79 (86)
                      +++|+++|++++|||+|..+ .++.|++||.|.+++.++.+.+++ ..+..+...+..+++.+|+  ++..+
T Consensus        72 ~~~~~~lfeig~vfr~e~~~-~~~~~~~ef~~l~~~~~g~~~~~~-~~~~~~~~~~~~~l~~lg~~~~~~~~  141 (211)
T cd00768          72 RKLPLRLAEIGPAFRNEGGR-RGLRRVREFTQLEGEVFGEDGEEA-SEFEELIELTEELLRALGIKLDIVFV  141 (211)
T ss_pred             ccCCEEEEEEcceeecCCCc-cccccceeEEEcCEEEEcCCchhH-HHHHHHHHHHHHHHHHcCCCcceEEE
Confidence            68999999999999999754 335689999999999999865433 3578899999999999997  45544

Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.

>PRK12420 histidyl-tRNA synthetase; Provisional

Probab=98.75  E-value=1.4e-08  Score=76.21  Aligned_cols=67  Identities=25%  Similarity=0.274  Sum_probs=56.9

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEec
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVR   82 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~   82 (86)
                      ..+|+|+|++++|||+|. +..|  |.|||+|.++..|..+...++   .+++.+..++++.||+++.....+
T Consensus        96 ~~~p~r~~y~g~vfR~~~-~~~g--r~rE~~Q~g~EiiG~~~~~ad---aEvi~la~~~l~~lg~~~~i~l~~  162 (423)
T PRK12420         96 IRLPFKRYEIGKVFRDGP-IKQG--RFREFIQCDVDIVGVESVMAE---AELMSMAFELFRRLNLEVTIQYNN  162 (423)
T ss_pred             CCCCeeEEEEcceECCCC-CCCC--ccceeEECCeeeECCCCCccc---HHHHHHHHHHHHHCCCCEEEEEcC
Confidence            467999999999999994 4456  999999999999998777777   779999999999999987655444

>TIGR00443 hisZ_biosyn_reg ATP phosphoribosyltransferase, regulatory subunit

Probab=98.71  E-value=3.5e-08  Score=71.55  Aligned_cols=65  Identities=28%  Similarity=0.336  Sum_probs=55.1

Q ss_pred             cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542           9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      +.++|+|++.+++|||+|..+ .|  |.|||+|.+++.|..+...++   .+++.+..++++.||++ +...
T Consensus        83 ~~~~p~r~~y~g~VfR~~~~~-~g--r~re~~Q~g~Eiig~~~~~ad---aEvi~l~~~~l~~lg~~~~~i~  148 (314)
T TIGR00443        83 DRPLPLRLCYAGNVFRTNESG-AG--RSREFTQAGVELIGAGGPAAD---AEVIALLIEALKALGLKDFKIE  148 (314)
T ss_pred             cCCCCeEEEEeceEeecCCCc-CC--CcccccccceEEeCCCCchhH---HHHHHHHHHHHHHcCCCCeEEE
Confidence            457899999999999999643 45  999999999999998766666   68999999999999995 4443

Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit.

>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional

Probab=98.61  E-value=9.2e-08  Score=71.32  Aligned_cols=64  Identities=25%  Similarity=0.340  Sum_probs=55.2

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      ...|+|+|.+++|||+| ++..|  |.|||+|.++.+|..+...++   .+++.+..++++.||++ +...
T Consensus        95 ~~~p~r~~y~g~vfR~~-~~~~g--r~ref~Q~g~EiiG~~~~~aD---aEvi~l~~~~l~~lgl~~~~i~  159 (391)
T PRK12292         95 RPGPLRLCYAGNVFRAQ-ERGLG--RSREFLQSGVELIGDAGLEAD---AEVILLLLEALKALGLPNFTLD  159 (391)
T ss_pred             CCCCeEEEeeceeeecC-CCcCC--CccchhccceEEeCCCCchHH---HHHHHHHHHHHHHcCCCCeEEE
Confidence            46899999999999999 56667  999999999999998777777   68999999999999996 4443

>PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional

Probab=98.45  E-value=5.2e-07  Score=67.55  Aligned_cols=64  Identities=11%  Similarity=-0.024  Sum_probs=54.7

Q ss_pred             CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEE
Q psy5542          11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVI   80 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~   80 (86)
                      ..|+|+|.+++|||.+. +..|  |.|||+|.++-.+..+...++   .+++.+..++++.||++ +....
T Consensus        99 ~~p~R~~Y~g~VfR~~~-~~~g--r~rEf~Q~GvEiiG~~~~~aD---aEvi~l~~e~l~~lgi~~~~l~i  163 (392)
T PRK12421         99 EGVARLCYAGSVLHTLP-QGLF--GSRTPLQLGAELYGHAGIEAD---LEIIRLMLGLLRNAGVPALHLDL  163 (392)
T ss_pred             CCceEEEEeeeEEEcCC-CcCC--CcCccceeceEEeCCCCchhH---HHHHHHHHHHHHHcCCCCeEEEe
Confidence            67999999999999884 5556  999999999999998877777   77999999999999996 44433

>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed

Probab=98.42  E-value=7.4e-07  Score=67.63  Aligned_cols=64  Identities=20%  Similarity=0.324  Sum_probs=52.4

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ++.++|++++++++|||+|..+..   +++||+|.++..+..+     ..+..+..+.+.+++.|||+|...
T Consensus       277 k~~~~P~RIFEIG~VFR~E~~g~~---hlrEf~Ql~~~iiGs~-----~~f~dL~~lleeLL~~LGI~f~i~  340 (417)
T PRK09537        277 RILPDPIKIFEIGPCYRKESDGKE---HLEEFTMVNFCQMGSG-----CTRENLENIIDDFLKHLGIDYEII  340 (417)
T ss_pred             hcccCCeeEEEEeceEecCCCCCC---CcceEEEEEEEEeCCc-----hHHHHHHHHHHHHHHHCCCCcEEe
Confidence            457889999999999999964433   8999999999988543     234668899999999999998766

>PLN02972 Histidyl-tRNA synthetase

Probab=98.42  E-value=4.3e-07  Score=73.04  Aligned_cols=64  Identities=22%  Similarity=0.340  Sum_probs=52.5

Q ss_pred             CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCC-hHhHHHHHHHHHHHHHHHHHHcCCc-EEEEE
Q psy5542          11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTAS-EVDANDVYNLVGKCYDDVFNTLGIK-YRKVI   80 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~   80 (86)
                      ..|+|+|+++++||+| +|..|  |.|||+|.++.++... ...++   .+++.+..++++.||++ +.+..
T Consensus       415 ~~p~KrYyiG~VFR~e-~pqkG--R~REF~Q~G~EIIG~~~~~~aD---AEVI~La~E~L~~LGi~df~I~I  480 (763)
T PLN02972        415 ITSFKRYQIAKVYRRD-NPSKG--RYREFYQCDFDIAGVYEPMGPD---FEIIKVLTELLDELDIGTYEVKL  480 (763)
T ss_pred             CCcceEEEeccEEecC-CCCCC--CCccceEEeEEEEcCCCcchhh---HHHHHHHHHHHHhCCCCceEEEe
Confidence            4599999999999999 46778  9999999999999873 33356   67999999999999995 44433

>TIGR02367 PylS pyrrolysyl-tRNA synthetase

Probab=98.19  E-value=4.1e-06  Score=64.07  Aligned_cols=62  Identities=16%  Similarity=0.265  Sum_probs=49.5

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ..+|+++|+++.|||+|.. ..|  |+|||+|.++.+++.+..-     .++......+++.||++|...
T Consensus       315 l~~PqKIFEIGkVFR~E~~-~~t--hlREF~QL~~eIaG~~atf-----aDlealL~e~Lr~LGIdfeit  376 (453)
T TIGR02367       315 LPDPIKIFEIGPCYRKESD-GKE--HLEEFTMLNFCQMGSGCTR-----ENLEAIIKDFLDHLEIDFEIV  376 (453)
T ss_pred             ccCCeeEEEEcCeEecCCC-CCC--CcCeEEEEEEEEECCCCCH-----HHHHHHHHHHHHHCCCceEEe
Confidence            3689999999999999954 445  8999999999999775332     345568888999999987664

PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase.

>PF13393 tRNA-synt_His: Histidyl-tRNA synthetase; PDB: 3HRI_E 3HRK_A 3LC0_A 1Z7N_A 1Z7M_D 3NET_A 1H4V_B 3OD1_A 4E51_B 3RAC_A

Probab=98.07  E-value=1.7e-05  Score=56.88  Aligned_cols=65  Identities=29%  Similarity=0.417  Sum_probs=54.2

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH-HcCCc-EEEEE
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN-TLGIK-YRKVI   80 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~-~lgi~-~~~~~   80 (86)
                      ...|.|+|.++++||++. +..|  |.|||.|.++.++..+...++   .+++.+..++++ .||+. +....
T Consensus        85 ~~~~~r~~y~g~vfR~~~-~~~g--~~re~~Q~g~Eiig~~~~~~d---aEvi~l~~e~l~~~l~~~~~~i~i  151 (311)
T PF13393_consen   85 LPRPKRYYYIGPVFRYER-PGKG--RPREFYQCGFEIIGSSSLEAD---AEVIKLADEILDRELGLENFTIRI  151 (311)
T ss_dssp             SSSSEEEEEEEEEEEEET-TTTT--BESEEEEEEEEEESSSSHHHH---HHHHHHHHHHHHHHHTTTSEEEEE
T ss_pred             cCCCceEEEEcceeeccc-cCCC--CCceeEEEEEEEECCCCHHHH---HHHHHHHHHHHHhhcCCCCcEEEE
Confidence            678999999999999994 4355  999999999999998866666   779999999997 89994 44443

...

>PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional

Probab=98.06  E-value=1.1e-05  Score=60.34  Aligned_cols=61  Identities=21%  Similarity=0.243  Sum_probs=50.2

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCCh-HhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASE-VDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~-~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      ...|+|+|.++++||+| +   |  |.|||+|.++..|..+. ..++   .+++.+..++++.||++ +...
T Consensus        79 ~~~p~R~~Y~g~VfR~~-~---g--r~rEf~Q~GvEiiG~~~~~~aD---aEvi~l~~~~L~~lgl~~~~i~  141 (373)
T PRK12295         79 GGEPARYAYLGEVFRQR-R---D--RASEFLQAGIESFGRADPAAAD---AEVLALALEALAALGPGDLEVR  141 (373)
T ss_pred             CCCCeEEEEEccEEECC-C---C--CCCcceEeeEEeeCCCCCccch---HHHHHHHHHHHHHcCCCceEEE
Confidence            46799999999999999 3   4  89999999999998633 4556   67999999999999985 4443

>PRK12293 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional

Probab=97.89  E-value=2.3e-05  Score=56.57  Aligned_cols=53  Identities=9%  Similarity=0.078  Sum_probs=45.9

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR   77 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~   77 (86)
                      ..+|+|+|.++++||+|.         |||+|.++-.+..+..      .+++.+..+++++||+++.
T Consensus        92 ~~~p~r~~Y~g~vfR~~~---------rEf~Q~GvEliG~~~~------~Evi~la~~~l~~lgl~~~  144 (281)
T PRK12293         92 STEHKKWFYIQPVFRYPS---------NEIYQIGAELIGEEDL------SEILNIAAEIFEELELEPI  144 (281)
T ss_pred             CCCceeEEEeccEEecCC---------CcccccCeEeeCCCCH------HHHHHHHHHHHHHcCCCCE
Confidence            368999999999999983         8999999999988643      3688999999999999865

>PRK07080 hypothetical protein; Validated

Probab=97.84  E-value=6.3e-05  Score=55.45  Aligned_cols=62  Identities=13%  Similarity=0.077  Sum_probs=51.2

Q ss_pred             eeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEec
Q psy5542          18 QFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVR   82 (86)
Q Consensus        18 q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~   82 (86)
                      -.+.|||+|.  ..++-|+.+|.|-|..-+.++ +++.+.-+..++....+.+.|||++.+..|+
T Consensus       157 v~g~CFR~E~--s~dl~Rl~~F~mrE~V~iGt~-e~v~~~r~~w~e~~~~l~~~LgL~~~ve~An  218 (317)
T PRK07080        157 VASYCFRHEP--SLDPARMQLFRMREYVRIGTP-EQIVAFRQSWIERGTAMADALGLPVEIDLAN  218 (317)
T ss_pred             eeeeeeccCC--CCCcHHHhheeeeEEEEecCH-HHHHHHHHHHHHHHHHHHHHhCCceeEeecC
Confidence            3467999996  368999999999999888875 5666666788888888899999999988776

>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain

Probab=97.66  E-value=0.00012  Score=52.55  Aligned_cols=40  Identities=25%  Similarity=0.339  Sum_probs=30.9

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDV   57 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~   57 (86)
                      ++|++++|||+| ..+.+  +++||+|.|++.-..+-+++.+.
T Consensus        71 ~vf~i~~~fR~e-~~~~~--hl~EF~~le~e~~~~~~~dvm~~  110 (269)
T cd00669          71 RVFEINRNFRNE-DLRAR--HQPEFTMMDLEMAFADYEDVIEL  110 (269)
T ss_pred             cEEEEecceeCC-CCCCC--cccceeEEEEEEecCCHHHHHHH
Confidence            889999999999 55555  99999999999554455554433

This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.

>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional

Probab=97.62  E-value=9.9e-05  Score=57.24  Aligned_cols=56  Identities=16%  Similarity=0.223  Sum_probs=46.5

Q ss_pred             cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      -|++++.++.|||+|. ...+  +++||+|.|+.++..+.     .+..++.+...+|+++|+.
T Consensus       356 ~P~k~fsigrVfR~d~-~Dat--H~~eFhQ~Eg~vi~~~~-----s~~~L~~~l~~f~~~lG~~  411 (494)
T PTZ00326        356 KPKKYFSIDRVFRNET-LDAT--HLAEFHQVEGFVIDRNL-----TLGDLIGTIREFFRRIGIT  411 (494)
T ss_pred             CCceEEecCCEecCCC-CCCC--cCceeEEEEEEEEeCCC-----CHHHHHHHHHHHHHhcCCC
Confidence            3999999999999995 4444  99999999999997754     2356888888999999873

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=97.38  E-value=0.00031  Score=54.12  Aligned_cols=59  Identities=12%  Similarity=0.179  Sum_probs=48.0

Q ss_pred             cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ....|+++|++++|||+|.. ..+  |++||.|.++.....+.     .+..+..+...++..||++
T Consensus       346 ~~~~p~rlFeiGrVFR~e~~-d~~--~l~Ef~ql~~~i~G~~~-----~f~elkg~l~~ll~~lGi~  404 (489)
T PRK04172        346 RPEPPQKYFSIGRVFRPDTI-DAT--HLPEFYQLEGIVMGEDV-----SFRDLLGILKEFYKRLGFE  404 (489)
T ss_pred             cCCCCeEEEEecceEcCCCC-Ccc--cCCchheEEEEEEeCCC-----CHHHHHHHHHHHHHHhCCc
Confidence            55789999999999999953 333  56899999999998642     2467888999999999994

>PRK09350 poxB regulator PoxA; Provisional

Probab=97.37  E-value=0.00012  Score=53.32  Aligned_cols=44  Identities=18%  Similarity=0.170  Sum_probs=33.3

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++|++++|||+|.++ .+  ++.||+|.|++....+-++..+..+.+
T Consensus        80 rvf~i~~~FR~e~~~-~~--H~~EFt~lE~y~~~~d~~dlm~~~E~l  123 (306)
T PRK09350         80 PIFQICKSFRNEEAG-RY--HNPEFTMLEWYRPHYDMYRLMNEVDDL  123 (306)
T ss_pred             ceEEecceeecCCCC-CC--CCcHHHhhhhhhhCCCHHHHHHHHHHH
Confidence            899999999999774 34  899999999997766655544333333

>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX

Probab=97.29  E-value=0.00021  Score=52.03  Aligned_cols=57  Identities=18%  Similarity=0.205  Sum_probs=37.8

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR   77 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~   77 (86)
                      ++|+++++||+|.++..   -+-||+|.|++....+-++..   ..+-+++..+++.+..|+.
T Consensus        75 rVfeigp~FRaE~~~~r---Hl~EFtmLE~e~~~~d~~d~m---~~~e~li~~i~~~~~~~~~  131 (304)
T TIGR00462        75 PIFQICKVFRNGERGRR---HNPEFTMLEWYRPGFDYHDLM---DEVEALLQELLGDPFAPWE  131 (304)
T ss_pred             CEEEEcCceeCCCCCCC---cccHHHhHHHHHHcCCHHHHH---HHHHHHHHHHHHhcCCCcE
Confidence            67999999999987544   688999999996655544444   3333344444544434443

Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.

>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type

Probab=97.27  E-value=0.00055  Score=54.08  Aligned_cols=45  Identities=24%  Similarity=0.213  Sum_probs=33.6

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|...+.   |--||+|.|++.-..+.++..+..+.++
T Consensus       208 rvfqI~~~FR~E~~~t~---r~pEFT~le~E~af~d~~dvm~~~E~li  252 (583)
T TIGR00459       208 RYYQIARCFRDEDLRAD---RQPEFTQIDMEMSFMTQEDVMELIEKLV  252 (583)
T ss_pred             cEEEEcceeeCCCCCCC---CCcccCcceeeecCCCHHHHHHHHHHHH
Confidence            68999999999976655   8899999999965556555554444433

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.

>cd00777 AspRS_core Asp tRNA synthetase (aspRS) class II core domain

Probab=97.26  E-value=0.00059  Score=49.25  Aligned_cols=45  Identities=22%  Similarity=0.177  Sum_probs=33.4

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++|+++++||+|...+ |  |..||+|.|++.-..+-++..+..+.++
T Consensus        71 ~v~~i~~~fR~e~~~~-~--r~~Ef~~~e~e~~~~~~~dlm~~~e~li  115 (280)
T cd00777          71 RYFQIARCFRDEDLRA-D--RQPEFTQIDIEMSFVDQEDIMSLIEGLL  115 (280)
T ss_pred             cEEEeccceeCCCCCC-C--ccceeEEeEeeeccCCHHHHHHHHHHHH
Confidence            6799999999997554 4  8889999999977666555544444433

Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain.

>PLN02903 aminoacyl-tRNA ligase

Probab=97.23  E-value=0.00066  Score=54.28  Aligned_cols=50  Identities=26%  Similarity=0.216  Sum_probs=35.6

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN   70 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~   70 (86)
                      ++||+++|||+|...+.   |--||+|.|++.-..+.++..+..+.+   +..+++
T Consensus       274 RvFqIa~~FR~E~~~t~---RhpEFTqLE~E~sf~d~~dvm~~~E~l---i~~v~~  323 (652)
T PLN02903        274 RYYQIARCFRDEDLRAD---RQPEFTQLDMELAFTPLEDMLKLNEDL---IRQVFK  323 (652)
T ss_pred             cEEEEehhhccCCCCCC---cccceeeeeeeecCCCHHHHHHHHHHH---HHHHHH
Confidence            58999999999976655   889999999996555555554343433   344444

>KOG1936|consensus

Probab=97.20  E-value=0.00021  Score=54.91  Aligned_cols=60  Identities=22%  Similarity=0.268  Sum_probs=47.0

Q ss_pred             CcchhhheeeceeecCCCC--CCCceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542          11 ALPLLLYQFTSKFRDELRP--KFGLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~--~~Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      ---++.|+|+.+||.+. |  +.|  |.|||.|.|..+...-++ -++   .+++.+..+++..|||.-
T Consensus       148 i~sikRy~iAkVyRRd~-P~mtrG--R~REFYQcDFDIAG~~d~M~pd---aE~lkiv~e~L~~l~Igd  210 (518)
T KOG1936|consen  148 ITSIKRYHIAKVYRRDQ-PAMTRG--RYREFYQCDFDIAGQFDPMIPD---AECLKIVVEILSRLGIGD  210 (518)
T ss_pred             cccceeeeEEEEEeccC-chhhch--hhhhhhccCccccccCCCCCch---HHHHHHHHHHHhhcCccc
Confidence            33467899999999994 5  458  999999999999875322 234   568888999999999953

>PF00152 tRNA-synt_2: tRNA synthetases class II (D, K and N) ; InterPro: IPR004364 The aminoacyl-tRNA synthetases (6

Probab=97.18  E-value=0.0016  Score=47.60  Aligned_cols=44  Identities=20%  Similarity=0.195  Sum_probs=31.7

Q ss_pred             hhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||+++|||+|.+ +..   =+-||+|.|++.-..+.+.+.+..+.+
T Consensus        95 ~vf~i~~~FR~E~~~~~r---Hl~EFtmLE~e~a~~~~~~lm~~~e~l  139 (335)
T PF00152_consen   95 RVFEIGPCFRNEESRTRR---HLPEFTMLEWEMAFADYDDLMDLIEEL  139 (335)
T ss_dssp             EEEEEEEEE-BSSSCBTT---BSSEEEEEEEEEETSSHHHHHHHHHHH
T ss_pred             hhhheecceeccCccccc---chhhhhhhhhccccCcHHHhHHHHHHH
Confidence            58999999999977 444   467999999999777665554343433

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry includes the asparagine, aspartic acid and lysine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1N9W_B 1BBU_A 1BBW_A 4EX5_B 3E9I_A 3E9H_C 3A74_C 1NNH_A 3M4P_C 3M4Q_B ....

>cd00775 LysRS_core Lys_tRNA synthetase (LysRS) class II core domain

Probab=97.15  E-value=0.0011  Score=48.76  Aligned_cols=45  Identities=24%  Similarity=0.251  Sum_probs=32.9

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||++++||+|..++.   .+-||+|.|++.-..+-++..+..+.++
T Consensus        78 ~vf~i~~~FR~E~~~~r---Hl~EFt~le~e~~~~~~~~~m~~~e~li  122 (329)
T cd00775          78 RVYEIGRNFRNEGIDLT---HNPEFTMIEFYEAYADYNDMMDLTEDLF  122 (329)
T ss_pred             cEEEEeccccCCCCCCC---CCCceEEEEEeeecCCHHHHHHHHHHHH
Confidence            68999999999987654   7889999999865555455443434333

Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.

>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=97.09  E-value=0.0012  Score=52.00  Aligned_cols=50  Identities=34%  Similarity=0.426  Sum_probs=34.6

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeee-EEcCChHhHHHHHHHHHHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLY-AFTASEVDANDVYNLVGKCYDDVFNT   71 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~-~f~~~~~~~~~~~~~~~~~~~~i~~~   71 (86)
                      |+|||.+|||+|- .+.-  |.-||+|.|+- ||+. +++..+..+   +++.++|+.
T Consensus       211 RYyQIarCFRDED-lRaD--RQPEFTQiD~EmSF~~-~edv~~~~E---~l~~~vf~~  261 (585)
T COG0173         211 RYYQIARCFRDED-LRAD--RQPEFTQIDLEMSFVD-EEDVMELIE---KLLRYVFKE  261 (585)
T ss_pred             ceeeeeeeecccc-cccc--cCCcceeEeEEeecCC-HHHHHHHHH---HHHHHHHHH
Confidence            7899999999995 3333  88999999996 5655 555554444   444555553

>PRK00484 lysS lysyl-tRNA synthetase; Reviewed

Probab=97.04  E-value=0.0017  Score=50.30  Aligned_cols=44  Identities=25%  Similarity=0.312  Sum_probs=32.8

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||++++||+|...+.   ++-||+|.|++.-..+-++..+..+.+
T Consensus       242 rVfei~~~FR~E~~~~r---H~pEFt~lE~e~a~~d~~d~m~~~E~l  285 (491)
T PRK00484        242 RVYEIGRNFRNEGIDTR---HNPEFTMLEFYQAYADYNDMMDLTEEL  285 (491)
T ss_pred             cEEEEecceecCCCCCC---cCCceEEEEEEEecCCHHHHHHHHHHH
Confidence            68999999999987654   889999999985555555554343433

>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional

Probab=97.04  E-value=0.00094  Score=53.83  Aligned_cols=45  Identities=24%  Similarity=0.168  Sum_probs=33.3

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|...+.   |--||+|.|++.-..+.++..+..+.++
T Consensus       226 rvfqI~~~FR~E~~~t~---r~pEFT~LE~E~af~d~~dvm~l~E~li  270 (706)
T PRK12820        226 RYFQLARCFRDEDLRPN---RQPEFTQLDIEASFIDEEFIFELIEELT  270 (706)
T ss_pred             cEEEEechhcCCCCCCC---cCccccccceeeccCCHHHHHHHHHHHH
Confidence            67999999999977655   7899999999954455555554444443

>PRK00476 aspS aspartyl-tRNA synthetase; Validated

Probab=97.00  E-value=0.0012  Score=52.14  Aligned_cols=45  Identities=24%  Similarity=0.174  Sum_probs=32.0

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|..-+.   |--||+|.|++.-..+.++..+..+.++
T Consensus       211 rvfqi~~~FR~E~~~~~---r~~EFt~le~e~af~~~~dvm~~~E~li  255 (588)
T PRK00476        211 RYYQIARCFRDEDLRAD---RQPEFTQIDIEMSFVTQEDVMALMEGLI  255 (588)
T ss_pred             ceEEEeceeecCCCCCC---cCcccccceeeecCCCHHHHHHHHHHHH
Confidence            68999999999974333   6669999999965556555554444433

>PRK06462 asparagine synthetase A; Reviewed

Probab=96.99  E-value=0.0013  Score=48.58  Aligned_cols=46  Identities=20%  Similarity=0.067  Sum_probs=32.5

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL   60 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~   60 (86)
                      ++||++++||+|...+.+=--+-||+|.|++....+-++..+..+.
T Consensus       104 rVfeI~p~FR~E~~~~~~~rHl~EFtmlE~e~~~~d~~dlm~~~e~  149 (335)
T PRK06462        104 KIFYLSPNFRLEPVDKDTGRHLYEFTQLDIEIEGADLDEVMDLIED  149 (335)
T ss_pred             cEEEEeccccCCCCCCCCCCCCCchheeeehhhcCCHHHHHHHHHH
Confidence            6799999999998766112268899999999655555554433333

>PRK12445 lysyl-tRNA synthetase; Reviewed

Probab=96.84  E-value=0.0021  Score=50.02  Aligned_cols=45  Identities=22%  Similarity=0.253  Sum_probs=34.0

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++|+++++||+|..+..   .+-||+|.|++.-..+-++..+..+.++
T Consensus       254 rVfeIg~~FRnE~~~~r---H~pEFTmlE~y~a~~d~~d~m~l~E~li  298 (505)
T PRK12445        254 RVFEINRNFRNEGISVR---HNPEFTMMELYMAYADYHDLIELTESLF  298 (505)
T ss_pred             cEEEEehhccCCCCCCC---cCcccceeeeeeecCCHHHHHHHHHHHH
Confidence            57999999999976544   7899999999987666666554444443

>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain

Probab=96.83  E-value=0.003  Score=46.34  Aligned_cols=46  Identities=17%  Similarity=0.113  Sum_probs=32.0

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcC-ChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTA-SEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~-~~~~~~~~~~~~~   62 (86)
                      ++|+++++||+|.+-+.  --+.||+|.|++.... +-++..+..+.++
T Consensus        91 ~vf~i~~~FR~E~~~~~--rHl~EFtmlE~e~~~~~~~~dlm~~~e~ll  137 (322)
T cd00776          91 RVYEIGPVFRAEKSNTR--RHLSEFWMLEAEMAFIEDYNEVMDLIEELI  137 (322)
T ss_pred             hhEEeccccccCCCCcC--CCcceeeccceeeeccCCHHHHHHHHHHHH
Confidence            68999999999963321  2578999999996655 5555544434333

Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.

>KOG2411|consensus

Probab=96.77  E-value=0.0014  Score=51.27  Aligned_cols=46  Identities=24%  Similarity=0.234  Sum_probs=33.6

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK   63 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~   63 (86)
                      ++||++.|||+|. .+.-  |--||+|.|+..-..+.+...+.++.++.
T Consensus       249 rYyQiARCfRDEd-lR~D--RQPEFTQvD~EMsF~~~~dim~liEdll~  294 (628)
T KOG2411|consen  249 RYYQIARCFRDED-LRAD--RQPEFTQVDMEMSFTDQEDIMKLIEDLLR  294 (628)
T ss_pred             hHHhHHhhhcccc-cCcc--cCCcceeeeeEEeccCHHHHHHHHHHHHH
Confidence            6899999999994 3334  89999999998666666665544444433

>PTZ00385 lysyl-tRNA synthetase; Provisional

Probab=96.77  E-value=0.0025  Score=51.08  Aligned_cols=44  Identities=20%  Similarity=0.254  Sum_probs=33.9

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||++++||+|...+.   .+-||+|.|++....+-++..+..+++
T Consensus       303 rVyeIg~~FRnE~~~~r---H~pEFTmlE~y~a~~d~~d~m~l~E~l  346 (659)
T PTZ00385        303 RIYEIGKVFRNEDADRS---HNPEFTSCEFYAAYHTYEDLMPMTEDI  346 (659)
T ss_pred             CEEEEeceecCCCCCCC---ccccccceeeeeecCCHHHHHHHHHHH
Confidence            68999999999987654   889999999997766655555443443

>PF01409 tRNA-synt_2d: tRNA synthetases class II core domain (F); InterPro: IPR002319 The aminoacyl-tRNA synthetases (6

Probab=96.75  E-value=0.0084  Score=42.70  Aligned_cols=61  Identities=13%  Similarity=0.275  Sum_probs=48.6

Q ss_pred             CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc-CCc
Q psy5542           7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL-GIK   75 (86)
Q Consensus         7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l-gi~   75 (86)
                      .+.+..|++++++|.|||+|.-...   .+.+|.|.|+-....+-     .+..+...++.+++.| |..
T Consensus        96 ~~~~~~p~kif~iG~VyR~D~~D~t---h~~~f~Qleg~~~~~~~-----~f~~Lk~~l~~l~~~lfG~~  157 (247)
T PF01409_consen   96 NKHRPPPIKIFEIGKVYRRDEIDAT---HLPEFHQLEGLVVDKNV-----TFEDLKGTLEELLKELFGID  157 (247)
T ss_dssp             TTTSHSSEEEEEEEEEESSSCSBSS---BESEEEEEEEEEEETTE------HHHHHHHHHHHHHHHHTTT
T ss_pred             HHhcCCCeEEEecCceEecCCcccc---cCccceeEeeEEEeccc-----chhHHHHHHHHHHHHHhhcc
Confidence            3567889999999999999986655   67899999998876531     3466888888888887 886

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [].; GO: 0000049 tRNA binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 3TUP_A 3HFV_A 3CMQ_A 3TEG_A 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B ....

>PLN02502 lysyl-tRNA synthetase

Probab=96.75  E-value=0.0019  Score=50.77  Aligned_cols=44  Identities=20%  Similarity=0.278  Sum_probs=32.7

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++|+++++||+|...+   -.+-||+|.|++.-..+-++..+..+.+
T Consensus       299 rVfeIg~~FRnE~~~~---rH~pEFtmlE~y~a~~d~~dlm~~~E~l  342 (553)
T PLN02502        299 RVYEIGRQFRNEGIST---RHNPEFTTCEFYQAYADYNDMMELTEEM  342 (553)
T ss_pred             CEEEEcCeeeCCCCCC---ccccceeehhhhhhcCCHHHHHHHHHHH
Confidence            5799999999997765   4889999999985555555554444433

>PRK05159 aspC aspartyl-tRNA synthetase; Provisional

Probab=96.62  E-value=0.0043  Score=47.24  Aligned_cols=43  Identities=16%  Similarity=0.150  Sum_probs=29.6

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCC-hHhHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTAS-EVDANDVYN   59 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~   59 (86)
                      ++||++++||+|...+.  -=+-||+|.|++.-..+ -++..+..+
T Consensus       204 rVf~i~~~FR~E~~~t~--rHl~EFt~lE~e~a~~~~~~~lm~~~e  247 (437)
T PRK05159        204 RVFEIGPVFRAEEHNTS--RHLNEYTSIDVEMGFIDDHEDVMDLLE  247 (437)
T ss_pred             cEEEEeceeeCCCCCCc--ccchhhheeeeeeeecccHHHHHHHHH
Confidence            67999999999976542  02579999999954444 444443333

>PTZ00417 lysine-tRNA ligase; Provisional

Probab=96.62  E-value=0.0034  Score=49.69  Aligned_cols=44  Identities=20%  Similarity=0.139  Sum_probs=33.0

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++|+++++||+|...+.   ..-||+|.|+|.-..+-++..+..+.+
T Consensus       323 rVfeIgp~FRnE~~~~r---HnpEFTmlE~y~ay~dy~dlM~l~E~L  366 (585)
T PTZ00417        323 KVYEIGKVFRNEGIDNT---HNPEFTSCEFYWAYADFYDLIKWSEDF  366 (585)
T ss_pred             CEEEEcccccCCCCCCC---ccceeeeeeeeeecCCHHHHHHHHHHH
Confidence            67999999999986654   778999999996666655554343433

>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial

Probab=96.61  E-value=0.0027  Score=49.23  Aligned_cols=45  Identities=24%  Similarity=0.275  Sum_probs=33.2

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++|+++++||+|...+.   .+-||+|.|+|.-..+-++..+..+.++
T Consensus       242 rVfeIg~~FRnE~~~~r---H~pEFTmlE~y~a~~d~~dlm~~~E~li  286 (496)
T TIGR00499       242 KVYEIGRNFRNEGVDTT---HNPEFTMIEFYQAYADYEDLMDLTENLF  286 (496)
T ss_pred             ceEEEecceecCCCCCc---ccchhheeehhhhcCCHHHHHHHHHHHH
Confidence            57999999999987654   7889999999965556555544444433

This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.

>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type

Probab=96.44  E-value=0.0078  Score=45.81  Aligned_cols=45  Identities=18%  Similarity=0.162  Sum_probs=31.8

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||++++||+|...+.  --+-||+|.|++.-..+.++..+..+++
T Consensus       201 rVf~i~~~FR~E~~~t~--rHl~EFt~lE~e~a~~~~~dlm~~~e~l  245 (428)
T TIGR00458       201 RVYEIGPIFRAEEHNTH--RHLNEATSIDIEMAFEDHHDVMDILEEL  245 (428)
T ss_pred             cEEEEecccccCCCCCc--cchheeeEeeeeeccCCHHHHHHHHHHH
Confidence            68999999999976542  1356999999996655655554444433

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).

>PRK03932 asnC asparaginyl-tRNA synthetase; Validated

Probab=96.36  E-value=0.008  Score=46.04  Aligned_cols=44  Identities=25%  Similarity=0.246  Sum_probs=30.3

Q ss_pred             hhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||+++|||+|.. +..   =+-||+|.|++.-..+-++.....+.+
T Consensus       209 rVf~i~~~FR~E~~~t~r---Hl~EFt~lE~e~~~~~~~~~m~~~e~l  253 (450)
T PRK03932        209 KVYTFGPTFRAENSNTRR---HLAEFWMIEPEMAFADLEDNMDLAEEM  253 (450)
T ss_pred             CeEEeeeccccCCCCCcc---ccccccccceEEeccCHHHHHHHHHHH
Confidence            57999999999965 222   356999999996555555544343433

>COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]

Probab=96.19  E-value=0.0055  Score=45.10  Aligned_cols=46  Identities=17%  Similarity=0.247  Sum_probs=35.2

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK   63 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~   63 (86)
                      .+||++.||||+-.|+.   ---||+|.|.|..+-+-....++...+++
T Consensus        91 ~ifql~kvfRN~E~G~~---H~PEFTMLEWYrv~~d~~~lm~e~~~Ll~  136 (322)
T COG2269          91 PIFQLGKVFRNEEMGRL---HNPEFTMLEWYRVGCDYYRLMNEVDDLLQ  136 (322)
T ss_pred             cchhhhHHHhccccccc---CCCceeEeeeeccCCcHHHHHHHHHHHHH
Confidence            47999999999987755   45699999999999887665544444444

>PRK02983 lysS lysyl-tRNA synthetase; Provisional

Probab=96.16  E-value=0.0055  Score=51.55  Aligned_cols=45  Identities=18%  Similarity=0.217  Sum_probs=34.6

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||++++||+|...+.   ..-||+|.|+|.-..+-++..+..++++
T Consensus       840 rVFEIg~~FRnE~~~~r---HnpEFTmLE~y~a~~dy~d~m~l~E~li  884 (1094)
T PRK02983        840 RVFELGRNFRNEGVDAT---HNPEFTLLEAYQAHADYDTMRDLTRELI  884 (1094)
T ss_pred             ceEEEcceecCCCCCCC---ccccccchhhhhhcCCHHHHHHHHHHHH
Confidence            67999999999987654   7889999999987776666554444443

>PLN02850 aspartate-tRNA ligase

Probab=95.99  E-value=0.0081  Score=47.04  Aligned_cols=42  Identities=21%  Similarity=0.204  Sum_probs=29.7

Q ss_pred             hhheeeceeecCCC-CCCCceeeceeeeeeee-EEcCChHhHHHHHH
Q psy5542          15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLY-AFTASEVDANDVYN   59 (86)
Q Consensus        15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~-~f~~~~~~~~~~~~   59 (86)
                      ++|+++++||+|.+ +..   =+-||+|.|++ .|..+-++..+..+
T Consensus       293 rVfeIgp~FRaE~s~t~R---Hl~EFt~Le~Em~~~~~y~evm~~~E  336 (530)
T PLN02850        293 RVFEIGPVFRAEDSFTHR---HLCEFTGLDLEMEIKEHYSEVLDVVD  336 (530)
T ss_pred             ceEEEecccccCCCCCCc---cchhhccchhhhhhhcCHHHHHHHHH
Confidence            68999999999974 322   35799999999 77655444433333

>TIGR00457 asnS asparaginyl-tRNA synthetase

Probab=95.93  E-value=0.017  Score=44.36  Aligned_cols=43  Identities=23%  Similarity=0.191  Sum_probs=29.4

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYN   59 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~   59 (86)
                      ++||++++||+|...+.  -=+-||+|.|++.-..+.+++.+..+
T Consensus       212 rVf~i~~~FR~E~~~t~--rHl~EFt~le~e~~~~~~~dvm~~~E  254 (453)
T TIGR00457       212 KVYTFGPTFRAEKSNTS--RHLSEFWMIEPEMAFANLNDLLQLAE  254 (453)
T ss_pred             CceEeeeccccCCCCCC--cCcchhccceeeeecCCHHHHHHHHH
Confidence            57999999999976532  12469999999955445555443333

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.

>PTZ00401 aspartyl-tRNA synthetase; Provisional

Probab=95.67  E-value=0.014  Score=46.05  Aligned_cols=45  Identities=16%  Similarity=0.203  Sum_probs=31.1

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeee-eEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDL-YAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~-~~f~~~~~~~~~~~~~~   61 (86)
                      ++||++++||+|.+.+.  --+-||+|.|+ +.|..+-++..+..+.+
T Consensus       281 rVfeI~p~FRaE~s~T~--RHl~EFt~Le~E~~~~~~y~evm~~~e~l  326 (550)
T PTZ00401        281 RVFEVGPVFRSENSNTH--RHLTEFVGLDVEMRINEHYYEVLDLAESL  326 (550)
T ss_pred             CEEEEeCeEeCCCCCCC--CCccchhhhhhhhHhcCCHHHHHHHHHHH
Confidence            57999999999976532  12569999999 57766544444343433

>PLN02532 asparagine-tRNA synthetase

Probab=95.63  E-value=0.024  Score=45.42  Aligned_cols=54  Identities=17%  Similarity=0.092  Sum_probs=34.8

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH-HHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV-GKCYDDVFN   70 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~-~~~~~~i~~   70 (86)
                      ++|+++++||+|.+-+.  --+-||+|.|++.--.+-+++.+..+.+ ..++..+++
T Consensus       391 rVYeIgP~FRAE~s~T~--RHL~EFtmlE~Emaf~d~~dvM~l~E~lI~~v~k~v~~  445 (633)
T PLN02532        391 NVYTFGPRFRADRIDSA--RHLAEMWMVEVEMAFSELEDAMNCAEDYFKFLCKWVLE  445 (633)
T ss_pred             ceEEEccceecCCCCCC--cccccccceeeeehhcCHHHHHHHHHHHHHHHHHHHHh
Confidence            57999999999977533  0378999999995444555544343433 333444443

>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase

Probab=95.62  E-value=0.03  Score=43.85  Aligned_cols=59  Identities=15%  Similarity=0.231  Sum_probs=46.6

Q ss_pred             cCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           9 HKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ...+|++++.++.|||+|.. ...   ++++|.|.++-..+.+-     ++..+......+++.||..
T Consensus       203 ~~~~PiRIFsIGRVfRrD~~~DaT---Hl~eFhQlEGLVVdedV-----Sf~DLKgvLe~LLr~LG~~  262 (533)
T TIGR00470       203 KRKLPLKLFSIDRCFRREQREDRS---HLMTYHSASCVVVDEEV-----SVDDGKAVAEGLLAQFGFT  262 (533)
T ss_pred             cCCCCeEEEeeeeEEecCCCCCCc---cCceeeeEEEEEECCCC-----CHHHHHHHHHHHHHHhCCc
Confidence            56799999999999999963 323   68999999999986642     3466777888888888864

This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.

>PTZ00425 asparagine-tRNA ligase; Provisional

Probab=95.30  E-value=0.048  Score=43.37  Aligned_cols=43  Identities=23%  Similarity=0.196  Sum_probs=29.2

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYN   59 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~   59 (86)
                      ++|+++++||+|.+-+.  --+-||+|.|++.-..+.++..+..+
T Consensus       345 rVf~i~p~FRaE~s~t~--RHL~EFt~lE~E~af~d~~d~m~~~E  387 (586)
T PTZ00425        345 DVYTFGPTFRAENSHTS--RHLAEFWMIEPEIAFADLYDNMELAE  387 (586)
T ss_pred             CEEEEeceEeCCCCCCC--CCCcccceEEEEEecCCHHHHHHHHH
Confidence            67999999999975322  13469999999955445454443333

>PLN02221 asparaginyl-tRNA synthetase

Probab=95.28  E-value=0.044  Score=43.47  Aligned_cols=38  Identities=26%  Similarity=0.229  Sum_probs=28.2

Q ss_pred             hhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHH
Q psy5542          15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDAN   55 (86)
Q Consensus        15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~   55 (86)
                      +.|+++++||+|.+ ...   =+-||+|.|++.-..+-++..
T Consensus       328 rVfeIgP~FRAE~s~T~R---HL~EFtmlE~Emaf~d~~dvm  366 (572)
T PLN02221        328 SVYTFGPTFRAENSHTSR---HLAEFWMVEPEIAFADLEDDM  366 (572)
T ss_pred             CeEEEccceecCCCCCCc---ccccccceeeeeecCCHHHHH
Confidence            68999999999986 333   478999999994434444443

>COG3705 HisZ ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]

Probab=95.14  E-value=0.013  Score=44.55  Aligned_cols=68  Identities=21%  Similarity=0.214  Sum_probs=55.3

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEe
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIV   81 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~   81 (86)
                      +-...|.|++..+++||.. ++..|  |..||+|.-+-.+..+...|+   .+++......++.+|++ +.....
T Consensus        90 ~~~~~P~Rl~Y~G~Vfr~~-~~~~g--~~~Ef~QaGiEllG~~~~~AD---aEvi~la~~~L~~~gl~~~~l~LG  158 (390)
T COG3705          90 LLAGTPLRLSYAGKVFRAR-EGRHG--RRAEFLQAGIELLGDDSAAAD---AEVIALALAALKALGLADLKLELG  158 (390)
T ss_pred             hcCCCCceeeecchhhhcc-hhccC--cccchhhhhhHHhCCCcchhh---HHHHHHHHHHHHHcCCcCeEEEec
Confidence            4445899999999999999 77778  888999998888888767777   67888888899999985 444433

>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain

Probab=95.02  E-value=0.077  Score=36.70  Aligned_cols=55  Identities=9%  Similarity=0.129  Sum_probs=41.7

Q ss_pred             CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcC
Q psy5542          11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLG   73 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lg   73 (86)
                      ..|++++++|++||.+..+..   ++.||.+..+.....+   .  .+..+..+.+.+++.+|
T Consensus        78 ~~~~~lFEiG~Vf~~~~~~~~---~~~E~~~l~~~~~g~~---~--df~dlkg~ve~ll~~l~  132 (218)
T cd00496          78 KPPIRIFSIGRVYRNDEIDAT---HLPEFHQIEGLVVDKG---L--TFADLKGTLEEFAKELF  132 (218)
T ss_pred             CCCeeEEEEcCeEECCCCCCC---cCCccEEEEEEEECCC---C--CHHHHHHHHHHHHHHhc
Confidence            679999999999998743222   2459999998887642   1  25778888888888888

PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.

>PLN02603 asparaginyl-tRNA synthetase

Probab=94.81  E-value=0.081  Score=41.93  Aligned_cols=39  Identities=26%  Similarity=0.178  Sum_probs=27.9

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDAN   55 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~   55 (86)
                      ++|+++++||+|.+-+.  --+-||+|.|++.-..+-++..
T Consensus       323 rVy~igp~FRaE~s~T~--RHL~EF~mlE~E~af~dl~d~m  361 (565)
T PLN02603        323 DVYTFGPTFRAENSNTS--RHLAEFWMIEPELAFADLNDDM  361 (565)
T ss_pred             ceEEEecceeCCCCCCc--cccccceeeeeeeecCCHHHHH
Confidence            47999999999976432  0357999999996444544443

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=94.68  E-value=0.064  Score=41.91  Aligned_cols=55  Identities=18%  Similarity=0.239  Sum_probs=43.2

Q ss_pred             cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC
Q psy5542          12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI   74 (86)
Q Consensus        12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi   74 (86)
                      -|++++.++.|||+|.--..   -+.+|+|.|+.+...+-     ++..+......+++++|+
T Consensus       341 ~p~k~fsigrVfR~d~iDat---H~~eFhQ~EG~vvd~~~-----t~~~L~g~l~~f~~~lg~  395 (492)
T PLN02853        341 KPKRYFSIDRVFRNEAVDRT---HLAEFHQVEGLVCDRGL-----TLGDLIGVLEDFFSRLGM  395 (492)
T ss_pred             CCcEEEeccceecCCCCCcc---cCccceeEEEEEEeCCC-----CHHHHHHHHHHHHHHcCC
Confidence            69999999999999974433   57899999999996532     235577778888888876

>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]

Probab=94.57  E-value=0.065  Score=41.29  Aligned_cols=53  Identities=23%  Similarity=0.231  Sum_probs=36.8

Q ss_pred             hhheeeceeecCCCCCCCcee-eceeeeeeeeEEcCChHhHHHHHHH-HHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMR-SREFLMKDLYAFTASEVDANDVYNL-VGKCYDDVFN   70 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R-~reF~~~d~~~f~~~~~~~~~~~~~-~~~~~~~i~~   70 (86)
                      +.|.+++.||.|.+-+.   | +-||+|.|+-.-..+.++..+..+. +.-+++++++
T Consensus       201 rVf~igP~FRAE~s~T~---RHL~EF~~ld~Emaf~~~~d~m~l~E~~i~~i~~~v~e  255 (435)
T COG0017         201 RVFTIGPTFRAEKSNTR---RHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVLE  255 (435)
T ss_pred             ceEEecCceecCCCCCc---chhhhHheecceeccCcHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999988766   5 8899999998777665554434333 2333444443

>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit

Probab=94.37  E-value=0.067  Score=38.85  Aligned_cols=56  Identities=9%  Similarity=0.152  Sum_probs=41.5

Q ss_pred             cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      .|++++++|.|||++.....   ++.||.+.++-....   ..  .+..+....+.+++.+|++
T Consensus       149 ~pirlFEiGrVfr~d~~d~~---~~pef~ql~gl~~~~---~~--~f~dLKg~le~ll~~l~~~  204 (294)
T TIGR00468       149 PPIRIFSPGRVFRNDTVDAT---HLPEFHQVEGLVIDK---NV--SFTNLKGFLEEFLKKMFGE  204 (294)
T ss_pred             CCceEEEecceEEcCCCCCc---cCChhhEEEEEEECC---CC--CHHHHHHHHHHHHHHhCCC
Confidence            89999999999999853322   245899888885542   11  2577888888888988885

Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment.

>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated

Probab=94.03  E-value=0.13  Score=38.40  Aligned_cols=55  Identities=9%  Similarity=0.132  Sum_probs=41.3

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL   72 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l   72 (86)
                      +..|+++..+|.|||++.-...   ++.+|+|.|+-..+.+-     .+..+......+++.+
T Consensus       182 ~~~Pirif~~G~VyR~D~~Dat---H~~~FhQleglvvd~~v-----tf~dLK~~L~~fl~~~  236 (339)
T PRK00488        182 QKPPIRIIAPGRVYRNDSDDAT---HSPMFHQVEGLVVDKNI-----SFADLKGTLEDFLKAF  236 (339)
T ss_pred             cCCCeEEEEeeeEEEcCCCCcc---cCcceeeEEEEEEeCCC-----CHHHHHHHHHHHHHHH
Confidence            6789999999999999964433   68899999999997642     2355556666666654

>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]

Probab=91.42  E-value=0.4  Score=35.85  Aligned_cols=53  Identities=9%  Similarity=0.136  Sum_probs=40.4

Q ss_pred             chhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcC
Q psy5542          13 PLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLG   73 (86)
Q Consensus        13 P~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lg   73 (86)
                      |+++..++.|||+|.--..   -+.+|.|.|+-+...+-.     +..+.-.++.++++++
T Consensus       192 P~k~~~~grvyR~D~~DaT---Hs~~FhQiEGlvvd~~~s-----~~~Lkg~L~~f~~~~f  244 (335)
T COG0016         192 PIKIFSPGRVYRNDTVDAT---HSPEFHQIEGLVVDKNIS-----FADLKGTLEEFAKKFF  244 (335)
T ss_pred             CceEecccceecCCCCCcc---cchheeeeEEEEEeCCcc-----HHHHHHHHHHHHHHhc
Confidence            9999999999999965544   678999999988866422     3556666677777654

>KOG2784|consensus

Probab=90.17  E-value=0.18  Score=38.62  Aligned_cols=56  Identities=16%  Similarity=0.130  Sum_probs=44.3

Q ss_pred             cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      -|.+++.|..+||||.--+.   -+-||.|.|+.+....-     +.-.++.....++.++|+.
T Consensus       332 ~p~K~FSIDrVFRNEtvDaT---HLAEFHQVEGviad~gl-----tLgdLig~l~~ff~~lg~t  387 (483)
T KOG2784|consen  332 KPAKYFSIDRVFRNETVDAT---HLAEFHQVEGVIADKGL-----TLGDLIGILMEFFTKLGAT  387 (483)
T ss_pred             CcccccchhhhhhccccchH---HHHHHhhhceeeecCCC-----cHHHHHHHHHHHHhccCCc
Confidence            38899999999999975544   57799999999987643     2345778888888888874

>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]

Probab=87.07  E-value=0.11  Score=39.96  Aligned_cols=63  Identities=16%  Similarity=0.231  Sum_probs=36.7

Q ss_pred             cCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           6 KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         6 i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      |+..+++|++++.|..|||.|++--..  ++-.+...-+.+...+ -..+    .=..+.+.+++.+|+.
T Consensus       200 i~~r~~~PlklFSIDRCFRREQ~ED~s--hLmtYhSASCVvvde~-vtvD----~GKaVAEglL~qfGFe  262 (536)
T COG2024         200 ILKREDPPLKLFSIDRCFRREQREDAS--HLMTYHSASCVVVDED-VTVD----DGKAVAEGLLRQFGFE  262 (536)
T ss_pred             HHhccCCCceeeehhHHhhhhhhcchh--hhhhhccceEEEEcCc-cccc----ccHHHHHHHHHHhCcc
Confidence            455679999999999999999876432  3333333444444221 1111    1123345566777763

>PRK12294 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional

Probab=86.20  E-value=1.6  Score=31.53  Aligned_cols=51  Identities=6%  Similarity=-0.081  Sum_probs=35.9

Q ss_pred             CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      .-|.|++.++++||++.          +|+|..+-.+..+ .+++   .+++.+..+.++.+|.+
T Consensus        82 ~~~~Rl~Y~g~VfR~~~----------~~~Q~GvEliG~~-~~a~---~e~l~la~~~l~~~g~~  132 (272)
T PRK12294         82 TAATKVAYAGLIIRNNE----------AAVQVGIENYAPS-LANV---QQSFKLFIQFIQQQLRD  132 (272)
T ss_pred             CCCceEEEeccEeccCC----------CcceeceEEECCC-chhH---HHHHHHHHHHHHHhCCC
Confidence            45779999999999983          3789988888743 2333   44556666777777543

>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]

Probab=85.59  E-value=0.7  Score=36.31  Aligned_cols=37  Identities=24%  Similarity=0.333  Sum_probs=27.9

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDA   54 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~   54 (86)
                      ++|+++..||||--...   -.-||+|.|.|-.-++-+..
T Consensus       250 rVfEIgr~FRNEGid~t---HNPEFTmlE~Y~AYaDy~D~  286 (502)
T COG1190         250 RVFEIGRNFRNEGIDTT---HNPEFTMLEFYQAYADYEDL  286 (502)
T ss_pred             hheeeccccccCCCccc---cCcchhhHHHHHHHhHHHHH
Confidence            78999999999954433   45699999999766654443

>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed

Probab=80.92  E-value=5.9  Score=31.20  Aligned_cols=61  Identities=13%  Similarity=0.219  Sum_probs=41.5

Q ss_pred             cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542           9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR   77 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~   77 (86)
                      .+..|++++++|.+|+.+..+..   -.+|+.+..+-....   ..  .|..+..+.+.++..+|+++.
T Consensus       434 ~~~~~~~lFEiG~Vf~~~~~~~~---~~~e~~~l~~~~~g~---~~--df~dlKg~ve~ll~~lgi~~~  494 (552)
T PRK09616        434 HREYPQKIFEIGDVVLIDESTET---GTRTERKLAAAIAHS---EA--SFTEIKSVVQALLRELGIEYE  494 (552)
T ss_pred             CCCCCeeEEEeeEEEecCCcccc---CcchhhEEEEEEECC---CC--CHHHHHHHHHHHHHHcCCeEE
Confidence            45789999999999987642211   124666666554443   22  267788888999999998643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	86
2i4l_A	458	Rhodopseudomonas Palustris Prolyl-trna Synthetase L		2e-14
2j3l_A	572	Prolyl-Trna Synthetase From Enterococcus Faecalis C		3e-14
1nj1_A	501	Crystal Structure Of Prolyl-Trna Synthetase From Me		1e-04

>pdb|2I4L|A Chain A, Rhodopseudomonas Palustris Prolyl-trna Synthetase Length = 458

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 35/68 (51%), Positives = 43/68 (63%)
Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDD 67
           S+K+LPL LY    KFRDE RP+FG+MR REFLMKD Y+F   E  A   YN +   Y  
Sbjct: 144 SYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLR 203
Query: 68  VFNTLGIK 75
            F  +G+K
Sbjct: 204 TFARMGLK 211

>pdb|2J3L|A Chain A, Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed With A Prolyl-Adenylate Analogue ('5'-O-(N-(L-Prolyl)- Sulfamoyl)adenosine) Length = 572

Iteration: 1
 Score = 73.2 bits (178), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 36/86 (41%), Positives = 52/86 (60%)
Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL LYQ  +K+RDE R + GL+R REF+MKD Y+F A E   +  Y  
Sbjct: 117 LIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRD 176
Query: 61  VGKCYDDVFNTLGIKYRKVIVRHGAV 86
             K Y  +F   G+++R +I   GA+
Sbjct: 177 YEKAYSRIFERCGLEFRAIIGDGGAM 202

>pdb|1NJ1|A Chain A, Crystal Structure Of Prolyl-Trna Synthetase From Methanothermobacter Thermautotrophicus Bound To Cysteine Sulfamoyl Adenylate Length = 501

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREF-LMKDLYAFTASEVDANDVYNLVGKCYD 66
           SH  LP+  YQ  + FR E +    L+R RE    K+ +   A+  +A +      + Y 
Sbjct: 152 SHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKEAHTIHATASEAEEQVERAVEIYK 211
Query: 67  DVFNTLGIKY 76
           + FN+LGI Y
Sbjct: 212 EFFNSLGIPY 221

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	86
2i4l_A	458	Proline-tRNA ligase; alpha beta; 2.00A {Rhodopseud	1e-30
2j3l_A	572	Prolyl-tRNA synthetase; class II aminoacyl- T synt	2e-29
2cja_A	522	Seryl-tRNA synthetase; ligase, zinc ION; HET: MSE	2e-06
1hc7_A	477	Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase,	1e-05
3mf2_A	346	BLL0957 protein; aminoacyl-tRNA synthetase, seryl-	2e-05
1nj8_A	459	Proline-tRNA synthetase, proline--tRNA ligase; cla	8e-05
1nj1_A	501	PROR, proline-tRNA synthetase, proline--tRNA ligas	8e-05
3ial_A	518	Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase,	1e-04
2zt5_A	693	Glycyl-tRNA synthetase; ligase, AP4A, glycine, ATP	5e-04
1ati_A	505	Glycyl-tRNA synthetase; protein biosynthesis, liga	6e-04

>2i4l_A Proline-tRNA ligase; alpha beta; 2.00A {Rhodopseudomonas palustris} PDB: 2i4m_A* 2i4n_A* 2i4o_A* Length = 458

 Score =  110 bits (278), Expect = 1e-30
 Identities = 35/80 (43%), Positives = 45/80 (56%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           +      S+K+LPL LY    KFRDE RP+FG+MR REFLMKD Y+F   E  A   YN 
Sbjct: 137 IFRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNK 196

Query: 61  VGKCYDDVFNTLGIKYRKVI 80
           +   Y   F  +G+K   + 
Sbjct: 197 MFVAYLRTFARMGLKAIPMR 216

>2j3l_A Prolyl-tRNA synthetase; class II aminoacyl- T synthetase, editing, translation; HET: P5A; 2.3A {Enterococcus faecalis} PDB: 2j3m_A* Length = 572

 Score =  108 bits (271), Expect = 2e-29
 Identities = 34/80 (42%), Positives = 49/80 (61%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
           ++ D   S+K LPL LYQ  +K+RDE R + GL+R REF+MKD Y+F A E   +  Y  
Sbjct: 117 LIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRD 176

Query: 61  VGKCYDDVFNTLGIKYRKVI 80
             K Y  +F   G+++R +I
Sbjct: 177 YEKAYSRIFERCGLEFRAII 196

>2cja_A Seryl-tRNA synthetase; ligase, zinc ION; HET: MSE ATP; 2.2A {Methanosarcina barkeri} PDB: 2cim_A* 2cj9_A* 2cjb_A Length = 522

 Score = 42.8 bits (100), Expect = 2e-06
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 1   MVADMKLSHKALPLLLYQFTSK-FRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYN 59
            VA   L ++ +P+ ++  +    R E     G+ R  EF   ++      E +      
Sbjct: 332 YVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKE-EVLKCAE 390

Query: 60  LVGKCYDDVFNT-LGIKYRKV 79
            +   Y  +FN  L I++RK 
Sbjct: 391 ELHDRYMHIFNDILDIEWRKA 411

>1hc7_A Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP + L-proline + tRNA(Pro) AMP + PPI + L-prolyl-tRNA(Pro); 2.43A {Thermus thermophilus} SCOP: c.51.1.1 d.68.5.1 d.104.1.1 PDB: 1h4q_A* 1h4t_A 1h4s_A Length = 477

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFL 40
           S + LP LL Q+ +  R E+R +   +R+ EFL
Sbjct: 126 SWRDLPQLLNQWGNVVRWEMRTRP-FLRTSEFL 157

>3mf2_A BLL0957 protein; aminoacyl-tRNA synthetase, seryl-tRNA synthetase, zinc ION, amino acid:[carrier protein] ligase; HET: AMP; 2.15A {Bradyrhizobium japonicum} PDB: 3mey_A* 3mf1_A* 3pzc_A* Length = 346

 Score = 39.6 bits (92), Expect = 2e-05
 Identities = 14/75 (18%), Positives = 23/75 (30%), Gaps = 3/75 (4%)

Query: 6   KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCY 65
           +       L        FR E  P   L R + F M++       + D +D         
Sbjct: 161 RGPLPKGGLRFDVAADCFRRE--PSKHLDRLQSFRMREYVCIGTPD-DVSDFRERWMVRA 217

Query: 66  DDVFNTLGIKYRKVI 80
             +   LG+ +R   
Sbjct: 218 QAIARDLGLTFRVDY 232

>1nj8_A Proline-tRNA synthetase, proline--tRNA ligase; class-II tRNA synthetase; 3.20A {Methanocaldococcus jannaschii} SCOP: c.51.1.1 d.68.5.1 d.104.1.1 Length = 459

 Score = 38.1 bits (89), Expect = 8e-05
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLM 41
            H  LP+ +YQ  + FR E +    L+R RE + 
Sbjct: 120 VHTDLPIKIYQIVNTFRYETKHTRPLIRLREIMT 153

>1nj1_A PROR, proline-tRNA synthetase, proline--tRNA ligase; protein-aminoacyladenylate complex class-II tRNA synthetase,; HET: 5CA; 2.55A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: c.51.1.1 d.68.5.1 d.104.1.1 PDB: 1nj2_A 1nj5_A* 1nj6_A* Length = 501

 Score = 38.2 bits (89), Expect = 8e-05
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLM 41
           SH  LP+  YQ  + FR E +    L+R RE   
Sbjct: 152 SHTDLPMRFYQVVNTFRYETKHTRPLIRVREITT 185

>3ial_A Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, prors, cysrs, RS, translation, ATP-binding, nucleotide-binding; HET: PR8; 2.20A {Giardia lamblia atcc 50803} Length = 518

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 13/33 (39%), Positives = 19/33 (57%)

Query: 8   SHKALPLLLYQFTSKFRDELRPKFGLMRSREFL 40
           S+K LPL ++Q  + FR E +    L+R RE  
Sbjct: 137 SYKDLPLKIHQTCTIFRHETKNTKPLIRVREIH 169

>2zt5_A Glycyl-tRNA synthetase; ligase, AP4A, glycine, ATP, Gly-AMP, aminoacyl-tRNA synthetase, ATP-binding, charcot-marie-tooth disease, disease mutation; HET: B4P; 2.50A {Homo sapiens} PDB: 2pme_A* 2zt6_A* 2zt7_A* 2zt8_A* 2zxf_A* 2pmf_A 2q5h_A 2q5i_A Length = 693

 Score = 36.2 bits (83), Expect = 5e-04
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 5   MKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61
           ++ +   LP    Q  + FR+E+ P+ GL+R REF M ++  F       +  +  V
Sbjct: 258 LEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNV 314

>1ati_A Glycyl-tRNA synthetase; protein biosynthesis, ligase, aminoacyl-tRNA SYN; 2.75A {Thermus thermophilus} SCOP: c.51.1.1 d.104.1.1 PDB: 1b76_A* 1ggm_A* Length = 505

 Score = 35.6 bits (82), Expect = 6e-04
 Identities = 12/49 (24%), Positives = 22/49 (44%)

Query: 5   MKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVD 53
           +  + + L   + Q    FR+E+ P+  + R REF   ++  F     D
Sbjct: 201 LDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGED 249

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	86
3lss_A	484	Seryl-tRNA synthetase; aminoacyl-tRNA synthetase,	99.93
3err_A	536	Fusion protein of microtubule binding domain from	99.93
3vbb_A	522	Seryl-tRNA synthetase, cytoplasmic; coiled-coil, l	99.92
1wle_A	501	Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bo	99.92
3qne_A	485	Seryl-tRNA synthetase, cytoplasmic; amino acid bio	99.91
3ial_A	518	Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase,	99.91
1ses_A	421	Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A	99.91
2dq0_A	455	Seryl-tRNA synthetase; coiled-coil, homodimer, str	99.89
4hvc_A	519	Bifunctional glutamate/proline--tRNA ligase; ligas	99.89
2i4l_A	458	Proline-tRNA ligase; alpha beta; 2.00A {Rhodopseud	99.89
2j3l_A	572	Prolyl-tRNA synthetase; class II aminoacyl- T synt	99.88
2dq3_A	425	Seryl-tRNA synthetase; coiled-coil, homodimer, str	99.88
1nj1_A	501	PROR, proline-tRNA synthetase, proline--tRNA ligas	99.86
1hc7_A	477	Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase,	99.86
1evl_A	401	Threonyl-tRNA synthetase; amino acid recognition,	99.85
1ati_A	505	Glycyl-tRNA synthetase; protein biosynthesis, liga	99.85
1nj8_A	459	Proline-tRNA synthetase, proline--tRNA ligase; cla	99.84
1qf6_A	642	THRRS, threonyl-tRNA synthetase; tRNA(Thr), AMP, m	99.84
3uh0_A	460	Threonyl-tRNA synthetase, mitochondrial; threonine	99.84
1nyr_A	645	Threonyl-tRNA synthetase 1; ATP, threonine, ligase	99.81
1g5h_A	454	Mitochondrial DNA polymerase accessory subunit; in	99.8
2cja_A	522	Seryl-tRNA synthetase; ligase, zinc ION; HET: MSE	99.79
3a32_A	471	Probable threonyl-tRNA synthetase 1; aeropyrum per	99.76
3ikl_A	459	DNA polymerase subunit gamma-2, mitochondrial; tra	99.75
2zt5_A	693	Glycyl-tRNA synthetase; ligase, AP4A, glycine, ATP	99.74
3mf2_A	346	BLL0957 protein; aminoacyl-tRNA synthetase, seryl-	99.69
1h4v_B	421	Histidyl-tRNA synthetase; class IIA aminoacyl-tRNA	99.65
1qe0_A	420	Histidyl-tRNA synthetase; class II tRNA synthetase	99.65
1wu7_A	434	Histidyl-tRNA synthetase; ligase, structural genom	99.62
1htt_A	423	Histidyl-tRNA synthetase; complex (tRNA synthetase	99.62
4e51_A	467	Histidine--tRNA ligase; seattle structural genomic	99.5
1z7m_A	344	ATP phosphoribosyltransferase regulatory subunit;	99.45
3od1_A	400	ATP phosphoribosyltransferase regulatory subunit;	99.32
3rac_A	373	Histidine-tRNA ligase; structural genomics, PSI-bi	99.3
3lc0_A	456	Histidyl-tRNA synthetase; tRNA-ligase, aminoacyl-t	99.27
4g84_A	464	Histidine--tRNA ligase, cytoplasmic; synthetase; 2	99.19
3net_A	465	Histidyl-tRNA synthetase; aminoacyl-tRNA synthetas	99.17
1usy_A	275	ATP phosphoribosyltransferase regulatory subunit;	99.14
3dsq_A	288	Pyrrolysyl-tRNA synthetase; homodimer, aminoacyl-t	99.11
4g85_A	517	Histidine-tRNA ligase, cytoplasmic; synthetase; 3.	99.1
3qtc_A	290	Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthet	98.63
3a5y_A	345	GENX, putative lysyl-tRNA synthetase; aminoacyl-tR	97.85
1nnh_A	294	Asparaginyl-tRNA synthetase-related peptide; struc	97.78
3a74_A	493	Lysyl-tRNA synthetase; aminoacyl tRNA synthetase,	97.68
1e1o_A	504	Lysyl-tRNA synthetase, heat inducible; ligase, ami	97.63
1x54_A	434	Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthe	97.57
1wyd_A	429	Hypothetical aspartyl-tRNA synthetase; archaea, LI	97.51
1eov_A	487	ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy	97.49
4ah6_A	617	Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo	97.44
1l0w_A	580	Aspartyl-tRNA synthetase; space-grown crystal, dim	97.39
1c0a_A	585	Aspartyl tRNA synthetase; protein-RNA complex, lig	97.38
3bju_A	521	Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase,	97.3
1n9w_A	422	Aspartyl-tRNA synthetase 2; biosynthetic protein;	97.29
4ex5_A	529	Lysine--tRNA ligase; structural genomics, niaid, n	97.25
2xgt_A	435	Asparaginyl-tRNA synthetase, cytoplasmic; ligase,	97.15
3i7f_A	548	Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-bi	96.87
3nem_A	438	Aspartyl-tRNA synthetase; rossmann fold, OB fold,	96.86
3m4p_A	456	Ehasnrs, asparaginyl-tRNA synthetase, putative; am	96.66
3l4g_A	508	Phenylalanyl-tRNA synthetase alpha chain; aminoacy	96.42
2du3_A	534	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	96.1
1b7y_A	350	Phers, protein (phenylalanyl-tRNA synthetase); enz	95.92
2rhq_A	294	Phenylalanyl-tRNA synthetase alpha chain; heterote	95.69
3pco_A	327	Phenylalanyl-tRNA synthetase, alpha subunit; amino	94.31
2odr_B	648	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.59
2odr_A	665	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.54
2odr_D	685	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.48
2du7_A	549	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	92.46
2odr_C	701	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.4
3l4g_B	589	Phenylalanyl-tRNA synthetase beta chain; aminoacyl	88.78

>3lss_A Seryl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, serrs, translation, ATP-binding, nucleotide-binding, structural genomics; HET: ATP; 1.95A {Trypanosoma brucei} PDB: 3lsq_A*

Probab=99.93  E-value=2e-26  Score=174.41  Aligned_cols=86  Identities=17%  Similarity=0.266  Sum_probs=80.0

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC----CCceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~----~Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ||+++++||++||++++++++|||+|+++.    .||+|+|||+|+|+|+||++++ ++.++++++++++++||+.||||
T Consensus       277 l~~~~i~sy~dLPlr~~~~s~cFR~Eags~Grdt~GL~RvrqF~kvE~~~f~~pe~~~s~~e~e~~~~~~e~il~~LGLp  356 (484)
T 3lss_A          277 YHRGRWFTELKEPLKYAGMSTCFRKEAGAHGRDTLGIFRVHQFDKIEQFVVCSPRQEESWRHLEDMITTSEEFNKSLGLP  356 (484)
T ss_dssp             HTTTCEESCCSSCEEEEEEEEEECCCTTCSSSCCSTTSSCSEEEEEEEEEEECSSTTHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             HHhccccchhhCCeeEEeecCccCCCCCcCCcccCCcceeeeEEEEEEEEEeCcchHHHHHHHHHHHHHHHHHHHHcCCc
Confidence            578999999999999999999999999653    5999999999999999999865 47889999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy5542          76 YRKVIVRHGAV   86 (86)
Q Consensus        76 ~~~~~~~~g~~   86 (86)
                      |+++.+|+|+|
T Consensus       357 yrvv~l~tgdl  367 (484)
T 3lss_A          357 YRVVNICSGAL  367 (484)
T ss_dssp             EEEEECCTTTC
T ss_pred             EEEEEcCCccc
Confidence            99999999986

>3err_A Fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA...; coiled coil, ligase; HET: AMP; 2.27A {Mus musculus} PDB: 3j1t_A 3j1u_A

Probab=99.93  E-value=3.8e-26  Score=174.49  Aligned_cols=86  Identities=24%  Similarity=0.390  Sum_probs=80.4

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCC----CCCCceeeceeeeeeeeEEcCCh-HhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELR----PKFGLMRSREFLMKDLYAFTASE-VDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~----~~~Gl~R~reF~~~d~~~f~~~~-~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      |++++++||++||++++|+++|||+|++    ++.||+|+|||+|+|+|+||+++ +++.++++++++.++++|++||||
T Consensus       342 l~~~~i~s~~~LPlr~~~~~~~fR~E~gs~Gr~~~GL~RvrqF~k~e~~~f~~pe~e~s~~~~e~~~~~~~~i~~~LgLp  421 (536)
T 3err_A          342 LHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELP  421 (536)
T ss_dssp             HTTTCEEEGGGCSEEEEEEEEEECCCTTCTTSSCSTTSSCSEEEEEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHhcccccHhhCCeeEEEecccccCCccccCCCCCCceeeeeeEEEEEEEEECCchHHHHHHHHHHHHHHHHHHHHcCCc
Confidence            5789999999999999999999999994    35699999999999999999987 577889999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy5542          76 YRKVIVRHGAV   86 (86)
Q Consensus        76 ~~~~~~~~g~~   86 (86)
                      |+++.+++|+|
T Consensus       422 yrvv~~~tgdl  432 (536)
T 3err_A          422 YRLVEVATGDM  432 (536)
T ss_dssp             EEEEECCTTTS
T ss_pred             EEEEEcCCccc
Confidence            99999999986

>3vbb_A Seryl-tRNA synthetase, cytoplasmic; coiled-coil, ligase; 2.89A {Homo sapiens}

Probab=99.92  E-value=8.4e-26  Score=172.16  Aligned_cols=86  Identities=19%  Similarity=0.398  Sum_probs=80.1

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ||+++++||++||++++++++|||+|+++    +.||+|+|||+|+|+|+||++++ ++.++++++++.++++|+.||||
T Consensus       279 l~~~ei~s~~dLPlr~~~~s~cFR~Eags~GrdtrGL~RvhQF~kvE~~~f~~pe~e~s~~e~e~ml~~~e~il~~LGLp  358 (522)
T 3vbb_A          279 LHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIP  358 (522)
T ss_dssp             TSTTCEECTTTCCEEEEEEEEEECSCCCC----CCCSSSCSEEEEEEEEEEECSSTTHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHhhhecccccCCeeEEEecccccCCCCcCCccCCCcceeeeeEEEEEEEEeCCChHHHHHHHHHHHHHHHHHHHHcCCc
Confidence            68999999999999999999999999964    46999999999999999999874 57889999999999999999999


Q ss_pred             EEEEEecCCCC
Q psy5542          76 YRKVIVRHGAV   86 (86)
Q Consensus        76 ~~~~~~~~g~~   86 (86)
                      |+++.+|+|+|
T Consensus       359 yrvv~l~tgdl  369 (522)
T 3vbb_A          359 YHIVNIVSGSL  369 (522)
T ss_dssp             EEEEECCGGGC
T ss_pred             eEEEEcCCccC
Confidence            99999999986

>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}

Probab=99.92  E-value=5.4e-26  Score=172.58  Aligned_cols=86  Identities=15%  Similarity=0.331  Sum_probs=80.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCC---CCCCceeeceeeeeeeeEEcCCh-HhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELR---PKFGLMRSREFLMKDLYAFTASE-VDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~---~~~Gl~R~reF~~~d~~~f~~~~-~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      ||+++++||++||++++|+++|||+|++   ++.||+|+|||+|+|+|+||+++ +++.+++++++++++++|+.|||||
T Consensus       290 l~~~~i~s~~~LPlrl~~~s~~FR~Ea~~G~d~~GL~RvhqF~kvE~~~f~~pe~e~s~~~~e~~l~~~~~il~~LgLpy  369 (501)
T 1wle_A          290 YFMDHSVAFRDLPIRMVCSSTCYRAETDTGKEPWGLYRVHHFTKVEMFGVTGPGLEQSSELLEEFLSLQMEILTELGLHF  369 (501)
T ss_dssp             HHTTEEEEGGGCSEEEEEEEEEECCCCSCC--CCSSSSCSEEEEEEEEEEECSSHHHHHHHHHHHHHHHHHHHHHTTCCE
T ss_pred             HHhhccCCcccCCeeEEeccCcccCCCCCCCCCcCceeeeeeeeeeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHCCCcE
Confidence            4789999999999999999999999987   35699999999999999999987 7888899999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +++.+++|+|
T Consensus       370 rvv~l~tgdl  379 (501)
T 1wle_A          370 RVLDMPTQEL  379 (501)
T ss_dssp             EEEECCGGGS
T ss_pred             EEEEccCccc
Confidence            9999999975

>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis, CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A* 3qo8_A* 3qo5_A

Probab=99.91  E-value=2.4e-25  Score=168.55  Aligned_cols=85  Identities=21%  Similarity=0.421  Sum_probs=77.6

Q ss_pred             CcccccCC--cCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC
Q psy5542           1 MVADMKLS--HKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI   74 (86)
Q Consensus         1 ~~~~~i~S--yr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi   74 (86)
                      |++++++|  |++||++++|+++|||+|+++    +.||+|+|||+|+|+|+||++ +++++++++++++++++|+.|||
T Consensus       254 l~~~ei~~S~y~dLPlr~~~~s~cfR~Eag~~Grdt~GL~RvhqF~kvE~~~f~~p-e~s~~e~e~ml~~~e~il~~LgL  332 (485)
T 3qne_A          254 YHAGEWFESPAEQLPVRYAGYSSCFRREAGSHGKDAWGIFRVHAFEKIEQFVLTEP-EKSWEEFDRMIGCSEEFYQSLGL  332 (485)
T ss_dssp             HTTTCEESSHHHHCCEEEEEEEEEECSCCC-----CCSSSSCSEEEEEEEEEEECG-GGHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHhccccccchhcCCeeEEEecccccCCCCCCCccCCCceeeeeeeeeeEEEEeCH-HHHHHHHHHHHHHHHHHHHHCCC
Confidence            46788887  999999999999999999976    459999999999999999997 46788999999999999999999


Q ss_pred             cEEEEEecCCCC
Q psy5542          75 KYRKVIVRHGAV   86 (86)
Q Consensus        75 ~~~~~~~~~g~~   86 (86)
                      ||+++.+|+|+|
T Consensus       333 pyrvv~~~tgdl  344 (485)
T 3qne_A          333 PYRVVGIVSGEL  344 (485)
T ss_dssp             CEEEEECCGGGC
T ss_pred             cEEEEEcCCccc
Confidence            999999999986

>3ial_A Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, prors, cysrs, RS, translation, ATP-binding, nucleotide-binding; HET: PR8; 2.20A {Giardia lamblia atcc 50803}

Probab=99.91  E-value=4.1e-25  Score=168.31  Aligned_cols=85  Identities=27%  Similarity=0.232  Sum_probs=79.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHH-HHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVF-NTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~-~~lgi~~~~~   79 (86)
                      +|+++++||++||+++||+++|||+|.+|+.||+|+|||+|+|+|+||.+++++++++..++++|.++| +.|||||+.+
T Consensus       130 ~~~~~i~SyrdLPlrl~q~~~~fR~E~~~~~GL~R~REF~q~e~h~f~~~~e~a~~e~~~~l~~~~~i~~~~LGlp~~~~  209 (518)
T 3ial_A          130 MFSKWVRSYKDLPLKIHQTCTIFRHETKNTKPLIRVREIHWNEAHCCHATAEDAVSQLSDYWKVIDTIFSDELCFKGQKL  209 (518)
T ss_dssp             HHHHHCCBGGGCCEEEEEEEEEECTTCCSCBTTTBCSEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHTTTTCCCCEEE
T ss_pred             HHHhhhcccccCCeEEEEEeceecCCCCCCCCCceeeEEEEeeEEEEECCHHHHHHHHHHHHHHHHHHHHHhcCCcEEee
Confidence            478899999999999999999999999999999999999999999998888999999999999999999 8999999998


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      ..+.++
T Consensus       210 ~~~~~e  215 (518)
T 3ial_A          210 RRVCWD  215 (518)
T ss_dssp             EECGGG
T ss_pred             ecChhh
Confidence            876543

>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A* 1set_A* 1sry_A

Probab=99.91  E-value=5.5e-25  Score=163.98  Aligned_cols=85  Identities=25%  Similarity=0.391  Sum_probs=79.2

Q ss_pred             CcccccCCcCCcchhhheeeceeecCC----CCCCCceeeceeeeeeeeEEcCC-hHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDEL----RPKFGLMRSREFLMKDLYAFTAS-EVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~----~~~~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ++++++.||++||++++|+++|||+|+    +++.||+|+|||+|+|+|+||.+ .+++++++.++++++.++|+.||||
T Consensus       233 ~~~~~~~s~~~LPlr~~~~g~~FR~E~g~~Gr~~~GL~R~rqF~q~E~~~f~~p~~e~s~~~~~e~~~~~~~il~~LGL~  312 (421)
T 1ses_A          233 LHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELP  312 (421)
T ss_dssp             TTTTCEEEGGGCSEEEEEEEEEECCCCSCCCSCCCTTSSCSEEEEEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HhcccccCchhCCEEEEecCCeecCCccccCcCCCCCeeeeeeeeeeEEEEeCCCHHHHHHHHHHHHHHHHHHHHHCCCc
Confidence            578999999999999999999999999    66779999999999999999998 4677889999999999999999999


Q ss_pred             EEEEEecCCC
Q psy5542          76 YRKVIVRHGA   85 (86)
Q Consensus        76 ~~~~~~~~g~   85 (86)
                      |+++.+++|+
T Consensus       313 ~rvv~l~t~d  322 (421)
T 1ses_A          313 YRLVEVATGD  322 (421)
T ss_dssp             EEEEECCHHH
T ss_pred             eEEEEecCcc
Confidence            9999998875

>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 2.60A {Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A

Probab=99.89  E-value=1e-23  Score=158.51  Aligned_cols=85  Identities=25%  Similarity=0.397  Sum_probs=78.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC----CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~----~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      +|+++++||++||++++++++|||+|.++.    .||+|+|||+|+|+|+||++ +++.++++++++.+.++|+.|||||
T Consensus       260 ~~~~~~~s~~~LPlr~~~~g~~FR~E~~~~G~~~~GL~R~rqF~kvE~~~f~~p-e~s~~~~~e~l~~~~~il~~LGL~y  338 (455)
T 2dq0_A          260 MHANEILDGKDLPLLYVGVSPCFRKEAGTAGKDTKGIFRVHQFHKVEQFVYSRP-EESWEWHEKIIRNAEELFQELEIPY  338 (455)
T ss_dssp             TTTTEEEETTTCSEEEEEEEEEECCCTTCSSCSCCSSSSCSEEEEEEEEEEECT-TTHHHHHHHHHHHHHHHHHHTTCCE
T ss_pred             HHHhCccCchhCCEEEEEecCcccCCCCccccccCCceeeeeeEeeeEEEecCH-HHHHHHHHHHHHHHHHHHHHcCCce
Confidence            578999999999999999999999998753    59999999999999999998 5677899999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +++..++|++
T Consensus       339 rv~~~~~gdl  348 (455)
T 2dq0_A          339 RVVNICTGDL  348 (455)
T ss_dssp             EEEECCGGGS
T ss_pred             EEEECCCccc
Confidence            9999998875

>4hvc_A Bifunctional glutamate/proline--tRNA ligase; ligase-ligase inhibitor complex; HET: ANP HFG; 2.00A {Homo sapiens}

Probab=99.89  E-value=1.2e-23  Score=160.16  Aligned_cols=85  Identities=25%  Similarity=0.268  Sum_probs=77.5

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc-CCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL-GIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l-gi~~~~~   79 (86)
                      +|+++++|||+||++++|+++|||+|.+|+.||+|+|||+|+|+|+|+.+++++++++..+++.|.++|+.| ||||+++
T Consensus       136 ~~~~~i~SyrdLPlrl~q~g~~fR~E~~~~~Gl~R~ReF~q~e~h~~~~~~e~a~~E~~~~l~~~~~i~~~ll~lp~~~~  215 (519)
T 4hvc_A          136 AYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKG  215 (519)
T ss_dssp             HHHHHCSSGGGCCEEEEEEEEEECCCCSCCBTTTBCSEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHTTSCCCCEEE
T ss_pred             HHHhhccccccCCeEEEEEcCeeeCCCCCCCCCcceeEEEEeeEEEEecCHHHHHHHHHHHHHHHHHHHHHhcCCcceee
Confidence            478899999999999999999999999999999999999999999966667888999999999999999996 9999998


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      ..+.++
T Consensus       216 ~~t~~e  221 (519)
T 4hvc_A          216 RKTEKE  221 (519)
T ss_dssp             ECCTTT
T ss_pred             ecCCcc
Confidence            866543

>2i4l_A Proline-tRNA ligase; alpha beta; 2.00A {Rhodopseudomonas palustris} PDB: 2i4m_A* 2i4n_A* 2i4o_A*

Probab=99.89  E-value=1.7e-23  Score=156.41  Aligned_cols=85  Identities=42%  Similarity=0.670  Sum_probs=79.9

Q ss_pred             cccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEe
Q psy5542           2 VADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIV   81 (86)
Q Consensus         2 ~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~   81 (86)
                      +++++.||++||+++||+++|||+|.+|+.||+|+|||+|.|+|+||.+.++++.++..+.+++.++|++|||+++.+.+
T Consensus       138 ~r~~~~s~~~lP~rl~~ig~~fR~E~~p~~Gl~R~REF~q~d~~~f~~~~~~ad~e~~~~~~~~~~i~~~lGl~~~~~~~  217 (458)
T 2i4l_A          138 FRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRA  217 (458)
T ss_dssp             HHHHCCBGGGCSEEEEEEEEEECCCSSCBTGGGBCSEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHTTTCCEEEEEC
T ss_pred             HHHHHhhccccCeeeEEecCEeeCCCCCCCCcccccceEEeEEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCceEEEEc
Confidence            56788899999999999999999999998899999999999999999888999999999999999999999999999998


Q ss_pred             cCCCC
Q psy5542          82 RHGAV   86 (86)
Q Consensus        82 ~~g~~   86 (86)
                      ++|.|
T Consensus       218 ~~g~~  222 (458)
T 2i4l_A          218 ETGPI  222 (458)
T ss_dssp             CCCSS
T ss_pred             ccccc
Confidence            88764

>2j3l_A Prolyl-tRNA synthetase; class II aminoacyl- T synthetase, editing, translation; HET: P5A; 2.3A {Enterococcus faecalis} PDB: 2j3m_A*

Probab=99.88  E-value=1.5e-23  Score=159.52  Aligned_cols=85  Identities=42%  Similarity=0.712  Sum_probs=79.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      ++++++.||++||+++||+++|||+|.+|+.||+|+|||+|.|+|+||.+++++++++..+++++.++|+.|||+|..+.
T Consensus       117 ~~~~~~~s~~~lP~r~~~~g~~fR~E~~~~~Gl~R~ReF~q~d~~~f~~~~~~~~~e~~~~~~~~~~~~~~lgl~~~~~~  196 (572)
T 2j3l_A          117 LIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRDYEKAYSRIFERCGLEFRAII  196 (572)
T ss_dssp             HHHHHCCBGGGCCEEEEEEEEEECCCSSCCTGGGSCSEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHhhccChhhcCHhhheecCeeccCcCcccCccccceeEEeeeEEEcCCHHHHHHHHHHHHHHHHHHHHHcCCcEEEEe
Confidence            36778899999999999999999999888779999999999999999998899999999999999999999999999998


Q ss_pred             ecCCC
Q psy5542          81 VRHGA   85 (86)
Q Consensus        81 ~~~g~   85 (86)
                      +++|.
T Consensus       197 ~~~g~  201 (572)
T 2j3l_A          197 GDGGA  201 (572)
T ss_dssp             CCGGG
T ss_pred             ccccc
Confidence            88764

>2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, nationa on protein structural and functional analyses; HET: SSA; 3.00A {Aquifex aeolicus}

Probab=99.88  E-value=4.6e-23  Score=153.69  Aligned_cols=85  Identities=24%  Similarity=0.391  Sum_probs=78.5

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~   76 (86)
                      +|++++.||++||++++++++|||+|.++    +.||+|+|||+|.|+|+||+++ ++++++.++++.+.++|+.|||||
T Consensus       239 ~~~~~i~s~~~LPlrl~~~g~~FR~E~~~~Gr~~~Gl~R~reF~q~E~~~f~~pe-~s~~~~~e~i~~~~~il~~LGL~~  317 (425)
T 2dq3_A          239 LYREEILKEENLPIYLTAYTPCYRREAGAYGKDIRGIIRQHQFDKVELVKIVHPD-TSYDELEKLVKDAEEVLQLLGLPY  317 (425)
T ss_dssp             GGTTEEEETTTCCEEEEEEEEEECCCCSCCSSSCSSSSSCSEEEEEEEEEEECGG-GHHHHHHHHHHHHHHHHHHHTCCE
T ss_pred             HHHhhccccccCCeEEEEecCEecCCCCcccccccCcccccceEEeeEEEECCHH-HHHHHHHHHHHHHHHHHHHCCCce
Confidence            57889999999999999999999999854    5699999999999999999975 577789999999999999999999


Q ss_pred             EEEEecCCCC
Q psy5542          77 RKVIVRHGAV   86 (86)
Q Consensus        77 ~~~~~~~g~~   86 (86)
                      +++..++|++
T Consensus       318 rvv~l~~gdl  327 (425)
T 2dq3_A          318 RVVELCTGDL  327 (425)
T ss_dssp             EEEECCTTTC
T ss_pred             EEEEecCCcC
Confidence            9999999975

>1nj1_A PROR, proline-tRNA synthetase, proline--tRNA ligase; protein-aminoacyladenylate complex class-II tRNA synthetase,; HET: 5CA; 2.55A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: c.51.1.1 d.68.5.1 d.104.1.1 PDB: 1nj2_A 1nj5_A* 1nj6_A*

Probab=99.86  E-value=3.5e-22  Score=151.23  Aligned_cols=85  Identities=29%  Similarity=0.386  Sum_probs=77.1

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceee-eeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFL-MKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~-~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +|++++.||++||+++||+++|||+|.++..||+|+|||+ |+|+|+|+.+.+++++++.++++++.++|+.|||||++.
T Consensus       145 ~~~~~~~s~~~LPlr~~q~g~~fR~E~~~~rGl~R~REF~~q~e~~~~~~~~e~a~~e~~~~l~~~~~i~~~Lgl~~~~~  224 (501)
T 1nj1_A          145 MFALWVRSHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKEAHTIHATASEAEEQVERAVEIYKEFFNSLGIPYLIT  224 (501)
T ss_dssp             HHHHHCCBTTTCCEEEEEEEEEECCCCSCCBTTTBCSEEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHTCCCEEE
T ss_pred             HHHhhhcccccCCEEEEeecCEeeCCCCCCCCCceeEEEeeeeeEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCeEEEE
Confidence            4678999999999999999999999987455999999999 999999888888999999999999999999999999988


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      ..+.++
T Consensus       225 ~~~~~e  230 (501)
T 1nj1_A          225 RRPPWD  230 (501)
T ss_dssp             ECCTTT
T ss_pred             eCCchh
Confidence            876554

>1hc7_A Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP + L-proline + tRNA(Pro) AMP + PPI + L-prolyl-tRNA(Pro); 2.43A {Thermus thermophilus} SCOP: c.51.1.1 d.68.5.1 d.104.1.1 PDB: 1h4q_A* 1h4t_A 1h4s_A

Probab=99.86  E-value=4.8e-22  Score=149.75  Aligned_cols=81  Identities=22%  Similarity=0.252  Sum_probs=73.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHH-HHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVF-NTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~-~~lgi~~~~~   79 (86)
                      +|++++.||++||+++||+++|||+|.+|+ ||+|+|||+|+|+|+|+.+.+++++++..++++|.++| +.|||||+..
T Consensus       119 ~~~~~~~s~r~LP~rl~qig~vfR~E~~~r-Gl~R~REF~q~d~~~~~~~~~~ad~E~~~~l~~~~~i~~~~Lgl~~~~~  197 (477)
T 1hc7_A          119 MWSKWIRSWRDLPQLLNQWGNVVRWEMRTR-PFLRTSEFLWQEGHTAHATREEAEEEVRRMLSIYARLAREYAAIPVIEG  197 (477)
T ss_dssp             HHHHHCCBGGGCCEEEEEEEEEECCCSSCB-TTTBCSEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_pred             HHHhhhhccccCCeeeEeecCEEeCCCCCC-CcceeEEEEEccEEEEeCCHHHHHHHHHHHHHHHHHHHHHhcCCeEEEE
Confidence            367889999999999999999999998877 99999999999999988888899999999999999999 7999997766


Q ss_pred             Eec
Q psy5542          80 IVR   82 (86)
Q Consensus        80 ~~~   82 (86)
                      ..+
T Consensus       198 ~~~  200 (477)
T 1hc7_A          198 LKT  200 (477)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            544

>1evl_A Threonyl-tRNA synthetase; amino acid recognition, zinc ION, adenylate analog, deletion mutant, ligase; HET: TSB; 1.55A {Escherichia coli} SCOP: c.51.1.1 d.104.1.1 PDB: 1evk_A* 1fyf_A* 1kog_A*

Probab=99.85  E-value=8.2e-22  Score=144.68  Aligned_cols=81  Identities=28%  Similarity=0.328  Sum_probs=73.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC-cEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI-KYRK   78 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi-~~~~   78 (86)
                      ++++++.||++||+++||+++|||+|.+ |+.||+|+|||+|.|+|+||+ .+++++++.++++++.++|++||| ++.+
T Consensus        99 ~~~~~~~s~~~lP~r~~~~g~~fR~E~~~p~~Gl~R~reF~q~d~~~f~~-~~~~~~e~~e~i~~~~~~~~~lgl~~~~~  177 (401)
T 1evl_A           99 IFNQGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCT-EEQIRDEVNGCIRLVYDMYSTFGFEKIVV  177 (401)
T ss_dssp             HHTSSCCBGGGCSEEEEEEEEEECCCCGGGCBTTTBCSEEEEEEEEEEEC-GGGHHHHHHHHHHHHHHHHHTTTCSCCEE
T ss_pred             HHHhhhhhhhhCChhhccccceecCCCCcccccccccCcEEecceEEeCC-HHHHHHHHHHHHHHHHHHHHHcCCCceEE
Confidence            3678899999999999999999999987 688999999999999999997 677888899999999999999999 7877


Q ss_pred             EEec
Q psy5542          79 VIVR   82 (86)
Q Consensus        79 ~~~~   82 (86)
                      ...+
T Consensus       178 ~~~~  181 (401)
T 1evl_A          178 KLST  181 (401)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            6554

>1ati_A Glycyl-tRNA synthetase; protein biosynthesis, ligase, aminoacyl-tRNA SYN; 2.75A {Thermus thermophilus} SCOP: c.51.1.1 d.104.1.1 PDB: 1b76_A* 1ggm_A*

Probab=99.85  E-value=2.7e-22  Score=151.97  Aligned_cols=80  Identities=15%  Similarity=0.191  Sum_probs=71.5

Q ss_pred             cccccCCc-CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           2 VADMKLSH-KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         2 ~~~~i~Sy-r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      |++++.|| ++||+++||+++|||+|++|+.||+|+|||+|+|+|.||++ +++.+++.++++++.++|++|||++..+.
T Consensus       197 ~~~~~~sy~r~LP~rl~qig~~FR~E~~pr~GL~R~REF~q~d~~~f~~~-e~~~~~~~~~i~~~~~i~~~LGl~~~~v~  275 (505)
T 1ati_A          197 FKNVLDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRP-GEDEYWHRYWVEERLKWWQEMGLSRENLV  275 (505)
T ss_dssp             HHHHHHHHTCCSSEEEEEEEEEEBCCSSCCTGGGSCSEEEEEEEEEEECG-GGHHHHHHHHHHHHHHHHHHTTCCGGGEE
T ss_pred             HHHHHHhcCCCCCEEEEEeeceeeCCCCCCCCCCcccceEEeeEEEEECH-HHHHHHHHHHHHHHHHHHHHcCCCeEEEE
Confidence            46788999 99999999999999999999999999999999999988875 56677899999999999999999865555


Q ss_pred             ec
Q psy5542          81 VR   82 (86)
Q Consensus        81 ~~   82 (86)
                      .+
T Consensus       276 ~~  277 (505)
T 1ati_A          276 PY  277 (505)
T ss_dssp             EE
T ss_pred             EC
Confidence            44

>1nj8_A Proline-tRNA synthetase, proline--tRNA ligase; class-II tRNA synthetase; 3.20A {Methanocaldococcus jannaschii} SCOP: c.51.1.1 d.68.5.1 d.104.1.1

Probab=99.84  E-value=1.8e-21  Score=145.89  Aligned_cols=82  Identities=27%  Similarity=0.378  Sum_probs=74.5

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceee-eeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFL-MKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~-~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +|++++.||++||+++||+++|||+|.++..||+|+|||+ |+|+|+|+.+.+++++++.++++++.++|+.||||+...
T Consensus       113 ~~~~~~~s~r~LP~rl~qig~~fR~E~~~~rGl~R~REF~qq~d~~~~~~~~~~a~~e~~~~i~~~~~~~~~LGl~~~~~  192 (459)
T 1nj8_A          113 MMKLWVKVHTDLPIKIYQIVNTFRYETKHTRPLIRLREIMTFKEAHTAHSTKEEAENQVKEAISIYKKFFDTLGIPYLIS  192 (459)
T ss_dssp             HHHTTCCBTTSCCCCEEEEECCBCCCCSCCBTTTBCSBCSCEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHTCCCEEE
T ss_pred             HHHHhhhhcccCCeEEEEEccEecCccCCCCCceEeeeeeccCcEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCceEEe
Confidence            3678999999999999999999999987355999999999 999999988889999999999999999999999998776


Q ss_pred             Eec
Q psy5542          80 IVR   82 (86)
Q Consensus        80 ~~~   82 (86)
                      ..+
T Consensus       193 ~~~  195 (459)
T 1nj8_A          193 KRP  195 (459)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            654

>1qf6_A THRRS, threonyl-tRNA synthetase; tRNA(Thr), AMP, mRNA, aminoacylati translational regulation, protein/RNA, ligase-RNA complex; HET: H2U AET G7M 5MU PSU AMP; 2.90A {Escherichia coli} SCOP: c.51.1.1 d.15.10.1 d.67.1.1 d.104.1.1

Probab=99.84  E-value=1.4e-21  Score=151.41  Aligned_cols=81  Identities=27%  Similarity=0.314  Sum_probs=72.6

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC-cEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI-KYRK   78 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi-~~~~   78 (86)
                      +|++++.|||+||+++||+++|||+|.+ ++.||+|+|||+|+|+|+||++ +++++++.++++++.++|++||| +|.+
T Consensus       340 ~~~~~~~syr~LPlr~~~~g~~fR~E~~g~~~GL~R~ReF~q~d~~~f~~~-~~~~~e~~~~i~~~~~i~~~lGl~~~~v  418 (642)
T 1qf6_A          340 IFNQGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTE-EQIRDEVNGCIRLVYDMYSTFGFEKIVV  418 (642)
T ss_dssp             HHTTSCEEGGGCSEEEEEEEEEECCCCGGGCBTTTBCSEEEEEEEEEEECG-GGHHHHHHHHHHHHHHHHGGGTCCCCEE
T ss_pred             HHHhhhhhccccCeEEEEeccEEecCCCccccCCceeeeEEEccEEEEcCH-HHHHHHHHHHHHHHHHHHHHcCCCceEE
Confidence            4678899999999999999999999988 4669999999999999999985 67888899999999999999999 7777


Q ss_pred             EEec
Q psy5542          79 VIVR   82 (86)
Q Consensus        79 ~~~~   82 (86)
                      ...+
T Consensus       419 ~l~~  422 (642)
T 1qf6_A          419 KLST  422 (642)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            5443

>3uh0_A Threonyl-tRNA synthetase, mitochondrial; threonine tRNA, threonyl ADE threonyl sulfamoyl adenylate; HET: TSB; 2.00A {Saccharomyces cerevisiae} PDB: 3ugt_A 3ugq_A* 4eo4_A*

Probab=99.84  E-value=1.7e-21  Score=146.37  Aligned_cols=74  Identities=23%  Similarity=0.236  Sum_probs=68.7

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHH-HHcCCc
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVF-NTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~-~~lgi~   75 (86)
                      +|+++++||++||++++|+++|||+|.++. .||+|+|||+|+|+|+||++ +++++++.++++.+.++| +.|||+
T Consensus       137 ~~~~~~~s~r~LPlrl~~~g~~fR~E~~~~~~GL~R~ReF~q~d~~~f~~~-e~~~~e~~~~i~~~~~~~~~~lGl~  212 (460)
T 3uh0_A          137 IFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTP-SQVKSEIFNSLKLIDIVYNKIFPFV  212 (460)
T ss_dssp             HHTTSCCBGGGCSEEEEECCEEECCCCTTTCBTTTBCSEEEEEEEEEEECG-GGHHHHHHHHHHHHHHHHTTTSCCC
T ss_pred             HHHhccccccccCeEEEEecCeeeCCCCCCCCCceeeeeEEEeeEEEEcCH-HHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            478899999999999999999999998884 69999999999999999996 577888899999999999 899998

>1nyr_A Threonyl-tRNA synthetase 1; ATP, threonine, ligase; HET: ATP; 2.80A {Staphylococcus aureus} SCOP: c.51.1.1 d.15.10.1 d.67.1.1 d.104.1.1 PDB: 1nyq_A*

Probab=99.81  E-value=2.2e-20  Score=144.31  Aligned_cols=80  Identities=21%  Similarity=0.324  Sum_probs=69.8

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCC-CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC-cEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRP-KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI-KYRK   78 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~-~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi-~~~~   78 (86)
                      +|++.+.||++||+++||+++|||+|.++ ..||+|+|||+|.|+|+||+++ ++.+++.++++++.++|++||| +|..
T Consensus       342 ~~~~~~~syr~LPlrl~~~g~~fR~E~~~~~~GL~R~ReF~Q~d~~~f~~~~-~~~d~~~e~i~~~~~~l~~lGl~~~~~  420 (645)
T 1nyr_A          342 IYANKPHSYRELPIRIAELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPD-QIKEEFKRVVNMIIDVYKDFGFEDYSF  420 (645)
T ss_dssp             HHHTSCCBGGGCCEEEEEEEEEECCCCTTTCBTTTBCSEEEEEEEEEEECGG-GHHHHHHHHHHHHHHHHHHTTCCCEEE
T ss_pred             HHHhhhhhccCCCeEEEEeccEEecCCCccccCcceeeeEEEccEEEEcCHH-HHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence            36788899999999999999999999884 4699999999999999999864 4555789999999999999999 6766


Q ss_pred             EEe
Q psy5542          79 VIV   81 (86)
Q Consensus        79 ~~~   81 (86)
                      ...
T Consensus       421 ~l~  423 (645)
T 1nyr_A          421 RLS  423 (645)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            443

>1g5h_A Mitochondrial DNA polymerase accessory subunit; intermolecular four helix bundle, DNA binding protein; 1.95A {Mus musculus} SCOP: c.51.1.1 d.104.1.1 PDB: 1g5i_A 2g4c_A* 3ikm_B*

Probab=99.80  E-value=1.4e-20  Score=141.20  Aligned_cols=74  Identities=14%  Similarity=0.039  Sum_probs=60.1

Q ss_pred             CcccccCCcC-Ccchhhheeeceee---cCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           1 MVADMKLSHK-ALPLLLYQFTSKFR---DELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr-~LP~~l~q~~~~fR---~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      +|++++.||+ +||++++|+++|||   ||.+|+.||+|+|||+|+|+|+||. ++++.+++..+++.+..++++|||+
T Consensus       150 ~f~~~~~s~r~~LP~~~aqig~~fR~~~nE~s~~~Gl~R~REF~q~E~~~F~~-pe~~~e~~~~~~~~~~~~~~~lgi~  227 (454)
T 1g5h_A          150 HYVNCLDLVNRKLPFGLAQIGVCFHPVSNSNQTPSSVTRVGEKTEASLVWFTP-TRTSSQWLDFWLRHRLLWWRKFAMS  227 (454)
T ss_dssp             THHHHHHHTTTBSCEEEEEEEEEEEEEC---------CEEEEEEEEEEEEEEC-HHHHHHHHHHHHHHHHHHHHTTCSS
T ss_pred             HHhhhHhhcccCCCEEEEEeeeeccCCcccccCCCCccccCceehhheEEEeC-HhhHHHHHHHHHHHHHHHHHHcCCC
Confidence            3677888888 99999999999999   6999988999999999999999997 5677889999999999999999997

>2cja_A Seryl-tRNA synthetase; ligase, zinc ION; HET: MSE ATP; 2.2A {Methanosarcina barkeri} PDB: 2cim_A* 2cj9_A* 2cjb_A

Probab=99.79  E-value=1e-19  Score=138.77  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=66.2

Q ss_pred             CcccccCCcCCcchhhhe-eeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH-HHHHHHHHHcCCcE
Q psy5542           1 MVADMKLSHKALPLLLYQ-FTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG-KCYDDVFNTLGIKY   76 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q-~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~-~~~~~i~~~lgi~~   76 (86)
                      +|++++.||++||++++| +++|||+|+++..||+|+|||+|.|+|+||++ +++.+++++++ +....+++.||||.
T Consensus       332 ~f~~~i~s~~~LPlrl~q~ig~~FR~Epgs~~GL~R~REF~q~E~~~F~~p-e~s~ee~ee~i~~~~~~~l~~LGLp~  408 (522)
T 2cja_A          332 YVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTK-EEVLKCAEELHDRYMHIFNDILDIEW  408 (522)
T ss_dssp             GTTTCEECGGGCSEEEEECSSEEECCCSSSCCCTTSCSEEEEEEEEEEEEH-HHHHHHHHHHHHHHHHHHHHTSCCCE
T ss_pred             HHHhcccccccCCeeEEEEcCceEeCCCCCCCCCeEeEEEEEeeEEEEeCh-HHHHHHHHHHHHHHHHHHHHHcCCCE
Confidence            478899999999999999 99999999544479999999999999999975 56677889999 77777789999993

>3a32_A Probable threonyl-tRNA synthetase 1; aeropyrum pernix K1, protein biosynthesis, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; 2.30A {Aeropyrum pernix} PDB: 3a31_A

Probab=99.76  E-value=2.7e-19  Score=134.07  Aligned_cols=81  Identities=20%  Similarity=0.284  Sum_probs=71.5

Q ss_pred             cccccCCcC---CcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHH-cCC--
Q psy5542           2 VADMKLSHK---ALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNT-LGI--   74 (86)
Q Consensus         2 ~~~~i~Syr---~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~-lgi--   74 (86)
                      |++++.|||   +||+++||+++|||+|.+++ .||+|+|||+|.|+|+||.++ .+.+++.++++++.++|++ |||  
T Consensus       119 ~~~~~~s~r~~~~lP~rl~~~g~vfR~E~~~~~~Gl~R~REF~Q~~~e~f~~~~-~~~de~~e~i~~~~~~l~~~lGl~~  197 (471)
T 3a32_A          119 FLNEVAKHRSKLPLPFKVFEFGRVHRYEPSGSIYGLLRVRGFTQDDAHIIVPGG-RVIDVVYDVFEEMKLVLERLFKLGV  197 (471)
T ss_dssp             HHHHHHHHGGGSCSSEEEEEEEEEECCCCGGGCBTTTBCSEEEEEEEEEEEEGG-GHHHHHHHHHHHHHHHHHHTSCCCC
T ss_pred             HHhhhhhccccccCCeEEeeccceeccCCCcccccceeEEEEEECCeEEEcChH-HHHHHHHHHHHHHHHHHHHhhCCCc
Confidence            567788998   99999999999999998877 699999999999999999865 4555789999999999999 999  


Q ss_pred             ---cEEEEEecC
Q psy5542          75 ---KYRKVIVRH   83 (86)
Q Consensus        75 ---~~~~~~~~~   83 (86)
                         ++..+..+.
T Consensus       198 ~~~~~~l~i~~~  209 (471)
T 3a32_A          198 SSETFKVRLSMS  209 (471)
T ss_dssp             STTTEEEEEECC
T ss_pred             CCCCeEEEEecC
Confidence               587776655

>3ikl_A DNA polymerase subunit gamma-2, mitochondrial; transferase; HET: DNA; 3.10A {Homo sapiens}

Probab=99.75  E-value=2.5e-18  Score=129.56  Aligned_cols=81  Identities=14%  Similarity=0.085  Sum_probs=66.9

Q ss_pred             cccccCCcC-CcchhhheeeceeecCC---CCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc--
Q psy5542           2 VADMKLSHK-ALPLLLYQFTSKFRDEL---RPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK--   75 (86)
Q Consensus         2 ~~~~i~Syr-~LP~~l~q~~~~fR~E~---~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~--   75 (86)
                      |++...||+ +||++++|+++|||+|+   ++..||+|+|||+|+|+|.||.++ ++++++..+++....+++.|||+  
T Consensus       161 fk~~~~s~r~~LP~~iaqig~~FR~E~g~~~~~~GL~RvrEFtq~E~~~F~~Pe-~~~e~~~~~~~~~~~~~~~LGi~~~  239 (459)
T 3ikl_A          161 YVNCLDLVNKRLPYGLAQIGVCFHPVFDTKQIRNGVKSIGEKTEASLVWFTPPR-TSNQWLDFWLRHRLQWWRKFAMSPS  239 (459)
T ss_dssp             TTTTTGGGTTBSSEEEEEEEEEECCC----------CCCCEEEEEEEEEEECGG-GHHHHHHHHHHHHHHHHHHHCSSGG
T ss_pred             HhhhhhhccccCCeEEEEEeeeeecccccccCCCCcccccceeeeeEEEEeChh-HHHHHHHHHHHHHHHHHHHhCCChh
Confidence            678899999 99999999999999996   455699999999999999999965 55678999999999999999998  


Q ss_pred             -EEEEEecC
Q psy5542          76 -YRKVIVRH   83 (86)
Q Consensus        76 -~~~~~~~~   83 (86)
                       ++....+.
T Consensus       240 ~~r~~~~~~  248 (459)
T 3ikl_A          240 NFSSSDCQD  248 (459)
T ss_dssp             GEEEEEECC
T ss_pred             hEEEeecCc
Confidence             87776643

>2zt5_A Glycyl-tRNA synthetase; ligase, AP4A, glycine, ATP, Gly-AMP, aminoacyl-tRNA synthetase, ATP-binding, charcot-marie-tooth disease, disease mutation; HET: B4P; 2.50A {Homo sapiens} PDB: 2pme_A* 2zt6_A* 2zt7_A* 2zt8_A* 2zxf_A* 2pmf_A 2q5h_A 2q5i_A

Probab=99.74  E-value=3.3e-19  Score=139.39  Aligned_cols=73  Identities=26%  Similarity=0.380  Sum_probs=63.7

Q ss_pred             ccccCC-cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhH---------------------------
Q psy5542           3 ADMKLS-HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDA---------------------------   54 (86)
Q Consensus         3 ~~~i~S-yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~---------------------------   54 (86)
                      ++...| |++||+++||+|++||||.+|+.||+|+|||+|.|+|+||.+++..                           
T Consensus       255 ~r~~~~~~~~LP~~~aqiG~~fRnEisPr~GLlR~REF~q~d~e~F~~p~~~~~~~y~~v~da~~~~~~~~~~~~~~~~~  334 (693)
T 2zt5_A          255 KRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSAR  334 (693)
T ss_dssp             HHHHHHTTTCSCEEEEEEEEEECCCSSCCSGGGSCSEEEEEEEEEEECTTCCCCTTGGGTTTCEEEEECHHHHHTTCCCE
T ss_pred             HHHHHHhCcCCCEEEEeecceecCCCCCCCCCccceeeEEccceEEeCcchhcchhHHHHHHHHHhhhhhhhhccccccc
Confidence            444455 8999999999999999999999999999999999999999876542                           


Q ss_pred             --------------HHHHHHHHHHHHHHHHHcCCc
Q psy5542          55 --------------NDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        55 --------------~~~~~~~~~~~~~i~~~lgi~   75 (86)
                                    .+++..++..+..++..|||+
T Consensus       335 ~~~~~ea~~~g~i~~e~~~~~i~~~~~f~~~lGi~  369 (693)
T 2zt5_A          335 KMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGIS  369 (693)
T ss_dssp             EEEHHHHHHHTSSCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             cchhhhhhhhcccchHHHHHHHHHHHHHHHHcCcC
Confidence                          256778999999999999996

>3mf2_A BLL0957 protein; aminoacyl-tRNA synthetase, seryl-tRNA synthetase, zinc ION, amino acid:[carrier protein] ligase; HET: AMP; 2.15A {Bradyrhizobium japonicum} PDB: 3mey_A* 3mf1_A* 3pzc_A*

Probab=99.69  E-value=4.4e-17  Score=119.15  Aligned_cols=75  Identities=20%  Similarity=0.154  Sum_probs=66.0

Q ss_pred             cccc-cCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           2 VADM-KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         2 ~~~~-i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      |+++ +++  +.|+++..+++|||+|++  .||+|+|||+|.|+|.||++ +++.++.+++++..+.+++.|||||+++.
T Consensus       158 ~~~eg~i~--~~plr~~~~g~CFR~EaS--~GL~RvhqF~kvE~v~~~tp-Eqs~~e~e~l~~~ae~il~~LgLpyrv~~  232 (346)
T 3mf2_A          158 AASRGPLP--KGGLRFDVAADCFRREPS--KHLDRLQSFRMREYVCIGTP-DDVSDFRERWMVRAQAIARDLGLTFRVDY  232 (346)
T ss_dssp             HHTTCSCC--TTCEEEEEEEEEECCCCC--SSTTSCSEEEEEEEEEEESH-HHHHHHHHHHHHHHHHHHHHTTCCCEEEE
T ss_pred             HccCCccc--ccCeEEEEECCccCCcCC--CCCeeeeeeEEEEEEEEeCH-HHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Confidence            5555 666  449999999999999983  69999999999999999985 55666889999999999999999999998


Q ss_pred             e
Q psy5542          81 V   81 (86)
Q Consensus        81 ~   81 (86)
                      +
T Consensus       233 ~  233 (346)
T 3mf2_A          233 A  233 (346)
T ss_dssp             C
T ss_pred             c
Confidence            7

>1h4v_B Histidyl-tRNA synthetase; class IIA aminoacyl-tRNA synthetase, ATP + L-histidine tRNA(His)-> AMP + PPI + L-histidyl-tRNA(His); 2.4A {Thermus thermophilus} SCOP: c.51.1.1 d.104.1.1 PDB: 1ady_A* 1adj_A

Probab=99.65  E-value=1.3e-16  Score=117.14  Aligned_cols=75  Identities=20%  Similarity=0.291  Sum_probs=64.7

Q ss_pred             cccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEec
Q psy5542           4 DMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVR   82 (86)
Q Consensus         4 ~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~   82 (86)
                      ....||++||+++||++++||+| +|+.|  |.|||+|.|+|+|+.+.+.++   .+++.++.++|++||++ +..+..+
T Consensus        92 ~~~~~~~~lP~rl~~~g~vfR~e-~p~~g--R~REf~Q~g~e~~g~~~~~ad---~e~i~~~~~~l~~lgl~~~~i~i~~  165 (421)
T 1h4v_B           92 EHGMKVWPQPVRLWMAGPMFRAE-RPQKG--RYRQFHQVNYEALGSENPILD---AEAVVLLYECLKELGLRRLKVKLSS  165 (421)
T ss_pred             hccccccCCCeEEEEecCeecCC-CCCCC--CcccEEEccEEEECCCChhhh---HHHHHHHHHHHHHcCCCceEEEEcC
Confidence            34567899999999999999999 78788  999999999999999877776   57889999999999997 7766655


Q ss_pred             CC
Q psy5542          83 HG   84 (86)
Q Consensus        83 ~g   84 (86)
                      .|
T Consensus       166 ~g  167 (421)
T 1h4v_B          166 VG  167 (421)
T ss_pred             CC
Confidence            44

>1qe0_A Histidyl-tRNA synthetase; class II tRNA synthetase, beta sheet, ligase; 2.70A {Staphylococcus aureus} SCOP: c.51.1.1 d.104.1.1

Probab=99.65  E-value=1.4e-16  Score=116.83  Aligned_cols=77  Identities=26%  Similarity=0.336  Sum_probs=61.3

Q ss_pred             cccccCCc-CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542           2 VADMKLSH-KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus         2 ~~~~i~Sy-r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      ++++..|| ++||+++||+++|||+| +|+.|  |+|||+|.|+|+|+.+.+.++   .+++.++.++|+.||++ +...
T Consensus        89 ~~~~~~~~~~~lP~r~~~~g~vfR~E-~~~~g--R~reF~q~~~e~~~~~~~~~d---~e~i~~~~~~l~~lgl~~~~i~  162 (420)
T 1qe0_A           89 YIEHKMQGNPNQPIKLYYNGPMFRYE-RKQKG--RYRQFNQFGVEAIGAENPSVD---AEVLAMVMHIYQSFGLKHLKLV  162 (420)
T ss_dssp             HHHTTGGGCSSCSEEEEEEEEEECC----------CCEEEEEEEEEESCCCHHHH---HHHHHHHHHHHHHTTCCCEEEE
T ss_pred             HHhccccccCCCCeEEEEecCEeecC-CCcCC--CcccEEEeeEEEECCCCchhH---HHHHHHHHHHHHHcCCCceEEE
Confidence            45677899 99999999999999999 66666  999999999999999877776   67889999999999998 7776


Q ss_pred             EecCC
Q psy5542          80 IVRHG   84 (86)
Q Consensus        80 ~~~~g   84 (86)
                      ..+.|
T Consensus       163 l~~~g  167 (420)
T 1qe0_A          163 INSVG  167 (420)
T ss_dssp             EEECC
T ss_pred             EcccC
Confidence            66544

>1wu7_A Histidyl-tRNA synthetase; ligase, structural genomics, dimer; 2.40A {Thermoplasma acidophilum} SCOP: c.51.1.1 d.104.1.1

Probab=99.62  E-value=4.6e-16  Score=114.95  Aligned_cols=71  Identities=25%  Similarity=0.360  Sum_probs=62.6

Q ss_pred             CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc--EEEEEecCC
Q psy5542           7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK--YRKVIVRHG   84 (86)
Q Consensus         7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~--~~~~~~~~g   84 (86)
                      .++ +||+++||++++||+| +|+.|  |.|||+|.|+|+|+.+...++   .+++.++.++|++||++  +..+.++.|
T Consensus        94 ~~~-~lP~rl~~~g~vfR~e-rp~~g--R~REF~Q~d~ei~g~~~~~ad---~E~i~~~~~~l~~lgl~~~~~i~l~~~g  166 (434)
T 1wu7_A           94 KDL-QRPLRWYSFPKVWRYE-EPQAG--RYREHYQFNADIFGSDSPEAD---AEVIALASSILDRLGLQDIYEIRINSRK  166 (434)
T ss_dssp             TTC-CSSEEEEECCEEECCC-CSCSS--CCSEEEEEEEEEESCCSHHHH---HHHHHHHHHHHHHTTTTTSEEEEEEEHH
T ss_pred             CCC-CCCeEEEEEcCeecCC-CCCCC--CccceEEeeEEEEcCCChHhh---HHHHHHHHHHHHHcCCCCceEEEECChh
Confidence            445 7999999999999999 88888  999999999999999877776   46889999999999997  888877654

>1htt_A Histidyl-tRNA synthetase; complex (tRNA synthetase/His-adenylate), aminoacyl-tRNA synthase, ligase; HET: HIS AMP; 2.60A {Escherichia coli} SCOP: c.51.1.1 d.104.1.1 PDB: 1kmm_A* 1kmn_A* 2el9_A*

Probab=99.62  E-value=1.1e-15  Score=112.26  Aligned_cols=72  Identities=22%  Similarity=0.198  Sum_probs=63.1

Q ss_pred             CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC--cEEEEEecCC
Q psy5542           7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI--KYRKVIVRHG   84 (86)
Q Consensus         7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi--~~~~~~~~~g   84 (86)
                      .+|++||+++||++++||+| +|+.|  |.|||+|.|+|+|+.+...++   .+++.++.++|++||+  ++..+..+.|
T Consensus        95 ~~~~~~P~rl~~~g~vfR~e-~p~~g--R~Ref~Q~d~e~~g~~~~~ad---~e~i~~~~~~l~~lgl~~~~~i~i~~~g  168 (423)
T 1htt_A           95 GLLYNQEQRLWYIGPMFRHE-RPQKG--RYRQFHQLGCEVFGLQGPDID---AELIMLTARWWRALGISEHVTLELNSIG  168 (423)
T ss_dssp             TCSTTCCEEEEEEEEEECCC-CCCSS--CCSEEEEEEEEEESCCSHHHH---HHHHHHHHHHHHHHTCGGGCEEEEEECC
T ss_pred             ccccCCCeEEEEEcCEecCC-CCCCC--ccceeEEeeEEEECCCCchhh---HHHHHHHHHHHHHCCCCCCcEEEEcCCC
Confidence            45889999999999999999 88888  999999999999999877776   4678999999999999  4877776654

>4e51_A Histidine--tRNA ligase; seattle structural genomics center for infectious disease, S aminoacylation, tRNA activation, charged tRNA; HET: HIS; 2.65A {Burkholderia thailandensis}

Probab=99.50  E-value=2.7e-14  Score=107.13  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=61.3

Q ss_pred             cccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEE
Q psy5542           2 VADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVI   80 (86)
Q Consensus         2 ~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~   80 (86)
                      +.....|| +||+|+|++++|||+| +|+.|  |+|||+|.|+|+|+.+...++   .+++.++.++++.||++ +....
T Consensus       120 ~~~~~~~~-~lP~r~~~~g~vfR~E-~~~~g--R~ReF~Q~d~ei~g~~~~~ad---aEvi~l~~~~l~~lGl~~~~i~i  192 (467)
T 4e51_A          120 AIEHNMLY-DGPKRLWYIGPMFRHE-RPQRG--RYRQFHQVGVEALGFAGPDAD---AEIVMMCQRLWEDLGLTGIKLEI  192 (467)
T ss_dssp             HHHTTTTT-TSCEEEEEEEEEECCC-CC-----CCSEEEEEEEEEETCCCSHHH---HHHHHHHHHHHHHHTCCCEEEEE
T ss_pred             HHHccccc-CCCEEEEEEccEEccC-CCCCC--CcCceEEEEEEEEeCCChHHH---HHHHHHHHHHHHHcCCCceEEEE
Confidence            34556788 6999999999999999 55556  999999999999999877776   78999999999999994 65555


Q ss_pred             ecCC
Q psy5542          81 VRHG   84 (86)
Q Consensus        81 ~~~g   84 (86)
                      .+.|
T Consensus       193 n~~g  196 (467)
T 4e51_A          193 NSLG  196 (467)
T ss_dssp             EECC
T ss_pred             eCCC
Confidence            4433

>1z7m_A ATP phosphoribosyltransferase regulatory subunit; ATP-PRT, histidine biosynthesis, hiszg, alloste evolution; 2.90A {Lactococcus lactis} SCOP: d.104.1.1 PDB: 1z7n_A*

Probab=99.45  E-value=8.3e-14  Score=101.12  Aligned_cols=70  Identities=20%  Similarity=0.121  Sum_probs=54.7

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecC
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRH   83 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~   83 (86)
                      +++++|+|+|++++|||+| +|+.|  |.|||+|.|+++|+.+...++   .+++.++.+++++||++ +.....+.
T Consensus       112 ~~~~~P~rl~y~g~vfR~e-~p~~g--R~REF~Q~g~ei~g~~~~~aD---aEvi~l~~~~l~~lgl~~~~i~l~~~  182 (344)
T 1z7m_A          112 IKDSTSARYSYFGKIFRKE-KRHKG--RSTENYQIGIELFGESADKSE---LEILSLALQVIEQLGLNKTVFEIGSA  182 (344)
T ss_dssp             CCSCCCEEEEEEEECCCCC-C---------CCEEEEEEEESSCHHHHH---HHHHHHHHHHHHHHTCSSEEEEEEEH
T ss_pred             cCCCCCeEEEEECcEEccC-CCCCC--CcceeEEEEEEEEcCCCcHHH---HHHHHHHHHHHHHCCCCcEEEEECCH
Confidence            3778999999999999999 77778  999999999999999876666   57999999999999996 76665544

>3od1_A ATP phosphoribosyltransferase regulatory subunit; structural genomics, PSI-2, protein structure initiative; 1.97A {Bacillus halodurans}

Probab=99.32  E-value=2.9e-12  Score=94.72  Aligned_cols=69  Identities=17%  Similarity=0.227  Sum_probs=57.1

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEec
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVR   82 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~   82 (86)
                      .++++|+|+|++++|||+| +|+.|  |.|||+|.|+++|+.+...++   .+++.+..++++.||++ +.....+
T Consensus        98 ~~~~~P~r~~y~g~vfR~e-~~~~g--R~Ref~Q~g~ei~G~~~~~aD---aEvi~l~~~~l~~lgl~~~~i~l~~  167 (400)
T 3od1_A           98 KDRAYPLRLAYQSNVYRAQ-QNEGG--KPAEFEQLGVELIGDGTASAD---GEVIALMIAALKRAGLSEFKVAIGH  167 (400)
T ss_dssp             SSSCSCEEEEEEEEEECCC-C---C--CCSEEEEEEEEEESCCSHHHH---HHHHHHHHHHHHHTTCCSEEEEEEE
T ss_pred             ccCCCCeEEEEEcCEEeCC-CCCCC--CCCccEEeEEEEECCCChHhH---HHHHHHHHHHHHHCCCCceEEEecC
Confidence            4689999999999999999 67677  999999999999999876666   67999999999999994 6555433

>3rac_A Histidine-tRNA ligase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, PSI-BIO; 2.30A {Alicyclobacillus acidocaldarius subsp}

Probab=99.30  E-value=4.5e-12  Score=92.97  Aligned_cols=71  Identities=15%  Similarity=0.160  Sum_probs=54.6

Q ss_pred             cCCcchhhheeeceeecCCCC-----CCCceeeceeeeeeeeEEcCC-hHhHHHHHHHHHHHHHHHHHHcCC-cEEEEEe
Q psy5542           9 HKALPLLLYQFTSKFRDELRP-----KFGLMRSREFLMKDLYAFTAS-EVDANDVYNLVGKCYDDVFNTLGI-KYRKVIV   81 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~-----~~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~~~~~~~~~i~~~lgi-~~~~~~~   81 (86)
                      .+++|+|+|++++|||+|..|     ..|  |.|||+|.|+++|+.+ ...++   .+++.++.++++.||+ ++.+...
T Consensus       113 ~~~~P~r~~y~g~vfR~e~~g~~~~~~~g--R~ReF~Q~g~ei~g~~d~~~aD---aEvi~l~~~~l~~lgl~~~~i~l~  187 (373)
T 3rac_A          113 AGRTPIRWCYCERVYRRTDDPASLSWASG--KAAESTQVGIERIGEEASVDVD---MDVLRLLHEASAAAGVRHHRIVVS  187 (373)
T ss_dssp             TTCCCCEEEEEEEEEECC--------------CEEEEEEEEEECSSCCCHHHH---HHHHHHHHHHHHHHTCCSCEEEEE
T ss_pred             cCCCCeEEEEEcceEccCCCcccccccCC--ccceeEEeeeEEECCCCCHHHH---HHHHHHHHHHHHHcCCCceEEEec
Confidence            378999999999999999654     446  9999999999999998 45555   6799999999999999 4666655


Q ss_pred             cCC
Q psy5542          82 RHG   84 (86)
Q Consensus        82 ~~g   84 (86)
                      +.|
T Consensus       188 ~~~  190 (373)
T 3rac_A          188 HAR  190 (373)
T ss_dssp             ETT
T ss_pred             CHH
Confidence            543

>3lc0_A Histidyl-tRNA synthetase; tRNA-ligase, aminoacyl-tRNA synthetase, ligase, structural G medical structural genomics of pathogenic protozoa; HET: HIS; 1.80A {Trypanosoma cruzi} PDB: 3hrk_A* 3hri_A

Probab=99.27  E-value=7.7e-12  Score=93.76  Aligned_cols=68  Identities=19%  Similarity=0.144  Sum_probs=54.3

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC---cEEEEEe
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI---KYRKVIV   81 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi---~~~~~~~   81 (86)
                      .++++|+|+|++++|||+| +|..|  |.|||+|.|+++|+.+...++   .+++.++.++++.||+   ++.....
T Consensus       118 ~~~~~P~r~~y~g~vfR~e-~~~~g--R~ReF~Q~g~ei~G~~~~~~D---aEvi~l~~~~l~~lgl~~~~~~i~in  188 (456)
T 3lc0_A          118 RSLLLPAKWYSIPQCWRYE-AITRG--RRREHYQWNMDIVGVKSVSAE---VELVCAACWAMRSLGLSSKDVGIKVN  188 (456)
T ss_dssp             TTCCSSEEEEECCEEECCC-C-------CCEEEEEEEEEESCCSTHHH---HHHHHHHHHHHHHTTCCTTTEEEEEE
T ss_pred             cccCCCEEEEEeccEEecC-CCCCC--CccceEEEEEEEEcCCChHhh---HHHHHHHHHHHHHcCCCCCceEEEEc
Confidence            4678999999999999999 57667  999999999999999876666   5799999999999999   3554443

>4g84_A Histidine--tRNA ligase, cytoplasmic; synthetase; 2.40A {Homo sapiens}

Probab=99.19  E-value=2.4e-11  Score=89.80  Aligned_cols=71  Identities=18%  Similarity=0.140  Sum_probs=53.8

Q ss_pred             cCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           6 KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         6 i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      ..+++.+|+++|+++++||+| +|+.|..|.|||+|.++++|+..+. .++   .+++.++.++++.||++-..+.
T Consensus        97 ~~~~~~~p~k~~y~g~vfR~e-rp~~~~gR~Ref~Q~g~ei~G~~~~~~aD---aEvi~l~~~~l~~lgl~~~~i~  168 (464)
T 4g84_A           97 LAMNKLTNIKRYHIAKVYRRD-NPAMTRGRYREFYQCDFDIAGNFDPMIPD---AECLKIMCEILSSLQIGDFLVK  168 (464)
T ss_dssp             HHHTTCSCEEEEEEEEEECCC-C------CCSEEEEEEEEEESCCSTTHHH---HHHHHHHHHHHHHHTCCCEEEE
T ss_pred             HHhcCCCCceeEEEecceecc-CCccccCccceeeecceeccCCccchhhH---HHHHHHHHHHHHHhCCCCccee
Confidence            346788999999999999999 8866666999999999999997543 345   5688999999999999644443

>3net_A Histidyl-tRNA synthetase; aminoacyl-tRNA synthetase, ligase, structural genomics, PSI- nostoc, protein structure initiative; 2.70A {Nostoc SP}

Probab=99.17  E-value=2.6e-11  Score=90.77  Aligned_cols=66  Identities=23%  Similarity=0.378  Sum_probs=52.6

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhH--HHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDA--NDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~--~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      .+..+|+|+|++++|||+| +|+.|  |.|||+|.++++|+.+...+  +   .+++.+..++++.||++ +...
T Consensus       115 ~~~~~p~r~~y~g~vfR~e-~~~~g--r~Ref~Q~g~ei~G~~~~~a~~D---aEvi~l~~~~l~~lgl~~~~i~  183 (465)
T 3net_A          115 NDLTFPFARYQMDVVFRGE-RAKDG--RFRQFRQCDIDVVGREKLSLLYD---AQMPAIITEIFEAVNIGDFVIR  183 (465)
T ss_dssp             GGSCSSEEEEECCEEECBC---------CCEEEEEEEEEECSSCCCHHHH---HHHHHHHHHHHHHHTCSCEEEE
T ss_pred             cccCCCeEEEEeccEEecC-CCCCC--CcceeEEeeEEEECCCCccchhh---HHHHHHHHHHHHHcCCCceEEE
Confidence            3568999999999999999 67777  99999999999999987667  5   57999999999999996 4443

>1usy_A ATP phosphoribosyltransferase regulatory subunit; aminoacyl-tRNA synthetase; HET: HIS; 2.52A {Thermotoga maritima} SCOP: d.104.1.1 PDB: 1usy_C*

Probab=99.14  E-value=7.7e-11  Score=83.09  Aligned_cols=67  Identities=7%  Similarity=-0.145  Sum_probs=56.0

Q ss_pred             CcCC-cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecC
Q psy5542           8 SHKA-LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRH   83 (86)
Q Consensus         8 Syr~-LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~   83 (86)
                      .+++ +|+|+|++++|||+|..+.      |||+|.|+|+|+.+...++   .+++.+..++++.||++ +.....+.
T Consensus        64 ~~~~~~p~R~~y~g~vfR~e~~~~------Ref~Q~g~ei~g~~~~~~D---aEvi~l~~~~l~~lgl~~~~i~l~~~  132 (275)
T 1usy_A           64 RYSPDSQIKVWYADFVYRYSGSDL------VAEYQLGLEKVPRNSLDDS---LEVLEIIVESASEFFEGPVIVEIGHT  132 (275)
T ss_dssp             TCTTCCCEEEECCEEEEEEETTEE------EEEEEEEEEEESCCSHHHH---HHHHHHHHHHHHHHCCSCEEEEEEET
T ss_pred             hcCCCCceEEEEeceEEecCCCCC------CeeeEeCEEEecCCCchhH---HHHHHHHHHHHHHcCCCCeEEEeCCH
Confidence            3667 9999999999999995442      9999999999999877666   78999999999999996 65554443

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

Probab=99.11  E-value=1.8e-10  Score=82.10  Aligned_cols=69  Identities=16%  Similarity=0.197  Sum_probs=56.7

Q ss_pred             cCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC-cEEEEEe
Q psy5542           6 KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI-KYRKVIV   81 (86)
Q Consensus         6 i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi-~~~~~~~   81 (86)
                      +.+ +++|++++++|+|||+|..+   ..|++||+|.|++.++.+++.   .+..+..+++.++++||+ ++..+..
T Consensus       143 ~~~-~~~PlrlfeiG~vFR~E~~~---~~r~~EF~qle~~i~g~~~~~---~f~elkg~le~ll~~LGl~~~~~~~~  212 (288)
T 3dsq_A          143 ERL-WDKPIRIFEIGTCYRKESQG---AQHLNEFTMLNLTELGTPLEE---RHQRLEDMARWVLEAAGIREFELVTE  212 (288)
T ss_dssp             TTT-SCSCEEEEEEEEEECSCCSS---SCCCSEEEEEEEEEETCCGGG---HHHHHHHHHHHHHHHHTCCCCEEEEC
T ss_pred             HhC-CCCCEEEEEEeeEEecCCCC---CCcCccEEEEEEEEEcCCchh---hHHHHHHHHHHHHHHcCCCCcEEecC
Confidence            344 89999999999999999654   348999999999999986433   368899999999999999 5665543

>4g85_A Histidine-tRNA ligase, cytoplasmic; synthetase; 3.11A {Homo sapiens}

Probab=99.10  E-value=1.1e-10  Score=88.05  Aligned_cols=69  Identities=20%  Similarity=0.208  Sum_probs=52.6

Q ss_pred             cCCcCCcchhhheeeceeecCCCCCC--CceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           6 KLSHKALPLLLYQFTSKFRDELRPKF--GLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         6 i~Syr~LP~~l~q~~~~fR~E~~~~~--Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      ..+++.+|+++|+++++||+| +|+.  |  |.|||+|.|+++|+..+. .++   .+++.++.++++.||+.-..+.
T Consensus       150 ~~~~~~~p~k~yyig~vfR~E-rp~~~~G--R~ReF~Q~g~ei~G~~~~~~aD---aEvi~l~~~~l~~lgl~~~~i~  221 (517)
T 4g85_A          150 LAMNKLTNIKRYHIAKVYRRD-NPAMTRG--RYREFYQCDFDIAGNFDPMIPD---AECLKIMCEILSSLQIGDFLVK  221 (517)
T ss_dssp             HHHTTCSCEEEEEEEEEECCC-C---------CCEEEEEEEEEESCCCTTHHH---HHHHHHHHHHHHHHCCCCEEEE
T ss_pred             HHhCCCCCceeEEEeceEecc-CcccccC--ccceeeeeceeccCCccchHHH---HHHHHHHHHHHHhhcCCccccc
Confidence            345788999999999999999 6643  6  999999999999997543 345   4688999999999999644333

>3qtc_A Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP B O-methyl tyrosine binding, magnesium binding, aminoacylatio esterification; HET: 0A1 ANP; 1.75A {Methanosarcina mazei} PDB: 2q7e_A* 2q7g_A* 2q7h_A* 2zim_A* 2zin_A* 2e3c_A* 2zcd_A* 2zce_A* 2zio_A* 3vqv_A* 3vqw_A* 3vqx_A* 3vqy_A*

Probab=98.63  E-value=7.7e-08  Score=68.01  Aligned_cols=65  Identities=18%  Similarity=0.272  Sum_probs=53.2

Q ss_pred             CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      .+...+|+++|++++|||+|..+ .+  |.+||+|.|+..+..+.     .+..+..+++.+++.||+++...
T Consensus       149 ~~~~~~p~rlfeiG~vFR~E~~~-~~--~~~Ef~ql~~~~~g~~~-----~f~elkg~le~ll~~lGl~~~~~  213 (290)
T 3qtc_A          149 DRALPDPIKIFEIGPCYRKESDG-KE--HLEEFTMLVFWQMGSGC-----TRENLESIITDFLNHLGIDFKIV  213 (290)
T ss_dssp             TTTSCSSEEEEEEEEEECCCSCS-SS--CCSEEEEEEEEEESTTC-----CHHHHHHHHHHHHHHHTCCCEEE
T ss_pred             hccCCCCeEEEEEcCEEecCCCC-Cc--CcchheEEEEEEEcCCh-----HHHHHHHHHHHHHHHcCCCcEEe
Confidence            34578999999999999999543 33  89999999999998753     24678899999999999987654

>3a5y_A GENX, putative lysyl-tRNA synthetase; aminoacyl-tRNA synthetase paralog, translation, lysyl- synthetase, lysyladenylate analog; HET: KAA; 1.90A {Escherichia coli} PDB: 3a5z_A* 3g1z_A*

Probab=97.85  E-value=2.5e-05  Score=56.85  Aligned_cols=46  Identities=17%  Similarity=0.240  Sum_probs=35.7

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK   63 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~   63 (86)
                      ++||+++|||+|..++.   ++.||+|.|++.-..+.++..+..+.++.
T Consensus       111 rvyqIg~~FR~E~~~~r---H~pEFt~lE~e~af~d~~d~m~~~E~li~  156 (345)
T 3a5y_A          111 PVFQLCRSFRNEEMGRY---HNPEFTMLEWYRPHYDMYRLMNEVDDLLQ  156 (345)
T ss_dssp             SEEEEEEEECCCCCBTT---BCSEEEEEEEEEETCCHHHHHHHHHHHHH
T ss_pred             cEEEEEcceeCCCCccc---ccchhheeeeeeeCCCHHHHHHHHHHHHH
Confidence            78999999999977544   99999999999888776655544444443

>1nnh_A Asparaginyl-tRNA synthetase-related peptide; structural genomics, PSI, protein structure initiative, southeast COLL for structural genomics; 1.65A {Pyrococcus furiosus} SCOP: d.104.1.1 PDB: 3p8t_A 3p8v_A 3p8y_A 3reu_A* 3rex_A* 3rl6_A*

Probab=97.78  E-value=3e-05  Score=55.04  Aligned_cols=44  Identities=20%  Similarity=0.173  Sum_probs=33.3

Q ss_pred             chhhheeeceeecCCCCC--CCceeec-eeeeeeeeEEcCChHhHHHHHH
Q psy5542          13 PLLLYQFTSKFRDELRPK--FGLMRSR-EFLMKDLYAFTASEVDANDVYN   59 (86)
Q Consensus        13 P~~l~q~~~~fR~E~~~~--~Gl~R~r-eF~~~d~~~f~~~~~~~~~~~~   59 (86)
                      |.++||+++|||+|. |+  .|  |-+ ||+|.|++....+.++.....+
T Consensus        88 ~~rvf~ig~~FR~E~-pq~~~~--RH~~EFtqle~e~~~~~~~~l~~~~e  134 (294)
T 1nnh_A           88 LKKIFVLSPNIRLES-RQKDDG--RHAYEFTQLDFEVERAKMEDIMRLIE  134 (294)
T ss_dssp             CCEEEEEEEEECCCC-GGGCSS--SCCSEEEEEEEEEETCCHHHHHHHHH
T ss_pred             ccceEEEEccEeCCC-CCCCCC--ccccceeEEEEEecCCCHHHHHHHHH
Confidence            779999999999995 22  14  667 9999999999887555443333

>3a74_A Lysyl-tRNA synthetase; aminoacyl tRNA synthetase, ligase, protein biosynthesis, AMI tRNA synthetase, ATP-binding, magnesium; HET: B4P LYN; 1.80A {Geobacillus stearothermophilus} PDB: 3e9h_A* 3e9i_A*

Probab=97.68  E-value=6.9e-05  Score=56.79  Aligned_cols=44  Identities=25%  Similarity=0.243  Sum_probs=34.9

Q ss_pred             hhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHH
Q psy5542          14 LLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL   60 (86)
Q Consensus        14 ~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~   60 (86)
                      -++||+++|||+|...+.   +..||+|.|++....+.++..+..+.
T Consensus       243 ~rVyeig~~FR~E~~~~r---H~pEFT~lE~e~af~d~~dlm~l~E~  286 (493)
T 3a74_A          243 EKVYEIGRVFRNEGISTR---HNPEFTMLELYEAYADFRDIMKLTEN  286 (493)
T ss_dssp             CEEEEEEEEECCCCCBTT---BCSEEEEEEEEEETCCHHHHHHHHHH
T ss_pred             CceEEECccccCCCCCcc---cCCceeEEEEEecCCCHHHHHHHHHH
Confidence            479999999999976553   99999999999998876655444333

>1e1o_A Lysyl-tRNA synthetase, heat inducible; ligase, aminoacyl-tRNA synthetase, protein biosynthesis; HET: LYS; 2.12A {Escherichia coli} SCOP: b.40.4.1 d.104.1.1 PDB: 1e1t_A* 1e22_A* 1e24_A* 1lyl_A 1bbu_A* 1bbw_A 1krs_A 1krt_A

Probab=97.63  E-value=8.4e-05  Score=56.48  Aligned_cols=43  Identities=23%  Similarity=0.291  Sum_probs=34.0

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL   60 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~   60 (86)
                      ++||+++|||+|...+.   +..||+|.|++....+.++..+..+.
T Consensus       253 rVyeIg~~FR~E~~~~r---H~pEFt~lE~e~af~d~~dlm~l~E~  295 (504)
T 1e1o_A          253 RVFEINRNFRNEGISVR---HNPEFTMMELYMAYADYHDLIELTES  295 (504)
T ss_dssp             EEEEEEEEECCCCCCC----CCSEEEEEEEEEESCCHHHHHHHHHH
T ss_pred             cEEEEcccccCCCCCcc---ccCceeeeeeeecCCCHHHHHHHHHH
Confidence            78999999999976543   99999999999988876665544333

>1x54_A Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken structural genomics/proteom initiative, RSGI, structural genomics, ligase; HET: 4AD; 1.45A {Pyrococcus horikoshii} PDB: 1x55_A* 1x56_A

Probab=97.57  E-value=0.00011  Score=54.78  Aligned_cols=46  Identities=24%  Similarity=0.171  Sum_probs=34.7

Q ss_pred             chhhheeeceeecCCCCCCCceeec-eeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          13 PLLLYQFTSKFRDELRPKFGLMRSR-EFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        13 P~~l~q~~~~fR~E~~~~~Gl~R~r-eF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      |.++||+++|||+|. +..|  |-+ ||+|.|++....+.++..+..+.+
T Consensus       200 ~~rvf~ig~~FR~E~-~~~~--RH~pEFtqle~e~~~~~~~dlm~~~e~l  246 (434)
T 1x54_A          200 LEKVWSLTPSFRAEK-SRTR--RHLTEFWHLELEAAWMDLWDIMKVEEEL  246 (434)
T ss_dssp             HSEEEEEEEEECCCC-CCCS--SCCSEEEEEEEEEETCCHHHHHHHHHHH
T ss_pred             ccceEEEecceecCC-CCCc--ccccEEEEeeEEEcCCCHHHHHHHHHHH
Confidence            679999999999994 3333  666 999999999988765554443333

>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE; 2.30A {Sulfolobus tokodaii}

Probab=97.51  E-value=0.00015  Score=53.97  Aligned_cols=45  Identities=16%  Similarity=0.102  Sum_probs=34.0

Q ss_pred             chhhheeeceeecCCCCCCCceeec-eeeeeeeeEEcCChHhHHHHHHH
Q psy5542          13 PLLLYQFTSKFRDELRPKFGLMRSR-EFLMKDLYAFTASEVDANDVYNL   60 (86)
Q Consensus        13 P~~l~q~~~~fR~E~~~~~Gl~R~r-eF~~~d~~~f~~~~~~~~~~~~~   60 (86)
                      |-++||+++|||+|.. ..|  |-+ ||+|.|++....+.++..+..+.
T Consensus       199 ~~rvf~ig~~FR~E~~-~~~--RH~pEFtqle~e~~~~~~~dlm~~~e~  244 (429)
T 1wyd_A          199 VERVFEVAPAWRAEES-DTP--FHLAEFISMDVEMAFADYNDVMQLLEK  244 (429)
T ss_dssp             HSEEEEEEEEECCCCC-CSS--SCCSEEEEEEEEEETCCHHHHHHHHHH
T ss_pred             cCceEEEcccccccCC-ccc--cccceeeEeeeeecCCCHHHHHHHHHH
Confidence            5689999999999943 333  666 99999999998876555444333

>1eov_A ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA synthetase, tRNA ligase, APO-enzyme, OB-fold,; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.1 d.104.1.1 PDB: 1asy_A* 1asz_A*

Probab=97.49  E-value=0.00015  Score=54.83  Aligned_cols=46  Identities=24%  Similarity=0.221  Sum_probs=32.5

Q ss_pred             chhhheeeceeecCCCCCCCceeec-eeeeeeee-EEcCChHhHHHHHHHH
Q psy5542          13 PLLLYQFTSKFRDELRPKFGLMRSR-EFLMKDLY-AFTASEVDANDVYNLV   61 (86)
Q Consensus        13 P~~l~q~~~~fR~E~~~~~Gl~R~r-eF~~~d~~-~f~~~~~~~~~~~~~~   61 (86)
                      +-++||+++|||+|.. ..+  |-+ ||+|.|++ +|..+.++..+..+.+
T Consensus       244 ~~rvy~ig~~FR~E~~-~~~--Rh~pEFt~le~e~af~~~~~dlm~l~E~l  291 (487)
T 1eov_A          244 FERVYEIGPVFRAENS-NTH--RHMTEFTGLDMEMAFEEHYHEVLDTLSEL  291 (487)
T ss_dssp             CCEEEEEEEEECCCCC-CCT--TCCSEEEEEEEEEECSSCTHHHHHHHHHH
T ss_pred             CCceEEEeccEecCCC-CCC--ccchhhhhhhhhhhhhcCHHHHHHHHHHH
Confidence            4589999999999954 334  777 99999996 4876544443333333

>4ah6_A Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo sapiens}

Probab=97.44  E-value=0.00019  Score=55.89  Aligned_cols=38  Identities=21%  Similarity=0.198  Sum_probs=31.5

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDAN   55 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~   55 (86)
                      ++||+++|||+|...+.   |..||+|.|++.-..+.++..
T Consensus       218 rvfqi~~~FR~E~~~t~---r~pEFt~lE~e~af~d~~d~m  255 (617)
T 4ah6_A          218 RYFQVARCYRDEGSRPD---RQPEFTQIDIEMSFVDQTGIQ  255 (617)
T ss_dssp             EEEEEEEEECCCSSCSS---SCSEEEEEEEEEESCCHHHHH
T ss_pred             cEEEEEhheecccCCCC---cCcceecceeeecCCCHHHHH
Confidence            78999999999976655   899999999998777655544

>1l0w_A Aspartyl-tRNA synthetase; space-grown crystal, dimeric enzyme, flexible domains, ligase; 2.01A {Thermus thermophilus} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1efw_A* 1g51_A

Probab=97.39  E-value=0.00029  Score=54.38  Aligned_cols=44  Identities=23%  Similarity=0.181  Sum_probs=34.3

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||+++|||+|...+.   |--||+|.|++.-..+.++..+..+.+
T Consensus       214 rvfqI~~~FR~E~~~~~---r~pEFT~lE~e~af~d~~dvm~~~E~l  257 (580)
T 1l0w_A          214 RYFQIARCFRDEDLRAD---RQPDFTQLDLEMSFVEVEDVLELNERL  257 (580)
T ss_dssp             EEEEEEEEECCCCCCSS---CCSEEEEEEEEEESCCHHHHHHHHHHH
T ss_pred             CeEEEeceeeCCCCCCC---cCCCccceeeeecCCCHHHHHHHHHHH
Confidence            68999999999976655   777999999998887766655443433

>1c0a_A Aspartyl tRNA synthetase; protein-RNA complex, ligase/RNA complex; HET: 4SU H2U QUO G7M 5MU PSU AMP AMO; 2.40A {Escherichia coli} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1il2_A* 1eqr_A*

Probab=97.38  E-value=0.00029  Score=54.35  Aligned_cols=45  Identities=24%  Similarity=0.214  Sum_probs=35.0

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|...+.   |--||+|.|++.-..+.++..+..+.++
T Consensus       208 rvfqI~~~FR~E~~~t~---r~pEFT~lE~e~af~d~~dvm~~~E~li  252 (585)
T 1c0a_A          208 RYYQIVKCFRDEDLRAD---RQPEFTQIDVETSFMTAPQVREVMEALV  252 (585)
T ss_dssp             EEEEEEEEECCCCCBTT---BCSEEEEEEEEEESCCHHHHHHHHHHHH
T ss_pred             ceEEEeceeecCCCCCC---cCcccceeeeeecCCCHHHHHHHHHHHH
Confidence            68999999999976655   7779999999988877666554444433

>3bju_A Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP- binding, cytoplasm, ligase, nucleotide-binding, phosphoprotein, polymorphism; HET: LYS ATP; 2.31A {Homo sapiens}

Probab=97.30  E-value=0.00042  Score=52.82  Aligned_cols=44  Identities=20%  Similarity=0.258  Sum_probs=34.8

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||++++||+|...+.   ++-||+|.|++.--.+-++..+..+.+
T Consensus       246 rVyeig~~FR~E~~~tr---H~pEFtmlE~e~af~d~~dlm~l~E~l  289 (521)
T 3bju_A          246 RVYEIGRQFRNEGIDLT---HNPEFTTCEFYMAYADYHDLMEITEKM  289 (521)
T ss_dssp             EEEEEEEEECCSCCBTT---BCSEEEEEEEEEETCCHHHHHHHHHHH
T ss_pred             ceEEEEcceeCCCCCCc---cchhhhhhhhhhhcCCHHHHHHHHHHH
Confidence            68999999999977664   889999999999888766655444433

>1n9w_A Aspartyl-tRNA synthetase 2; biosynthetic protein; 2.30A {Thermus thermophilus} SCOP: b.40.4.1 d.104.1.1 PDB: 3kfu_A*

Probab=97.29  E-value=0.00025  Score=52.70  Aligned_cols=42  Identities=21%  Similarity=0.138  Sum_probs=23.9

Q ss_pred             chhhheeeceeecCCCCCCCceeec-eeeeeeeeEEcC-ChHhHHHH
Q psy5542          13 PLLLYQFTSKFRDELRPKFGLMRSR-EFLMKDLYAFTA-SEVDANDV   57 (86)
Q Consensus        13 P~~l~q~~~~fR~E~~~~~Gl~R~r-eF~~~d~~~f~~-~~~~~~~~   57 (86)
                      +-++||+++|||+|. +..|  |-+ ||+|.|++.... +.++..+.
T Consensus       190 ~~rvf~ig~~FR~E~-~~~~--RH~pEFtqle~e~~~~~d~~dlm~l  233 (422)
T 1n9w_A          190 FERVYEVAPVWRMEE-HHTS--RHLNEYLSLDVEMGFIADEEDLMRL  233 (422)
T ss_dssp             HSEEEEEEEC----------------CCEEEEEEEESCSSHHHHHHH
T ss_pred             CCceeEEeCceECCC-CCCC--cccceeEEeeeeeeCCCCHHHHHHH
Confidence            358999999999994 4334  776 999999999988 65544433

>4ex5_A Lysine--tRNA ligase; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: LYS; 2.40A {Burkholderia thailandensis}

Probab=97.25  E-value=0.00052  Score=52.52  Aligned_cols=45  Identities=20%  Similarity=0.197  Sum_probs=34.8

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|...+.   +.-||+|.|++.-..+.++..+..+.++
T Consensus       274 rVyeIg~~FR~E~~~~r---H~pEFtmlE~e~af~d~~dlm~l~E~li  318 (529)
T 4ex5_A          274 RVFEINRNFRNEGVSPR---HNPEFTMMEFYAAYTDYRWLMDFTERLI  318 (529)
T ss_dssp             EEEEEEEEECCSCCBTT---BCSEEEEEEEEEETCCHHHHHHHHHHHH
T ss_pred             cEEEeehheecCCCCCC---cccHhHhhhhhhhcCCHHHHHHHHHHHH
Confidence            67999999999976654   8999999999988777666554444333

>2xgt_A Asparaginyl-tRNA synthetase, cytoplasmic; ligase, ATP-binding, protein biosynthesis; HET: NSS; 1.90A {Brugia malayi} PDB: 2xti_A*

Probab=97.15  E-value=0.00075  Score=50.27  Aligned_cols=45  Identities=11%  Similarity=0.021  Sum_probs=32.9

Q ss_pred             hhheeeceeecCCCCCCCceeec-eeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSR-EFLMKDLYAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~r-eF~~~d~~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|...+.   |=. ||+|.|++.-..+.++..+..+.++
T Consensus       199 rvfeIg~~FR~E~~~t~---RH~~EFT~lE~e~af~d~~d~m~~~E~li  244 (435)
T 2xgt_A          199 DVFCIAQSYRAEKSRTR---RHLAEYAHVEAECPFITLDDLMEKIEELV  244 (435)
T ss_dssp             SEEEEEEEECCCSSCCT---TCCSEEEEEEEEEESCCHHHHHHHHHHHH
T ss_pred             ceEEEecceecCCCCcc---ccccceeEEEEEEecCCHHHHHHHHHHHH
Confidence            78999999999963221   334 9999999998887766554444443

>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding, aminoacyl-tRNA synthetase, LI nucleotide-binding, protein biosynthesis; 2.80A {Entamoeba histolytica}

Probab=96.87  E-value=0.0015  Score=50.26  Aligned_cols=45  Identities=18%  Similarity=0.163  Sum_probs=30.3

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeee-EEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLY-AFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~-~f~~~~~~~~~~~~~~   61 (86)
                      ++||+++|||+|...+.  -=+-||+|.|++ +|..+.++..+..+.+
T Consensus       312 rVfeI~~~FR~E~~~t~--RHl~EFtmlE~e~af~~d~~d~m~~~E~l  357 (548)
T 3i7f_A          312 KVFEVGPVFRAENSNTR--RHLTEFEGLDIEMEIVENYHECIDVMEKL  357 (548)
T ss_dssp             EEEEEEEECCCSCCCSS--SCCSCEEEEEEEEECSSCTHHHHHHHHHH
T ss_pred             cEEEEeeeEecCCCCCC--CcchhhhchhhhhhhhcCHHHHHHHHHHH
Confidence            68999999999965322  024699999999 5775545444343433

>3nem_A Aspartyl-tRNA synthetase; rossmann fold, OB fold, ligase; HET: AMO ATP; 1.89A {Thermococcus kodakarensis} PDB: 3nel_A* 3nen_A 1b8a_A*

Probab=96.86  E-value=0.0025  Score=47.65  Aligned_cols=45  Identities=18%  Similarity=0.099  Sum_probs=32.5

Q ss_pred             hhheeeceeecCCCCCCCcee-eceeeeeeeeEEcCC-hHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMR-SREFLMKDLYAFTAS-EVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R-~reF~~~d~~~f~~~-~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|...+.   | ..||+|.|++.-..+ .++..+..+.++
T Consensus       205 rvf~i~~~FR~E~~~t~---RH~pEFt~le~e~a~~~~~~d~m~~~E~li  251 (438)
T 3nem_A          205 RVYEIAPIFRAEEHNTT---RHLNEAWSIDSEMAFIEDEEEVMSFLERLV  251 (438)
T ss_dssp             EEEEEEEEECCCSSCCT---TCCSEEEEEEEEEESCSSHHHHHHHHHHHH
T ss_pred             ceEEEcceEECCCCCCc---ccccceeeeeeeeccCccHHHHHHHHHHHH
Confidence            78999999999965432   3 359999999987776 665544444433

>3m4p_A Ehasnrs, asparaginyl-tRNA synthetase, putative; aminoacyl-tRNA synthetase, tRNA ligase, AARS, translation, ATP-binding, nucleotide-binding; HET: 4AD; 2.83A {Entamoeba histolytica} PDB: 3m4q_A

Probab=96.66  E-value=0.0037  Score=46.91  Aligned_cols=45  Identities=16%  Similarity=0.031  Sum_probs=31.8

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||+++|||+|...+.  -=+-||+|.|++.-..+.++..+..+.+
T Consensus       223 rVyeig~~FR~E~~~t~--rH~pEFtmlE~e~af~d~~d~m~~~E~l  267 (456)
T 3m4p_A          223 KSFCMLSSYRAEQSRTV--RHLAEYLHLEAELPFISFEDLLNHLEDL  267 (456)
T ss_dssp             SEEEEEEEECCCSCCCS--SCCSEEEEEEEEEESCCHHHHHHHHHHH
T ss_pred             cEEEEEhheecCCCCCC--cchHHHHHhHHHHhcCCHHHHHHHHHHH
Confidence            68999999999964221  0235999999999877766654444433

>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}

Probab=96.42  E-value=0.0042  Score=47.37  Aligned_cols=58  Identities=17%  Similarity=0.206  Sum_probs=45.0

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      +..|++++++++|||+|.....   ++.+|.|.++.....+   +  .+..+..+.+.++++||+.
T Consensus       344 ~~~PiriFeiGrVFR~d~~Dat---HlpeFhQlegl~~~~~---v--~f~dLKg~Le~~l~~lG~~  401 (508)
T 3l4g_A          344 PFTPVKYFSIDRVFRNETLDAT---HLAEFHQIEGVVADHG---L--TLGHLMGVLREFFTKLGIT  401 (508)
T ss_dssp             SCCCEEEEEEEEEECCSCCCSS---SCSEEEEEEEEEEEES---C--CHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCceEEEEccEEecCCCCCC---cCCeEEEEEEEEECCC---C--CHHHHHHHHHHHHHHcCCc
Confidence            4689999999999999964433   6789999999887542   1  3466778888889999873

>2du3_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase/RNA complex; HET: SEP; 2.60A {Archaeoglobus fulgidus} PDB: 2du4_A 2du5_A* 2du6_A*

Probab=96.10  E-value=0.019  Score=44.00  Aligned_cols=65  Identities=14%  Similarity=0.192  Sum_probs=48.6

Q ss_pred             CcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVI   80 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~   80 (86)
                      +.+..|++++++|.|||.|.. ...   +.+||.|.++.....+.     .+..+....+.+++.||+. +....
T Consensus       200 ~r~~~pvrLFEIG~VFr~d~~~d~t---h~~Ef~qLagli~G~~v-----df~dLKgilE~LL~~LGi~~~r~~~  266 (534)
T 2du3_A          200 DKLPLPIKLFSIDRCFRREQGEDAT---RLYTYFSASCVLVDEEL-----SVDDGKAVAEALLRQFGFENFRFRK  266 (534)
T ss_dssp             TTSCSSEEEEEEEEEECCCTTCSSS---CCSEEEEEEEEEECSSC-----CHHHHHHHHHHHHGGGTCCEEEEEE
T ss_pred             hCCCCCeeEEEEeeEEecCcccccc---ccceeeEEEEEEECCCC-----CHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            456899999999999998742 222   56899999999887532     1356778888999999985 54443

>1b7y_A Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta homodimer, ligase; HET: FYA; 2.50A {Thermus thermophilus} SCOP: d.104.1.1 PDB: 1b70_A* 1eiy_A 1jjc_A* 1pys_A 2iy5_A* 3hfz_A* 3teh_A* 2aly_A* 2akw_A* 2amc_A*

Probab=95.92  E-value=0.015  Score=42.25  Aligned_cols=57  Identities=12%  Similarity=0.041  Sum_probs=43.1

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc-CC
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL-GI   74 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l-gi   74 (86)
                      +..|++++++|.|||+|.....   ...||+|.+++....+-     .+..+....+.+++.+ |+
T Consensus       190 ~~~piriFEiGrVFR~d~~d~t---H~pEF~qlegl~~g~~v-----~f~dLKg~le~ll~~lfG~  247 (350)
T 1b7y_A          190 HTPPFRIVVPGRVFRFEQTDAT---HEAVFHQLEGLVVGEGI-----AMAHLKGAIYELAQALFGP  247 (350)
T ss_dssp             CCSSEEEEEEEEEECCCCCCSS---CCSEEEEEEEEEEETTC-----CHHHHHHHHHHHHHHHSCS
T ss_pred             cCCCeeEEEeeeEEECCCCCCC---CCChhHEEEEEEECCCC-----CHHHHHHHHHHHHHhhcCC
Confidence            4679999999999998753322   45899999999997631     2456677777888876 75

>2rhq_A Phenylalanyl-tRNA synthetase alpha chain; heterotetramer, phenylalanine, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus haemolyticus} PDB: 2rhs_A*

Probab=95.69  E-value=0.022  Score=40.09  Aligned_cols=58  Identities=12%  Similarity=0.062  Sum_probs=42.2

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc-CCc
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL-GIK   75 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l-gi~   75 (86)
                      ++.|++++++|.|||+|.....   ...||+|.+++....+-     .+..+....+.+++.| |++
T Consensus       129 ~~~~~riFEiG~Vfr~d~~d~~---h~~Ef~~Le~~~~g~~~-----df~dlKg~le~ll~~l~g~~  187 (294)
T 2rhq_A          129 GQGPVKIICPGKVYRRDSDDAT---HSHQFTQIEGLVVDKNI-----KMSDLKGTLELVAKKLFGAD  187 (294)
T ss_dssp             TCSCEEEEEEEEEECCCCCBTT---BCSEEEEEEEEEEESSC-----CHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCccEEEEcCEEecCCCCCC---CCChhhEEEEEEECCCC-----CHHHHHHHHHHHHHHHhCCC
Confidence            3679999999999998642322   34699999999987532     1455667777778876 763

>3pco_A Phenylalanyl-tRNA synthetase, alpha subunit; aminoacylation, tRNA-binding, DNA-binding domain, four-helix aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP; 3.02A {Escherichia coli}

Probab=94.31  E-value=0.15  Score=36.81  Aligned_cols=56  Identities=7%  Similarity=0.134  Sum_probs=38.6

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL   72 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l   72 (86)
                      +++..|++++++|.|||++ ....   .+.+|.|.++.....+-     .+..+....+.+++.|
T Consensus       179 ~~~~~pirifeiGrVyR~d-~d~t---h~p~fhqlegl~v~~~v-----~f~dLKg~Le~~l~~l  234 (327)
T 3pco_A          179 KAQQPPIRIIAPGRVYRND-YDQT---HTPMFHQMEGLIVDTNI-----SFTNLKGTLHDFLRNF  234 (327)
T ss_dssp             TTCCSSCCBCCEECCBCSC-CBTT---BCSBCCEEEEEEEETTC-----CHHHHHHHHHHHHHHH
T ss_pred             HhCCCCeeEEeeccEEecC-CCcc---cCCcccEEEEEEECCCC-----CHHHHHHHHHHHHHHH
Confidence            4567899999999999998 2322   45679999887764321     1355666666666665

>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.59  E-value=0.27  Score=38.57  Aligned_cols=64  Identities=16%  Similarity=0.219  Sum_probs=47.0

Q ss_pred             CcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      +.++.|+++++++.|||++.. ...   ...||.|.++-....+-     .+..+....+.+++.||++ ++..
T Consensus       219 ~R~~~pvRLFEIGrVFR~D~~lDat---h~~Ef~qLeGlv~G~~v-----dF~DLKGvLE~LL~~LGi~~vrfr  284 (648)
T 2odr_B          219 NKKPLPFKLFSIDRCFRREQKEDKS---HLMTYHSASCAIAGEGV-----DINDGKAIAEGLLSQFGFTNFKFI  284 (648)
T ss_dssp             TTSCSCEEEEEEEEEECCCSCCCSS---CCSEEEEEEEEEECTTC-----CHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             hcCCCCeEEEEEeeEEecCcccccc---CCCcceEEEEEEECCCC-----CHHHHHHHHHHHHHHcCCCeEEEE
Confidence            345889999999999997642 222   24899999999886521     2466788888889999983 4443

>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.54  E-value=0.28  Score=38.61  Aligned_cols=64  Identities=16%  Similarity=0.219  Sum_probs=47.0

Q ss_pred             CcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      +.++.|+++++++.|||++.. ...   ...||.|.++-....+-     .+..+....+.+++.||++ ++..
T Consensus       219 ~R~~~pvRLFEIGrVFR~D~~lDat---h~~Ef~qLeGlv~G~~v-----dF~DLKGvLE~LL~~LGi~~vrfr  284 (665)
T 2odr_A          219 NKKPLPFKLFSIDRCFRREQKEDKS---HLMTYHSASCAIAGEGV-----DINDGKAIAEGLLSQFGFTNFKFI  284 (665)
T ss_dssp             TTSCSCEEEEEEEEEECCCSCCCSS---CCSEEEEEEEEEECTTC-----CHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             hcCCCCeEEEEEeeEEecCcccccc---CCCcceEEEEEEECCCC-----CHHHHHHHHHHHHHHcCCCeEEEE
Confidence            345889999999999997642 222   24899999999886521     2466788888889999983 4443

>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.48  E-value=0.28  Score=38.67  Aligned_cols=64  Identities=16%  Similarity=0.219  Sum_probs=47.0

Q ss_pred             CcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      +.++.|+++++++.|||++.. ...   ...||.|.++-....+-     .+..+....+.+++.||++ ++..
T Consensus       219 ~R~~~pvRLFEIGrVFR~D~~lDat---h~~Ef~qLeGlv~G~~v-----DF~DLKGvLE~LL~~LGi~~vrfr  284 (685)
T 2odr_D          219 NKKPLPFKLFSIDRCFRREQKEDKS---HLMTYHSASCAIAGEGV-----DINDGKAIAEGLLSQFGFTNFKFI  284 (685)
T ss_dssp             TTSCSCEEEEEEEEEECCCSCCCSS---CCSEEEEEEEEEECTTC-----CHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             hCCCCCeEEEEeccEEecCcccccc---CCCcceEEEEEEECCCC-----CHHHHHHHHHHHHHHcCCCeEEEE
Confidence            345889999999999997642 222   24899999999886521     2466788888889999983 4443

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

Probab=92.46  E-value=0.26  Score=37.99  Aligned_cols=60  Identities=15%  Similarity=0.218  Sum_probs=45.6

Q ss_pred             CcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           8 SHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      +.+..|++++++|.|||.+.. ...   ..+||.|.++-....+-     .+..+....+.+++.||++
T Consensus       212 ~r~~~pvrlFEiGrVFr~D~~~d~t---h~~ef~qLaglv~G~~v-----dF~DLKG~Le~ll~~LGi~  272 (549)
T 2du7_A          212 KKRKLPLKLFSIDRCFRREQREDRS---HLMSYHSASCVVVGEDV-----SVDDGKVVAEGLLAQFGFT  272 (549)
T ss_dssp             TTSCSSEEEEEEEEECCCCSSCSSS---CCSCEEEEEEEEECTTC-----CHHHHHHHHHHHHGGGTCC
T ss_pred             hcCCCCeEEEEEeeEEecCCcccCc---CCCcceEEEEEEECCCC-----CHHHHHHHHHHHHHHcCCC
Confidence            345889999999999997642 222   45899999999987631     3566888888899999873

>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.40  E-value=0.29  Score=38.68  Aligned_cols=64  Identities=16%  Similarity=0.219  Sum_probs=47.0

Q ss_pred             CcCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV   79 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~   79 (86)
                      +.++.|+++++++.|||++.. ...   ...||.|.++-....+-     .+..+....+.+++.||++ ++..
T Consensus       219 ~R~~~pvRLFEIGrVFR~D~~lDat---h~~EfhqLeGlv~G~~v-----DF~DLKGvLE~LL~~LGi~~vrfr  284 (701)
T 2odr_C          219 NKKPLPFKLFSIDRCFRREQKEDKS---HLMTYHSASCAIAGEGV-----DINDGKAIAEGLLSQFGFTNFKFI  284 (701)
T ss_dssp             TTSCSCEEEEEEEEEECCCSCCCSS---CCSEEEEEEEEEECTTC-----CHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             hCCCCCeEEEEEeeEEccCcccccc---CCCcceEEEEEEECCCC-----CHHHHHHHHHHHHHHcCCCeEEEE
Confidence            345889999999999997642 222   24899999999886521     2466788888889999983 4443

>3l4g_B Phenylalanyl-tRNA synthetase beta chain; aminoacylation, tRNA-binding, DNA-binding domain, four-helix acetylation, aminoacyl-tRNA synthetase; HET: PHE; 3.30A {Homo sapiens}

Probab=88.78  E-value=1  Score=34.58  Aligned_cols=58  Identities=12%  Similarity=0.302  Sum_probs=41.2

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ++.|++++++|.+||.+.....|   .+|+.+..+.......     .|..+....+.+++.||++
T Consensus       468 ~~~~vrlFEiG~Vf~~d~~~~~~---~~e~~~la~~~~g~~~-----~f~~lkg~le~ll~~lg~~  525 (589)
T 3l4g_B          468 MPLPLKLFEISDIVIKDSNTDVG---AKNYRHLCAVYYNKNP-----GFEIIHGLLDRIMQLLDVP  525 (589)
T ss_dssp             SCSCEEEEEEEEEEEECTTSTTS---EEEEEEEEEEEESSSC-----CHHHHHHHHHHHHHHTTCC
T ss_pred             CCCceEEEEeeeEEecCCccccC---CccccEEEEEEECCCC-----CHHHHHHHHHHHHHHcCCC
Confidence            35799999999999976543333   4677777776554321     2566777778889999986

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	86
d1qf6a4	291	d.104.1.1 (A:242-532) Threonyl-tRNA synthetase (Th	1e-09
d1b76a2	331	d.104.1.1 (A:1-394) Glycyl-tRNA synthetase (GlyRS)	2e-09
d1nj8a3	268	d.104.1.1 (A:0-267) Prolyl-tRNA synthetase (ProRS)	2e-06
d1nj1a3	265	d.104.1.1 (A:19-283) Prolyl-tRNA synthetase (ProRS	9e-06
d1atia2	394	d.104.1.1 (A:1-394) Glycyl-tRNA synthetase (GlyRS)	0.002

>d1qf6a4 d.104.1.1 (A:242-532) Threonyl-tRNA synthetase (ThrRS) {Escherichia coli [TaxId: 562]} Length = 291

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: Threonyl-tRNA synthetase (ThrRS)
species: Escherichia coli [TaxId: 562]

 Score = 50.8 bits (121), Expect = 1e-09
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 2/80 (2%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYN 59
           +      S++ LPL + +F S  R+E      GLMR R F   D + F   E   ++V  
Sbjct: 99  IFNQGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEEQIRDEVNG 158

Query: 60  LVGKCYDDVFNTLGIKYRKV 79
            + +   D+++T G +   V
Sbjct: 159 CI-RLVYDMYSTFGFEKIVV 177

>d1b76a2 d.104.1.1 (A:1-394) Glycyl-tRNA synthetase (GlyRS) {Thermus thermophilus [TaxId: 274]} Length = 331

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)
species: Thermus thermophilus [TaxId: 274]

 Score = 50.2 bits (119), Expect = 2e-09
 Identities = 14/84 (16%), Positives = 27/84 (32%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
               +  + + L   + Q    FR+E+ P+  + R REF   ++  F     D       
Sbjct: 134 FKNVLDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYW 193

Query: 61  VGKCYDDVFNTLGIKYRKVIVRHG 84
           V +           +   V  +  
Sbjct: 194 VEERLKWWQEMGLSRENLVPYQQP 217

>d1nj8a3 d.104.1.1 (A:0-267) Prolyl-tRNA synthetase (ProRS) {Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190]} Length = 268

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: Prolyl-tRNA synthetase (ProRS)
species: Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190]

 Score = 41.4 bits (96), Expect = 2e-06
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 1   MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFL-MKDLYAFTASEVDANDVYN 59
           M+      H  LP+ +YQ  + FR E +    L+R RE +  K+ +   +++ +A +   
Sbjct: 110 MMKLWVKVHTDLPIKIYQIVNTFRYETKHTRPLIRLREIMTFKEAHTAHSTKEEAENQVK 169

Query: 60  LVGKCYDDVFNTLGIKYRKVIVRHG 84
                Y   F+TLGI Y        
Sbjct: 170 EAISIYKKFFDTLGIPYLISKRPEW 194

>d1nj1a3 d.104.1.1 (A:19-283) Prolyl-tRNA synthetase (ProRS) {Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262]} Length = 265

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: Prolyl-tRNA synthetase (ProRS)
species: Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262]

 Score = 39.5 bits (91), Expect = 9e-06
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 7   LSHKALPLLLYQFTSKFRDELRPKFGLMRSREF-LMKDLYAFTASEVDANDVYNLVGKCY 65
            SH  LP+  YQ  + FR E +    L+R RE    K+ +   A+  +A +      + Y
Sbjct: 113 RSHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKEAHTIHATASEAEEQVERAVEIY 172

Query: 66  DDVFNTLGIKYRKV 79
            + FN+LGI Y   
Sbjct: 173 KEFFNSLGIPYLIT 186

>d1atia2 d.104.1.1 (A:1-394) Glycyl-tRNA synthetase (GlyRS) {Thermus thermophilus [TaxId: 274]} Length = 394

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)
species: Thermus thermophilus [TaxId: 274]

 Score = 32.7 bits (74), Expect = 0.002
 Identities = 14/79 (17%), Positives = 27/79 (34%)

Query: 5   MKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKC 64
           +  + + L   + Q    FR+E+ P+  + R REF   ++  F     D       V + 
Sbjct: 201 LDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYWVEER 260

Query: 65  YDDVFNTLGIKYRKVIVRH 83
                     +   V  + 
Sbjct: 261 LKWWQEMGLSRENLVPYQQ 279

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	86
d1nyra4	291	Threonyl-tRNA synthetase (ThrRS) {Staphylococcus a	99.94
d1qf6a4	291	Threonyl-tRNA synthetase (ThrRS) {Escherichia coli	99.94
d1nj8a3	268	Prolyl-tRNA synthetase (ProRS) {Archaeon (Methanoc	99.93
d1nj1a3	265	Prolyl-tRNA synthetase (ProRS) {Arhaeon (Methanoth	99.91
d1seta2	311	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	99.84
d1b76a2	331	Glycyl-tRNA synthetase (GlyRS) {Thermus thermophil	99.81
d1hc7a2	272	Prolyl-tRNA synthetase (ProRS) {Thermus thermophil	99.74
d1g5ha2	290	The aaRS-like accessory subunit of mitochondrial p	99.67
d1atia2	394	Glycyl-tRNA synthetase (GlyRS) {Thermus thermophil	99.36
d1z7ma1	318	ATP phosphoribosyltransferase regulatory subunit H	98.64
d1qe0a2	325	Histidyl-tRNA synthetase (HisRS) {Staphylococcus a	98.55
d1wu7a2	327	Histidyl-tRNA synthetase (HisRS) {Archaeon Thermop	98.28
d1kmma2	322	Histidyl-tRNA synthetase (HisRS) {Escherichia coli	98.24
d1h4vb2	324	Histidyl-tRNA synthetase (HisRS) {Thermus thermoph	98.23
d1usya_	275	ATP phosphoribosyltransferase regulatory subunit H	98.05
d1e1oa2	342	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	97.42
d1c0aa3	346	Aspartyl-tRNA synthetase (AspRS) {Escherichia coli	97.39
d1l0wa3	356	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	97.24
d1nnha_	293	Hypothetical protein PF1951 {Archaeon Pyrococcus f	97.04
d1eova2	353	Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S	96.64
d1b8aa2	335	Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ	96.39
d1n9wa2	304	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	95.38
d1jjca_	266	Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS	91.61

>d1nyra4 d.104.1.1 (A:242-532) Threonyl-tRNA synthetase (ThrRS) {Staphylococcus aureus [TaxId: 1280]}

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: Threonyl-tRNA synthetase (ThrRS)
species: Staphylococcus aureus [TaxId: 1280]

Probab=99.94  E-value=9.5e-28  Score=170.03  Aligned_cols=85  Identities=19%  Similarity=0.267  Sum_probs=78.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      |++++++|||+||++++|+++|||+|++|+. ||+|+|||+|+|+|+||+++ ++.+++.++++.+.+++++||++++.+
T Consensus       101 ~~~~~~~sy~dLPlr~~~~~~~fR~E~~~~~~Gl~Rvr~F~~~d~~~f~~~e-q~~~e~~~~~~~~~~i~~~lGl~~~~v  179 (291)
T d1nyra4         101 IYANKPHSYRELPIRIAELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPD-QIKEEFKRVVNMIIDVYKDFGFEDYSF  179 (291)
T ss_dssp             HHHTSCCBGGGCCEEEEEEEEEECCCCTTTCBTTTBCSEEEEEEEEEEECGG-GHHHHHHHHHHHHHHHHHHTTCCCEEE
T ss_pred             hhhcEeccccccceEEeeccceeecCCCcccccccceeeeeeeeheeecCCc-ccHHHHHHHHHHHHHHhhhcCcCceEE
Confidence            4789999999999999999999999999986 99999999999999999865 555578999999999999999999999


Q ss_pred             EecCCCC
Q psy5542          80 IVRHGAV   86 (86)
Q Consensus        80 ~~~~g~~   86 (86)
                      ..++|++
T Consensus       180 ~~~~~d~  186 (291)
T d1nyra4         180 RLSYRDP  186 (291)
T ss_dssp             EEEECCC
T ss_pred             EEecCCC
Confidence            9998864

>d1qf6a4 d.104.1.1 (A:242-532) Threonyl-tRNA synthetase (ThrRS) {Escherichia coli [TaxId: 562]}

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: Threonyl-tRNA synthetase (ThrRS)
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=6e-28  Score=171.04  Aligned_cols=84  Identities=26%  Similarity=0.292  Sum_probs=77.3

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      ||+++++|||+||+++||+++|||+|++|+. ||+|+|||+|+|+|+||++++.++ ++.++++++.++|++||++++.+
T Consensus        99 ~~~~~~~sy~~LPl~~~q~~~~fR~E~~~~~~Gl~R~reF~~~d~h~f~~~e~~~~-e~~~~~~~~~~i~~~lGl~~~~v  177 (291)
T d1qf6a4          99 IFNQGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEEQIRD-EVNGCIRLVYDMYSTFGFEKIVV  177 (291)
T ss_dssp             HHTTSCEEGGGCSEEEEEEEEEECCCCGGGCBTTTBCSEEEEEEEEEEECGGGHHH-HHHHHHHHHHHHHGGGTCCCCEE
T ss_pred             HHHccccchhhcCeeEeecceeeecccccccccccccccceeccceeEecchhhHH-HHHHHHHHHHHHHHHcCCceEEE
Confidence            4789999999999999999999999999986 999999999999999999876655 56789999999999999999999


Q ss_pred             EecCCC
Q psy5542          80 IVRHGA   85 (86)
Q Consensus        80 ~~~~g~   85 (86)
                      .+++|.
T Consensus       178 ~~s~~~  183 (291)
T d1qf6a4         178 KLSTRP  183 (291)
T ss_dssp             EEECCC
T ss_pred             EEecCC
Confidence            999875

>d1nj8a3 d.104.1.1 (A:0-267) Prolyl-tRNA synthetase (ProRS) {Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190]}

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: Prolyl-tRNA synthetase (ProRS)
species: Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190]

Probab=99.93  E-value=2.1e-26  Score=160.75  Aligned_cols=86  Identities=26%  Similarity=0.339  Sum_probs=81.2

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceee-eeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFL-MKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~-~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +|+++++|||+||+++||+++|||+|+++..|++|+|||+ |+|+|+||.+++++++++.+++++|.++|++||++++.+
T Consensus       110 i~~~~~~Syr~LP~r~~e~~~~fR~E~~~~~GllR~reF~~~dd~~~~~~~~~~~~~~~~~~~~~y~~if~~l~l~~~~~  189 (268)
T d1nj8a3         110 MMKLWVKVHTDLPIKIYQIVNTFRYETKHTRPLIRLREIMTFKEAHTAHSTKEEAENQVKEAISIYKKFFDTLGIPYLIS  189 (268)
T ss_dssp             HHHTTCCBTTSCCCCEEEEECCBCCCCSCCBTTTBCSBCSCEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHTCCCEEE
T ss_pred             hhhhhccchhhhheEEeeccccccccccccccceeEEEEeeechhceeccccchhhHHHHHHHHHHHHHHHhcCcceeec
Confidence            4789999999999999999999999988888999999997 888999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy5542          80 IVRHGAV   86 (86)
Q Consensus        80 ~~~~g~~   86 (86)
                      .++++++
T Consensus       190 ~~~~~~~  196 (268)
T d1nj8a3         190 KRPEWDK  196 (268)
T ss_dssp             EECTTSC
T ss_pred             ccccccc
Confidence            9998874

>d1nj1a3 d.104.1.1 (A:19-283) Prolyl-tRNA synthetase (ProRS) {Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262]}

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: Prolyl-tRNA synthetase (ProRS)
species: Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262]

Probab=99.91  E-value=1.8e-25  Score=154.94  Aligned_cols=86  Identities=29%  Similarity=0.375  Sum_probs=80.9

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceee-eeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFL-MKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV   79 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~-~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~   79 (86)
                      +++++++|||+||+++||+++|||+|.+++.||+|+|||+ |+|.|+|+.+++++++++..+++.|.++++++|+|++++
T Consensus       107 ~~~~~~~SyrdLPlr~~q~~~~fR~E~~~~~Gl~R~reF~~~~d~~~~~~~~~~~~~e~~~~~~~~~~~~~~l~l~~~~~  186 (265)
T d1nj1a3         107 MFALWVRSHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKEAHTIHATASEAEEQVERAVEIYKEFFNSLGIPYLIT  186 (265)
T ss_dssp             HHHHHCCBTTTCCEEEEEEEEEECCCCSCCBTTTBCSEEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHTCCCEEE
T ss_pred             eeeeeeccccccceEEEeeccceeeecccCcCCEEEEEEEEeccceeecCCHHHHHHHhhhhHHHHHHHHhhcCCceeEE
Confidence            4788999999999999999999999998889999999995 789999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q psy5542          80 IVRHGAV   86 (86)
Q Consensus        80 ~~~~g~~   86 (86)
                      .++++++
T Consensus       187 ~~~~~~~  193 (265)
T d1nj1a3         187 RRPPWDK  193 (265)
T ss_dssp             ECCTTTS
T ss_pred             EccCccc
Confidence            9998864

>d1seta2 d.104.1.1 (A:111-421) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

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: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=99.84  E-value=1.7e-21  Score=139.04  Aligned_cols=86  Identities=24%  Similarity=0.376  Sum_probs=79.1

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCC----CCceeeceeeeeeeeEEcCC-hHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFTAS-EVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~----~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      |++++++++++||++++++++|||.|+++.    .||+|+|||++.|+|++|.+ ++++.+.++++++..+.+++.||||
T Consensus       123 ~~~~~i~~~~~LPlr~~~~s~cfR~Eag~~g~~trGL~RvhQF~kvE~~~~~~~~~e~s~~~~~~~~~~~~~~~~~L~lp  202 (311)
T d1seta2         123 LHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELP  202 (311)
T ss_dssp             TTTTCEEEGGGCSEEEEEEEEEECCCCSCTTSSCSTTSSCSEEEEEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             hhhhhhhhhhhccceEEeecccchhhhccccccchhhhhhcccchhhhheeeccccccchhHHHHHHHHHHHHHHhhCCc
Confidence            689999999999999999999999998653    49999999999999999974 4667778899999999999999999


Q ss_pred             EEEEEecCCCC
Q psy5542          76 YRKVIVRHGAV   86 (86)
Q Consensus        76 ~~~~~~~~g~~   86 (86)
                      |+++..++||+
T Consensus       203 yrvv~~~~~dl  213 (311)
T d1seta2         203 YRLVEVATGDM  213 (311)
T ss_dssp             EEEEECCTTTS
T ss_pred             chhccccCCCC
Confidence            99999999986

>d1b76a2 d.104.1.1 (A:1-394) Glycyl-tRNA synthetase (GlyRS) {Thermus thermophilus [TaxId: 274]}

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)
species: Thermus thermophilus [TaxId: 274]

Probab=99.81  E-value=3.9e-21  Score=137.44  Aligned_cols=75  Identities=17%  Similarity=0.216  Sum_probs=63.1

Q ss_pred             ccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC-cEEE
Q psy5542           3 ADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI-KYRK   78 (86)
Q Consensus         3 ~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi-~~~~   78 (86)
                      +....|||+||++++|+++|||+|++|+.||+|+|||+|+|+|+||++++..+ ++..+++.+...+.++|+ ++..
T Consensus       136 ~~~~~syk~LP~~~aqig~~fR~E~s~~~gl~RvReFtq~D~~~F~~~~q~~~-~~~~~~~~~~~~~~~~g~~~~~l  211 (331)
T d1b76a2         136 NVLDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEY-WHRYWVEERLKWWQEMGLSRENL  211 (331)
T ss_dssp             HHHHHHTCCSSEEEEEEEEEECCCSSCCTTTTSCSEEEEEEEEEEECGGGHHH-HHHHHHHHHHHHHHHTTCCGGGE
T ss_pred             hHHhccccccchhhhhccceecccccccccccccchhhhhhhhhhcCCcchhH-HHHHHHHHHHHHHHHhhccchhe
Confidence            45678999999999999999999999999999999999999999999765544 667777777777777776 4443

>d1hc7a2 d.104.1.1 (A:5-276) Prolyl-tRNA synthetase (ProRS) {Thermus thermophilus [TaxId: 274]}

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: Prolyl-tRNA synthetase (ProRS)
species: Thermus thermophilus [TaxId: 274]

Probab=99.74  E-value=7.9e-19  Score=120.24  Aligned_cols=80  Identities=21%  Similarity=0.209  Sum_probs=70.9

Q ss_pred             CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542           1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI   80 (86)
Q Consensus         1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~   80 (86)
                      |++++++||++||++++|+++|||+|++|+ |+.|.|+|.|.|+|+|+.++++++.++..+.+.+..++..+++....+.
T Consensus       115 ~~~~~~~s~~~LPlr~~~~~~~fR~E~~~~-g~~r~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (272)
T d1hc7a2         115 MWSKWIRSWRDLPQLLNQWGNVVRWEMRTR-PFLRTSEFLWQEGHTAHATREEAEEEVRRMLSIYARLAREYAAIPVIEG  193 (272)
T ss_dssp             HHHHHCCBGGGCCEEEEEEEEEECCCSSCB-TTTBCSEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_pred             hhhceeccccccceeeeecccccccccccc-cccceEEEEEEhhhhhhcccccchhHHHHHHHHHHHHHHHhcchhhhcC
Confidence            468899999999999999999999999886 6789999999999999999999999999999999999998766444443


Q ss_pred             e
Q psy5542          81 V   81 (86)
Q Consensus        81 ~   81 (86)
                      .
T Consensus       194 ~  194 (272)
T d1hc7a2         194 L  194 (272)
T ss_dssp             E
T ss_pred             c
Confidence            3

>d1g5ha2 d.104.1.1 (A:41-330) The aaRS-like accessory subunit of mitochondrial polymerase gamma, N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

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: The aaRS-like accessory subunit of mitochondrial polymerase gamma, N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.3e-17  Score=117.49  Aligned_cols=75  Identities=15%  Similarity=0.080  Sum_probs=60.8

Q ss_pred             cCCcCCcchhhheeeceeecCCCC---CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEe
Q psy5542           6 KLSHKALPLLLYQFTSKFRDELRP---KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIV   81 (86)
Q Consensus         6 i~Syr~LP~~l~q~~~~fR~E~~~---~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~   81 (86)
                      ..|+++||++++|+|+|||+|+++   ..||+|+|||+|.|+|.||.+ ++.+++++.+++....++++|||+...+..
T Consensus       132 ~~~~~~LPf~iaq~g~~fR~E~~~~~~~~gl~RvReF~q~E~~~F~~p-e~~~~~~~~~~~~~~~~~~~lGi~~~~~~~  209 (290)
T d1g5ha2         132 DLVNRKLPFGLAQIGVCFHPVSNSNQTPSSVTRVGEKTEASLVWFTPT-RTSSQWLDFWLRHRLLWWRKFAMSPSNFSS  209 (290)
T ss_dssp             HHTTTBSCEEEEEEEEEEEEEC---------CEEEEEEEEEEEEEECH-HHHHHHHHHHHHHHHHHHHTTCSSGGGEEE
T ss_pred             hhccCCCCcEEEEeccccccccccCCcccccceeeEeEeeeeEEEeCC-cchHHHHHHHHHHHHHHHHHcCCChhheee
Confidence            479999999999999999977544   459999999999999999996 566779999999999999999997554443

>d1atia2 d.104.1.1 (A:1-394) Glycyl-tRNA synthetase (GlyRS) {Thermus thermophilus [TaxId: 274]}

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)
species: Thermus thermophilus [TaxId: 274]

Probab=99.36  E-value=4.6e-13  Score=97.54  Aligned_cols=66  Identities=18%  Similarity=0.225  Sum_probs=59.7

Q ss_pred             cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      -..||+.++|||.+||||.+|+.|++|+|||+|.|+-.|+.+.+ ..+++...++.....+.++||+
T Consensus       205 r~KlPFGiAQIGk~FRNEIsPr~~l~R~REF~q~EiE~Fv~P~~-~~~~~~yw~~~~~~f~~~lGi~  270 (394)
T d1atia2         205 SRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGE-DEYWHRYWVEERLKWWQEMGLS  270 (394)
T ss_dssp             TCCSSEEEEEEEEEEBCCSSCCTGGGSCSEEEEEEEEEEECGGG-HHHHHHHHHHHHHHHHHHTTCC
T ss_pred             ccCCCceeeeeccccccccCcccCCcccccceeeeeEEEEeCCc-chHHHHHHHHHHHHHHHHhcCC
Confidence            46899999999999999999999999999999999999999754 4668888888888889999995

>d1z7ma1 d.104.1.1 (A:6-323) ATP phosphoribosyltransferase regulatory subunit HisZ {Lactococcus lactis [TaxId: 1358]}

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: ATP phosphoribosyltransferase regulatory subunit HisZ
species: Lactococcus lactis [TaxId: 1358]

Probab=98.64  E-value=3.1e-08  Score=68.25  Aligned_cols=65  Identities=20%  Similarity=0.133  Sum_probs=50.0

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEE
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRK   78 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~   78 (86)
                      ...+.|.|++++++|||+|. +..|  |.|||+|.++.+|..+...++   .+++.+..++++.||++-..
T Consensus        91 ~~~~~~~r~~Y~g~vfR~~~-~~~~--r~rE~~Q~g~EiiG~~~~~ad---~Eii~l~~e~l~~lgi~~~~  155 (318)
T d1z7ma1          91 IKDSTSARYSYFGKIFRKEK-RHKG--RSTENYQIGIELFGESADKSE---LEILSLALQVIEQLGLNKTV  155 (318)
T ss_dssp             CCSCCCEEEEEEEECCCCCC----------CCEEEEEEEESSCHHHHH---HHHHHHHHHHHHHHTCSSEE
T ss_pred             hcccCCcccccccceeEEcc-cccc--ccchhhhhheeccccchhhHH---HHHHHHHHHHHHHhhhcccc
Confidence            45688999999999999994 4445  999999999999998766665   78999999999999997333

>d1qe0a2 d.104.1.1 (A:1-325) Histidyl-tRNA synthetase (HisRS) {Staphylococcus aureus [TaxId: 1280]}

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: Histidyl-tRNA synthetase (HisRS)
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.55  E-value=7e-08  Score=66.59  Aligned_cols=68  Identities=26%  Similarity=0.349  Sum_probs=52.2

Q ss_pred             CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEE
Q psy5542           7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVI   80 (86)
Q Consensus         7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~   80 (86)
                      .+....|+|+|.+++|||.+ ++..|  |.|||+|.++-.+..+...++   .+++.+..++++.+|+. +....
T Consensus        95 ~~~~~~p~R~~Y~g~VfR~~-~~~~~--~~rE~~Q~G~EiiG~~~~~ad---~Eii~l~~~~l~~~g~~~~~i~i  163 (325)
T d1qe0a2          95 QGNPNQPIKLYYNGPMFRYE-RKQKG--RYRQFNQFGVEAIGAENPSVD---AEVLAMVMHIYQSFGLKHLKLVI  163 (325)
T ss_dssp             GGCSSCSEEEEEEEEEECC----------CCEEEEEEEEEESCCCHHHH---HHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             ccccccchhhheecceeeec-cccCC--ccceeeecceeecCCcCcHHH---HHHHHHHHHHHHhhCCcCcceee
Confidence            34567999999999999999 44455  999999999999999877777   77899999999999995 44433

>d1wu7a2 d.104.1.1 (A:3-329) Histidyl-tRNA synthetase (HisRS) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

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: Histidyl-tRNA synthetase (HisRS)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=98.28  E-value=9.9e-07  Score=60.85  Aligned_cols=60  Identities=27%  Similarity=0.404  Sum_probs=52.4

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ...|+|+|.+++|||++ ++..|  |.|||+|.++-.+..+...++   .+++.+..++++.+|++
T Consensus        94 ~~~p~k~~y~g~VfR~~-~~~~g--~~re~~Q~G~EiiG~~~~~~D---~Eii~l~~~~l~~~~~~  153 (327)
T d1wu7a2          94 LQRPLRWYSFPKVWRYE-EPQAG--RYREHYQFNADIFGSDSPEAD---AEVIALASSILDRLGLQ  153 (327)
T ss_dssp             CCSSEEEEECCEEECCC-CSCSS--CCSEEEEEEEEEESCCSHHHH---HHHHHHHHHHHHHTTTT
T ss_pred             ccccceeeccCcceecc-ccccC--CcchhhhhhhhhcCCcchHHH---HHHHHHHHHHHhccccc
Confidence            46799999999999999 55556  999999999999998877777   67889999999999983

>d1kmma2 d.104.1.1 (A:4-325) Histidyl-tRNA synthetase (HisRS) {Escherichia coli [TaxId: 562]}

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: Histidyl-tRNA synthetase (HisRS)
species: Escherichia coli [TaxId: 562]

Probab=98.24  E-value=1.2e-06  Score=60.07  Aligned_cols=62  Identities=24%  Similarity=0.253  Sum_probs=53.3

Q ss_pred             CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542           8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus         8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      .....|+++|+++++||.| ++..|  |.|||+|.++..+..+...++   .+++.+...+++.+|+.
T Consensus        94 ~~~~~p~r~~y~g~v~r~~-~~~~g--r~re~~Q~g~EiiG~~~~~ad---~Eii~l~~~~l~~lgl~  155 (322)
T d1kmma2          94 LLYNQEQRLWYIGPMFRHE-RPQKG--RYRQFHQLGCEVFGLQGPDID---AELIMLTARWWRALGIS  155 (322)
T ss_dssp             CSTTCCEEEEEEEEEECCC-CCBTT--BCSEEEEEEEEEESCCSHHHH---HHHHHHHHHHHHHHTCG
T ss_pred             hhhhhhhhHhhcccccccC-CCCCC--ccchhhhhhHHHhccccchhH---HHHHHHHHHHHHhcCCC
Confidence            3457899999999999999 45556  999999999999998777776   67888888999999985

>d1h4vb2 d.104.1.1 (B:2-325) Histidyl-tRNA synthetase (HisRS) {Thermus thermophilus [TaxId: 274]}

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: Histidyl-tRNA synthetase (HisRS)
species: Thermus thermophilus [TaxId: 274]

Probab=98.23  E-value=1.2e-06  Score=60.35  Aligned_cols=60  Identities=22%  Similarity=0.288  Sum_probs=49.4

Q ss_pred             CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542          10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK   75 (86)
Q Consensus        10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~   75 (86)
                      ...|+|++.++++||.+. +..|  |.|||+|.++-.+..+...++   .+++.+..++++.+|+.
T Consensus        97 ~~~p~r~~Y~g~VfR~~~-~~~g--r~re~~Q~g~EiiG~~~~~ad---~Eii~l~~~~l~~l~~~  156 (324)
T d1h4vb2          97 WPQPVRLWMAGPMFRAER-PQKG--RYRQFHQVNYEALGSENPILD---AEAVVLLYECLKELGLR  156 (324)
T ss_dssp             SSSSEEEEEEEEEECCCC-C------CCEEEEEEEEEESCCCHHHH---HHHHHHHHHHHHHTTCC
T ss_pred             hchhhhheeeCcccccCc-ccCC--CcceeccccccccCCCChHHH---HHHHHHHHHHHHHhccc
Confidence            357999999999999994 4456  999999999999998777777   67889999999999986

>d1usya_ d.104.1.1 (A:) ATP phosphoribosyltransferase regulatory subunit HisZ {Thermotoga maritima [TaxId: 2336]}

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: ATP phosphoribosyltransferase regulatory subunit HisZ
species: Thermotoga maritima [TaxId: 2336]

Probab=98.05  E-value=6.9e-06  Score=55.72  Aligned_cols=64  Identities=8%  Similarity=-0.144  Sum_probs=52.5

Q ss_pred             cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEe
Q psy5542           9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIV   81 (86)
Q Consensus         9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~   81 (86)
                      ..+.|+|+|.+++|||.+. +     +.|||.|..+-.+..+...++   .+++.+..++++.+|++ +.....
T Consensus        66 ~~~~p~k~~Y~g~VfR~~~-~-----~~re~~Q~G~EiiG~~~~~aD---~Evi~l~~~~l~~lgi~~~~i~l~  130 (275)
T d1usya_          66 SPDSQIKVWYADFVYRYSG-S-----DLVAEYQLGLEKVPRNSLDDS---LEVLEIIVESASEFFEGPVIVEIG  130 (275)
T ss_dssp             TTCCCEEEECCEEEEEEET-T-----EEEEEEEEEEEEESCCSHHHH---HHHHHHHHHHHHHHCCSCEEEEEE
T ss_pred             CCCCCeeeeEEeeEEEeCC-C-----cccceeecCceeechhhHHHH---HHHHHHHHHHHHhhcccccEEEec
Confidence            4567999999999999983 3     579999999999988766666   77899999999999996 444433

>d1e1oa2 d.104.1.1 (A:161-502) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]}

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: Lysyl-tRNA synthetase (LysRS)
species: Escherichia coli, gene lysU [TaxId: 562]

Probab=97.42  E-value=0.00013  Score=50.62  Aligned_cols=44  Identities=23%  Similarity=0.298  Sum_probs=33.4

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||+++|||+|..++.   ++-||+|.|++.-..+.++..+..+.+
T Consensus        93 ~vf~i~p~FR~E~~~~r---Hl~EFtmlE~e~a~~~~~d~m~~~e~l  136 (342)
T d1e1oa2          93 RVFEINRNFRNEGISVR---HNPEFTMMELYMAYADYHDLIELTESL  136 (342)
T ss_dssp             EEEEEEEEECCCCCCC----CCSEEEEEEEEEESCCHHHHHHHHHHH
T ss_pred             ceeeecccccccccccc---chHHHHHHHHHHHhhhhhhHHHhhhHH
Confidence            68999999999976654   889999999999877765554333333

>d1c0aa3 d.104.1.1 (A:107-287,A:421-585) Aspartyl-tRNA synthetase (AspRS) {Escherichia coli [TaxId: 562]}

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: Aspartyl-tRNA synthetase (AspRS)
species: Escherichia coli [TaxId: 562]

Probab=97.39  E-value=0.0002  Score=49.85  Aligned_cols=44  Identities=25%  Similarity=0.243  Sum_probs=34.2

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||++++||+|..++.   +.-||+|.|++.-..+.++..+..+.+
T Consensus       102 ~Vf~i~~~FR~E~~~~~---H~~EFtmLE~e~a~~~~~~~m~~~E~l  145 (346)
T d1c0aa3         102 RYYQIVKCFRDEDLRAD---RQPEFTQIDVETSFMTAPQVREVMEAL  145 (346)
T ss_dssp             EEEEEEEEECCCCCBTT---BCSEEEEEEEEEESCCHHHHHHHHHHH
T ss_pred             ceEEEeeeccccccCch---hhhHhhhhccccccccHhHhHHHHHHH
Confidence            68999999999987766   779999999998777665555443433

>d1l0wa3 d.104.1.1 (A:105-294,A:415-580) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]}

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: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-1 [TaxId: 274]

Probab=97.24  E-value=0.00032  Score=49.02  Aligned_cols=50  Identities=24%  Similarity=0.224  Sum_probs=37.5

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN   70 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~   70 (86)
                      ++||++++||+|.+++.   +.-||+|.|++....+-+++.+.   +-+++..+++
T Consensus       110 ~Vf~i~~~FRaE~~~t~---H~~EFtmLE~e~~~~~~~~~m~~---~E~li~~v~~  159 (356)
T d1l0wa3         110 RYFQIARCFRDEDLRAD---RQPDFTQLDLEMSFVEVEDVLEL---NERLMAHVFR  159 (356)
T ss_dssp             EEEEEEEEECCCCCCSS---CCSEEEEEEEEEESCCHHHHHHH---HHHHHHHHHH
T ss_pred             cEEEEeccccccccCCc---chhhhhHHHHhhhHHHHHHHHHH---HHHHHHHHHH
Confidence            67999999999988876   67899999999998876665433   3333444444

>d1nnha_ d.104.1.1 (A:) Hypothetical protein PF1951 {Archaeon Pyrococcus furiosus [TaxId: 2261]}

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: Hypothetical protein PF1951
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.04  E-value=0.00065  Score=46.44  Aligned_cols=47  Identities=19%  Similarity=0.123  Sum_probs=31.7

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~   61 (86)
                      ++||++++||+|.....+---+-||+|.|++.-..+-++..+..+.+
T Consensus        89 ~Vf~I~~~FR~E~~~s~t~RH~~EFtmLE~e~~~~d~~d~m~~~e~l  135 (293)
T d1nnha_          89 KIFVLSPNIRLESRQKDDGRHAYEFTQLDFEVERAKMEDIMRLIERL  135 (293)
T ss_dssp             EEEEEEEEECCCCGGGCSSSCCSEEEEEEEEEETCCHHHHHHHHHHH
T ss_pred             cceeechhhhcCcccCCCCccchhhhhhccccccccHHHHHHHHHHH
Confidence            68999999999953222212456999999998766665554444443

>d1eova2 d.104.1.1 (A:205-557) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

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: Aspartyl-tRNA synthetase (AspRS)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.64  E-value=0.0017  Score=44.89  Aligned_cols=45  Identities=18%  Similarity=0.144  Sum_probs=30.1

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCC-hHhHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTAS-EVDANDVYNLV   61 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~~~   61 (86)
                      ++||+++|||+|...+.  --.-||+|.|+|.-..+ -+.+.+..+.+
T Consensus       112 ~vf~I~~~FR~E~~~~~--rH~pEFtmLE~y~a~~d~~~~i~~~~e~l  157 (353)
T d1eova2         112 RVYEIGPVFRAENSNTH--RHMTEFTGLDMEMAFEEHYHEVLDTLSEL  157 (353)
T ss_dssp             EEEEEEEEECCCCCCCT--TCCSEEEEEEEEEECSSCTHHHHHHHHHH
T ss_pred             cceeechhhhccccccc--cccchhcccccccccchhhHHHHHHHHHH
Confidence            68999999999964432  02469999999976544 34444343433

>d1b8aa2 d.104.1.1 (A:104-438) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]}

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: Aspartyl-tRNA synthetase (AspRS)
species: Archaeon Pyrococcus kodakaraensis [TaxId: 311400]

Probab=96.39  E-value=0.0036  Score=42.75  Aligned_cols=46  Identities=20%  Similarity=0.182  Sum_probs=29.6

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeee-eEEcCChHhHHHHHHHHH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDL-YAFTASEVDANDVYNLVG   62 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~-~~f~~~~~~~~~~~~~~~   62 (86)
                      ++||+++|||+|..+..  --.-||+|.+. +.+..+..++.+..+.++
T Consensus       102 ~if~i~~~FR~e~~~~~--rh~~Ef~~le~~~~~~~~~~~l~~~~e~~~  148 (335)
T d1b8aa2         102 RVYEIAPIFRAEEHNTT--RHLNEAWSIDSEMAFIEDEEEVMSFLERLV  148 (335)
T ss_dssp             EEEEEEEEECCCSSCCS--SCCSEEEEEEEEEESCSSHHHHHHHHHHHH
T ss_pred             hHHHhhccccccccccc--ccchHHHhhhHHHHHHHhhhhHHHHHHHHH
Confidence            68999999999965432  02349999954 445466655554444443

>d1n9wa2 d.104.1.1 (A:111-414) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]}

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: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-2 [TaxId: 274]

Probab=95.38  E-value=0.0079  Score=40.50  Aligned_cols=38  Identities=24%  Similarity=0.191  Sum_probs=18.9

Q ss_pred             hhheeeceeecCCCCCCCceeeceeeeeeeeEEc-CChHhH
Q psy5542          15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFT-ASEVDA   54 (86)
Q Consensus        15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~-~~~~~~   54 (86)
                      ++||+++|||+|..+..  -..-||+|.|.+.-. .+.+..
T Consensus        82 ~if~i~~~FR~ee~~~~--rh~~EF~~le~~~~~~~~~~~~  120 (304)
T d1n9wa2          82 RVYEVAPVWRMEEHHTS--RHLNEYLSLDVEMGFIADEEDL  120 (304)
T ss_dssp             EEEEEEEC---------------CCEEEEEEEESCSSHHHH
T ss_pred             cceeehhhccccccccc--ccccHHHHHHHHHhhhhhHHHH
Confidence            58999999999854322  146799999998743 443333

>d1jjca_ d.104.1.1 (A:) Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS {Thermus thermophilus [TaxId: 274]}

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: Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS
species: Thermus thermophilus [TaxId: 274]

Probab=91.61  E-value=0.13  Score=34.54  Aligned_cols=54  Identities=11%  Similarity=-0.002  Sum_probs=37.9

Q ss_pred             CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc
Q psy5542          11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL   72 (86)
Q Consensus        11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l   72 (86)
                      .-|+++...+.|||+|.--+.   .+.+|.|.|+.....+-.-     ..+......+++.+
T Consensus       107 ~~p~~~~~~g~VyRrd~iD~t---H~p~FhQ~eg~~vd~~~~~-----~~Lk~~l~~~~~~~  160 (266)
T d1jjca_         107 TPPFRIVVPGRVFRFEQTDAT---HEAVFHQLEGLVVGEGIAM-----AHLKGAIYELAQAL  160 (266)
T ss_dssp             CSSEEEEEEEEEECCSCCCSS---CCSEEEEEEEEEEETTCCH-----HHHHHHHHHHHHHH
T ss_pred             CCCceEEecccceecCCCCCc---ccccceeeeeeeccccccH-----HHHHHHHHHHHHHh
Confidence            358999999999999865544   6889999999998764322     23444445555553