Psyllid ID: psy2399

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230--
Protein Sequence
MKKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEIFF
Secondary Structure (PSIPRED)
ccccccccccccEEEEEEccccccccccccHHccHHcHHHHHHHHcccccccccccEEEEEccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHcccEEEEEEEEEEEcccccccccccEEEccccccccccccccccHHccccccccccccccccccccccEEEEccEEEEEcccHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEEcccEcccccEHHHHHHHHHHHHHHHHHHHcHHcccccEEEEEEEEEcccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEEEEEEEccccEEccHHHEEEEccccccccEEccEccccccEccHHHcEEEEEcccccccEEEEEEEEEEcHccHHHHHHHHHHHHccccccccEcc
Coil and Loop (DISEMBL)
mkkhdsefkDVRRIFVTtalpyangelhIGHIMEYIQADIWVRFQCmqqdngksrqvyFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFyikfdnwystdsienIDLVQKIYDTLYNKAKLIINKKINqffdpikniflpdryikgecpicnakdqygdfceccssiytptklinpysilsgtkpiikssKHFFFKLSDKRCIDFLRKWAihdkrlqpeiff
Flexible Loop (DISEMBL)
mkkhdsefkdvrriFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWaihdkrlqpeiff
Low Complexity Region (SEG)
MKKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYnkakliinkkinQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEIFF
Disordered region (IsUnstruct)
*********DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRL******
Disordered Region (DISOPRED)
**************FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEIFF
Disordered Region (DISEMBL)
********KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEIFF
Disordered Region (DISPRO)
********KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEIFF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEIFF
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	232	2.2.26 [Sep-21-2011]
A6SX05	700	Methionine--tRNA ligase O	yes	N/A	0.922	0.305	0.634	1e-85
A1VKF9	707	Methionine--tRNA ligase O	yes	N/A	0.918	0.301	0.651	2e-84
A1TTU1	706	Methionine--tRNA ligase O	yes	N/A	0.913	0.300	0.639	1e-83
A4G3S6	710	Methionine--tRNA ligase O	yes	N/A	0.870	0.284	0.668	5e-83
Q12F12	689	Methionine--tRNA ligase O	yes	N/A	0.913	0.307	0.643	2e-81
A1WBH1	688	Methionine--tRNA ligase O	yes	N/A	0.922	0.311	0.636	6e-81
B9MEX0	688	Methionine--tRNA ligase O	yes	N/A	0.922	0.311	0.636	6e-81
A2SEY3	697	Methionine--tRNA ligase O	yes	N/A	0.922	0.307	0.597	8e-80
Q21TB9	700	Methionine--tRNA ligase O	yes	N/A	0.922	0.305	0.6	9e-80
B1XWM2	689	Methionine--tRNA ligase O	yes	N/A	0.922	0.310	0.609	1e-79

>sp|A6SX05|SYM_JANMA Methionine--tRNA ligase OS=Janthinobacterium sp. (strain Marseille) GN=metG PE=3 SV=1

 Score =  315 bits (808), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 139/219 (63%), Positives = 175/219 (79%), Gaps = 5/219 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  H+GHIMEYIQADIWVRFQ MQ +     +V+F+ ADDAHGA IM
Sbjct: 7   RKLFVTTALPYANGAFHVGHIMEYIQADIWVRFQRMQGN-----EVHFVGADDAHGAPIM 61

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG+TP++F+ NI++ RK+YLDGF+I+FDNW STDS EN +L ++IY  L + AKL
Sbjct: 62  IAAEKAGLTPQQFVANIAAGRKQYLDGFHIEFDNWSSTDSPENHELSREIYRRLRDDAKL 121

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K + QF+DP+K +FLPDRYIKGECP C  KDQYGD CE CS++Y PT L +PYS L+
Sbjct: 122 ITTKSVEQFYDPVKEMFLPDRYIKGECPKCGTKDQYGDSCENCSAVYAPTDLKHPYSTLT 181

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P+ KSS HFFF+LSD +C+ FLR+WA+  +RLQ E+
Sbjct: 182 GATPVRKSSDHFFFRLSDPKCVAFLREWALDGQRLQSEV 220

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.
Janthinobacterium sp. (strain Marseille) (taxid: 375286)
EC: 6EC: .EC: 1EC: .EC: 1EC: .EC: 1EC: 0

>sp|A1VKF9|SYM_POLNA Methionine--tRNA ligase OS=Polaromonas naphthalenivorans (strain CJ2) GN=metG PE=3 SV=1

 Score =  311 bits (797), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 144/221 (65%), Positives = 171/221 (77%), Gaps = 8/221 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           RR+FVTTALPYANG  HIGHIMEYIQADIWVR+Q MQ +      V F+ ADDAHGA IM
Sbjct: 4   RRLFVTTALPYANGNFHIGHIMEYIQADIWVRYQRMQGN-----AVNFVGADDAHGAPIM 58

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYN--KA 129
           IAAEKAG TP++F+ +I+S RK YLDGF+I FDNW STDS EN +L ++IY  L +  + 
Sbjct: 59  IAAEKAGKTPQQFVADIASGRKPYLDGFHISFDNWSSTDSPENHELARQIYRDLRDNPQG 118

Query: 130 KLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSI 189
            LI  K I QFFDP KN+FLPDR+IKGECP C+AKDQYGD CE C ++Y PT LINPYS 
Sbjct: 119 SLIETKTIEQFFDPEKNMFLPDRFIKGECPKCHAKDQYGDNCEVCGAVYAPTDLINPYSA 178

Query: 190 LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           LSG  P++KSS+HFFFKLSD RC++FL  W   D +LQPE+
Sbjct: 179 LSGVTPVLKSSEHFFFKLSDARCVEFLESWT-QDGKLQPEV 218

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Polaromonas naphthalenivorans (strain CJ2) (taxid: 365044)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|A1TTU1|SYM_ACIAC Methionine--tRNA ligase OS=Acidovorax citrulli (strain AAC00-1) GN=metG PE=3 SV=1

 Score =  309 bits (791), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 140/219 (63%), Positives = 171/219 (78%), Gaps = 7/219 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R+IFVTTALPYANG  HIGHIMEYIQADIWVRFQ MQ       +V F+ ADD HGA IM
Sbjct: 4   RKIFVTTALPYANGNFHIGHIMEYIQADIWVRFQRMQ-----GAEVNFVGADDTHGAPIM 58

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG TP++F+ +I++ RK YL+GF+I+FDNW+STD+ EN +L ++IY  L   A L
Sbjct: 59  IAAEKAGKTPQQFVADIAAGRKPYLEGFHIRFDNWHSTDAPENHELARQIYRDL-QAAGL 117

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  + I QFFDP KN+FLPDR+IKGECP C+A+DQYGD CE C ++Y PT LI PYS LS
Sbjct: 118 IETRTIEQFFDPEKNMFLPDRFIKGECPRCHARDQYGDNCENCGAVYAPTDLIEPYSALS 177

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G KP++KSS HFFF+LSD RC+ FL++W   D RLQPE+
Sbjct: 178 GAKPVLKSSDHFFFQLSDPRCVAFLQEWT-QDGRLQPEV 215

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Acidovorax citrulli (strain AAC00-1) (taxid: 397945)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|A4G3S6|SYM_HERAR Methionine--tRNA ligase OS=Herminiimonas arsenicoxydans GN=metG PE=3 SV=1

 Score =  307 bits (786), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 139/208 (66%), Positives = 167/208 (80%), Gaps = 6/208 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVRFQ MQ +     QV F+ ADDAHGA IM
Sbjct: 7   RKLFVTTALPYANGAFHIGHIMEYIQADIWVRFQRMQGN-----QVDFVGADDAHGAPIM 61

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG+TP++F++NI++ RK+YLDGF+I FDNW STDS EN  L Q+IY  L  KA L
Sbjct: 62  IAAEKAGLTPQQFVSNIAAGRKQYLDGFHIAFDNWSSTDSPENHQLAQQIYLDL-KKAGL 120

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I +K + QFFDP KN+FLPDRYIKGECP C+ KDQYGD CE C+++Y+PT LINPYS L+
Sbjct: 121 IASKTVEQFFDPEKNMFLPDRYIKGECPKCHTKDQYGDNCEVCAAVYSPTDLINPYSALT 180

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKW 219
           G  P++K S+HFFF LSD RC+ FL +W
Sbjct: 181 GATPVLKHSEHFFFTLSDPRCVAFLEEW 208

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Herminiimonas arsenicoxydans (taxid: 204773)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q12F12|SYM_POLSJ Methionine--tRNA ligase OS=Polaromonas sp. (strain JS666 / ATCC BAA-500) GN=metG PE=3 SV=1

 Score =  301 bits (772), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 141/219 (64%), Positives = 167/219 (76%), Gaps = 7/219 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           RR+FVTTALPYANG  HIGHIMEYIQADIWVR+Q MQ       +V F+ ADDAHGA IM
Sbjct: 4   RRLFVTTALPYANGNFHIGHIMEYIQADIWVRYQRMQ-----GHEVNFVGADDAHGAPIM 58

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG TP++F+ +I++ RK YLDGF+I FDNW+STD  EN  L Q+IY  L  KA L
Sbjct: 59  IAAEKAGKTPQQFVADIAAGRKPYLDGFHISFDNWHSTDGPENHQLAQQIYLDL-KKAGL 117

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K + QFFDP KN+FLPDR+IKG+CP C AKDQYGD CE C ++Y PT LINPYS LS
Sbjct: 118 IETKTVEQFFDPDKNMFLPDRFIKGQCPKCGAKDQYGDNCEVCGAVYAPTDLINPYSALS 177

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P++KSS+HFFF+LSD RC+ FL +W   D  LQ E+
Sbjct: 178 GATPVLKSSEHFFFRLSDPRCVAFLEQWT-QDGMLQTEV 215

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Polaromonas sp. (strain JS666 / ATCC BAA-500) (taxid: 296591)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|A1WBH1|SYM_ACISJ Methionine--tRNA ligase OS=Acidovorax sp. (strain JS42) GN=metG PE=3 SV=1

 Score =  300 bits (768), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 140/220 (63%), Positives = 169/220 (76%), Gaps = 6/220 (2%)

Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            R+IFVTTALPYANG  HIGHIMEYIQAD WVR Q MQ        V F+ ADDAHGA I
Sbjct: 3   ARKIFVTTALPYANGNFHIGHIMEYIQADTWVRAQRMQ-----GNAVNFVGADDAHGAPI 57

Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAK 130
           MIAAEKAG TP++F+ +I++ RK+YLDGF+I FDNW +TDS EN +L Q+IY  L   A 
Sbjct: 58  MIAAEKAGKTPQQFVADIAAGRKQYLDGFHIAFDNWSNTDSPENHELSQQIYLDL-KAAG 116

Query: 131 LIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
            I  + I QFFDP KN+FLPDR+IKGECP C+AKDQYGD CE CSS+Y PT LINPYS L
Sbjct: 117 FIETRTIEQFFDPEKNMFLPDRFIKGECPRCHAKDQYGDNCEVCSSVYAPTDLINPYSAL 176

Query: 191 SGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           SG KP++K+S+HFFFKLSD R ++FL +W  + + +QPE+
Sbjct: 177 SGAKPVLKTSEHFFFKLSDPRAVEFLTEWTQNGQHVQPEV 216

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Acidovorax sp. (strain JS42) (taxid: 232721)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|B9MEX0|SYM_ACIET Methionine--tRNA ligase OS=Acidovorax ebreus (strain TPSY) GN=metG PE=3 SV=1

 Score =  300 bits (768), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 140/220 (63%), Positives = 169/220 (76%), Gaps = 6/220 (2%)

Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            R+IFVTTALPYANG  HIGHIMEYIQAD WVR Q MQ        V F+ ADDAHGA I
Sbjct: 3   ARKIFVTTALPYANGNFHIGHIMEYIQADTWVRAQRMQ-----GNAVNFVGADDAHGAPI 57

Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAK 130
           MIAAEKAG TP++F+ +I++ RK+YLDGF+I FDNW +TDS EN +L Q+IY  L   A 
Sbjct: 58  MIAAEKAGKTPQQFVADIAAGRKQYLDGFHIAFDNWSNTDSPENHELSQQIYLDL-KAAG 116

Query: 131 LIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
            I  + I QFFDP KN+FLPDR+IKGECP C+AKDQYGD CE CSS+Y PT LINPYS L
Sbjct: 117 FIETRTIEQFFDPEKNMFLPDRFIKGECPRCHAKDQYGDNCEVCSSVYAPTDLINPYSAL 176

Query: 191 SGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           SG KP++K+S+HFFFKLSD R ++FL +W  + + +QPE+
Sbjct: 177 SGAKPVLKTSEHFFFKLSDPRAVEFLTEWTQNGQHVQPEV 216

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Acidovorax ebreus (strain TPSY) (taxid: 535289)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|A2SEY3|SYM_METPP Methionine--tRNA ligase OS=Methylibium petroleiphilum (strain PM1) GN=metG PE=3 SV=1

 Score =  296 bits (758), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 135/226 (59%), Positives = 164/226 (72%), Gaps = 12/226 (5%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVRFQ MQ        V+F+ ADDAHGA IM
Sbjct: 3   RQLFVTTALPYANGHFHIGHIMEYIQADIWVRFQRMQ-----GHAVHFVGADDAHGAPIM 57

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG TP++F+ +I++ RK YLDGF+I FDNW+STD  EN  L Q  Y  L  +  L
Sbjct: 58  IAAEKAGKTPQQFVADIAAGRKPYLDGFHIAFDNWHSTDGPENHQLAQDTYRAL-RRNGL 116

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  ++I QFFDP+K +FLPDRYIKGECP C AKDQYGD CE C ++Y PT+L NPYS L+
Sbjct: 117 IFTREIEQFFDPVKAMFLPDRYIKGECPKCGAKDQYGDSCEVCGAVYAPTELKNPYSTLT 176

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWA------IHDKRLQPEIF 231
           G  P++K+S+H FF+LS  RC+DFL+ W           RLQ E+ 
Sbjct: 177 GATPVMKTSEHHFFQLSSPRCLDFLKDWTHGSAPISGQPRLQAEVL 222

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Methylibium petroleiphilum (strain PM1) (taxid: 420662)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q21TB9|SYM_RHOFD Methionine--tRNA ligase OS=Rhodoferax ferrireducens (strain DSM 15236 / ATCC BAA-621 / T118) GN=metG PE=3 SV=1

 Score =  296 bits (758), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 135/225 (60%), Positives = 166/225 (73%), Gaps = 11/225 (4%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVR+Q M  +      V+F+CADD HGA IM
Sbjct: 3   RQLFVTTALPYANGNFHIGHIMEYIQADIWVRYQRMMGN-----AVHFVCADDCHGAPIM 57

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEK G TP++F+ +I+S RK YLDGF+I FDNW+STD  EN +L Q IY  L   A L
Sbjct: 58  IAAEKVGKTPQQFVADIASGRKPYLDGFHIGFDNWHSTDGAENHELAQAIYRDL-KAAGL 116

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  + I QFFD  KN+FLPDR+IKGECP C AKDQYGD CE C ++Y+PT+L NPYS LS
Sbjct: 117 ISTRVIAQFFDTEKNMFLPDRFIKGECPKCGAKDQYGDNCEECGAVYSPTELKNPYSALS 176

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-----DKRLQPEIF 231
           G  P+++ S+H+FFKLSD RC++FL +W          RLQ E++
Sbjct: 177 GVTPVLRDSEHYFFKLSDPRCVEFLEQWTTDTNPRGQSRLQAEVY 221

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Rhodoferax ferrireducens (strain DSM 15236 / ATCC BAA-621 / T118) (taxid: 338969)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|B1XWM2|SYM_LEPCP Methionine--tRNA ligase OS=Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) GN=metG PE=3 SV=1

 Score =  295 bits (756), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 134/220 (60%), Positives = 166/220 (75%), Gaps = 6/220 (2%)

Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            R++FVTTALPYANG+ HIGHIMEYIQADIWVRFQ +        QV+F+ ADDAHGA I
Sbjct: 2   TRQLFVTTALPYANGKFHIGHIMEYIQADIWVRFQRLM-----GHQVHFVGADDAHGAPI 56

Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAK 130
           MIAAEKAG TP++F+ +I++ R++YLDGF+I FDNW+STD  EN +L Q IY  L +   
Sbjct: 57  MIAAEKAGKTPQQFVADIAAGRREYLDGFHISFDNWHSTDGPENHELAQSIYRALRDNG- 115

Query: 131 LIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
           LI  + I QFFDP K +FLPDR+IKGECP C AKDQYGD CE C ++YTPT++ NPYS L
Sbjct: 116 LIEVRSIEQFFDPEKGMFLPDRFIKGECPKCGAKDQYGDSCEVCGAVYTPTEVRNPYSAL 175

Query: 191 SGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           SG  P++KSS H+FFKLSD RC  +L +W     +LQ E+
Sbjct: 176 SGATPVLKSSDHYFFKLSDPRCAAYLEQWTHEGGKLQQEV 215

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.

Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (taxid: 395495)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 0

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	232
300312383	690	methionyl-tRNA synthetase [Herbaspirillu	0.922	0.310	0.671	3e-87
398836261	692	protein containing beta chain of methion	0.922	0.309	0.666	1e-85
399017208	687	protein containing beta chain of methion	0.922	0.311	0.662	2e-85
329915423	731	Methionyl-tRNA synthetase [Oxalobacterac	0.922	0.292	0.639	2e-84
237746649	695	methionyl-tRNA synthetase [Oxalobacter f	0.939	0.313	0.650	5e-84
152979917	700	methionyl-tRNA synthetase [Janthinobacte	0.922	0.305	0.634	8e-84
395010429	701	protein containing beta chain of methion	0.918	0.303	0.647	3e-83
351730919	722	methionyl-tRNA synthetase [Acidovorax ra	0.918	0.295	0.647	5e-83
237748784	695	methionyl-tRNA synthetase [Oxalobacter f	0.939	0.313	0.627	8e-83
121603729	707	methionyl-tRNA synthetase [Polaromonas n	0.918	0.301	0.651	1e-82

>gi|300312383|ref|YP_003776475.1| methionyl-tRNA synthetase [Herbaspirillum seropedicae SmR1] gi|300075168|gb|ADJ64567.1| methionyl-tRNA synthetase protein [Herbaspirillum seropedicae SmR1]

 Score =  327 bits (837), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 147/219 (67%), Positives = 180/219 (82%), Gaps = 5/219 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVRFQ MQ +     +V+F+ ADDAHGA IM
Sbjct: 7   RQLFVTTALPYANGAFHIGHIMEYIQADIWVRFQRMQGN-----EVHFVGADDAHGAPIM 61

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG+TP++F+ NI++ RK+YLDGF+I FDNW STDS EN +L Q+IY  L ++AKL
Sbjct: 62  IAAEKAGITPQQFVANIAAGRKQYLDGFHIAFDNWSSTDSPENHELSQEIYRALRDEAKL 121

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K I+QF+DP+KN+FLPDRYIKGECP C  KDQYGD CE CS++Y+PT L NPYS LS
Sbjct: 122 ISTKTIDQFYDPVKNMFLPDRYIKGECPKCGTKDQYGDSCENCSAVYSPTDLKNPYSTLS 181

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P++KSS+HFFFKLSD +C+ FLR+WA+   RLQPE+
Sbjct: 182 GATPVMKSSEHFFFKLSDPKCVAFLREWALDSNRLQPEV 220

Source: Herbaspirillum seropedicae SmR1

Species: Herbaspirillum seropedicae

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|398836261|ref|ZP_10593602.1| protein containing beta chain of methionyl-tRNA synthetase [Herbaspirillum sp. YR522] gi|398212579|gb|EJM99183.1| protein containing beta chain of methionyl-tRNA synthetase [Herbaspirillum sp. YR522]

 Score =  321 bits (823), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 146/219 (66%), Positives = 174/219 (79%), Gaps = 5/219 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVRFQ MQ +     +V+F+ ADDAHGA IM
Sbjct: 7   RQLFVTTALPYANGAFHIGHIMEYIQADIWVRFQRMQGN-----EVHFVGADDAHGAPIM 61

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKA +TP++F+ NI++ RK+YLDGF+I FDNW STDS EN  L Q IY  L + A L
Sbjct: 62  IAAEKANVTPQQFVANIAAGRKQYLDGFHIAFDNWSSTDSPENHQLSQDIYRALRDDAGL 121

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K I QFFDP+KN+FLPDRYIKGECP C  KDQYGD CE CS++Y PT LINPYS LS
Sbjct: 122 ISTKTIEQFFDPVKNMFLPDRYIKGECPKCGTKDQYGDSCENCSAVYAPTDLINPYSTLS 181

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P++KSS+HFFF+LSD +C+ FLR+WA+   RLQPE+
Sbjct: 182 GATPVMKSSEHFFFRLSDPKCVAFLREWALDGDRLQPEV 220

Source: Herbaspirillum sp. YR522

Species: Herbaspirillum sp. YR522

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|399017208|ref|ZP_10719406.1| protein containing beta chain of methionyl-tRNA synthetase [Herbaspirillum sp. CF444] gi|398104112|gb|EJL94266.1| protein containing beta chain of methionyl-tRNA synthetase [Herbaspirillum sp. CF444]

 Score =  321 bits (822), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 145/219 (66%), Positives = 176/219 (80%), Gaps = 5/219 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVRFQ MQ       +V+F+ ADDAHGA IM
Sbjct: 7   RQLFVTTALPYANGAFHIGHIMEYIQADIWVRFQRMQ-----GHEVHFVGADDAHGAPIM 61

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG+TP++F+ +I++ RK+YLDGF+I FDNW STDS EN  L Q IY  L + A+L
Sbjct: 62  IAAEKAGVTPQQFVADIAAGRKQYLDGFHIAFDNWSSTDSQENHQLSQDIYRALRDDARL 121

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K I+QFFDP+K++FLPDRYIKGECP C  KDQYGD CE CS++Y PT L NPYS LS
Sbjct: 122 ITTKTIDQFFDPVKSMFLPDRYIKGECPKCGTKDQYGDSCENCSAVYAPTDLKNPYSTLS 181

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P++KSS+HFFFKLSD +C+ FLR+WA+ + RLQPE+
Sbjct: 182 GATPVMKSSEHFFFKLSDPKCVAFLREWALDNNRLQPEV 220

Source: Herbaspirillum sp. CF444

Species: Herbaspirillum sp. CF444

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|329915423|ref|ZP_08276269.1| Methionyl-tRNA synthetase [Oxalobacteraceae bacterium IMCC9480] gi|327544901|gb|EGF30259.1| Methionyl-tRNA synthetase [Oxalobacteraceae bacterium IMCC9480]

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 140/219 (63%), Positives = 173/219 (78%), Gaps = 5/219 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYAN   HIGHIMEYIQADIWVRFQ MQ       +V+F+CADDAHGA IM
Sbjct: 42  RQLFVTTALPYANAAFHIGHIMEYIQADIWVRFQRMQ-----GHEVHFVCADDAHGAPIM 96

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAA+ AG+TP+EF+  I++ R+  LDGF+I FDNW+STD  EN  L ++IY +L + A+L
Sbjct: 97  IAADNAGVTPQEFVARIAAGRQAPLDGFHIGFDNWHSTDGEENHALSKEIYRSLRDNAQL 156

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K I QFFDP+KN+FL DRYIKGECP C AKDQYGD CE C ++Y PT+L NPYS LS
Sbjct: 157 ITTKTIEQFFDPVKNMFLADRYIKGECPKCGAKDQYGDSCEVCGAVYAPTELKNPYSALS 216

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P++KSS+HFFFKLSD +C++FLR+WA  + RLQPE+
Sbjct: 217 GAVPVMKSSEHFFFKLSDHKCVEFLREWAFTEGRLQPEV 255

Source: Oxalobacteraceae bacterium IMCC9480

Species: Oxalobacteraceae bacterium IMCC9480

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|237746649|ref|ZP_04577129.1| methionyl-tRNA synthetase [Oxalobacter formigenes HOxBLS] gi|229378000|gb|EEO28091.1| methionyl-tRNA synthetase [Oxalobacter formigenes HOxBLS]

 Score =  316 bits (810), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 145/223 (65%), Positives = 174/223 (78%), Gaps = 5/223 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYAN   HIGHIMEYIQADIWVRFQ MQQDNGK R+V+F+ ADD HGA IM
Sbjct: 3   RKLFVTTALPYANAPFHIGHIMEYIQADIWVRFQRMQQDNGKQREVHFVGADDVHGAPIM 62

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG TP+EF+  I++ R   L+GF I FDNW+STD  EN +L ++IY  L  K  L
Sbjct: 63  IAAEKAGKTPQEFVAEIAAGRAAPLNGFLISFDNWHSTDGSENYELSREIYRRLKAKG-L 121

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I +K I QFFDP+K +FLPDRYIKGECP C AKDQYGD CE CSS+YTPT+L NPYSIL+
Sbjct: 122 IESKTIEQFFDPVKEMFLPDRYIKGECPKCGAKDQYGDTCESCSSVYTPTELKNPYSILT 181

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAI----HDKRLQPEI 230
           G  P++K S+HFFFKLSD +C  FL++W +     + RLQPE+
Sbjct: 182 GATPVMKQSEHFFFKLSDPQCTAFLKEWTLGNVDGEPRLQPEV 224

Source: Oxalobacter formigenes HOxBLS

Species: Oxalobacter formigenes

Genus: Oxalobacter

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|152979917|ref|YP_001352802.1| methionyl-tRNA synthetase [Janthinobacterium sp. Marseille] gi|187647729|sp|A6SX05.1|SYM_JANMA RecName: Full=Methionine--tRNA ligase; AltName: Full=Methionyl-tRNA synthetase; Short=MetRS gi|151279994|gb|ABR88404.1| Methionyl-tRNA synthetase [Janthinobacterium sp. Marseille]

 Score =  315 bits (808), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 139/219 (63%), Positives = 175/219 (79%), Gaps = 5/219 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  H+GHIMEYIQADIWVRFQ MQ +     +V+F+ ADDAHGA IM
Sbjct: 7   RKLFVTTALPYANGAFHVGHIMEYIQADIWVRFQRMQGN-----EVHFVGADDAHGAPIM 61

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG+TP++F+ NI++ RK+YLDGF+I+FDNW STDS EN +L ++IY  L + AKL
Sbjct: 62  IAAEKAGLTPQQFVANIAAGRKQYLDGFHIEFDNWSSTDSPENHELSREIYRRLRDDAKL 121

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K + QF+DP+K +FLPDRYIKGECP C  KDQYGD CE CS++Y PT L +PYS L+
Sbjct: 122 ITTKSVEQFYDPVKEMFLPDRYIKGECPKCGTKDQYGDSCENCSAVYAPTDLKHPYSTLT 181

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P+ KSS HFFF+LSD +C+ FLR+WA+  +RLQ E+
Sbjct: 182 GATPVRKSSDHFFFRLSDPKCVAFLREWALDGQRLQSEV 220

Source: Janthinobacterium sp. Marseille

Species: Janthinobacterium sp. Marseille

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|395010429|ref|ZP_10393809.1| protein containing beta chain of methionyl-tRNA synthetase [Acidovorax sp. CF316] gi|394311461|gb|EJE48803.1| protein containing beta chain of methionyl-tRNA synthetase [Acidovorax sp. CF316]

 Score =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 143/221 (64%), Positives = 171/221 (77%), Gaps = 8/221 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVRFQ MQ +      V F+ ADD HGA IM
Sbjct: 6   RKLFVTTALPYANGNFHIGHIMEYIQADIWVRFQRMQGN-----AVNFVGADDTHGAPIM 60

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKA-- 129
           IAAEKAG TP++F+ +I++ RK+YLDGF+I FDNW+STD  EN DL ++IY  L ++A  
Sbjct: 61  IAAEKAGKTPQQFVADIAAGRKQYLDGFHISFDNWHSTDGPENHDLARQIYRDLRDRADG 120

Query: 130 KLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSI 189
            LI  + I QFFDP KN+FLPDR+IKGECP C AKDQYGD CE C S+Y PT LINP+S 
Sbjct: 121 SLIETRTIEQFFDPEKNMFLPDRFIKGECPKCRAKDQYGDNCEVCGSVYAPTDLINPFSA 180

Query: 190 LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           LSG KP +KSS+HFFFKLSD RC++FL  W   D +LQPE+
Sbjct: 181 LSGVKPELKSSEHFFFKLSDPRCVEFLENWT-QDGKLQPEV 220

Source: Acidovorax sp. CF316

Species: Acidovorax sp. CF316

Genus: Acidovorax

Family: Comamonadaceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|351730919|ref|ZP_08948610.1| methionyl-tRNA synthetase [Acidovorax radicis N35]

 Score =  313 bits (801), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 143/221 (64%), Positives = 173/221 (78%), Gaps = 8/221 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYANG  HIGHIMEYIQADIWVR+Q MQ        V F+ ADD HGA IM
Sbjct: 6   RKLFVTTALPYANGNFHIGHIMEYIQADIWVRYQRMQ-----GHAVNFVGADDTHGAPIM 60

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKA-- 129
           IAAEKAG TP++F+ +I++ RK+YLDGF+I FDNW+STD+ EN DL ++IY  L ++A  
Sbjct: 61  IAAEKAGKTPQQFVADIAAGRKQYLDGFHISFDNWHSTDAPENHDLARQIYRDLRDRADG 120

Query: 130 KLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSI 189
            LI  + I QFFDP KN+FLPDRYIKGECP C+AKDQYGD CE C S+Y PT LINP+S 
Sbjct: 121 SLIEVRTIEQFFDPEKNMFLPDRYIKGECPKCHAKDQYGDNCEVCGSVYAPTDLINPFSA 180

Query: 190 LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           LSG KP +K+S+HFFFKLSD RC++FL KW   D +LQPE+
Sbjct: 181 LSGAKPELKNSEHFFFKLSDPRCVEFLEKWT-QDGKLQPEV 220

Source: Acidovorax radicis N35

Species: Acidovorax radicis

Genus: Acidovorax

Family: Comamonadaceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|237748784|ref|ZP_04579264.1| methionyl-tRNA synthetase [Oxalobacter formigenes OXCC13] gi|229380146|gb|EEO30237.1| methionyl-tRNA synthetase [Oxalobacter formigenes OXCC13]

 Score =  312 bits (799), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 140/223 (62%), Positives = 175/223 (78%), Gaps = 5/223 (2%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R++FVTTALPYAN   HIGHIMEYIQADIWVRFQ MQ+D+GK R+V+F+ ADD HGA IM
Sbjct: 3   RKLFVTTALPYANAPFHIGHIMEYIQADIWVRFQRMQKDDGKQREVHFVGADDVHGAPIM 62

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           IAAEKAG TP+EF+  I++ RK  L+GF I FDNW+STD  EN +L ++IY  L  K  L
Sbjct: 63  IAAEKAGKTPQEFVAEIAAGRKAPLNGFLISFDNWHSTDGPENYELSREIYRRLKAKG-L 121

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I+++ I QFFDP+K +FLPDRYIKGECP C AKDQYGD CE CS++Y PT+L NPYSIL+
Sbjct: 122 IVSRTIEQFFDPVKEMFLPDRYIKGECPKCGAKDQYGDTCEVCSTVYAPTELKNPYSILT 181

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHD----KRLQPEI 230
           G  P++K S+HFFF+LSD +C +FL++W +       RLQPE+
Sbjct: 182 GATPVMKQSEHFFFRLSDPQCTEFLKEWTLGKVNGHPRLQPEV 224

Source: Oxalobacter formigenes OXCC13

Species: Oxalobacter formigenes

Genus: Oxalobacter

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|121603729|ref|YP_981058.1| methionyl-tRNA synthetase [Polaromonas naphthalenivorans CJ2] gi|187647741|sp|A1VKF9.1|SYM_POLNA RecName: Full=Methionine--tRNA ligase; AltName: Full=Methionyl-tRNA synthetase; Short=MetRS gi|120592698|gb|ABM36137.1| methionyl-tRNA synthetase [Polaromonas naphthalenivorans CJ2]

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 144/221 (65%), Positives = 171/221 (77%), Gaps = 8/221 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           RR+FVTTALPYANG  HIGHIMEYIQADIWVR+Q MQ +      V F+ ADDAHGA IM
Sbjct: 4   RRLFVTTALPYANGNFHIGHIMEYIQADIWVRYQRMQGN-----AVNFVGADDAHGAPIM 58

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYN--KA 129
           IAAEKAG TP++F+ +I+S RK YLDGF+I FDNW STDS EN +L ++IY  L +  + 
Sbjct: 59  IAAEKAGKTPQQFVADIASGRKPYLDGFHISFDNWSSTDSPENHELARQIYRDLRDNPQG 118

Query: 130 KLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSI 189
            LI  K I QFFDP KN+FLPDR+IKGECP C+AKDQYGD CE C ++Y PT LINPYS 
Sbjct: 119 SLIETKTIEQFFDPEKNMFLPDRFIKGECPKCHAKDQYGDNCEVCGAVYAPTDLINPYSA 178

Query: 190 LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           LSG  P++KSS+HFFFKLSD RC++FL  W   D +LQPE+
Sbjct: 179 LSGVTPVLKSSEHFFFKLSDARCVEFLESWT-QDGKLQPEV 218

Source: Polaromonas naphthalenivorans CJ2

Species: Polaromonas naphthalenivorans

Genus: Polaromonas

Family: Comamonadaceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

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	232
TIGR_CMR|CBU_1695	546	CBU_1695 "methionyl-tRNA synth	0.905	0.384	0.497	4.3e-54
UNIPROTKB|Q9KT69	683	metG "Methionine--tRNA ligase"	0.909	0.308	0.472	1.1e-50
TIGR_CMR|VC_1036	683	VC_1036 "methionyl-tRNA synthe	0.909	0.308	0.472	1.1e-50
TIGR_CMR|CPS_2839	713	CPS_2839 "methionyl-tRNA synth	0.892	0.290	0.441	2.8e-50
UNIPROTKB|P00959	677	metG "methionyl-tRNA synthetas	0.905	0.310	0.442	5.2e-49
TIGR_CMR|SO_2619	676	SO_2619 "methionyl-tRNA synthe	0.905	0.310	0.442	3.7e-48
DICTYBASE|DDB_G0279113	736	metS "methionyl-tRNA synthetas	0.823	0.259	0.319	6.7e-25
SGD|S000003496	751	MES1 "Methionyl-tRNA synthetas	0.875	0.270	0.327	2.4e-24
CGD|CAL0003012	748	MES1 [Candida albicans (taxid:	0.879	0.272	0.300	3.1e-24
UNIPROTKB|Q5AK65	748	MES1 "Potential cytoplasmic me	0.879	0.272	0.300	3.1e-24

TIGR_CMR|CBU_1695 CBU_1695 "methionyl-tRNA synthetase" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 109/219 (49%), Positives = 143/219 (65%)

Query:    12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
             R+I VT ALPYANG +H+GH++E+IQADIWVRFQ +     K     FIC +DAHG AIM
Sbjct:     6 RQILVTAALPYANGPIHLGHMVEHIQADIWVRFQRL-----KGNDCLFICGEDAHGTAIM 60

Query:    72 IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXX 131
             I A+K G+ P+  +  +     + L GF I++DN+Y+T S EN +L + IY  L      
Sbjct:    61 ITAQKQGLPPEALVAKMHKEHARDLGGFLIEYDNFYTTHSPENRELAELIYTRL-KDKGD 119

Query:   132 XXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
                    Q +DP+K IFLPDR+I+G CP C AKDQYGD CE C + Y+PT+LI+P S LS
Sbjct:   120 IFAKTISQAYDPVKEIFLPDRFIRGTCPRCGAKDQYGDVCEVCGATYSPTELIDPVSALS 179

Query:   192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
             G KPI K+S+HFFF L+  R    L+KW I    LQP++
Sbjct:   180 GAKPIEKNSEHFFFSLN--RYTQLLKKW-IDAGHLQPQV 215

GO:0004825 "methionine-tRNA ligase activity" evidence=ISS

GO:0006431 "methionyl-tRNA aminoacylation" evidence=ISS

UNIPROTKB|Q9KT69 metG "Methionine--tRNA ligase" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 104/220 (47%), Positives = 140/220 (63%)

Query:    10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAA 69
             D R++ VT ALPYANG +H+GH++E+IQADIWVR+Q ++   G +  V FICADDAHG  
Sbjct:     4 DPRKLLVTCALPYANGSIHLGHMLEHIQADIWVRYQRLR---GNT--VNFICADDAHGTP 58

Query:    70 IMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXX 129
             IM+ A++ GMTP+  I  +S   ++   GF I FDN++ST S EN +L   IY  L    
Sbjct:    59 IMLKAQQMGMTPEAMIEMVSEEHQRDFAGFDISFDNYHSTHSDENRELASHIYLQL-KKN 117

Query:   130 XXXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSI 189
                      Q FDP K +FLPDR++KG CP C ++DQYGD C+ C   Y+PT+LINP S 
Sbjct:   118 GFISSRTISQLFDPEKEMFLPDRFVKGTCPKCKSEDQYGDNCDACGETYSPTELINPKSA 177

Query:   190 LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE 229
             +SG  P++K S+HFFF L     +  L++W      LQ E
Sbjct:   178 VSGATPVMKDSEHFFFDLPQFESM--LKEWT-RSGSLQSE 214

GO:0004825 "methionine-tRNA ligase activity" evidence=ISS

GO:0006431 "methionyl-tRNA aminoacylation" evidence=ISS

TIGR_CMR|VC_1036 VC_1036 "methionyl-tRNA synthetase" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 104/220 (47%), Positives = 140/220 (63%)

Query:    10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAA 69
             D R++ VT ALPYANG +H+GH++E+IQADIWVR+Q ++   G +  V FICADDAHG  
Sbjct:     4 DPRKLLVTCALPYANGSIHLGHMLEHIQADIWVRYQRLR---GNT--VNFICADDAHGTP 58

Query:    70 IMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXX 129
             IM+ A++ GMTP+  I  +S   ++   GF I FDN++ST S EN +L   IY  L    
Sbjct:    59 IMLKAQQMGMTPEAMIEMVSEEHQRDFAGFDISFDNYHSTHSDENRELASHIYLQL-KKN 117

Query:   130 XXXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSI 189
                      Q FDP K +FLPDR++KG CP C ++DQYGD C+ C   Y+PT+LINP S 
Sbjct:   118 GFISSRTISQLFDPEKEMFLPDRFVKGTCPKCKSEDQYGDNCDACGETYSPTELINPKSA 177

Query:   190 LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE 229
             +SG  P++K S+HFFF L     +  L++W      LQ E
Sbjct:   178 VSGATPVMKDSEHFFFDLPQFESM--LKEWT-RSGSLQSE 214

GO:0004825 "methionine-tRNA ligase activity" evidence=ISS

GO:0006431 "methionyl-tRNA aminoacylation" evidence=ISS

TIGR_CMR|CPS_2839 CPS_2839 "methionyl-tRNA synthetase, beta subunit" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 523 (189.2 bits), Expect = 2.8e-50, P = 2.8e-50
 Identities = 95/215 (44%), Positives = 141/215 (65%)

Query:    12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
             R+I VT ALPYANG +H+GH++E+IQ DIWVRFQ M     +  + YF+CADDAHG  IM
Sbjct:    22 RKILVTCALPYANGSIHLGHMLEHIQTDIWVRFQRM-----RGHETYFVCADDAHGTPIM 76

Query:    72 IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXX 131
             + A++ G+TP+E IN +   R K    F+I FDN+++T S EN +  +KIY+ L+     
Sbjct:    77 LKAQELGITPEEMINGVREERIKEFSDFHISFDNYHTTHSDENKEYSEKIYNALHAKGHI 136

Query:   132 XXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
                    Q +DP K +FL DR++KG CP C ++D+ GD C+ C + Y+PT+++NP S +S
Sbjct:   137 KTRIIS-QLYDPEKGMFLADRFVKGTCPKCKSEDENGDSCDNCGATYSPTEVLNPRSAIS 195

Query:   192 GTKPIIKSSKHFFFKLS--DKRCIDFLRKWAIHDK 224
             G  PI+K S+H+FF L   +    D++R  A+ ++
Sbjct:   196 GATPILKDSEHYFFDLPAFETMLSDWIRSGALQEE 230

GO:0004825 "methionine-tRNA ligase activity" evidence=ISS

GO:0006431 "methionyl-tRNA aminoacylation" evidence=ISS

UNIPROTKB|P00959 metG "methionyl-tRNA synthetase" [Escherichia coli K-12 (taxid:83333)]

 Score = 511 (184.9 bits), Expect = 5.2e-49, P = 5.2e-49
 Identities = 97/219 (44%), Positives = 138/219 (63%)

Query:    12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
             ++I VT ALPYANG +H+GH++E+IQAD+WVR+Q M     +  +V FICADDAHG  IM
Sbjct:     6 KKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRM-----RGHEVNFICADDAHGTPIM 60

Query:    72 IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXX 131
             + A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + IY  L      
Sbjct:    61 LKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRL-KENGF 119

Query:   132 XXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
                    Q +DP K +FLPDR++KG CP C + DQYGD CE C + Y+PT+LI P S++S
Sbjct:   120 IKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKSVVS 179

Query:   192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
             G  P+++ S+HFFF L      + L+ W      LQ ++
Sbjct:   180 GATPVMRDSEHFFFDLPSFS--EMLQAWT-RSGALQEQV 215

GO:0006431 "methionyl-tRNA aminoacylation" evidence=IEA

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

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

GO:0004825 "methionine-tRNA ligase activity" evidence=IEA

TIGR_CMR|SO_2619 SO_2619 "methionyl-tRNA synthetase" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 503 (182.1 bits), Expect = 3.7e-48, P = 3.7e-48
 Identities = 97/219 (44%), Positives = 137/219 (62%)

Query:    12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
             R+I VT+ALPYANG +H+GH++EYIQ DIW R+Q +     +  + ++ICADDAHG  IM
Sbjct:     6 RKILVTSALPYANGPIHLGHMLEYIQTDIWSRYQKL-----RGHECHYICADDAHGTPIM 60

Query:    72 IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXX 131
             + A++ GM P+E I  ++   ++    F I FDN++ST S EN  L   IY  L      
Sbjct:    61 LKAQQLGMAPEEMIAQVNKEHQQDFADFNIAFDNYHSTHSEENRVLASDIYLKL-RANGY 119

Query:   132 XXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
                    Q FDP +++FLPDR++KG CP C + DQYGD C+ C + Y+PT+LINP S +S
Sbjct:   120 IKSKSISQLFDPEQSMFLPDRFVKGTCPKCKSPDQYGDNCDACGATYSPTELINPKSAVS 179

Query:   192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
             G  P++K ++HFFF L      D L++W      LQ E+
Sbjct:   180 GATPVMKDTEHFFFDLPAFE--DMLKEWT-RSGALQTEM 215

GO:0004825 "methionine-tRNA ligase activity" evidence=ISS

GO:0006431 "methionyl-tRNA aminoacylation" evidence=ISS

DICTYBASE|DDB_G0279113 metS "methionyl-tRNA synthetase" [Dictyostelium discoideum (taxid:44689)]

 Score = 293 (108.2 bits), Expect = 6.7e-25, P = 6.7e-25
 Identities = 63/197 (31%), Positives = 98/197 (49%)

Query:    12 RRIFVTTALPYANGELHIGHIMEYI-QADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
             R I +T+ALPY N   H+G+I+  +  AD++ R+ C      K+    +IC  D +G A 
Sbjct:    16 RNILITSALPYVNNVPHLGNIIGCVLSADVYARY-CRL----KNYNCIYICGTDEYGTAT 70

Query:    71 MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXX 130
                A   G TPKE  +      K+  + F I FD +  T +    ++ Q I++ +     
Sbjct:    71 ETKALSEGCTPKEICDKYHEIHKEIYEWFNISFDKFGRTSTNSQTEIAQDIFNKIKDNGY 130

Query:   131 XXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
                      + +    +FL DR+++G CP C  +D  GD C+ CS +  PT+LINP   +
Sbjct:   131 TLTQEIEQLYCEQTCKMFLADRFVEGTCPHCKFEDARGDQCDGCSKLLNPTELINPRCKV 190

Query:   191 SGTKPIIKSSKHFFFKL 207
                 P+IKS+KH F  L
Sbjct:   191 CSKPPVIKSTKHIFIDL 207

GO:0006431 "methionyl-tRNA aminoacylation" evidence=IEA;ISS

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

GO:0005737 "cytoplasm" evidence=IEA;ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0004825 "methionine-tRNA ligase activity" evidence=IEA;ISS

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

GO:0017102 "methionyl glutamyl tRNA synthetase complex" evidence=ISS

GO:0016874 "ligase activity" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

SGD|S000003496 MES1 "Methionyl-tRNA synthetase" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 288 (106.4 bits), Expect = 2.4e-24, P = 2.4e-24
 Identities = 70/214 (32%), Positives = 104/214 (48%)

Query:     1 MKKHDSEF---KDVRRIFVTTALPYANGELHIGHIM-EYIQADIWVRFQCMQQDNGKSRQ 56
             +K  DSE     + R I +T+ALPY N   H+G+I+   + ADI+ R+ C     G++  
Sbjct:   182 VKPKDSEILPKPNERNILITSALPYVNNVPHLGNIIGSVLSADIFARY-C----KGRNYN 236

Query:    57 VYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENID 116
               FIC  D +G A    A + G+TP++  +            F I FD +  T + +  +
Sbjct:   237 ALFICGTDEYGTATETKALEEGVTPRQLCDKYHKIHSDVYKWFQIGFDYFGRTTTDKQTE 296

Query:   117 LVQKIYDTLYXXXXXXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSS 176
             + Q I+  L             Q + P+ N +L DRY++GECP C+  D  GD C+ C +
Sbjct:   297 IAQHIFTKL-NSNGYLEEQSMKQLYCPVHNSYLADRYVEGECPKCHYDDARGDQCDKCGA 355

Query:   177 IYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDK 210
             +  P +LINP   L    P  K S H F  L DK
Sbjct:   356 LLDPFELINPRCKLDDASPEPKYSDHIFLSL-DK 388

GO:0004825 "methionine-tRNA ligase activity" evidence=IEA;IDA

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

GO:0017102 "methionyl glutamyl tRNA synthetase complex" evidence=IDA

GO:0006431 "methionyl-tRNA aminoacylation" evidence=IEA;IDA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0006412 "translation" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

CGD|CAL0003012 MES1 [Candida albicans (taxid:5476)]

 Score = 287 (106.1 bits), Expect = 3.1e-24, P = 3.1e-24
 Identities = 64/213 (30%), Positives = 109/213 (51%)

Query:    10 DVRRIFVTTALPYANGELHIGHIM-EYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGA 68
             D R I +T+ALPY N   H+G+I+   + ADI+ R+        ++    FIC  D +G 
Sbjct:   185 DERNILITSALPYVNNVPHLGNIIGSVLSADIYSRYA-----KNRNYNTLFICGTDEYGT 239

Query:    69 AIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXX 128
             A    A +  +TP++  +   +  K+  D F I FD +  T +    ++ Q I+  L+  
Sbjct:   240 ATETKALEEKVTPQQLCDKYHAIHKEVYDWFDIGFDYFGRTTTSLQTEIAQDIFLKLHNK 299

Query:   129 XXXXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYS 188
                        + +  K+ FL DR+++G CP C+ +D  GD C+ C ++  P +LINP  
Sbjct:   300 GYLEEKTTEQLYCEHHKS-FLADRFVEGTCPKCDYEDARGDQCDKCGNLLDPLELINPRC 358

Query:   189 ILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAI 221
              + G  P++K S H + KL+D    + L++W +
Sbjct:   359 KVDGNTPVVKESTHIYLKLNDLE--EPLKEWVL 389

GO:0004825 "methionine-tRNA ligase activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

GO:0017102 "methionyl glutamyl tRNA synthetase complex" evidence=IEA

GO:0006431 "methionyl-tRNA aminoacylation" evidence=IEA

UNIPROTKB|Q5AK65 MES1 "Potential cytoplasmic methionyl tRNA synthetase" [Candida albicans SC5314 (taxid:237561)]

 Score = 287 (106.1 bits), Expect = 3.1e-24, P = 3.1e-24
 Identities = 64/213 (30%), Positives = 109/213 (51%)

Query:    10 DVRRIFVTTALPYANGELHIGHIM-EYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGA 68
             D R I +T+ALPY N   H+G+I+   + ADI+ R+        ++    FIC  D +G 
Sbjct:   185 DERNILITSALPYVNNVPHLGNIIGSVLSADIYSRYA-----KNRNYNTLFICGTDEYGT 239

Query:    69 AIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXX 128
             A    A +  +TP++  +   +  K+  D F I FD +  T +    ++ Q I+  L+  
Sbjct:   240 ATETKALEEKVTPQQLCDKYHAIHKEVYDWFDIGFDYFGRTTTSLQTEIAQDIFLKLHNK 299

Query:   129 XXXXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYS 188
                        + +  K+ FL DR+++G CP C+ +D  GD C+ C ++  P +LINP  
Sbjct:   300 GYLEEKTTEQLYCEHHKS-FLADRFVEGTCPKCDYEDARGDQCDKCGNLLDPLELINPRC 358

Query:   189 ILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAI 221
              + G  P++K S H + KL+D    + L++W +
Sbjct:   359 KVDGNTPVVKESTHIYLKLNDLE--EPLKEWVL 389

GO:0004825 "methionine-tRNA ligase activity" evidence=ISS

GO:0005737 "cytoplasm" 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)
B9MEX0	SYM_ACIET	6, ., 1, ., 1, ., 1, 0	0.6363	0.9224	0.3110	yes	N/A
A1WBH1	SYM_ACISJ	6, ., 1, ., 1, ., 1, 0	0.6363	0.9224	0.3110	yes	N/A
Q63W90	SYM_BURPS	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
Q2Y7P0	SYM_NITMU	6, ., 1, ., 1, ., 1, 0	0.5205	0.9181	0.2925	yes	N/A
A1VKF9	SYM_POLNA	6, ., 1, ., 1, ., 1, 0	0.6515	0.9181	0.3012	yes	N/A
B1YUT2	SYM_BURA4	6, ., 1, ., 1, ., 1, 0	0.5366	0.9051	0.2916	yes	N/A
Q7W1D8	SYM_BORPA	6, ., 1, ., 1, ., 1, 0	0.5714	0.9181	0.3078	yes	N/A
Q143I7	SYM_BURXL	6, ., 1, ., 1, ., 1, 0	0.5528	0.8706	0.2845	yes	N/A
A0K9L0	SYM_BURCH	6, ., 1, ., 1, ., 1, 0	0.5458	0.9051	0.2924	yes	N/A
Q7WP45	SYM_BORBR	6, ., 1, ., 1, ., 1, 0	0.5714	0.9181	0.3078	yes	N/A
Q7NYR7	SYM_CHRVO	6, ., 1, ., 1, ., 1, 0	0.5066	0.9051	0.3047	yes	N/A
Q7W0F7	SYM_BORPE	6, ., 1, ., 1, ., 1, 0	0.5714	0.9181	0.3078	yes	N/A
Q8XWT9	SYM_RALSO	6, ., 1, ., 1, ., 1, 0	0.5528	0.8706	0.2936	yes	N/A
A5EY62	SYM_DICNV	6, ., 1, ., 1, ., 1, 0	0.5227	0.9094	0.3135	yes	N/A
Q39DV4	SYM_BURS3	6, ., 1, ., 1, ., 1, 0	0.5625	0.8706	0.2805	yes	N/A
A3MLM5	SYM_BURM7	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
A4JGW6	SYM_BURVG	6, ., 1, ., 1, ., 1, 0	0.5412	0.9051	0.2912	yes	N/A
A9AHJ8	SYM_BURM1	6, ., 1, ., 1, ., 1, 0	0.5458	0.9051	0.2908	yes	N/A
B1XWM2	SYM_LEPCP	6, ., 1, ., 1, ., 1, 0	0.6090	0.9224	0.3105	yes	N/A
A2SEY3	SYM_METPP	6, ., 1, ., 1, ., 1, 0	0.5973	0.9224	0.3070	yes	N/A
Q1BUH6	SYM_BURCA	6, ., 1, ., 1, ., 1, 0	0.5458	0.9051	0.2924	yes	N/A
Q3JUY1	SYM_BURP1	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
A2SAF7	SYM_BURM9	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
Q47IK0	SYM_DECAR	6, ., 1, ., 1, ., 1, 0	0.5188	0.8879	0.2959	yes	N/A
Q2KYS4	SYM_BORA1	6, ., 1, ., 1, ., 1, 0	0.5714	0.9181	0.3082	yes	N/A
Q2T087	SYM_BURTA	6, ., 1, ., 1, ., 1, 0	0.5137	0.9051	0.2924	yes	N/A
Q12F12	SYM_POLSJ	6, ., 1, ., 1, ., 1, 0	0.6438	0.9137	0.3076	yes	N/A
B1JWS3	SYM_BURCC	6, ., 1, ., 1, ., 1, 0	0.5458	0.9051	0.2932	yes	N/A
Q60CR0	SYM_METCA	6, ., 1, ., 1, ., 1, 0	0.5144	0.8620	0.2881	yes	N/A
Q0BCT3	SYM_BURCM	6, ., 1, ., 1, ., 1, 0	0.5366	0.9051	0.2916	yes	N/A
Q1H2F4	SYM_METFK	6, ., 1, ., 1, ., 1, 0	0.5183	0.9008	0.3020	yes	N/A
B4E8E0	SYM_BURCJ	6, ., 1, ., 1, ., 1, 0	0.5550	0.9051	0.2924	yes	N/A
A1TTU1	SYM_ACIAC	6, ., 1, ., 1, ., 1, 0	0.6392	0.9137	0.3002	yes	N/A
A3N6Y1	SYM_BURP6	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
Q0AES9	SYM_NITEC	6, ., 1, ., 1, ., 1, 0	0.5479	0.9181	0.3038	yes	N/A
A1WRC4	SYM_VEREI	6, ., 1, ., 1, ., 1, 0	0.6036	0.9224	0.3096	yes	N/A
Q1LJN4	SYM_RALME	6, ., 1, ., 1, ., 1, 0	0.5693	0.875	0.2942	yes	N/A
Q62LE0	SYM_BURMA	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
A1V5W0	SYM_BURMS	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
B3R678	SYM_CUPTR	6, ., 1, ., 1, ., 1, 0	0.5645	0.875	0.2950	yes	N/A
Q21TB9	SYM_RHOFD	6, ., 1, ., 1, ., 1, 0	0.6	0.9224	0.3057	yes	N/A
A4G3S6	SYM_HERAR	6, ., 1, ., 1, ., 1, 0	0.6682	0.8706	0.2845	yes	N/A
A3NSL6	SYM_BURP0	6, ., 1, ., 1, ., 1, 0	0.5091	0.9051	0.2896	yes	N/A
Q82WP0	SYM_NITEU	6, ., 1, ., 1, ., 1, 0	0.5296	0.9181	0.3016	yes	N/A
Q474X7	SYM_CUPPJ	6, ., 1, ., 1, ., 1, 0	0.5693	0.875	0.2950	yes	N/A
Q0K7K0	SYM_CUPNH	6, ., 1, ., 1, ., 1, 0	0.5693	0.875	0.2959	yes	N/A
A6SX05	SYM_JANMA	6, ., 1, ., 1, ., 1, 0	0.6347	0.9224	0.3057	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.1.1	LOW CONFIDENCE prediction!

---

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	232
PRK00133	673	PRK00133, metG, methionyl-tRNA synthetase; Reviewe	1e-113
PRK12268	556	PRK12268, PRK12268, methionyl-tRNA synthetase; Rev	3e-82
pfam09334	388	pfam09334, tRNA-synt_1g, tRNA synthetases class I	1e-76
COG0143	558	COG0143, MetG, Methionyl-tRNA synthetase [Translat	1e-72
TIGR00398	530	TIGR00398, metG, methionyl-tRNA synthetase	3e-64
cd00814	319	cd00814, MetRS_core, catalytic core domain of meth	3e-40
PLN02610	801	PLN02610, PLN02610, probable methionyl-tRNA synthe	2e-28
PRK11893	511	PRK11893, PRK11893, methionyl-tRNA synthetase; Rev	4e-22
cd00668	312	cd00668, Ile_Leu_Val_MetRS_core, catalytic core do	2e-21
PRK12267	648	PRK12267, PRK12267, methionyl-tRNA synthetase; Rev	6e-18
cd00812	314	cd00812, LeuRS_core, catalytic core domain of leuc	8e-11
PLN02843	974	PLN02843, PLN02843, isoleucyl-tRNA synthetase	7e-08
COG0495	814	COG0495, LeuS, Leucyl-tRNA synthetase [Translation	9e-08
cd00818	338	cd00818, IleRS_core, catalytic core domain of isol	5e-07
TIGR00392	861	TIGR00392, ileS, isoleucyl-tRNA synthetase	1e-06
COG0060	933	COG0060, IleS, Isoleucyl-tRNA synthetase [Translat	4e-06
PLN02224	616	PLN02224, PLN02224, methionine-tRNA ligase	6e-06
PRK13208	800	PRK13208, valS, valyl-tRNA synthetase; Reviewed	7e-05
TIGR00395	938	TIGR00395, leuS_arch, leucyl-tRNA synthetase, arch	8e-05
pfam00133	606	pfam00133, tRNA-synt_1, tRNA synthetases class I (	2e-04
PRK13804	961	PRK13804, ileS, isoleucyl-tRNA synthetase; Provisi	5e-04
PRK05743	912	PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewe	5e-04
cd00817	382	cd00817, ValRS_core, catalytic core domain of valy	0.001
COG0525	877	COG0525, ValS, Valyl-tRNA synthetase [Translation,	0.002

>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed

 Score =  337 bits (868), Expect = e-113
 Identities = 114/219 (52%), Positives = 148/219 (67%), Gaps = 8/219 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R+I VT ALPYANG +H+GH++EYIQADIWVR+Q M     +  +V F+CADDAHG  IM
Sbjct: 2   RKILVTCALPYANGPIHLGHLVEYIQADIWVRYQRM-----RGHEVLFVCADDAHGTPIM 56

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           + AEK G+TP+E I    +  K+   GF I FDN+ ST S EN +L Q+IY  L  +   
Sbjct: 57  LKAEKEGITPEELIARYHAEHKRDFAGFGISFDNYGSTHSEENRELAQEIYLKLK-ENGY 115

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           I  K I Q +DP K +FLPDR++KG CP C A+DQYGD CE C + Y+PT+LINP S +S
Sbjct: 116 IYEKTIEQLYDPEKGMFLPDRFVKGTCPKCGAEDQYGDNCEVCGATYSPTELINPKSAIS 175

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G  P++K S+HFFFKL   R  +FL++W      LQP +
Sbjct: 176 GATPVLKESEHFFFKLP--RFEEFLKEWITRSGELQPNV 212

Length = 673

>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed

 Score =  254 bits (652), Expect = 3e-82
 Identities = 77/219 (35%), Positives = 115/219 (52%), Gaps = 10/219 (4%)

Query: 12  RRIFVTTALPYANGELHIGHIME-YIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            RI +T+A PYANG LH+GH+    + AD++ R+Q ++ +      V F+   D HG  I
Sbjct: 3   MRILITSAWPYANGPLHLGHLAGSGLPADVFARYQRLKGNE-----VLFVSGSDEHGTPI 57

Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAK 130
            +AA+K G+TP+E  +      K+      I +D +  T S  + ++VQ+ +  LY    
Sbjct: 58  ELAAKKEGVTPQELADKYHEEHKEDFKKLGISYDLFTRTTSPNHHEVVQEFFLKLYEN-G 116

Query: 131 LIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
            I  K I Q + P    FLPDRY++G CP C  +   GD C+ C ++  PT LINP S +
Sbjct: 117 YIYKKTIEQAYCPSDGRFLPDRYVEGTCPYCGYEGARGDQCDNCGALLDPTDLINPRSKI 176

Query: 191 SGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE 229
           SG+ P  + ++HFF  L      + LR W I      P 
Sbjct: 177 SGSTPEFRETEHFFLDLP--AFAERLRAW-IESSGDWPP 212

Length = 556

>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M)

 Score =  235 bits (602), Expect = 1e-76
 Identities = 80/216 (37%), Positives = 117/216 (54%), Gaps = 8/216 (3%)

Query: 14  IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIA 73
             +TTALPY NG  HIGH+   I AD++ R+  ++        V F+   D HG  I +A
Sbjct: 1   FLITTALPYVNGPPHIGHLYTTIPADVYARYLRLR-----GYDVLFVTGTDEHGTKIELA 55

Query: 74  AEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLII 133
           AEK G+TP+E ++      K+    F I FD++  T S  + +LVQ+ +  LY K   I 
Sbjct: 56  AEKEGVTPQELVDRYHEEFKELFKKFNISFDDFIRTTSERHKELVQEFFLKLYEK-GDIY 114

Query: 134 NKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGT 193
             +   ++      FLPDRY++G CP C ++D  GD CE C     PT+LINP S +SG+
Sbjct: 115 EGEYEGWYCVSDERFLPDRYVEGTCPYCGSEDARGDQCEVCGRPLEPTELINPRSAISGS 174

Query: 194 KPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE 229
            P +K  +H+FF+LS  +  D L +W   +    P 
Sbjct: 175 TPELKEEEHYFFRLSKFQ--DKLLEWIKENPDEPPS 208

This family includes methionyl tRNA synthetases. Length = 388

>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score =  230 bits (589), Expect = 1e-72
 Identities = 78/211 (36%), Positives = 120/211 (56%), Gaps = 8/211 (3%)

Query: 9   KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGA 68
           K +++I VTTALPY NG  H+GH+  Y+ AD++ R+  ++       +V+F+   D HG 
Sbjct: 2   KMMKKILVTTALPYPNGPPHLGHLYTYLAADVYARYLRLR-----GYEVFFLTGTDEHGT 56

Query: 69  AIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNK 128
            I + AEK G+TP+E ++      K+      I FDN+  T S E+ +LVQ+ +  LY +
Sbjct: 57  KIELKAEKEGITPQELVDKNHEEFKELFKALNISFDNFIRTTSPEHKELVQEFFLKLY-E 115

Query: 129 AKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYS 188
              I  ++    +      FLPDRY++G CP C  +D  GD CE C     PT+LINP  
Sbjct: 116 NGDIYLREYEGLYCVSCERFLPDRYVEGTCPKCGGEDARGDQCENCGRTLDPTELINPVC 175

Query: 189 ILSGTKPIIKSSKHFFFKLSDKRCIDFLRKW 219
           ++SG  P ++  +H+FF+LS  +  D L +W
Sbjct: 176 VISGATPEVREEEHYFFRLS--KFQDKLLEW 204

Length = 558

>gnl|CDD|232957 TIGR00398, metG, methionyl-tRNA synthetase

 Score =  208 bits (530), Expect = 3e-64
 Identities = 80/206 (38%), Positives = 115/206 (55%), Gaps = 8/206 (3%)

Query: 14  IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIA 73
           I +TTALPYANG+ H+GH    I AD++ R++ ++        V F+C  D HG  I + 
Sbjct: 1   ILITTALPYANGKPHLGHAYTTILADVYARYKRLRGYE-----VLFVCGTDEHGTKIELK 55

Query: 74  AEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLII 133
           AE+ G+TPKE ++      K       I FD +  T   E+ ++VQKI+  L      I 
Sbjct: 56  AEQEGLTPKELVDKYHEEFKDDWKWLNISFDRFIRTTDEEHKEIVQKIFQKLKEN-GYIY 114

Query: 134 NKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGT 193
            K+I Q + P   +FLPDRY++G CP C ++D  GD CE C     PT+LINP   + G 
Sbjct: 115 EKEIKQLYCPECEMFLPDRYVEGTCPKCGSEDARGDHCEVCGRHLEPTELINPRCKICGA 174

Query: 194 KPIIKSSKHFFFKLSDKRCIDFLRKW 219
           KP ++ S+H+FF+LS       L +W
Sbjct: 175 KPELRDSEHYFFRLS--AFEKELEEW 198

The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to This model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (small) subunit; this model does not include the C-terminal region corresponding to the beta chain [Protein synthesis, tRNA aminoacylation]. Length = 530

>gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA synthetases

 Score =  139 bits (354), Expect = 3e-40
 Identities = 49/207 (23%), Positives = 79/207 (38%), Gaps = 53/207 (25%)

Query: 13  RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMI 72
           ++ +TTALPY NG  H+GH+   + AD++ R+Q +     +   V F+   D HG  I  
Sbjct: 1   KVLITTALPYVNGVPHLGHLYGTVLADVFARYQRL-----RGYDVLFVTGTDEHGTKIEQ 55

Query: 73  AAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLI 132
            AE+ G+TP+E  +      K       I FD +  T S  + ++VQ+ +  LY     I
Sbjct: 56  KAEEEGVTPQELCDKYHEIFKDLFKWLNISFDYFIRTTSPRHKEIVQEFFKKLYEN-GYI 114

Query: 133 INKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSG 192
              +    +      FL                                           
Sbjct: 115 YEGEYEGLYCVSCERFL------------------------------------------- 131

Query: 193 TKPIIKSSKHFFFKLSDKRCIDFLRKW 219
             P  +  +H+FF+LS  +  D L +W
Sbjct: 132 --PEWREEEHYFFRLSKFQ--DRLLEW 154

Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function. Length = 319

>gnl|CDD|215329 PLN02610, PLN02610, probable methionyl-tRNA synthetase

 Score =  112 bits (282), Expect = 2e-28
 Identities = 64/205 (31%), Positives = 97/205 (47%), Gaps = 12/205 (5%)

Query: 12  RRIFVTTALPYANGELHIGHIME-YIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
           R I +T+ALPY N   H+G+I+   + AD++ R+  ++  N       +IC  D +G A 
Sbjct: 17  RNILITSALPYVNNVPHLGNIIGCVLSADVFARYCRLRGYN-----AIYICGTDEYGTAT 71

Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAK 130
              A +   TPKE  +   +  K+  D F I FD +  T + +  ++ Q I+  L     
Sbjct: 72  ETKALEENCTPKEICDKYHAIHKEVYDWFDISFDKFGRTSTPQQTEICQAIFKKLMENNW 131

Query: 131 LIINKKINQFFDPIKNIFLPDRYIKGECPI--CNAKDQYGDFCECCSSIYTPTKLINPYS 188
           L  N  + Q +      FL DR ++G CP   CN     GD CE C  +  PT+LI+P  
Sbjct: 132 LSENT-MQQLYCDTCQKFLADRLVEGTCPTEGCNYDSARGDQCEKCGKLLNPTELIDPKC 190

Query: 189 ILSGTKPIIKSSKHFFF---KLSDK 210
            +    P I+ + H F     L DK
Sbjct: 191 KVCKNTPRIRDTDHLFLELPLLKDK 215

Length = 801

>gnl|CDD|237012 PRK11893, PRK11893, methionyl-tRNA synthetase; Reviewed

 Score = 93.8 bits (234), Expect = 4e-22
 Identities = 54/222 (24%), Positives = 95/222 (42%), Gaps = 42/222 (18%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           ++ ++TT + Y NG+ HIGH    + AD+  RF+ ++   G    V+F+   D HG  I 
Sbjct: 1   KKFYITTPIYYPNGKPHIGHAYTTLAADVLARFKRLR---GYD--VFFLTGTDEHGQKIQ 55

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
             AE+AG++P+E  +  S+  K+  +   I +D++  T    + + VQ+I+  L      
Sbjct: 56  RKAEEAGISPQELADRNSAAFKRLWEALNISYDDFIRTTDPRHKEAVQEIFQRLLA---- 111

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQY-GDFCECCSSIYTPTKLINP--YS 188
                                   G+  I     +Y G +C  C   YT ++LI      
Sbjct: 112 -----------------------NGD--IY--LGKYEGWYCVRCEEFYTESELIEDGYRC 144

Query: 189 ILSGTKPIIKSSKHFFFKLSDKRCIDFLRK-WAIHDKRLQPE 229
             +G        + +FF+LS     D L + +  +   +QP 
Sbjct: 145 PPTGAPVEWVEEESYFFRLSKY--QDKLLELYEANPDFIQPA 184

Length = 511

>gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases

 Score = 90.2 bits (224), Expect = 2e-21
 Identities = 42/131 (32%), Positives = 60/131 (45%), Gaps = 20/131 (15%)

Query: 13  RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMI 72
           + +VTT  PYANG LH+GH + +I AD   R++ M+        V F+   D HG  I +
Sbjct: 1   KFYVTTPPPYANGSLHLGHALTHIIADFIARYKRMRGYE-----VPFLPGWDTHGLPIEL 55

Query: 73  AAEKAGM-------------TPKEFINNISSNRKKYLDGFYIKFD--NWYSTDSIENIDL 117
            AE+ G               PKEF+  +S   K+      I +D  + Y T   E    
Sbjct: 56  KAERKGGRKKKTIWIEEFREDPKEFVEEMSGEHKEDFRRLGISYDWSDEYITTEPEYSKA 115

Query: 118 VQKIYDTLYNK 128
           V+ I+  LY K
Sbjct: 116 VELIFSRLYEK 126

Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function. Length = 312

>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed

 Score = 81.8 bits (203), Expect = 6e-18
 Identities = 57/196 (29%), Positives = 92/196 (46%), Gaps = 38/196 (19%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           ++TT + Y NG+ HIGH    I AD   R++ +Q   G    V+F+   D HG  I  AA
Sbjct: 7   YITTPIYYPNGKPHIGHAYTTIAADALARYKRLQ---GY--DVFFLTGTDEHGQKIQQAA 61

Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN 134
           EKAG TP+E+++ IS+  K+      I +D +  T    +  +VQKI++ LY +      
Sbjct: 62  EKAGKTPQEYVDEISAGFKELWKKLDISYDKFIRTTDERHKKVVQKIFEKLYEQG----- 116

Query: 135 KKINQFFDPIKNIFLPDRYIKGECPICNAKDQY-GDFCECCSSIYTPTKLIN-PYSILSG 192
                           D Y KGE         Y G +C  C + +T ++L++       G
Sbjct: 117 ----------------DIY-KGE---------YEGWYCVSCETFFTESQLVDGGKCPDCG 150

Query: 193 TKPIIKSSKHFFFKLS 208
            +  +   + +FF++S
Sbjct: 151 REVELVKEESYFFRMS 166

Length = 648

>gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA synthetases

 Score = 60.3 bits (147), Expect = 8e-11
 Identities = 34/118 (28%), Positives = 49/118 (41%), Gaps = 11/118 (9%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           ++    PY +G LH+GH+  Y   DI  R++ MQ   G    V F    DA G     AA
Sbjct: 3   YILVMFPYPSGALHVGHVRTYTIGDIIARYKRMQ---GY--NVLFPMGFDAFGLPAENAA 57

Query: 75  EKAGMTP----KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNK 128
            K G  P    +  I  +    K+   GF   +   ++T   E     Q ++  LY K
Sbjct: 58  IKIGRDPEDWTEYNIKKMKEQLKRM--GFSYDWRREFTTCDPEYYKFTQWLFLKLYEK 113

Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. Length = 314

>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase

 Score = 52.1 bits (125), Expect = 7e-08
 Identities = 29/107 (27%), Positives = 49/107 (45%), Gaps = 25/107 (23%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI-------MIA 73
           PYANG+LHIGH +  I  D   R+Q +Q      ++V+++   D HG  I       +  
Sbjct: 41  PYANGDLHIGHALNKILKDFINRYQLLQ-----GKKVHYVPGWDCHGLPIELKVLQSLDQ 95

Query: 74  AEKAGMTP-----------KEFINNISSNRKKYLDGFYIKFDNWYST 109
             +  +TP           K+ ++    + K+Y  G +  ++N Y T
Sbjct: 96  EARKELTPIKLRAKAAKFAKKTVDTQRESFKRY--GVWGDWENPYLT 140

Length = 974

>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 51.9 bits (125), Expect = 9e-08
 Identities = 34/121 (28%), Positives = 48/121 (39%), Gaps = 11/121 (9%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
            + +V    PY +G LH+GH+  Y   D+  R++ MQ  N     V      DA G    
Sbjct: 34  EKFYVLVMFPYPSGALHVGHVRNYTIGDVIARYKRMQGYN-----VLHPMGWDAFGLPAE 88

Query: 72  IAAEKAGMTPK----EFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYN 127
            AA K G  P       I  +    K    GF I +   ++T   E    +Q  +  LY 
Sbjct: 89  NAAIKIGTDPAKWTYYNIAYMKKQLKSL--GFSIDWRREFATCDPEYYKWIQWQFLKLYE 146

Query: 128 K 128
           K
Sbjct: 147 K 147

Length = 814

>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA synthetases

 Score = 49.2 bits (118), Expect = 5e-07
 Identities = 34/127 (26%), Positives = 49/127 (38%), Gaps = 24/127 (18%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAG-- 78
           PYANG  H GH +  I  DI  R++ MQ        V      D HG  I +  EK    
Sbjct: 10  PYANGLPHYGHALNKILKDIINRYKTMQ-----GYYVPRRPGWDCHGLPIELKVEKELGI 64

Query: 79  --------MTPKEFINNISSNRKKYLD---------GFYIKFDNWYSTDSIENIDLVQKI 121
                   M   EF         +Y+D         G ++ ++N Y T   E ++ V  +
Sbjct: 65  SGKKDIEKMGIAEFNAKCREFALRYVDEQEEQFQRLGVWVDWENPYKTMDPEYMESVWWV 124

Query: 122 YDTLYNK 128
           +  L+ K
Sbjct: 125 FKQLHEK 131

Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. Length = 338

>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase

 Score = 48.5 bits (116), Expect = 1e-06
 Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-GM 79
           PYANG +H+GH +  I  DI +R++ MQ   G    V      D HG  I    EK  G+
Sbjct: 45  PYANGSIHLGHALNKILKDIILRYKTMQ---GF--NVTRKPGWDTHGLPIEHKVEKKLGI 99

Query: 80  TPKEFINNIS 89
           + K+ I+++ 
Sbjct: 100 SGKKEISSLE 109

The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms [Protein synthesis, tRNA aminoacylation]. Length = 861

>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 46.8 bits (112), Expect = 4e-06
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 5/56 (8%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK 76
           PYANG +HIGH +  I  DI VR++ MQ   G    V ++   D HG  I +  EK
Sbjct: 58  PYANGNIHIGHALNKILKDIIVRYKTMQ---GYD--VPYVPGWDCHGLPIELKVEK 108

Length = 933

>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase

 Score = 46.2 bits (109), Expect = 6e-06
 Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 5/111 (4%)

Query: 16  VTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAE 75
           +TT L Y N   H+G     I AD   RFQ +       ++V FI   D HG  I  +A 
Sbjct: 73  LTTPLYYVNAPPHMGSAYTTIAADSIARFQRLL-----GKKVIFITGTDEHGEKIATSAA 127

Query: 76  KAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLY 126
             G  P E  + IS + +       I +D +  T   ++  +V++ Y  ++
Sbjct: 128 ANGRNPPEHCDIISQSYRTLWKDLDIAYDKFIRTTDPKHEAIVKEFYARVF 178

Length = 616

>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed

 Score = 43.3 bits (103), Expect = 7e-05
 Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 7/48 (14%)

Query: 21 PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYF-ICADDAHG 67
          P  +G LHIGH+  Y   D   R+Q M+  N     V+F    DD +G
Sbjct: 47 PTVSGSLHIGHVFSYTHTDFIARYQRMRGYN-----VFFPQGWDD-NG 88

Length = 800

>gnl|CDD|232955 TIGR00395, leuS_arch, leucyl-tRNA synthetase, archaeal and cytosolic family

 Score = 42.9 bits (101), Expect = 8e-05
 Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 5/67 (7%)

Query: 10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAA 69
          D  + F+T A PY NG +H GH   +   ++  RF+ M+  N     V F       G  
Sbjct: 23 DREKFFLTMAYPYLNGVMHAGHCRTFTIPEVSARFERMKGKN-----VLFPLGFHVTGTP 77

Query: 70 IMIAAEK 76
          I+  AE 
Sbjct: 78 ILGLAEL 84

The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS [Protein synthesis, tRNA aminoacylation]. Length = 938

>gnl|CDD|215739 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V)

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 30/127 (23%), Positives = 47/127 (37%), Gaps = 24/127 (18%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK---- 76
           P A G LHIGH +     DI +R++ MQ   G    V ++   D HG       EK    
Sbjct: 32  PNATGLLHIGHALNKTLKDIVIRYKRMQ---GFD--VLWVPGWDHHGLPTEQKVEKKLGI 86

Query: 77  ------AGMTPKEFINNISSNRKKYLD---------GFYIKFDNWYSTDSIENIDLVQKI 121
                   +  ++F       + +Y D         G    +D  Y T        V ++
Sbjct: 87  KGKKDRHKLGREKFREKCREWKMEYADEIRSQFKRLGVSGDWDREYFTLDPGLEAAVWRV 146

Query: 122 YDTLYNK 128
           +  L++K
Sbjct: 147 FVRLHDK 153

Other tRNA synthetase sub-families are too dissimilar to be included. Length = 606

>gnl|CDD|237514 PRK13804, ileS, isoleucyl-tRNA synthetase; Provisional

 Score = 40.7 bits (96), Expect = 5e-04
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 21 PYANGELHIGHIMEYIQADIWVRFQCMQ 48
          PYANG +HIGH +  I  D+ VR + M 
Sbjct: 63 PYANGNIHIGHALNKILKDVIVRSKQML 90

Length = 961

>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed

 Score = 40.5 bits (96), Expect = 5e-04
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 11/70 (15%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK---- 76
           PYANG++HIGH +  I  DI V+ + M    G      ++   D HG  I +  EK    
Sbjct: 58  PYANGDIHIGHALNKILKDIIVKSKTMS---GF--DAPYVPGWDCHGLPIELKVEKKLGK 112

Query: 77  --AGMTPKEF 84
               ++  EF
Sbjct: 113 KGKKLSAAEF 122

Length = 912

>gnl|CDD|185677 cd00817, ValRS_core, catalytic core domain of valyl-tRNA synthetases

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 21 PYANGELHIGHIMEYIQADIWVRFQCMQQDN 51
          P   G LH+GH +     DI  R++ M+  N
Sbjct: 10 PNVTGSLHMGHALNNTIQDIIARYKRMKGYN 40

Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. Length = 382

>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 21 PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK 76
          P   G LH+GH + Y   DI  R++ M+  N     V +    D  G A  +  EK
Sbjct: 42 PNVTGSLHMGHALNYTLQDILARYKRMRGYN-----VLWPPGTDHAGIATQVVVEK 92

Length = 877

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	232
COG0143	558	MetG Methionyl-tRNA synthetase [Translation, ribos	100.0
PF09334	391	tRNA-synt_1g: tRNA synthetases class I (M); InterP	100.0
PLN02610	801	probable methionyl-tRNA synthetase	100.0
PRK00133	673	metG methionyl-tRNA synthetase; Reviewed	100.0
PRK12268	556	methionyl-tRNA synthetase; Reviewed	100.0
TIGR00398	530	metG methionyl-tRNA synthetase. The methionyl-tRNA	100.0
PLN02224	616	methionine-tRNA ligase	100.0
PRK12267	648	methionyl-tRNA synthetase; Reviewed	100.0
cd00817	382	ValRS_core catalytic core domain of valyl-tRNA syn	100.0
PRK11893	511	methionyl-tRNA synthetase; Reviewed	100.0
KOG0436|consensus	578		100.0
PLN02563	963	aminoacyl-tRNA ligase	100.0
TIGR00396	842	leuS_bact leucyl-tRNA synthetase, eubacterial and	100.0
cd00814	319	MetRS_core catalytic core domain of methioninyl-tR	100.0
KOG1247|consensus	567		100.0
PRK13208	800	valS valyl-tRNA synthetase; Reviewed	100.0
PRK00390	805	leuS leucyl-tRNA synthetase; Validated	100.0
TIGR00422	861	valS valyl-tRNA synthetase. The valyl-tRNA synthet	100.0
COG0495	814	LeuS Leucyl-tRNA synthetase [Translation, ribosoma	100.0
PRK05729	874	valS valyl-tRNA synthetase; Reviewed	100.0
cd00812	314	LeuRS_core catalytic core domain of leucyl-tRNA sy	100.0
cd00818	338	IleRS_core catalytic core domain of isoleucyl-tRNA	100.0
KOG0435|consensus	876		100.0
cd00668	312	Ile_Leu_Val_MetRS_core catalytic core domain of is	100.0
PLN02943	958	aminoacyl-tRNA ligase	99.98
PRK05743	912	ileS isoleucyl-tRNA synthetase; Reviewed	99.98
TIGR00392	861	ileS isoleucyl-tRNA synthetase. The isoleucyl tRNA	99.97
PRK06039	975	ileS isoleucyl-tRNA synthetase; Reviewed	99.97
PRK13804	961	ileS isoleucyl-tRNA synthetase; Provisional	99.97
PF00133	601	tRNA-synt_1: tRNA synthetases class I (I, L, M and	99.97
PLN02882	1159	aminoacyl-tRNA ligase	99.97
PLN02843	974	isoleucyl-tRNA synthetase	99.97
PTZ00427	1205	isoleucine-tRNA ligase, putative; Provisional	99.97
PLN02381	1066	valyl-tRNA synthetase	99.97
TIGR00395	938	leuS_arch leucyl-tRNA synthetase, archaeal and cyt	99.97
PTZ00419	995	valyl-tRNA synthetase-like protein; Provisional	99.96
PRK14900	1052	valS valyl-tRNA synthetase; Provisional	99.96
COG0525	877	ValS Valyl-tRNA synthetase [Translation, ribosomal	99.96
COG0060	933	IleS Isoleucyl-tRNA synthetase [Translation, ribos	99.96
PLN02959	1084	aminoacyl-tRNA ligase	99.95
TIGR03447	411	mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-	99.94
PRK12418	384	cysteinyl-tRNA synthetase; Provisional	99.93
PRK00260	463	cysS cysteinyl-tRNA synthetase; Validated	99.93
cd00671	212	ArgRS_core catalytic core domain of arginyl-tRNA s	99.93
TIGR00435	465	cysS cysteinyl-tRNA synthetase. This model finds t	99.93
cd00674	353	LysRS_core_class_I catalytic core domain of class	99.92
PLN02946	557	cysteine-tRNA ligase	99.92
PRK14536	490	cysS cysteinyl-tRNA synthetase; Provisional	99.92
PRK14535	699	cysS cysteinyl-tRNA synthetase; Provisional	99.91
PRK12300	897	leuS leucyl-tRNA synthetase; Reviewed	99.9
PTZ00399	651	cysteinyl-tRNA-synthetase; Provisional	99.89
PRK14534	481	cysS cysteinyl-tRNA synthetase; Provisional	99.89
cd00672	213	CysRS_core catalytic core domain of cysteinyl tRNA	99.89
PRK01611	507	argS arginyl-tRNA synthetase; Reviewed	99.89
PF01406	300	tRNA-synt_1e: tRNA synthetases class I (C) catalyt	99.86
PRK00750	510	lysK lysyl-tRNA synthetase; Reviewed	99.86
KOG0432|consensus	995		99.85
KOG0433|consensus	937		99.82
COG0215	464	CysS Cysteinyl-tRNA synthetase [Translation, ribos	99.81
KOG0434|consensus	1070		99.8
TIGR00467	515	lysS_arch lysyl-tRNA synthetase, archaeal and spir	99.79
cd00802	143	class_I_aaRS_core catalytic core domain of class I	99.72
KOG2007|consensus	586		99.68
KOG0437|consensus	1080		99.62
PF00750	354	tRNA-synt_1d: tRNA synthetases class I (R); InterP	99.58
COG0018	577	ArgS Arginyl-tRNA synthetase [Translation, ribosom	99.57
TIGR00456	566	argS arginyl-tRNA synthetase. This model recognize	99.57
PRK12451	562	arginyl-tRNA synthetase; Reviewed	99.56
PF01921	360	tRNA-synt_1f: tRNA synthetases class I (K); InterP	99.53
COG1384	521	LysS Lysyl-tRNA synthetase (class I) [Translation,	99.47
PLN02286	576	arginine-tRNA ligase	99.46
cd09287	240	GluRS_non_core catalytic core domain of non-discri	99.34
PRK04156	567	gltX glutamyl-tRNA synthetase; Provisional	99.25
TIGR00463	560	gltX_arch glutamyl-tRNA synthetase, archaeal and e	99.21
cd00807	238	GlnRS_core catalytic core domain of glutaminyl-tRN	99.14
PRK12558	445	glutamyl-tRNA synthetase; Provisional	99.13
PLN03233	523	putative glutamate-tRNA ligase; Provisional	99.11
COG0008	472	GlnS Glutamyl- and glutaminyl-tRNA synthetases [Tr	99.09
PTZ00402	601	glutamyl-tRNA synthetase; Provisional	99.08
TIGR03838	272	queuosine_YadB glutamyl-queuosine tRNA(Asp) synthe	99.08
PTZ00437	574	glutaminyl-tRNA synthetase; Provisional	99.05
PRK05710	299	glutamyl-Q tRNA(Asp) synthetase; Reviewed	99.05
PF00749	314	tRNA-synt_1c: tRNA synthetases class I (E and Q),	99.03
PLN02907	722	glutamate-tRNA ligase	99.03
TIGR00440	522	glnS glutaminyl-tRNA synthetase. This protein is a	98.97
cd00418	230	GlxRS_core catalytic core domain of glutamyl-tRNA	98.97
PRK05347	554	glutaminyl-tRNA synthetase; Provisional	98.96
TIGR00464	470	gltX_bact glutamyl-tRNA synthetase, bacterial fami	98.94
PRK12410	433	glutamylglutaminyl-tRNA synthetase; Provisional	98.93
PRK14895	513	gltX glutamyl-tRNA synthetase; Provisional	98.92
PRK14703	771	glutaminyl-tRNA synthetase/YqeY domain fusion prot	98.91
PLN02859	788	glutamine-tRNA ligase	98.89
PRK01406	476	gltX glutamyl-tRNA synthetase; Reviewed	98.89
PLN02627	535	glutamyl-tRNA synthetase	98.87
cd00808	239	GluRS_core catalytic core domain of discriminating	98.86
KOG1147|consensus	712		98.54
KOG4426|consensus	656		98.39
KOG1195|consensus	567		98.24
KOG1148|consensus	764		97.63
KOG1149|consensus	524		97.61
PRK12285	368	tryptophanyl-tRNA synthetase; Reviewed	96.83
PLN02486	383	aminoacyl-tRNA ligase	96.72
COG0180	314	TrpS Tryptophanyl-tRNA synthetase [Translation, ri	96.25
PRK14714	1337	DNA polymerase II large subunit; Provisional	96.24
PRK12284	431	tryptophanyl-tRNA synthetase; Reviewed	95.95
COG1656	165	Uncharacterized conserved protein [Function unknow	95.87
TIGR00233	328	trpS tryptophanyl-tRNA synthetase. This model repr	95.84
PRK08560	329	tyrosyl-tRNA synthetase; Validated	95.72
PRK06039	975	ileS isoleucyl-tRNA synthetase; Reviewed	95.72
cd00806	280	TrpRS_core catalytic core domain of tryptophanyl-t	95.34
PF12773	50	DZR: Double zinc ribbon	94.73
PRK04023	1121	DNA polymerase II large subunit; Validated	94.72
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	94.69
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	94.57
PRK14900	1052	valS valyl-tRNA synthetase; Provisional	94.34
PTZ00126	383	tyrosyl-tRNA synthetase; Provisional	94.31
PLN02886	389	aminoacyl-tRNA ligase	94.26
cd00395	273	Tyr_Trp_RS_core catalytic core domain of tyrosinyl	94.25
PF00579	292	tRNA-synt_1b: tRNA synthetases class I (W and Y);	94.15
PRK05912	408	tyrosyl-tRNA synthetase; Validated	94.09
TIGR00392	861	ileS isoleucyl-tRNA synthetase. The isoleucyl tRNA	94.0
PRK00927	333	tryptophanyl-tRNA synthetase; Reviewed	93.62
PF13248	26	zf-ribbon_3: zinc-ribbon domain	93.61
PRK13354	410	tyrosyl-tRNA synthetase; Provisional	93.56
PRK12556	332	tryptophanyl-tRNA synthetase; Provisional	93.05
PLN02882	1159	aminoacyl-tRNA ligase	92.91
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	92.85
PRK12283	398	tryptophanyl-tRNA synthetase; Reviewed	92.84
PTZ00348	682	tyrosyl-tRNA synthetase; Provisional	92.81
PTZ00419	995	valyl-tRNA synthetase-like protein; Provisional	92.25
cd00805	269	TyrRS_core catalytic core domain of tyrosinyl-tRNA	92.21
PRK12282	333	tryptophanyl-tRNA synthetase II; Reviewed	91.4
PTZ00427	1205	isoleucine-tRNA ligase, putative; Provisional	91.4
PRK05743	912	ileS isoleucyl-tRNA synthetase; Reviewed	91.17
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	90.98
PRK14714	1337	DNA polymerase II large subunit; Provisional	90.85
PRK14559	645	putative protein serine/threonine phosphatase; Pro	90.71
TIGR00395	938	leuS_arch leucyl-tRNA synthetase, archaeal and cyt	90.67
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	90.04
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	89.88
PRK14559	645	putative protein serine/threonine phosphatase; Pro	89.86
PF12773	50	DZR: Double zinc ribbon	89.4
PF00133	601	tRNA-synt_1: tRNA synthetases class I (I, L, M and	89.29
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	88.45
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	88.45
TIGR00234	377	tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA sy	88.41
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	87.87
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	87.4
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	87.18
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	87.01
COG0060	933	IleS Isoleucyl-tRNA synthetase [Translation, ribos	86.87
KOG2713|consensus	347		86.86
PRK05978	148	hypothetical protein; Provisional	86.11
PLN02843	974	isoleucyl-tRNA synthetase	85.91
COG0162	401	TyrS Tyrosyl-tRNA synthetase [Translation, ribosom	85.73
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	85.26
PRK06266	178	transcription initiation factor E subunit alpha; V	84.49
PRK13804	961	ileS isoleucyl-tRNA synthetase; Provisional	84.4
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	84.37
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	83.99
COG5349	126	Uncharacterized protein conserved in bacteria [Fun	83.68
PF03833	900	PolC_DP2: DNA polymerase II large subunit DP2; Int	83.21
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	82.9
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	82.55
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	81.61
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	81.35
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	80.98
PRK12496	164	hypothetical protein; Provisional	80.66
PRK12300	897	leuS leucyl-tRNA synthetase; Reviewed	80.57
PRK00420	112	hypothetical protein; Validated	80.43

>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3e-61  Score=451.32  Aligned_cols=211  Identities=36%  Similarity=0.736  Sum_probs=205.1

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      .+++++||+|+|||||+|||||++++|.||+++||+|++|     ++|.|++|+|+||+||+.+|+++|++|++++++++
T Consensus         3 ~~~~~~VTtalpY~Ng~~HlGH~~~~l~ADv~aRy~Rl~G-----~~v~fvtGtDeHGt~I~~~A~~~g~tP~el~d~~~   77 (558)
T COG0143           3 MMKKILVTTALPYPNGPPHLGHLYTYLAADVYARYLRLRG-----YEVFFLTGTDEHGTKIELKAEKEGITPQELVDKNH   77 (558)
T ss_pred             CCCcEEEecCCCCCCCCcchhhHHHHHHHHHHHHHHHhcC-----CeEEEEeccCCCCCHHHHHHHHcCCCHHHHHHHHH
Confidence            3578999999999999999999999999999999999999     99999999999999999999999999999999999


Q ss_pred             HHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCC
Q psy2399          90 SNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGD  169 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~  169 (232)
                      +.+++++++|+|++|.|+||+++.|.+.++++|.+|+ ++|+||.++..+|||++|++||+|++|+|+||+|+...++||
T Consensus        78 ~~~~~~~~~l~IsfD~F~rTt~~~h~~~vq~~f~~L~-~~G~I~~~~~~~~Yc~~~e~fl~dr~v~g~cp~cg~~~arGD  156 (558)
T COG0143          78 EEFKELFKALNISFDNFIRTTSPEHKELVQEFFLKLY-ENGDIYLREYEGLYCVSCERFLPDRYVEGTCPKCGGEDARGD  156 (558)
T ss_pred             HHHHHHHHHhCCcccccccCCCHHHHHHHHHHHHHHH-HCCCEeccceeeeEcccccccccchheeccCCCcCccccCcc
Confidence            9999999999999999999999999999999999999 999999999999999999999999999999999999999999


Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc--CCCCCCC
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH--DKRLQPE  229 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~--~~~~~p~  229 (232)
                      +||+||+.++|.+|++|+|.+||++||+|+++||||+|  ++|+++|++| ++  +.++.|.
T Consensus       157 ~Ce~Cg~~~~P~~l~~p~~~i~g~~p~~r~~~hyFf~L--~~~~~~L~~~-~~~~~~~~~p~  215 (558)
T COG0143         157 QCENCGRTLDPTELINPVCVISGATPEVREEEHYFFRL--SKFQDKLLEW-YESNPDFIWPA  215 (558)
T ss_pred             hhhhccCcCCchhcCCCeeEeeCCCcccccceeEEEEH--HHhHHHHHHH-HHhCccccCCh
Confidence            99999999999999999999999999999999999999  9999999999 64  3566664

>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6

Probab=100.00  E-value=2.7e-58  Score=419.79  Aligned_cols=199  Identities=34%  Similarity=0.757  Sum_probs=183.9

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      |+||+|+|||||+|||||+++++.||+++||+|++|     ++|.+++|+|+||++|+.+|+++|++|+++++++++.|+
T Consensus         1 ~~ITt~~pY~Ng~lHlGH~~~~l~ADv~aR~~r~~G-----~~v~~~tGtDehG~~i~~~A~~~g~~p~~~~~~~~~~~~   75 (391)
T PF09334_consen    1 FYITTPIPYPNGDLHLGHLYPYLAADVLARYLRLRG-----HDVLFVTGTDEHGSKIETAAEKQGIDPEEFCDKYSAKFK   75 (391)
T ss_dssp             EEEEEEEEETSSS-BHHHHHHHHHHHHHHHHHHHTT------EEEEEEEEE-SSHHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred             CEEecCCCCCCCCCCCChhHHHHHHHHHHHHHhhcc-----cceeeEEecchhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999     999999999999999999999999999999999999999


Q ss_pred             HHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCcc
Q psy2399          94 KYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCEC  173 (232)
Q Consensus        94 ~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~  173 (232)
                      ++|++|||++|.|++|+++.|.+.|+++|.+|+ ++|+||+++..+|||+.|++||+|++|+|+||+|+...++|++||+
T Consensus        76 ~~~~~~~I~~D~F~rTt~~~h~~~v~~i~~~L~-~~G~I~~~~~~~~Yc~~~e~fl~e~~v~g~CP~C~~~~a~g~~Ce~  154 (391)
T PF09334_consen   76 ELLEALNISYDRFIRTTDDRHKEFVQEIFKRLY-DNGYIYKREYEGWYCPSCERFLPESFVEGTCPYCGSDKARGDQCEN  154 (391)
T ss_dssp             HHHHHTT---SEEEETTSHHHHHHHHHHHHHHH-HTTSEEEEEEEEEEETTTTEEE-GGGETCEETTT--SSCTTTEETT
T ss_pred             HHHHHcCCCCcceeCCCCHHHHHHHHHHHHHHH-hcCceeecccceeEecCcCcccccceeeccccCcCccccCCCcccC
Confidence            999999999999999999999999999999999 9999999999999999999999999999999999988899999999


Q ss_pred             CCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhh
Q psy2399         174 CSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWA  220 (232)
Q Consensus       174 Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~  220 (232)
                      ||+.+++++|++|+|++||++++++++++|||+|  ++|+++|++|+
T Consensus       155 cG~~~~~~~l~~p~~~~~g~~~~~r~e~~~ff~L--~~~~~~L~~~l  199 (391)
T PF09334_consen  155 CGRPLEPEELINPVCKICGSPPEVREEENYFFKL--SKFRDQLREWL  199 (391)
T ss_dssp             TSSBEECCCSECEEETTTS-B-EEEEEEEEEE-G--GGGHHHHHHHH
T ss_pred             CCCCcccccccCCccccccccCccccceEEEEeh--HHhHHHHHHHH
Confidence            9999999999999999999999999999999999  99999999994

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 is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....

>PLN02610 probable methionyl-tRNA synthetase

Probab=100.00  E-value=3.4e-57  Score=441.62  Aligned_cols=211  Identities=29%  Similarity=0.568  Sum_probs=202.7

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHh-HHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIME-YIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINN   87 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~-~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~   87 (232)
                      .++++++||+|+|||||+|||||+++ ++.+|+++||+|++|     ++|.|++|+|+||++|+.+|++.|++|++++++
T Consensus        14 ~~~~~~~ITt~~pY~Ng~~HlGH~~~~~l~aDv~aRy~r~~G-----~~v~f~~GtDehG~~i~~~A~~~g~~p~e~~d~   88 (801)
T PLN02610         14 PGKRNILITSALPYVNNVPHLGNIIGCVLSADVFARYCRLRG-----YNAIYICGTDEYGTATETKALEENCTPKEICDK   88 (801)
T ss_pred             CCCCCEEEeCCCCCCCCCcccchhhhhHHHHHHHHHHHHhCC-----CceEecccccCCcHHHHHHHHHcCCCHHHHHHH
Confidence            34578999999999999999999995 788999999999999     999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCC--CCccc
Q psy2399          88 ISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPI--CNAKD  165 (232)
Q Consensus        88 ~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~--c~~~~  165 (232)
                      +++.+++++++|||++|.|++|+++.|.+.|+++|.+|+ ++|+||++++.+|||+.|++||+|++|+|+||.  |++.+
T Consensus        89 ~~~~~~~~~~~l~i~~D~f~rT~~~~h~~~vq~~f~~L~-~~G~Iy~~~~~~~yc~~~e~fl~d~~v~G~CP~~~C~~~~  167 (801)
T PLN02610         89 YHAIHKEVYDWFDISFDKFGRTSTPQQTEICQAIFKKLM-ENNWLSENTMQQLYCDTCQKFLADRLVEGTCPTEGCNYDS  167 (801)
T ss_pred             HHHHHHHHHHHcCCccccCccCCCHHHHHHHHHHHHHHH-HCCCEEEeeEEEeecCCCCCCcchHHhcCcCCccccCccc
Confidence            999999999999999999999999999999999999999 999999999999999999999999999999999  99999


Q ss_pred             cCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCC
Q psy2399         166 QYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQP  228 (232)
Q Consensus       166 ~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p  228 (232)
                      ++|++||+||+.++|.+|++|+|++||+++++++++||||+|  ++|+++|.+| ++++.++|
T Consensus       168 a~Gd~Ce~Cg~~~~p~eLi~p~c~~~g~~~~~~~~~~~ff~L--s~~~~~L~~~-~~~~~~~~  227 (801)
T PLN02610        168 ARGDQCEKCGKLLNPTELIDPKCKVCKNTPRIRDTDHLFLEL--PLLKDKLVEY-INETSVAG  227 (801)
T ss_pred             cccchhhhccccCChhhhcCCcccCCCCcceEEEcceEEEEh--HHHHHHHHHH-HHhCCCCC
Confidence            999999999999999999999999999999999999999999  9999999999 65433443

>PRK00133 metG methionyl-tRNA synthetase; Reviewed

Probab=100.00  E-value=1.9e-54  Score=418.28  Aligned_cols=210  Identities=54%  Similarity=1.005  Sum_probs=202.4

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++++||+|||||||.|||||+++++++|+++||+|++|     ++|.+++|+|+||+||+.+|++.|++|.++++++++.
T Consensus         2 ~~~~itt~~py~ng~~HiGH~~~~l~aDv~aR~~r~~G-----~~V~~~~g~D~hG~~i~~~A~~~g~~p~e~~~~~~~~   76 (673)
T PRK00133          2 RKILVTCALPYANGPIHLGHLVEYIQADIWVRYQRMRG-----HEVLFVCADDAHGTPIMLKAEKEGITPEELIARYHAE   76 (673)
T ss_pred             CCEEEeCCCCCCCCcccccchHHHHHHHHHHHHHHhcC-----CeeEEeCccCCCChHHHHHHHHcCCCHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcC
Q psy2399          92 RKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFC  171 (232)
Q Consensus        92 ~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~C  171 (232)
                      |++++++|||++|.|++|+++.|.+.++++|.+|+ ++|+||++++.+|||+.|++||+|++|.|+||+|++.+++|++|
T Consensus        77 ~~~~~~~l~i~~d~f~rtt~~~h~~~v~~~~~~L~-~~G~iy~~~~~~~y~~~~~~~l~~~~v~g~cp~C~~~d~~g~~c  155 (673)
T PRK00133         77 HKRDFAGFGISFDNYGSTHSEENRELAQEIYLKLK-ENGYIYEKTIEQLYDPEKGMFLPDRFVKGTCPKCGAEDQYGDNC  155 (673)
T ss_pred             HHHHHHHhCCCCCCCccCCcHHHHHHHHHHHHHHH-HCCCEEEeeeEEEEeCCCCCCccchheecccCCCCCcccCCchh
Confidence            99999999999999999999999999999999999 99999999999999999999999999999999999998999999


Q ss_pred             ccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         172 ECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       172 e~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                      |.||+.+++.+|++|+|..||+++|+++++||||+|  ++|+++|.+|+.+...|+|.
T Consensus       156 e~cg~~~~~~~l~~~~~~~~g~~~e~~~~~~~f~~l--~~~~~~l~~~~~~~~~~~~~  211 (673)
T PRK00133        156 EVCGATYSPTELINPKSAISGATPVLKESEHFFFKL--PRFEEFLKEWITRSGELQPN  211 (673)
T ss_pred             hhccccCChHhhcCCccccCCCcceEEecceEEEEH--HHHHHHHHHHHhcCCCCCHH
Confidence            999999999999999999999999999999999999  99999999994333456553

>PRK12268 methionyl-tRNA synthetase; Reviewed

Probab=100.00  E-value=1.8e-52  Score=397.28  Aligned_cols=209  Identities=37%  Similarity=0.734  Sum_probs=201.3

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhH-HHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEY-IQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~-v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      +++++||+|||||||.|||||++++ |.+|+++||+|++|     ++|.+++|+|+||++|+.+|++.|+++.++++++.
T Consensus         2 ~~~~~i~~~~py~ng~~HiGH~~~~~~~~D~~~R~~r~~G-----~~v~~~~g~d~~g~~i~~~a~~~g~~~~~~~~~~~   76 (556)
T PRK12268          2 MMRILITSAWPYANGPLHLGHLAGSGLPADVFARYQRLKG-----NEVLFVSGSDEHGTPIELAAKKEGVTPQELADKYH   76 (556)
T ss_pred             CCcEEEecCCCCCCCCccccccccchhHHHHHHHHHHhcC-----CceEecCcCCCcccHHHHHHHHcCCCHHHHHHHHH
Confidence            4679999999999999999999997 99999999999999     99999999999999999999999999999999999


Q ss_pred             HHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCC
Q psy2399          90 SNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGD  169 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~  169 (232)
                      +.|++++++|||++|.|++|++++|.+.++++|.+|+ ++|+||++++.+|||+.|++||++++|.|+||.|++.+.+|+
T Consensus        77 ~~~~~~~~~l~i~~d~~~~t~~~~~~~~~~~~~~~L~-~~G~~y~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~G~  155 (556)
T PRK12268         77 EEHKEDFKKLGISYDLFTRTTSPNHHEVVQEFFLKLY-ENGYIYKKTIEQAYCPSDGRFLPDRYVEGTCPYCGYEGARGD  155 (556)
T ss_pred             HHHHHHHHHcCCcCCCCcCCCCHHHHHHHHHHHHHHH-HCCCeEEeeeEEEecCCCCcCcCccceeccCCCCCCcccCCc
Confidence            9999999999999999999999999999999999999 999999999999999999999999999999999998888999


Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCC-CCCC
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDK-RLQP  228 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~-~~~p  228 (232)
                      +||.||+.+++.+|++|+|..||++++++++++|||+|  ++|+++|.++ ++.. +++|
T Consensus       156 ~ce~cg~~~~~~~l~~p~~~~~~~~~e~~~~~qwF~~l--~~~~~~l~~~-~~~~~~~p~  212 (556)
T PRK12268        156 QCDNCGALLDPTDLINPRSKISGSTPEFRETEHFFLDL--PAFAERLRAW-IESSGDWPP  212 (556)
T ss_pred             hhhhccccCChHHhcCCccccCCCcCeEEecceEEEEh--HHHHHHHHHH-HhhccCCCH
Confidence            99999999999999999999999999999999999999  9999999999 6543 4444

>TIGR00398 metG methionyl-tRNA synthetase

Probab=100.00  E-value=8.9e-52  Score=390.52  Aligned_cols=200  Identities=40%  Similarity=0.787  Sum_probs=196.8

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      ++||+|||||||.|||||+++++.+|+++||+|++|     ++|.+++|+|+||++|+.+|++.|++|.++++.+.+.|+
T Consensus         1 ~~it~~~P~~ng~lHiGH~~~~~~aDvl~R~~r~~G-----~~V~~v~g~D~~g~~i~~~a~~~g~~~~e~~~~~~~~~~   75 (530)
T TIGR00398         1 ILITTALPYANGKPHLGHAYTTILADVYARYKRLRG-----YEVLFVCGTDEHGTKIELKAEQEGLTPKELVDKYHEEFK   75 (530)
T ss_pred             CEEecCCCCCCCCcccchhHHHHHHHHHHHHHHhcC-----CeEEEecccCCCCcHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999     999999999999999999999999999999999999999


Q ss_pred             HHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCcc
Q psy2399          94 KYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCEC  173 (232)
Q Consensus        94 ~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~  173 (232)
                      +++++|||++|.+++|+++.|...++++|.+|. ++|+||++++.+|||+.|++||+|++|+|.||.|++.+++|++||.
T Consensus        76 ~~l~~LgI~~D~~~~t~~~~~~~~v~~~~~~L~-~kG~iY~~~~~v~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~ce~  154 (530)
T TIGR00398        76 DDWKWLNISFDRFIRTTDEEHKEIVQKIFQKLK-ENGYIYEKEIKQLYCPECEMFLPDRYVEGTCPKCGSEDARGDHCEV  154 (530)
T ss_pred             HHHHHhCCCCCCCccCCCHHHHHHHHHHHHHHH-HCCCEEEeeeEEEecCCCCcCCchhhhcCCCCCCCCcccccchhhh
Confidence            999999999999999999999999999999999 9999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc
Q psy2399         174 CSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH  222 (232)
Q Consensus       174 Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~  222 (232)
                      ||+.+++.+|++|+|..||.++|+++++||||+|  ++|+++|.+| ++
T Consensus       155 cg~~~~~~~l~~p~~~~~~~~~e~~~~~~~f~~l--~~~~~~l~~~-~~  200 (530)
T TIGR00398       155 CGRHLEPTELINPRCKICGAKPELRDSEHYFFRL--SAFEKELEEW-IR  200 (530)
T ss_pred             ccccCCHHHhcCCccccCCCcceEEecceEEEEh--HHHHHHHHHH-HH
Confidence            9999999999999999999999999999999999  9999999999 55

The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma

>PLN02224 methionine-tRNA ligase

Probab=100.00  E-value=6.7e-45  Score=346.66  Aligned_cols=189  Identities=22%  Similarity=0.371  Sum_probs=171.7

Q ss_pred             CCccCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHH
Q psy2399           4 HDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKE   83 (232)
Q Consensus         4 ~~~~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e   83 (232)
                      ++++...+++|+|++|||||||+|||||+++++++|+++||+|++|     ++|.|++|+|+||+||+.+|++.|++|.+
T Consensus        61 ~~~~~~~~~~~~ittp~pY~NG~~HiGHa~~~~~aDviaR~~r~~G-----~~V~fv~G~DehG~kI~~~A~~~g~~p~e  135 (616)
T PLN02224         61 QESTVDEADTFVLTTPLYYVNAPPHMGSAYTTIAADSIARFQRLLG-----KKVIFITGTDEHGEKIATSAAANGRNPPE  135 (616)
T ss_pred             cccCCCCCCeEEEeCCCCCCCCCCchhccHHHHHHHHHHHHHHhcC-----CceEEecCcCCcchHHHHHHHHcCCChHH
Confidence            4455566788999999999999999999999999999999999999     99999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCc
Q psy2399          84 FINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNA  163 (232)
Q Consensus        84 ~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~  163 (232)
                      +++++++.+++.+++|||++|.|++|+++.|.+.|+++|.+|+ ++|+||++++.+|||+                    
T Consensus       136 ~~~~~~~~~~~~~~~l~I~~D~f~rTt~~~h~~~vq~~f~~L~-~~G~Iy~~~~~~~yc~--------------------  194 (616)
T PLN02224        136 HCDIISQSYRTLWKDLDIAYDKFIRTTDPKHEAIVKEFYARVF-ANGDIYRADYEGLYCV--------------------  194 (616)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCcCeeCCCHHHHHHHHHHHHHHH-HCCCEEEeeeeeeecC--------------------
Confidence            9999999999999999999999999999999999999999999 9999999999999954                    


Q ss_pred             cccCCCcCccCCCCCCCccccC-CcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCCC
Q psy2399         164 KDQYGDFCECCSSIYTPTKLIN-PYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQPE  229 (232)
Q Consensus       164 ~~~~g~~Ce~Cg~~~~~~~l~~-~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p~  229 (232)
                               .|++++++.+|++ +.|+.||+++++++++||||+|  ++|+++|++|+.+ +.+++|+
T Consensus       195 ---------~ce~f~~~~~l~~~~~~~~~~~~~~~~~e~~~ff~L--s~~~~~L~~~~~~~~~~~~p~  251 (616)
T PLN02224        195 ---------NCEEYKDEKELLENNCCPVHQMPCVARKEDNYFFAL--SKYQKPLEDILAQNPRFVQPS  251 (616)
T ss_pred             ---------CCCCCCCHHHHcCCCCCCCCCCcceEEecceEEEEh--HHHHHHHHHHHHhCCCccCCH
Confidence                     4555555555553 5788999999999999999999  9999999999432 4578775

>PRK12267 methionyl-tRNA synthetase; Reviewed

Probab=100.00  E-value=5.1e-43  Score=337.81  Aligned_cols=181  Identities=28%  Similarity=0.501  Sum_probs=168.0

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++++||+|+|||||++||||+++++++|+++||+|++|     ++|.|++|+|+||++|+.+|++.|++|+++++++++.
T Consensus         4 ~~~~it~~~py~ng~~HiGH~~~~~~aDv~~R~~r~~G-----~~v~~~~g~D~~g~~i~~~A~~~g~~~~e~~d~~~~~   78 (648)
T PRK12267          4 KTFYITTPIYYPNGKPHIGHAYTTIAADALARYKRLQG-----YDVFFLTGTDEHGQKIQQAAEKAGKTPQEYVDEISAG   78 (648)
T ss_pred             CCEEEeeCCCCCCCCcccccchHHHHHHHHHHHHHhcC-----CceEeecCCCCcchHHHHHHHHcCCCHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcC
Q psy2399          92 RKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFC  171 (232)
Q Consensus        92 ~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~C  171 (232)
                      |+++|++|||++|.|++|+++.|.+.++++|.+|. ++|+||++++.+|||+.|++||+++++                 
T Consensus        79 fk~~l~~lgI~~D~f~rTt~~~h~~~v~~~~~~L~-~kG~IY~~~~~~~yc~~~~~~l~~~~l-----------------  140 (648)
T PRK12267         79 FKELWKKLDISYDKFIRTTDERHKKVVQKIFEKLY-EQGDIYKGEYEGWYCVSCETFFTESQL-----------------  140 (648)
T ss_pred             HHHHHHHcCCCCCCCeeCCCHHHHHHHHHHHHHHH-HCCCEEEeeEEEeecCCCCccCChHHh-----------------
Confidence            99999999999999999999999999999999999 999999999999998888888887764                 


Q ss_pred             ccCCCCCCCccccC-CcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCCC
Q psy2399         172 ECCSSIYTPTKLIN-PYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQPE  229 (232)
Q Consensus       172 e~Cg~~~~~~~l~~-~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p~  229 (232)
                                  ++ |+|+.||+++++++++||||+|  ++|+++|.+|+-+ +.++.|+
T Consensus       141 ------------~~~~~c~~cg~~~e~~~~~~~f~~l--~~~~~~l~~~~~~~~~~~~p~  186 (648)
T PRK12267        141 ------------VDGGKCPDCGREVELVKEESYFFRM--SKYQDRLLEYYEENPDFIQPE  186 (648)
T ss_pred             ------------ccCCcCCCCCCcCeEEecceEEEEc--HHHHHHHHHHHhhCCcccCCH
Confidence                        33 5677788999999999999999  9999999999432 3456665

>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases

Probab=100.00  E-value=2.2e-42  Score=314.78  Aligned_cols=176  Identities=20%  Similarity=0.247  Sum_probs=159.9

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc---------CCCHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA---------GMTPK   82 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~---------g~~~~   82 (232)
                      ++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|+|+||+||+..|++.         +++++
T Consensus         1 ~~f~i~~~pPy~nG~lHiGH~~~~~~~Dv~~Ry~r~~G-----~~V~~~~G~D~hG~pie~~a~k~~~~~~~~~~~~~~~   75 (382)
T cd00817           1 PVFVIDTPPPNVTGSLHMGHALNNTIQDIIARYKRMKG-----YNVLWPPGTDHAGIATQVVVEKKLGIEGKTRHDLGRE   75 (382)
T ss_pred             CcEEEecCCCCCCCcchHHHHHHHHHHHHHHHHHHhcC-----CcccccCccCCCCChHHHHHHHHhcccccchhcCCHH
Confidence            47999999999999999999999999999999999999     99999999999999999999874         45544


Q ss_pred             -------HHHHHHHHHHHHHHhccCCc--CCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccce
Q psy2399          83 -------EFINNISSNRKKYLDGFYIK--FDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRY  153 (232)
Q Consensus        83 -------e~~~~~~~~~~~~l~~lgI~--~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~  153 (232)
                             ++++++++.+++++++|||+  |+++++|+++.|.+.|+++|.+|+ ++|+||++.++++||+.|+++|++++
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~lgi~~Dw~~~~~T~~~~~~~~v~~~f~~L~-~~G~iy~~~~~~~yc~~~~t~l~~~e  154 (382)
T cd00817          76 EFLEKCWEWKEESGGKIREQLKRLGASVDWSREYFTMDPGLSRAVQEAFVRLY-EKGLIYRDNRLVNWCPKLRTAISDIE  154 (382)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCceeecCCCcCCCCHHHHHHHHHHHHHHH-HCCCEEeeeeEEeecCCcCCCCCcch
Confidence                   57899999999999999995  459999999999999999999999 99999999999999999999999988


Q ss_pred             eccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcC--CCCCCC
Q psy2399         154 IKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHD--KRLQPE  229 (232)
Q Consensus       154 v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~--~~~~p~  229 (232)
                      |                                 |..||++++++.++||||+|  ++|+++|.++ +++  ..+.|+
T Consensus       155 v---------------------------------c~~cg~~~~~~~~~qwf~~l--~~~~~~l~~~-~~~~~~~~~P~  196 (382)
T cd00817         155 V---------------------------------CSRSGDVIEPLLKPQWFVKV--KDLAKKALEA-VKEGDIKFVPE  196 (382)
T ss_pred             h---------------------------------cccCCCeEEEEecCeeEEeh--HHHHHHHHHH-HhcCCcEEECh
Confidence            7                                 34478899999999999999  9999999999 654  345554

Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.

>PRK11893 methionyl-tRNA synthetase; Reviewed

Probab=100.00  E-value=6.7e-41  Score=314.87  Aligned_cols=180  Identities=25%  Similarity=0.434  Sum_probs=167.5

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++++|++|||||||.+||||+++++.+|+++||+|++|     ++|.+++|+|+||++|+..|++.|++|.++++++.+.
T Consensus         1 ~~~~i~~~~P~~~g~~HiGh~~~~~~~Dv~~R~~r~~G-----~~v~~v~g~dd~g~~i~~~a~~~g~~~~~~~~~~~~~   75 (511)
T PRK11893          1 KKFYITTPIYYPNGKPHIGHAYTTLAADVLARFKRLRG-----YDVFFLTGTDEHGQKIQRKAEEAGISPQELADRNSAA   75 (511)
T ss_pred             CCEEEecCCCCCCCCcccchhHHHHHHHHHHHHHHhcC-----CcEEecCCCCCCChHHHHHHHHcCCCHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcC
Q psy2399          92 RKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFC  171 (232)
Q Consensus        92 ~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~C  171 (232)
                      |+++|++|||++|.|++|+++.|.+.|+++|.+|. ++|++|+++..+|||+.|+++|+++++.                
T Consensus        76 ~~~~l~~l~I~~D~~~~t~~~~~~~~v~~~~~~L~-~~G~iY~~~~~~~~~~~~~~~l~~~~l~----------------  138 (511)
T PRK11893         76 FKRLWEALNISYDDFIRTTDPRHKEAVQEIFQRLL-ANGDIYLGKYEGWYCVRCEEFYTESELI----------------  138 (511)
T ss_pred             HHHHHHHhCCCcCCceeCCCHHHHHHHHHHHHHHH-HCCCEEEeeeeeeccccccccCCHHHhc----------------
Confidence            99999999999999999999999999999999999 9999999999999977777777776643                


Q ss_pred             ccCCCCCCCccccC--CcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcC--CCCCCC
Q psy2399         172 ECCSSIYTPTKLIN--PYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHD--KRLQPE  229 (232)
Q Consensus       172 e~Cg~~~~~~~l~~--~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~--~~~~p~  229 (232)
                                   +  |.|..||++++++++++|||+|  +.|+++|.++ ++.  ..+.|.
T Consensus       139 -------------~~~p~~~~~~~~~~~~~~~~~f~~l--~~~~~~l~~~-~~~~~~~~~p~  184 (511)
T PRK11893        139 -------------EDGYRCPPTGAPVEWVEEESYFFRL--SKYQDKLLEL-YEANPDFIQPA  184 (511)
T ss_pred             -------------CCCCCCCCCCCcceEEecCeEEEEc--HHHHHHHHHH-HHhCCCccCCH
Confidence                         3  6699999999999999999999  9999999999 543  455554

>KOG0436|consensus

Probab=100.00  E-value=4.9e-40  Score=292.48  Aligned_cols=193  Identities=23%  Similarity=0.393  Sum_probs=177.2

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      ...+++++|||+.|||..+||||+++.+++|+++||++.+|     ..|.|.+|+|+||++|+.+|+..|.+|.+++|++
T Consensus        36 ~~~~~~~lTTPifYvNAaPHlGhlYS~llaDai~R~q~lkg-----~~v~fsTGTDEHGlKIqtaaatnG~~P~e~cDr~  110 (578)
T KOG0436|consen   36 DEGETFVLTTPIFYVNAAPHLGHLYSTLLADAIARFQRLKG-----KKVIFSTGTDEHGLKIQTAAATNGRNPPELCDRI  110 (578)
T ss_pred             cCCceeEEecceeecCCCcchhHHHHHHHHHHHHHHHhhcC-----CceEeecCCCccchhhhhhHhhcCCChHHHHhhh
Confidence            34468999999999999999999999999999999999999     9999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCC
Q psy2399          89 SSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYG  168 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g  168 (232)
                      ++.|.++++.+||.++.|+||++|.|+..|+++|..+. ++|+||++++.+|||++|++|++++.|... |.        
T Consensus       111 s~~f~qL~k~~gi~yt~FIRTTdpkH~a~Vqefw~~~~-knG~iy~g~~eGwYcvsdEtf~pEskv~k~-p~--------  180 (578)
T KOG0436|consen  111 SQSFRQLWKDAGIAYTKFIRTTDPKHEAIVQEFWARVF-KNGDIYRGDYEGWYCVSDETFYPESKVLKN-PC--------  180 (578)
T ss_pred             hHHHHHHHHHhCcchhheeecCCchHHHHHHHHHHHHH-hCCceeeecccceEeccccccCCHHHHhcC-CC--------
Confidence            99999999999999999999999999999999999999 999999999999999999999999998641 11        


Q ss_pred             CcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhh-cCCCCCCCCC
Q psy2399         169 DFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAI-HDKRLQPEIF  231 (232)
Q Consensus       169 ~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~-~~~~~~p~~~  231 (232)
                        |.  |         -+++..+|++++|++|++|||+|  |+|+..|.+|+. ++.||+|+.+
T Consensus       181 --~~--g---------k~vsmEsg~~vv~~kE~NY~FrL--Skfqk~l~d~lrkNP~fvqPs~~  229 (578)
T KOG0436|consen  181 --PP--G---------KVVSMESGNPVVWRKEDNYFFRL--SKFQKPLEDHLRKNPRFVQPSYF  229 (578)
T ss_pred             --CC--C---------ceeeeccCCceeEecccceeeeH--HhhhhHHHHHHhcCCCccCchHH
Confidence              11  1         24566789999999999999999  999999999954 3679999864

>PLN02563 aminoacyl-tRNA ligase

Probab=100.00  E-value=6.4e-40  Score=324.91  Aligned_cols=176  Identities=23%  Similarity=0.274  Sum_probs=162.9

Q ss_pred             CCCCCcEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           8 FKDVRRIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      ++++++|+|+++||||||. |||||+++++++|+++||+||+|     ++|.+++|||+||+|++.+|.+.|..|.++++
T Consensus       106 ~~~k~k~~v~~~~PYpnG~~lHiGH~~~y~~~DviaRy~Rm~G-----~~Vl~~~G~D~~GlPiE~~a~~~g~~p~~~~~  180 (963)
T PLN02563        106 DTSKPKFYVLDMFPYPSGAGLHVGHPEGYTATDILARYKRMQG-----YNVLHPMGWDAFGLPAEQYAIETGTHPKITTL  180 (963)
T ss_pred             cCCCCCEEEEeCCCCCCCcccchhhHHHHHHHHHHHHHHHhcC-----CeecccccccccCcHHHHHHHHcCCChHHhHH
Confidence            3456789999999999996 99999999999999999999999     99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcc
Q psy2399          87 NISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAK  164 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~  164 (232)
                      ++++.++++|++||+  +|+++++|+++.|.++++++|.+|+ ++|+||+++..++|||.                    
T Consensus       181 ~~i~~~~~q~~~lG~s~DW~r~~~T~dp~y~~~~q~~F~~L~-~~GliY~~~~~v~wcp~--------------------  239 (963)
T PLN02563        181 KNIARFRSQLKSLGFSYDWDREISTTEPEYYKWTQWIFLQLL-KRGLAYQAEVPVNWCPA--------------------  239 (963)
T ss_pred             HHHHHHHHHHHHhCcEeeCCCCeecCCHHHHHHHHHHHHHHH-HCCCEEeeeeeeeecCC--------------------
Confidence            999999999999997  6678999999999999999999999 99999999999999554                    


Q ss_pred             ccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhh
Q psy2399         165 DQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWA  220 (232)
Q Consensus       165 ~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~  220 (232)
                               |+..++++|+++++|..||++++.++++||||+|  ++|+++|.++|
T Consensus       240 ---------~~T~La~~Ev~~~~~~~~~~~~~~~~~~q~f~~i--t~ya~~L~~~l  284 (963)
T PLN02563        240 ---------LGTVLANEEVVDGLSERGGHPVIRKPMRQWMLKI--TAYADRLLEDL  284 (963)
T ss_pred             ---------cCCCCCHHHhhcCCCcCCCCceEEEecceeEEec--chhHHHHHHhh
Confidence                     4555555566677888999999999999999999  99999999994

>TIGR00396 leuS_bact leucyl-tRNA synthetase, eubacterial and mitochondrial family

Probab=100.00  E-value=9.5e-40  Score=321.77  Aligned_cols=176  Identities=24%  Similarity=0.316  Sum_probs=164.1

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      .++++++|+++||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+.+|++.|++|.++++++
T Consensus        26 ~~k~k~~v~~~pPy~nG~lHiGH~~~~~~~Dvi~Ry~rm~G-----~~V~~~~G~D~~Glpie~~a~~~g~~p~~~~~~~  100 (842)
T TIGR00396        26 SNKPKYYILDMFPYPSGALHMGHVRNYTITDVLSRYYRMKG-----YNVLHPMGWDAFGLPAENAAIKRGIHPAKWTYEN  100 (842)
T ss_pred             CCCCCEEEEcCCCCCCCccccchhHHHHHHHHHHHHHHhcC-----CceeccCCcCCCChHHHHHHHHcCCCHHHHHHHH
Confidence            45677999999999999999999999999999999999999     9999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcccc
Q psy2399          89 SSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQ  166 (232)
Q Consensus        89 ~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~  166 (232)
                      .+.++++|++||+  +||++++|+++.|.+.++++|.+|+ ++|+||++..+++|||.|+++|++.+|..          
T Consensus       101 ~~~~~~~~~~lG~~~Dw~~~~~T~d~~y~~~~~~~F~~L~-~kGliy~~~~~v~wcp~~~t~La~~ev~~----------  169 (842)
T TIGR00396       101 IANMKKQLQALGFSYDWDREIATCDPEYYKWTQWIFLELF-EKGLAYVKEADVNWCPNDGTVLANEQVDS----------  169 (842)
T ss_pred             HHHHHHHHHHhCCcccCCCCcccCCHHHHHHHHHHHHHHH-HCCCeEeeccceEEeCCCCCCccHHHHhh----------
Confidence            9999999999998  5678999999999999999999999 99999999999999999999999998831          


Q ss_pred             CCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhh
Q psy2399         167 YGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWA  220 (232)
Q Consensus       167 ~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~  220 (232)
                                        ++.|..||.+++.+++++|||+|  ++|+++|.++|
T Consensus       170 ------------------~g~~~~~g~~v~~~~~~~~f~~i--~~~~~~l~~~l  203 (842)
T TIGR00396       170 ------------------DGRSWRGGTPVEKKELKQWFLKI--TAYAEELLNDL  203 (842)
T ss_pred             ------------------cCccccCCCcceEeecceeEEeh--hhhHHHHHHHH
Confidence                              13455677889999999999999  99999999983

The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches.

>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases

Probab=100.00  E-value=1.9e-39  Score=289.11  Aligned_cols=156  Identities=31%  Similarity=0.591  Sum_probs=149.5

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      +++||+|+|||||+|||||+++++++|+++||+|++|     ++|.+++|+|+||+||+.+|+++|++|+++++.+.+.|
T Consensus         1 ~~~it~~~Py~ng~~HlGH~~~~~~~Dv~~R~~r~~G-----~~V~~~~g~Dd~g~~i~~~a~~~g~~~~e~~~~~~~~~   75 (319)
T cd00814           1 KVLITTALPYVNGVPHLGHLYGTVLADVFARYQRLRG-----YDVLFVTGTDEHGTKIEQKAEEEGVTPQELCDKYHEIF   75 (319)
T ss_pred             CEEEEeCCCCCCCCcchhhHHHHHHHHHHHHHHHhCC-----CcccccCccCCCCcHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999     99999999999999999999999999999999999999


Q ss_pred             HHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCc
Q psy2399          93 KKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCE  172 (232)
Q Consensus        93 ~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce  172 (232)
                      +++|++|||++|.|++|+++.|.+.++++|++|. ++|++|+++..++||+.|++||+                      
T Consensus        76 ~~~l~~LgI~~D~~~~tt~~~~~~~v~~i~~~L~-ekG~iY~~~~~~~yc~~~~~~l~----------------------  132 (319)
T cd00814          76 KDLFKWLNISFDYFIRTTSPRHKEIVQEFFKKLY-ENGYIYEGEYEGLYCVSCERFLP----------------------  132 (319)
T ss_pred             HHHHHHcCCcCCCCeeCCCHHHHHHHHHHHHHHH-HCCCEEeeeeeeeECCCCCcEee----------------------
Confidence            9999999999999999999899999999999999 99999999999999776666654                      


Q ss_pred             cCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc
Q psy2399         173 CCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH  222 (232)
Q Consensus       173 ~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~  222 (232)
                                             |+++++||||+|  ++|+++|++| ++
T Consensus       133 -----------------------e~~~~~~~ff~l--~~~~~~l~~~-~~  156 (319)
T cd00814         133 -----------------------EWREEEHYFFRL--SKFQDRLLEW-LE  156 (319)
T ss_pred             -----------------------EEEeeeeEEEEh--HHHHHHHHHH-HH
Confidence                                   899999999999  9999999999 55

Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.

>KOG1247|consensus

Probab=100.00  E-value=5.1e-40  Score=291.90  Aligned_cols=214  Identities=27%  Similarity=0.578  Sum_probs=203.4

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHh-HHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIME-YIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~-~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      ..+.+.++|+++.||+|..+|+|++-+ .+.|||+|||-+.+|     ++..+++|+|+.|..++..|-+.|++|+++++
T Consensus        10 ~~n~rnilitsalpyvnnvphlgNIIg~vlsAdV~Aryc~~r~-----~~~~yicGTDEYgtatetkaleeg~tP~elcd   84 (567)
T KOG1247|consen   10 APNERNILITSALPYVNNVPHLGNIIGSVLSADVFARYCPLRG-----PNTLYICGTDEYGTATETKALEEGLTPQELCD   84 (567)
T ss_pred             CCCccceeeecccceecccccccceeeEEeehhhhcccccCCC-----CceEEeccccccchhhHHHHHHccCCHHHHHH
Confidence            355678999999999999999999995 678999999999999     99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcccc
Q psy2399          87 NISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQ  166 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~  166 (232)
                      +++..++..+++++|++|.|.+|+.+.+.+.+|.+|.+|+ ++|++-+..-.+.||..|++||+|++|+|.||.|+..++
T Consensus        85 Kyh~ihk~vy~Wf~IdfD~fgrtTT~~qT~i~Q~iF~kl~-~ng~~se~tv~qLyC~vc~~fladr~veg~cp~C~yd~A  163 (567)
T KOG1247|consen   85 KYHGIHKVVYDWFKIDFDEFGRTTTKTQTEICQDIFSKLY-DNGYLSEQTVKQLYCEVCDTFLADRFVEGKCPFCGYDDA  163 (567)
T ss_pred             hcchhHHHHHHhhcccccccCcccCcchhHHHHHHhhchh-hcCCcccceeeeEEehhhcccccchhhhccCCCCCCccc
Confidence            9999999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             CCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcC---CCCCCC
Q psy2399         167 YGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHD---KRLQPE  229 (232)
Q Consensus       167 ~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~---~~~~p~  229 (232)
                      +|++|++||..+.+.+|++|+|.+|...|+.+...|+||.|  ++++++|.+|+-++   +.|.++
T Consensus       164 RGDqcd~cG~l~N~~el~~pkc~ic~~~p~~~~t~h~Fl~L--~kl~~~lee~~~~~~~~~~WS~N  227 (567)
T KOG1247|consen  164 RGDQCDKCGKLVNAAELKIPKCKICQAGPVVRQTQHLFLSL--DKLEPRLEEWLRRTLVEGDWSQN  227 (567)
T ss_pred             cchhhhhhhhhcCHHHhcCcchheeccCCeeeeeeEEEEEh--HHhHHHHHHHHHhccccCCCccc
Confidence            99999999999999999999999999999999999999999  99999999995432   346554

>PRK13208 valS valyl-tRNA synthetase; Reviewed

Probab=100.00  E-value=5.2e-39  Score=316.21  Aligned_cols=140  Identities=24%  Similarity=0.319  Sum_probs=132.3

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-cCCCHH------
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-AGMTPK------   82 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~g~~~~------   82 (232)
                      ++++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+.+|++ +|++++      
T Consensus        36 ~~~~f~i~~ppPy~nG~lHiGH~~~~~~~D~~~R~~r~~G-----~~v~~~~G~D~~Glpie~~~ek~~g~~~~~~~~~~  110 (800)
T PRK13208         36 RKPVYSIDTPPPTVSGSLHIGHVFSYTHTDFIARYQRMRG-----YNVFFPQGWDDNGLPTERKVEKYYGIRKDDISREE  110 (800)
T ss_pred             CCCcEEEecCcCCCCCCccHHHHHhHHHHHHHHHHHHcCC-----CcccCCCCcCCCcchHHHHHHHHhCCCcccCCHHH
Confidence            3577999999999999999999999999999999999999     9999999999999999999998 588876      


Q ss_pred             ------HHHHHHHHHHHHHHhccCCc--CCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccccccee
Q psy2399          83 ------EFINNISSNRKKYLDGFYIK--FDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYI  154 (232)
Q Consensus        83 ------e~~~~~~~~~~~~l~~lgI~--~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v  154 (232)
                            ++++++.+.++++|++||++  |+++++|+++.|.+.++++|.+|+ ++|+||++.+.++|||.|+|+|+|.+|
T Consensus       111 f~~~~~~~~~~~~~~~~~~~~~lg~s~Dw~~~~~T~d~~~~~~v~~~f~~L~-~~Gliy~~~~~v~wcp~~~t~Lsd~ev  189 (800)
T PRK13208        111 FIELCRELTDEDEKKFRELWRRLGLSVDWSLEYQTISPEYRRISQKSFLDLY-KKGLIYRAEAPVLWCPRCETAIAQAEV  189 (800)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCeeeccCCCcccCCHHHHHHHHHHHHHHH-HCCCeeecCcccccCCCCCCccchhhh
Confidence                  58999999999999999994  558999999999999999999999 999999999999999999999999966


Q ss_pred             c
Q psy2399         155 K  155 (232)
Q Consensus       155 ~  155 (232)
                      +
T Consensus       190 ~  190 (800)
T PRK13208        190 E  190 (800)
T ss_pred             c
Confidence            3

>PRK00390 leuS leucyl-tRNA synthetase; Validated

Probab=100.00  E-value=1e-38  Score=313.60  Aligned_cols=172  Identities=25%  Similarity=0.331  Sum_probs=161.2

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++++|+++||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+.+|++.|++|.++++++.+.
T Consensus        32 ~~~~i~~~pPy~nG~lHiGH~~~~~~~Dii~Ry~rm~G-----~~V~~~~G~D~~Glpie~~a~~~g~~~~~~~~~~~~~  106 (805)
T PRK00390         32 KKYYVLDMFPYPSGGLHMGHVRNYTIGDVIARYKRMQG-----YNVLHPMGWDAFGLPAENAAIKTGTHPAEWTYENIAN  106 (805)
T ss_pred             CCEEEEccCCCCCCCcchhhhHHHHHHHHHHHHHHhcC-----CcccccCccCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Confidence            47999999999999999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCC
Q psy2399          92 RKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGD  169 (232)
Q Consensus        92 ~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~  169 (232)
                      ++++|++|||  +|+++++|+++.|.+.++++|.+|+ ++|+||++...++||+.|+++|++.+|+              
T Consensus       107 ~~~~~~~lGi~~Dw~~~~~T~~~~~~~~v~~~f~~L~-~~Gliy~~~~~v~wcp~~~t~La~~ev~--------------  171 (805)
T PRK00390        107 MKKQLKSLGFSYDWSREIATCDPEYYKWTQWIFLKLY-EKGLAYRKESPVNWCPVDGTVLANEQVI--------------  171 (805)
T ss_pred             HHHHHHHhCCcccCCCCeecCCHHHHHHHHHHHHHHH-HCCCEEEecCEEEecCCcCCCCCHHHhh--------------
Confidence            9999999999  5568999999999999999999999 9999999999999988888888888775              


Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhh
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWA  220 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~  220 (232)
                                     ++.|..||.+++.+++++|||+|  ++|+++|.++|
T Consensus       172 ---------------~~~~~~~~~~~~~~~~~~~f~~i--~~~~~~L~~~l  205 (805)
T PRK00390        172 ---------------DGRCWRCGAPVEKKELRQWFLKI--TDYADELLDDL  205 (805)
T ss_pred             ---------------CCeecccCCeeEEEecceeeEec--chhHHHHHHHH
Confidence                           23355677899999999999999  99999999994

>TIGR00422 valS valyl-tRNA synthetase

Probab=100.00  E-value=3.8e-38  Score=312.17  Aligned_cols=211  Identities=22%  Similarity=0.262  Sum_probs=181.2

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc----CCCH----
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA----GMTP----   81 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~----g~~~----   81 (232)
                      ++++|+|++||||+||.|||||+++++++|+++||+||+|     ++|.+++|+|+||+||+.++++.    |.++    
T Consensus        31 ~~~~f~i~~ppPy~nG~lHiGH~~~~~~~D~~~Ry~rm~G-----~~vl~~~G~D~~Glp~e~~vek~~~~~g~~~~~~~  105 (861)
T TIGR00422        31 NKPPFCIDIPPPNVTGSLHIGHALNWSIQDIIARYKRMKG-----YNVLWLPGTDHAGIATQVKVEKKLGAEGKTKHDLG  105 (861)
T ss_pred             CCCeEEEEeCCCCCCCCCcHHHhHHHHHHHHHHHHHHhcC-----CcccCCCCcCcCCCcHHHHHHHHhcccCCchhhCC
Confidence            4577999999999999999999999999999999999999     99999999999999999998863    5555    


Q ss_pred             --------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccccc
Q psy2399          82 --------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPD  151 (232)
Q Consensus        82 --------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~  151 (232)
                              .++++++.+.++++|++||+  +|++.+.|+++.|.+.|+++|.+|+ ++|+||++.+.++|||.|+|+|+|
T Consensus       106 ~e~f~~~~~~~~~~~~~~~~~~~~~lG~s~Dw~r~~~T~d~~~~~~v~~~F~~L~-~~GlIy~~~~~v~wcp~~~t~lsd  184 (861)
T TIGR00422       106 REEFREKIWEWKEESGGTIKNQIKRLGASLDWSRERFTMDEGLSKAVKEAFVRLY-EKGLIYRGEYLVNWDPKLNTAISD  184 (861)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCeeeecCCCcCcCCHHHHHHHHHHHHHHH-HCCCeeecCcccccCCCCCCcchH
Confidence                    36789999999999999998  4556677999999999999999999 999999999999999999999999


Q ss_pred             ceec----------------------------------------------------------------------------
Q psy2399         152 RYIK----------------------------------------------------------------------------  155 (232)
Q Consensus       152 ~~v~----------------------------------------------------------------------------  155 (232)
                      .+|+                                                                            
T Consensus       185 ~Ev~~~~~~~~~~~i~f~~~~~~~~~l~vaTtrPeTl~~~~av~V~P~~~ry~~l~g~~~~~P~~~~~ipii~~~~V~~~  264 (861)
T TIGR00422       185 IEVEYKEVKGKLYYIRYPLANGSKDYLVVATTRPETMFGDTAVAVHPEDERYKHLIGKKVILPLTGRKIPIIADEYVDME  264 (861)
T ss_pred             hHhhcccccceEEEEEEEecCCCCCEEEEEeCCcchhhhCeEEEECCCchHHHHhcCCEEEcCCCCCcceeeecCCCCcc
Confidence            8641                                                                            


Q ss_pred             -c-----CCCCCCcc----------------ccCCCcCccCCCC------------------------CCCccccCCccc
Q psy2399         156 -G-----ECPICNAK----------------DQYGDFCECCSSI------------------------YTPTKLINPYSI  189 (232)
Q Consensus       156 -g-----~cp~c~~~----------------~~~g~~Ce~Cg~~------------------------~~~~~l~~~~~~  189 (232)
                       |     .||.++..                +..|..|++||.+                        ..+-+...|.|.
T Consensus       265 ~GTG~V~~~Pah~~~D~~~~~~~~l~~~~~id~~G~~~~~~~~~~G~~~~~ar~~i~~~L~~~g~l~~~~~~~~~~p~~~  344 (861)
T TIGR00422       265 FGTGAVKVTPAHDFNDYEWGKRHNLEFINILDEDGLLNENAGKYQGLTRFEARKKIVEDLKEEGLLVKIEPHTHNVGTCW  344 (861)
T ss_pred             cCCCceEecCCCChHHHHHHHHcCCCccceeCCCCeEcCCCcccCCcCHHHhHHHHHHHHHhCCCeeeeeeeeccCCEeC
Confidence             2     37776543                3567888888875                        223344678999


Q ss_pred             CCCCccEEEEccceeEecCChhhHHHHHhhhhcCC--CCCCC
Q psy2399         190 LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDK--RLQPE  229 (232)
Q Consensus       190 ~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~--~~~p~  229 (232)
                      .||.+++.+.++||||++  +++++++.++ ++++  .+.|+
T Consensus       345 R~g~~ve~~~~~qWFi~~--~~~~~~~~~~-~~~~~i~~~P~  383 (861)
T TIGR00422       345 RSGTVVEPLLSKQWFVKV--EKLADKALEA-AEEGEIKFVPK  383 (861)
T ss_pred             CCCCEEEEEecCcceEec--HHHHHHHHHH-hhcCCeEEECh
Confidence            999999999999999999  9999999999 5432  34554

The valyl-tRNA synthetase (ValS) is a class I amino acyl-tRNA ligase and is particularly closely related to the isoleucyl tRNA synthetase.

>COG0495 LeuS Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2.4e-37  Score=299.09  Aligned_cols=181  Identities=25%  Similarity=0.332  Sum_probs=163.3

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++|||+.+.|||||.||+||.|+|+++|+++||+||+|     |+|+|.+|||..|+|++..|.+.|.+|..++..+++.
T Consensus        34 ~Kfyvl~mfPYpSG~LHvGH~r~Yti~Dv~aRykRm~G-----yNVL~PMGwdafGlPae~~A~~~~~~P~~wt~~ni~~  108 (814)
T COG0495          34 EKFYVLVMFPYPSGALHVGHVRNYTIGDVIARYKRMQG-----YNVLHPMGWDAFGLPAENAAIKIGTDPAKWTYYNIAY  108 (814)
T ss_pred             CceEEEeCCCCCCCCcccCccccccHHHHHHHHHHhcC-----CeecccCcccccCchHHHHHHHhCCChHHHHHHHHHH
Confidence            59999999999999999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCC
Q psy2399          92 RKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGD  169 (232)
Q Consensus        92 ~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~  169 (232)
                      ++++|++||.  ||++-+.|+||+|..++|++|.+|+ ++|+||+++..+.|||.+++.|.+.+|               
T Consensus       109 ~k~qlk~lG~siDW~Ref~T~Dp~Yyk~~QW~F~kL~-ekGL~y~~~~~VnwcP~d~tvlaneqv---------------  172 (814)
T COG0495         109 MKKQLKSLGFSIDWRREFATCDPEYYKWIQWQFLKLY-EKGLAYRKEAPVNWCPVDGTVLANEQV---------------  172 (814)
T ss_pred             HHHHHHHhCCccccccceecCCccHHHHHHHHHHHHH-HCCCEEeccccceeCCCcCCcccccee---------------
Confidence            9999999996  7778899999999999999999999 999999999999996666666555544               


Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                                    +++.|..||.+++.++..+|||++  ++|.++|++-|..-.-.+|+
T Consensus       173 --------------~~g~~~r~~~~V~~kel~qw~~ki--t~yae~ll~~l~~l~~~wPE  216 (814)
T COG0495         173 --------------IDGGCWRCGEPVEIKELTQWFFKI--TDYADELLDDLDKLATLWPE  216 (814)
T ss_pred             --------------ecCCcccCCCceeEeeeEEEEEEe--chhHHHHHhhhhhhccCCch
Confidence                          556677899999999999999999  99999999874332323444

>PRK05729 valS valyl-tRNA synthetase; Reviewed

Probab=100.00  E-value=5.2e-36  Score=297.17  Aligned_cols=210  Identities=20%  Similarity=0.244  Sum_probs=175.8

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH----cCCCHHH---
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK----AGMTPKE---   83 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~----~g~~~~e---   83 (232)
                      +++|+|++||||+||.|||||+++++++|+++||+||+|     ++|.+++|||+||++++.++++    .|+++.+   
T Consensus        35 ~~~f~i~~ppP~~~G~lHiGHa~~~~~~D~~~Ry~rm~G-----~~vl~~~G~D~~Gi~~e~~ve~~l~~~g~~~~~~~r  109 (874)
T PRK05729         35 KKPFSIVIPPPNVTGSLHMGHALNNTLQDILIRYKRMQG-----YNTLWLPGTDHAGIATQMVVERQLAAEGKSRHDLGR  109 (874)
T ss_pred             CCCEEEecCCCCCCCcchHHHHHHHHHHHHHHHHHHhCC-----CcccCCCCCCccchhhHHHHHHHHHhcCCChHHCCH
Confidence            456999999999999999999999999999999999999     9999999999999998887765    3776654   


Q ss_pred             ---------HHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccc
Q psy2399          84 ---------FINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDR  152 (232)
Q Consensus        84 ---------~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~  152 (232)
                               +++++.+.++++|++||+  +|++.+.|+++.|.+.|+++|.+|+ ++|+||++.+.++|||.|+|+|+|.
T Consensus       110 e~f~~~~~~w~~~~~~~~~~~~~~lG~s~Dw~r~~~T~d~~~~~~v~~~F~~L~-~~GlIyr~~~~v~wcp~~~talsd~  188 (874)
T PRK05729        110 EKFLEKVWEWKEESGGTITNQLRRLGASCDWSRERFTMDEGLSKAVREVFVRLY-EKGLIYRGKRLVNWDPKLQTALSDL  188 (874)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCcceecCCCcccCCHHHHHHHHHHHHHHH-HCCCEeecCcccccCCCCCCcchhh
Confidence                     488899999999999998  5667788999999999999999999 9999999999999999999999999


Q ss_pred             eec-----c-------------------------------------------------CCCCCCc----------cc---
Q psy2399         153 YIK-----G-------------------------------------------------ECPICNA----------KD---  165 (232)
Q Consensus       153 ~v~-----g-------------------------------------------------~cp~c~~----------~~---  165 (232)
                      +|+     |                                                 .||.|+.          ..   
T Consensus       189 EV~~~~~~~~~~~i~f~~~~~~~~l~vaTtrPeTl~~~~avaV~P~d~ry~~l~g~~~~~P~~~~~ipii~~~~V~~~~G  268 (874)
T PRK05729        189 EVEYKEVKGKLWHIRYPLADGSDYLVVATTRPETMLGDTAVAVNPEDERYKHLIGKTVILPLVGREIPIIADEYVDPEFG  268 (874)
T ss_pred             hcccccccceEEEEEEEecCCCcEEEEEeCCcchhhcCeeEeECCCccHHHHhcCCEEECCCCCCeeeEecCccCCCCCC
Confidence            997     1                                                 3777664          11   


Q ss_pred             ------------------------------cCCCcCccCCCCCC------------------------CccccCCcccCC
Q psy2399         166 ------------------------------QYGDFCECCSSIYT------------------------PTKLINPYSILS  191 (232)
Q Consensus       166 ------------------------------~~g~~Ce~Cg~~~~------------------------~~~l~~~~~~~~  191 (232)
                                                    ..|..+++||.+-.                        +.+...|.|..|
T Consensus       269 TG~V~~~Pah~~~D~~~~~~~~l~~~~~i~~~G~~~~~~~~~~G~~~~~ar~~i~~~L~~~g~l~~~~~~~~~~p~~~R~  348 (874)
T PRK05729        269 TGAVKITPAHDPNDFEVGKRHNLPMINIMDEDGTINENPGEYQGLDRFEARKAIVADLEELGLLVKIEPHTHSVGHSDRS  348 (874)
T ss_pred             CcceEecCCCCHHHHHHHHHcCCCcccccCCCCeEcCCCcccCCCCHHHHHHHHHHHHHhCCCeeeeEEeeccCCeeCCC
Confidence                                          23334444543211                        112346899999


Q ss_pred             CCccEEEEccceeEecCChhhHHHHHhhhhcCC--CCCCC
Q psy2399         192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDK--RLQPE  229 (232)
Q Consensus       192 g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~--~~~p~  229 (232)
                      |.+++.+..+||||++  +++++++.++ ++++  .+.|+
T Consensus       349 ~~~i~~~~~~QWFi~~--~~~~~~~~~~-v~~~~i~~~P~  385 (874)
T PRK05729        349 GVVIEPYLSDQWFVKM--KPLAKPALEA-VENGEIKFVPE  385 (874)
T ss_pred             CceEEEEecCcceEeh--HHHHHHHHHH-HhcCCcEEECh
Confidence            9999999999999999  9999999999 5432  45554

>cd00812 LeuRS_core catalytic core domain of leucyl-tRNA synthetases

Probab=100.00  E-value=1.2e-35  Score=264.09  Aligned_cols=150  Identities=26%  Similarity=0.382  Sum_probs=142.5

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      |++||+|||||||.+||||+++++.+|+++||+|++|     ++|.+++|+|+||+||+.+|++.|++|+++++++.+.+
T Consensus         1 k~~it~~~Py~ng~~HiGH~~~~v~~Dv~~R~lr~~G-----~~V~~v~g~Dd~g~~i~~~a~~~g~~~~e~~~~~~~~~   75 (314)
T cd00812           1 KFYILVMFPYPSGALHVGHVRTYTIGDIIARYKRMQG-----YNVLFPMGFDAFGLPAENAAIKIGRDPEDWTEYNIKKM   75 (314)
T ss_pred             CeEEecCCCCCCCCccccchHHHHHHHHHHHHHHHcC-----CCcCCCCCcCCCCCHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999     99999999999999999999999999999999999999


Q ss_pred             HHHHhccCCcCC--ccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCc
Q psy2399          93 KKYLDGFYIKFD--NWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDF  170 (232)
Q Consensus        93 ~~~l~~lgI~~d--~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~  170 (232)
                      +++|++|||++|  .+++|++++|.+.++++|.+|+ ++|+||+++..++||                            
T Consensus        76 ~~~~~~lgi~~d~~~~~~t~~~~~~~~v~~~f~~L~-~~G~iy~~~~~v~~~----------------------------  126 (314)
T cd00812          76 KEQLKRMGFSYDWRREFTTCDPEYYKFTQWLFLKLY-EKGLAYKKEAPVNWC----------------------------  126 (314)
T ss_pred             HHHHHHhccceecccccccCCHHHHHHHHHHHHHHH-HCCCEEecCceeeee----------------------------
Confidence            999999999877  6789999999999999999999 999999999999993                            


Q ss_pred             CccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCC
Q psy2399         171 CECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDK  224 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~  224 (232)
                                                 +.++||||+|+.++|++.|.+| +++.
T Consensus       127 ---------------------------~~~~~~f~~l~~~~~~~~l~~~-l~~~  152 (314)
T cd00812         127 ---------------------------KLLDQWFLKYSETEWKEKLLKD-LEKL  152 (314)
T ss_pred             ---------------------------CccceEEEEcCcHHHHHHHHHH-HHhc
Confidence                                       7789999999778999999999 5443

Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.

>cd00818 IleRS_core catalytic core domain of isoleucyl-tRNA synthetases

Probab=100.00  E-value=2.2e-35  Score=264.91  Aligned_cols=157  Identities=24%  Similarity=0.316  Sum_probs=145.6

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-CCCH---------
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-GMTP---------   81 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-g~~~---------   81 (232)
                      ++|+|.+|||||||++||||+++++++|+++||+|++|     ++|.+++|+|+||++|+.+|++. |+++         
T Consensus         1 ~~f~i~~~pP~vnG~lHiGHa~~~~~~Dvl~Ry~r~~G-----~~V~~~~g~D~hG~~ie~ka~k~lg~~~~~~~~~~~~   75 (338)
T cd00818           1 PEFVFHDGPPYANGLPHYGHALNKILKDIINRYKTMQG-----YYVPRRPGWDCHGLPIELKVEKELGISGKKDIEKMGI   75 (338)
T ss_pred             CCeEEecCCCCCCCCchHHHHHHHHHHHHHHHHHHhcC-----CccCCcCCcCCCCchhHHHHHHHhCCCCCcchhhcCH
Confidence            46999999999999999999999999999999999999     99999999999999999999985 8764         


Q ss_pred             -------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccc
Q psy2399          82 -------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDR  152 (232)
Q Consensus        82 -------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~  152 (232)
                             +++++++.+.|+++|++|||  ++|.+++|++++|.+.++++|.+|+ ++|+||++++.++|           
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~lgi~~~~~~~~~T~~~~~~~~v~~~f~~L~-~~G~iY~~~~~v~~-----------  143 (338)
T cd00818          76 AEFNAKCREFALRYVDEQEEQFQRLGVWVDWENPYKTMDPEYMESVWWVFKQLH-EKGLLYRGYKVVPW-----------  143 (338)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCceecCCCCeECCCHHHHHHHHHHHHHHH-HCCCEeccCCeeee-----------
Confidence                   68999999999999999999  8889999999999999999999999 99999999999988           


Q ss_pred             eeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         153 YIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       153 ~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                                                               ++++++++||||+|  ++++++|.++ ++...+.|+
T Consensus       144 -----------------------------------------~v~~~~~~qwf~~l--~~~~~~l~~~-~~~~~~~P~  176 (338)
T cd00818         144 -----------------------------------------PLIYRATPQWFIRV--TKIKDRLLEA-NDKVNWIPE  176 (338)
T ss_pred             -----------------------------------------EEEEEecCeEEEEc--HHHHHHHHHH-HhcCcEECH
Confidence                                                     77899999999999  9999999999 554334454

Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.

>KOG0435|consensus

Probab=100.00  E-value=2.4e-35  Score=274.18  Aligned_cols=178  Identities=25%  Similarity=0.327  Sum_probs=168.4

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      .++++++ ||+++.|||+|.|||||.|-|+++|+++||.||+|     |+|.+.+|||.+|+|.+.+|.+.|++|..+..
T Consensus        53 ~d~sk~K-YiLsMFPYPSG~LHiGHvRVYTIsD~laRf~rm~G-----ynVihPMGWDaFGLPAENAAiergv~P~sWT~  126 (876)
T KOG0435|consen   53 SDKSKKK-YILSMFPYPSGALHIGHVRVYTISDILARFYRMKG-----YNVIHPMGWDAFGLPAENAAIERGVHPASWTI  126 (876)
T ss_pred             cccCCCc-eEEEecCCCCCcccccceEEEEehHHHHHHHHhcC-----ceeecCCcccccCCchhhHHHhcCCCchhhhH
Confidence            3556666 99999999999999999999999999999999999     99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcc
Q psy2399          87 NISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAK  164 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~  164 (232)
                      .+++.++++|++|||  +||+.++|.+|+|..+.|++|.+|+ ++|++|+.+..+.|||.++|.|++.+|.         
T Consensus       127 ~NI~~Mk~Ql~~lg~~FDWdrEiSTC~PdYYKWTQwiFlkLf-e~GLAYq~Ea~VNWDPvD~TVLAnEQVD---------  196 (876)
T KOG0435|consen  127 NNIAKMKQQLKSLGISFDWDREISTCEPDYYKWTQWIFLKLF-EKGLAYQAEAEVNWDPVDKTVLANEQVD---------  196 (876)
T ss_pred             HHHHHHHHHHHHcCcccccccccccCCcchhHHHHHHHHHHH-HhhhhhccccccccCcccceeecchhhc---------
Confidence            999999999999999  7889999999999999999999999 9999999999999999999999988884         


Q ss_pred             ccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhh
Q psy2399         165 DQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAI  221 (232)
Q Consensus       165 ~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~  221 (232)
                                         .++++..+|+++|.+...+||+++  ++|+++|.+.|.
T Consensus       197 -------------------~~G~SWRSGA~VEkK~LrQWfikt--taYAk~L~d~L~  232 (876)
T KOG0435|consen  197 -------------------ADGCSWRSGAKVEKKKLRQWFIKT--TAYAKRLLDGLE  232 (876)
T ss_pred             -------------------ccCccccccchhhHHHHHHHHhhh--hHHHHHHHHHHH
Confidence                               356788999999999999999999  999999999854

>cd00668 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases

Probab=100.00  E-value=5.1e-33  Score=246.88  Aligned_cols=150  Identities=33%  Similarity=0.547  Sum_probs=138.7

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCC-------------
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGM-------------   79 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~-------------   79 (232)
                      +|+|++|||||||.+||||+++++++|+++||+|++|     ++|.+++|+|+||+||+.+|++.+.             
T Consensus         1 ~~~i~~~pP~~~g~~HiGH~~~~i~~D~i~R~~r~~G-----~~v~~~~g~D~~g~~i~~~a~~~~~~~~~~~~~~~~~~   75 (312)
T cd00668           1 KFYVTTPPPYANGSLHLGHALTHIIADFIARYKRMRG-----YEVPFLPGWDTHGLPIELKAERKGGRKKKTIWIEEFRE   75 (312)
T ss_pred             CEEEecCCCCCCCCcchhHHHHHHHHHHHHHHHHhCC-----CCCCCCCccCCCCHHHHHHHHHhcCcccccccHHHHHH
Confidence            5899999999999999999999999999999999999     9999999999999999999999887             


Q ss_pred             CHHHHHHHHHHHHHHHHhccCCcCC--ccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccC
Q psy2399          80 TPKEFINNISSNRKKYLDGFYIKFD--NWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGE  157 (232)
Q Consensus        80 ~~~e~~~~~~~~~~~~l~~lgI~~d--~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~  157 (232)
                      ++.++++++.+.|+++|++|||++|  .+++|+++.|.+.++++|.+|. ++|+||++...+                  
T Consensus        76 ~~~~~~~~~~~~~~~~l~~lgI~~Dw~~~~~T~~~~~~~~v~~~f~~L~-~~G~iY~~~~~v------------------  136 (312)
T cd00668          76 DPKEFVEEMSGEHKEDFRRLGISYDWSDEYITTEPEYSKAVELIFSRLY-EKGLIYRGTHPV------------------  136 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCccccCCCCeECCCHHHHHHHHHHHHHHH-HCCCEEeeccee------------------
Confidence            8999999999999999999999766  9999999999999999999999 999999987544                  


Q ss_pred             CCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         158 CPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       158 cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                                                              +.+++|||++  +++++++.++ ++...+.|+
T Consensus       137 ----------------------------------------~~~~~~f~~~--~~l~~~~~~~-~~~~~~~p~  165 (312)
T cd00668         137 ----------------------------------------RITEQWFFDM--PKFKEKLLKA-LRRGKIVPE  165 (312)
T ss_pred             ----------------------------------------EeeeeEEEEc--HHHHHHHHHH-HhcCCcCCh
Confidence                                                    7888999999  9999999999 544435554

Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function.

>PLN02943 aminoacyl-tRNA ligase

Probab=99.98  E-value=8e-32  Score=268.67  Aligned_cols=141  Identities=20%  Similarity=0.231  Sum_probs=129.7

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc----CCCHH---
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA----GMTPK---   82 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~----g~~~~---   82 (232)
                      ++++|+|+.||||+||.|||||+++++++|+++||+||+|     ++|.++.|||+||++++.++++.    |+++.   
T Consensus        86 ~~~~f~i~~pPP~~tG~lHiGHa~~~~~~D~~~Ry~rm~G-----~~vl~~~G~D~~Gl~~e~~vek~l~~~~~~~~~~~  160 (958)
T PLN02943         86 GGDPFVIPMPPPNVTGSLHMGHAMFVTLEDIMVRYNRMKG-----RPTLWIPGTDHAGIATQLVVEKMLASEGIKRTDLG  160 (958)
T ss_pred             CCCCEEEecCCCCCCCchhHHHHHHHHHHHHHHHHHHhcC-----CeeecCCCCCcccchhHHHHHHHHHHcCCChhhCC
Confidence            4567999999999999999999999999999999999999     99999999999999999988763    65443   


Q ss_pred             ---------HHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccccc
Q psy2399          83 ---------EFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPD  151 (232)
Q Consensus        83 ---------e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~  151 (232)
                               ++++++.+.+++++++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++.++++|||.|+|.|++
T Consensus       161 re~f~~~~~~~~~~~~~~~~~~~~~lG~s~Dw~~~~~T~d~~~~~~v~~~F~~l~-~~Gliyr~~~~V~wcp~~~Tals~  239 (958)
T PLN02943        161 RDEFTKRVWEWKEKYGGTITNQIKRLGASCDWSRERFTLDEQLSRAVVEAFVRLH-EKGLIYQGSYMVNWSPNLQTAVSD  239 (958)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCcceecCCCcccCCHHHHHHHHHHHHHHH-HCCCEEecCceeccCCCCCCCcCH
Confidence                     3567889999999999998  6778999999999999999999999 999999999999999999999999


Q ss_pred             ceecc
Q psy2399         152 RYIKG  156 (232)
Q Consensus       152 ~~v~g  156 (232)
                      .+|+.
T Consensus       240 ~Evey  244 (958)
T PLN02943        240 LEVEY  244 (958)
T ss_pred             HHhhc
Confidence            98863

>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed

Probab=99.98  E-value=4.3e-32  Score=269.81  Aligned_cols=142  Identities=20%  Similarity=0.300  Sum_probs=134.7

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc------CCCH
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA------GMTP   81 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~------g~~~   81 (232)
                      ++++++|+|++||||+||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+.+|++.      ++++
T Consensus        45 ~~~~~~f~i~~~pPyanG~lHiGHa~~~~~~Dii~Ry~rm~G-----~~v~~~~G~D~~Glpie~~~ek~l~~~~~~~~~  119 (912)
T PRK05743         45 NKGKPKFILHDGPPYANGDIHIGHALNKILKDIIVKSKTMSG-----FDAPYVPGWDCHGLPIELKVEKKLGKKGKKLSA  119 (912)
T ss_pred             cCCCCcEEEeCCCCCCCCCccHHHHHHHHHHHHHHHHHHccC-----CcccCCCCcCCCccHhHHHHHHHcCCccccCCH
Confidence            355677999999999999999999999999999999999999     99999999999999999999884      6777


Q ss_pred             HH-------HHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccc
Q psy2399          82 KE-------FINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDR  152 (232)
Q Consensus        82 ~e-------~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~  152 (232)
                      ++       +++++.+.++++|++||+  +|++++.|+++.|.+.++++|.+|+ ++|+||++.++++|||.|+|.|+|.
T Consensus       120 ~~f~~~c~~~~~~~~~~~~~~~~~lG~~~dw~~~~~T~~~~~~~~v~~~f~~l~-~~Gliy~~~~~v~w~p~~~TaLad~  198 (912)
T PRK05743        120 AEFRKKCREYALEQVDIQREDFKRLGVLGDWDNPYLTMDFKYEANIIRALGKMA-KKGYLYKGLKPVYWCPDCGSALAEA  198 (912)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCcCCCCHHHHHHHHHHHHHHH-HCCCEEecceeEecCCCcCCCchhh
Confidence            75       788889999999999999  8999999999999999999999999 9999999999999999999999999


Q ss_pred             eec
Q psy2399         153 YIK  155 (232)
Q Consensus       153 ~v~  155 (232)
                      +|+
T Consensus       199 Eve  201 (912)
T PRK05743        199 EVE  201 (912)
T ss_pred             Hhh
Confidence            997

>TIGR00392 ileS isoleucyl-tRNA synthetase

Probab=99.97  E-value=2e-31  Score=264.35  Aligned_cols=143  Identities=22%  Similarity=0.303  Sum_probs=134.0

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-CCC------
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-GMT------   80 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-g~~------   80 (232)
                      ++++++|+|+.|||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+.+|++. |++      
T Consensus        32 ~~~~~~f~i~~~pPy~nG~lH~GH~~~~~~~D~~~Ry~rm~G-----~~v~~~~G~D~~Glpie~~~ek~l~~~~~~~~~  106 (861)
T TIGR00392        32 NKGKPEFIFHDGPPYANGSIHLGHALNKILKDIILRYKTMQG-----FNVTRKPGWDTHGLPIEHKVEKKLGISGKKEIS  106 (861)
T ss_pred             cCCCCCeEEecCCCCCCCCccHHHHHHHHHHHHHHHHHHcCC-----CccCCCCCcCCCccHHHHHHHHHhCcccccccc
Confidence            345678999999999999999999999999999999999999     99999999999999999999875 654      


Q ss_pred             H----------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcc
Q psy2399          81 P----------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIF  148 (232)
Q Consensus        81 ~----------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~  148 (232)
                      +          .++++++.+.++++|++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++..+++|||.|+|.
T Consensus       107 ~~~~~~f~~~c~~~~~~~~~~~~~~~~~lG~~~dw~~~y~T~~p~y~~~~~~~f~~l~-~~gliyr~~~~v~w~p~~~T~  185 (861)
T TIGR00392       107 SLEIEEFREKCREFALKQIEEQREQFQRLGVWGDWENPYKTMDPSYEESQWWLFKEAH-EKGLLYRGLKPVYWSPRCRTA  185 (861)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHhCceecCCCCcCcCCHHHHHHHHHHHHHHH-HCCCEeecceeeecCCCcCCc
Confidence            3          36888999999999999999  8899999999999999999999999 999999999999999999999


Q ss_pred             cccceecc
Q psy2399         149 LPDRYIKG  156 (232)
Q Consensus       149 l~~~~v~g  156 (232)
                      |++.+|+.
T Consensus       186 La~~Ev~~  193 (861)
T TIGR00392       186 LAEAEVEY  193 (861)
T ss_pred             ccHHHHhc
Confidence            99999964

The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms.

>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed

Probab=99.97  E-value=3e-31  Score=265.39  Aligned_cols=141  Identities=22%  Similarity=0.265  Sum_probs=133.9

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-cCCC-------
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-AGMT-------   80 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~g~~-------   80 (232)
                      .++++|+++.|||||||.||+||+++++++|+++||+||+|     ++|.++.|||+||+||+.++++ +|++       
T Consensus        38 ~~~~~f~i~~~PPy~nG~lH~GH~l~~t~kD~i~Ry~rm~G-----~~v~~~~GwD~~GlPie~~vek~l~~~~~~~i~~  112 (975)
T PRK06039         38 EGGPEFVFYDGPPTANGLPHYGHLLTRTIKDVVPRYKTMKG-----YKVERRAGWDTHGLPVELEVEKELGISGKKDIEE  112 (975)
T ss_pred             CCCCCEEEeCCCCCCCCCccHhhhHhhHHHHHHHHHHHhCC-----CcccCcCCcCCCccHHHHHHHHHhCcccccchhh
Confidence            45678999999999999999999999999999999999999     9999999999999999999987 5765       


Q ss_pred             ---------HHHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccc
Q psy2399          81 ---------PKEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFL  149 (232)
Q Consensus        81 ---------~~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l  149 (232)
                               +.+++.++.+.+++++++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++.+.++|||.|+|.|
T Consensus       113 ~g~~~f~~~c~~~~~~~~~~~~~~~~rlG~~~Dw~~~y~T~d~~y~~~v~~~F~~l~-~kGliyr~~~~v~wcp~~~T~L  191 (975)
T PRK06039        113 YGIEKFNEKCRESVLRYTDEWEEYTERLGRWVDFDNPYKTLDNEYMESVWWALKQLY-DKGLLYKGYRVVPYCPRCETPL  191 (975)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHhCceeecCCCcCcCCHHHHHHHHHHHHHHH-HCCCEEecceeeeecCCCCCCc
Confidence                     567899999999999999995  8999999999999999999999999 9999999999999999999999


Q ss_pred             ccceec
Q psy2399         150 PDRYIK  155 (232)
Q Consensus       150 ~~~~v~  155 (232)
                      ++.+|+
T Consensus       192 s~~Ev~  197 (975)
T PRK06039        192 SNHEVA  197 (975)
T ss_pred             cHHHHh
Confidence            999997

>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional

Probab=99.97  E-value=4.3e-31  Score=263.51  Aligned_cols=142  Identities=20%  Similarity=0.304  Sum_probs=130.5

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc----CC----
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA----GM----   79 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~----g~----   79 (232)
                      ++++++|+|++||||+||.|||||++++++.|+++||+||+|     ++|.++.|||+||+||+.++++.    |.    
T Consensus        50 ~~~~~~f~l~dgPPyanG~lHiGHaln~~lkDii~Ry~rm~G-----~~v~~~pGwD~hGlPiE~~vek~~~~~~~~~~~  124 (961)
T PRK13804         50 AKGRPKFVLHDGPPYANGNIHIGHALNKILKDVIVRSKQMLG-----FDANYVPGWDCHGLPIEWKIEEKYRAKGKNKDE  124 (961)
T ss_pred             cCCCCcEEEeCCCCCCCCCccHHHHHHHHHHHHHHHHHHhcC-----CcccCCCCcCCCCcHHHHHHHHhhhhcCCChHh
Confidence            356678999999999999999999999999999999999999     99999999999999999999764    33    


Q ss_pred             -CH-------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccc
Q psy2399          80 -TP-------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFL  149 (232)
Q Consensus        80 -~~-------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l  149 (232)
                       ++       .++++++.+.++++|++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++..+++|||.|+|.|
T Consensus       125 ~~~~~f~~~c~~~a~~~i~~~~~~~~rlG~~~Dw~~~y~T~d~~y~~~~~~~F~~l~-~kGliyr~~kpV~Wcp~~~TaL  203 (961)
T PRK13804        125 VPVAEFRKECREYALSWIDVQREEFKRLGVLGDWDNPYTTMDFHAEARIAREFGKFA-AKGQLYRGSKPVMWSVVERTAL  203 (961)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHhCceecCCCCcCcCCHHHHHHHHHHHHHHH-HCCCEEeCCcceecCCCCCCCc
Confidence             23       34677888899999999999  6889999999999999999999999 9999999999999999999999


Q ss_pred             ccceec
Q psy2399         150 PDRYIK  155 (232)
Q Consensus       150 ~~~~v~  155 (232)
                      +|.+|+
T Consensus       204 a~~Eve  209 (961)
T PRK13804        204 AEAEIE  209 (961)
T ss_pred             cchhcc
Confidence            997775

>PF00133 tRNA-synt_1: tRNA synthetases class I (I, L, M and V); InterPro: IPR002300 The aminoacyl-tRNA synthetases (6

Probab=99.97  E-value=6.3e-31  Score=251.81  Aligned_cols=144  Identities=28%  Similarity=0.391  Sum_probs=125.4

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-CC------
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-GM------   79 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-g~------   79 (232)
                      .++++++|+|++||||+||.||+||++++++.|+++||+||+|     ++|.++.|+|+||+||+.++++. |.      
T Consensus        18 ~~~~~~~f~i~~~PPy~nG~lH~GH~~~~~~~D~i~Ry~rm~G-----~~v~~~~G~D~~Glpie~~vek~l~~~~~~~~   92 (601)
T PF00133_consen   18 KNKNKPKFFIHDPPPYANGDLHIGHALNKTIKDIIARYKRMQG-----YNVLFPPGWDCHGLPIEAKVEKKLGIKEKKDR   92 (601)
T ss_dssp             CTTTSGEEEEEE---BTSSS-BHHHHHHHHHHHHHHHHHHCTT-----SEEEEEEEEB--SHHHHHHHHHHTTTTSHHHC
T ss_pred             cCCCCCcEEEEeCCCCCCCcccHHHHHHHHHHHHHHHHHHhCC-----cEeCCCCCcCCCCcchhhhHHHhhcccccccc
Confidence            3566788999999999999999999999999999999999999     99999999999999999999873 43      


Q ss_pred             ---C-------HHHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCc
Q psy2399          80 ---T-------PKEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNI  147 (232)
Q Consensus        80 ---~-------~~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~  147 (232)
                         +       +.++++++.+.+++++++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++.++++|||.|++
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lG~~~Dw~~~y~T~d~~y~~~v~~~F~~l~-~kglIyr~~~pv~w~p~~~t  171 (601)
T PF00133_consen   93 KDLGREEFREECREWAEEFIEEQKEQFKRLGVSIDWDREYFTMDPEYEKFVWWQFKKLY-EKGLIYRGKKPVNWCPSCQT  171 (601)
T ss_dssp             SCSTHHHHHHHHHHHHHHHHHHHHHHHHHTT--SECTCEEETTSHHHHHHHHHHHHHHH-HTTSEEEEEEEEEEETTTTE
T ss_pred             cccccccchhhhcchhhhhhhhhhhhhhheeeecccCCceEECCccHhHHHHHHHHHHH-hcCcEEeeCCCCCcCccccc
Confidence               1       456788889999999999997  7788999999999999999999999 99999999999999999999


Q ss_pred             ccccceecc
Q psy2399         148 FLPDRYIKG  156 (232)
Q Consensus       148 ~l~~~~v~g  156 (232)
                      .|+|.+|+.
T Consensus       172 ~lsd~Ev~~  180 (601)
T PF00133_consen  172 ALSDHEVEY  180 (601)
T ss_dssp             EE-GGGEEE
T ss_pred             chhhhhccc
Confidence            999999863

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. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1OBC_A 2AJH_B 4ARI_A 2AJG_B 4AQ7_D 2AJI_B 4ARC_A 4AS1_A 1QU3_A 1QU2_A ....

>PLN02882 aminoacyl-tRNA ligase

Probab=99.97  E-value=2e-30  Score=261.90  Aligned_cols=141  Identities=21%  Similarity=0.251  Sum_probs=130.4

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-cCCC------
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-AGMT------   80 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~g~~------   80 (232)
                      ++++++|++++||||+||.||+||+++++++|+++||+||+|     ++|.+++|||+||+||+..+++ +|++      
T Consensus        34 ~~~~~~f~~~dgPPyanG~~HiGH~~~~~ikDii~Ry~rm~G-----~~V~~~~GwD~hGlPiE~~vek~lgi~~~~~i~  108 (1159)
T PLN02882         34 TEGLPEYIFYDGPPFATGLPHYGHILAGTIKDIVTRYQSMTG-----HHVTRRFGWDCHGLPVEYEIDKKLGIKRRDDVL  108 (1159)
T ss_pred             cCCCCCEEEeCCCCCCCCcchhhHHHHHHHHHHHHHHHHcCC-----CcccccCccCCCCcHHHHHHHHHcCCCCccchh
Confidence            345677999999999999999999999999999999999999     9999999999999999999965 5653      


Q ss_pred             ----------HHHHHHHHHHHHHHHHhccC--CcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcc
Q psy2399          81 ----------PKEFINNISSNRKKYLDGFY--IKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIF  148 (232)
Q Consensus        81 ----------~~e~~~~~~~~~~~~l~~lg--I~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~  148 (232)
                                +.+++.++.+.+++++++||  ++||+.++|+++.|.+.++++|.+|+ ++|+||++.+.++|||.|+|.
T Consensus       109 ~~g~~~f~~~c~~~~~~~~~~~~~~~~rlG~~~D~~~~y~T~d~~~~~~v~~~f~~l~-~kGliyr~~~~v~wcp~~~Ta  187 (1159)
T PLN02882        109 KMGIDKYNEECRSIVTRYSKEWEKTVTRTGRWIDFENDYKTMDPKFMESVWWVFKQLF-EKGLVYKGFKVMPYSTACKTP  187 (1159)
T ss_pred             hcCHHHHHHHHHHHHHHHHHHHHHHHHHcCcEEECCCCcCcCCHHHHHHHHHHHHHHH-HCCCEEecceeEeecCCCCCC
Confidence                      34578889999999999999  59999999999999999999999999 999999999999999999999


Q ss_pred             ccccee
Q psy2399         149 LPDRYI  154 (232)
Q Consensus       149 l~~~~v  154 (232)
                      |++.++
T Consensus       188 Ls~~E~  193 (1159)
T PLN02882        188 LSNFEA  193 (1159)
T ss_pred             cchhhh
Confidence            997555

>PLN02843 isoleucyl-tRNA synthetase

Probab=99.97  E-value=2.2e-30  Score=258.57  Aligned_cols=140  Identities=21%  Similarity=0.359  Sum_probs=129.7

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-------CCCHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-------GMTPKE   83 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-------g~~~~e   83 (232)
                      +++|+|++||||+||.|||||+++++++|+++||+||+|     ++|.++.|||+||+||+.++++.       ++++.+
T Consensus        31 ~~~f~i~~~PPy~nG~lHiGHa~~~~lkDii~Ry~rm~G-----~~v~~~pG~D~hGlpie~~vek~l~~~~~~~~~~~~  105 (974)
T PLN02843         31 GESFTLHDGPPYANGDLHIGHALNKILKDFINRYQLLQG-----KKVHYVPGWDCHGLPIELKVLQSLDQEARKELTPIK  105 (974)
T ss_pred             CCCEEEeCCCCCCCCCcchhHHHHHHHHHHHHHHHHhcC-----CccccCCccCCCCcHHHHHHHHHhchhhhccCCHHH
Confidence            466999999999999999999999999999999999999     99999999999999999998552       345655


Q ss_pred             H-------HHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccccccee
Q psy2399          84 F-------INNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYI  154 (232)
Q Consensus        84 ~-------~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v  154 (232)
                      +       ++++.+.++++|++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++.++++|||.|+|.|+|.+|
T Consensus       106 f~~~c~~~~~~~~~~~~~~~~~lG~~~Dw~~~y~T~d~~~~~~v~~~f~~l~-~~GlIyr~~kpV~Wcp~~~Talae~Ev  184 (974)
T PLN02843        106 LRAKAAKFAKKTVDTQRESFKRYGVWGDWENPYLTLDPEYEAAQIEVFGQMF-LNGYIYRGRKPVHWSPSSRTALAEAEL  184 (974)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCceecCCCCccCCHHHHHHHHHHHHHHH-HCCCEEecceeeeecCCCCCcchHhHh
Confidence            5       66777888999999999  8999999999999999999999999 999999999999999999999999999


Q ss_pred             cc
Q psy2399         155 KG  156 (232)
Q Consensus       155 ~g  156 (232)
                      +-
T Consensus       185 ey  186 (974)
T PLN02843        185 EY  186 (974)
T ss_pred             cc
Confidence            74

>PTZ00427 isoleucine-tRNA ligase, putative; Provisional

Probab=99.97  E-value=2e-30  Score=261.66  Aligned_cols=141  Identities=21%  Similarity=0.209  Sum_probs=131.2

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-cCC--------
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-AGM--------   79 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~g~--------   79 (232)
                      +++++|++++||||+||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+..+++ +|+        
T Consensus        99 ~~~~~Fv~~~gPPyanG~lHiGHal~~tikDii~Ry~rm~G-----~~V~~~~GwD~hGlPiE~~vEk~lg~~~k~~i~~  173 (1205)
T PTZ00427         99 KNKKAYIFYDGPPFATGLPHYGHLLAGIIKDCVTRYFYQCG-----FSVERKFGWDCHGLPIEYEIEKENNINKKEDILK  173 (1205)
T ss_pred             CCCCcEEEecCCCCCCCCcchhHHHHHHHHHHHHHHHHcCC-----CeeccCCccCCCCcHHHHHHHHHhCCCcccchhh
Confidence            45677999999999999999999999999999999999999     9999999999999999999986 342        


Q ss_pred             -C-------HHHHHHHHHHHHHHHHhccC--CcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccc
Q psy2399          80 -T-------PKEFINNISSNRKKYLDGFY--IKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFL  149 (232)
Q Consensus        80 -~-------~~e~~~~~~~~~~~~l~~lg--I~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l  149 (232)
                       .       +.++++++.+.+++++++||  ++||+.++|+++.|.+.++++|.+|+ ++|+||++.+.++|||.|+|.|
T Consensus       174 ~g~~~f~e~c~~~~~~~~~~~~~~~~rlG~~iDw~~~y~T~d~~~~~~v~~~f~~L~-ekGlIYr~~k~V~wcp~c~TaL  252 (1205)
T PTZ00427        174 MGIDVYNEKCRGIVLKYSNEWVKTVERIGRWIDFKNDYKTMDKTFMESVWWVFSELY-KNNYVYKSFKVMPYSCKCNTPI  252 (1205)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHhCcEEecCCCcCcCCHHHHHHHHHHHHHHH-HCCCEEecceeeccCCCCCCch
Confidence             1       35678888999999999999  69999999999999999999999999 9999999999999999999999


Q ss_pred             ccceec
Q psy2399         150 PDRYIK  155 (232)
Q Consensus       150 ~~~~v~  155 (232)
                      ++.+|.
T Consensus       253 S~~EV~  258 (1205)
T PTZ00427        253 SNFELN  258 (1205)
T ss_pred             hHHHhh
Confidence            999883

>PLN02381 valyl-tRNA synthetase

Probab=99.97  E-value=2.3e-30  Score=259.99  Aligned_cols=141  Identities=18%  Similarity=0.219  Sum_probs=129.7

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-----cCCCHH-
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-----AGMTPK-   82 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-----~g~~~~-   82 (232)
                      .++++|+|++||||+||.|||||+++++++|+++||+||+|     ++|.+++|||+||++++.++++     .|+++. 
T Consensus       125 ~~~~~f~i~~ppPy~nG~lHiGHa~~~ti~Dii~Ry~rm~G-----~~vl~~~G~D~~Glp~e~~vek~l~~~~~~~~~~  199 (1066)
T PLN02381        125 SSKPPFVIVLPPPNVTGALHIGHALTAAIEDTIIRWKRMSG-----YNALWVPGVDHAGIATQVVVEKKLMRERHLTRHD  199 (1066)
T ss_pred             CCCCcEEEEeCCCCCCCCccHHHHHHHHHHHHHHHHHHhCC-----CcccccCCCCCCcChHHHHHHHHhHhhcCCChhh
Confidence            44677999999999999999999999999999999999999     9999999999999999999976     255432 


Q ss_pred             -----------HHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccc
Q psy2399          83 -----------EFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFL  149 (232)
Q Consensus        83 -----------e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l  149 (232)
                                 ++++++.+.+++++++||+  +|++.+.|+++.|.+.|+++|.+|+ ++|+||++.+.++|||.|+|.|
T Consensus       200 ~~re~f~~~~~~~~~~~~~~~~~q~~~lG~s~Dw~~~~~T~d~~~~~~v~~~F~~L~-~~GlIyr~~~~VnWcP~~~TaL  278 (1066)
T PLN02381        200 IGREEFVSEVWKWKDEYGGTILNQLRRLGASLDWSRECFTMDEQRSKAVTEAFVRLY-KEGLIYRDIRLVNWDCTLRTAI  278 (1066)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHhCchhccCCccccCCHHHHHHHHHHHHHHH-HCCCEEeccccccCCCCCCCCc
Confidence                       5678889999999999997  6778889999999999999999999 9999999999999999999999


Q ss_pred             ccceec
Q psy2399         150 PDRYIK  155 (232)
Q Consensus       150 ~~~~v~  155 (232)
                      ++.+|+
T Consensus       279 Sd~EVe  284 (1066)
T PLN02381        279 SDVEVD  284 (1066)
T ss_pred             cHHHhh
Confidence            999664

>TIGR00395 leuS_arch leucyl-tRNA synthetase, archaeal and cytosolic family

Probab=99.97  E-value=2.8e-30  Score=257.42  Aligned_cols=140  Identities=20%  Similarity=0.285  Sum_probs=130.5

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcC-----------
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAG-----------   78 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g-----------   78 (232)
                      ++++|+|+.||||+||.|||||+++++++|+++||+||+|     ++|+|++|+|+||+||+..|++..           
T Consensus        23 ~~~kf~i~~ppPy~nG~lH~GH~~~~~~~D~~aRy~Rm~G-----~~vl~p~G~d~~G~pi~~~aek~~~~~~~~~~~~~   97 (938)
T TIGR00395        23 DREKFFLTMAYPYLNGVMHAGHCRTFTIPEVSARFERMKG-----KNVLFPLGFHVTGTPILGLAELIKRRDELTIKNYT   97 (938)
T ss_pred             CCCceEEecCCCCCCCCcccchhhhhhHHHHHHHHHHhcC-----CccCCCCccCCCCCchHHHHHHhhhhhhhccccch
Confidence            4678999999999999999999999999999999999999     999999999999999999998721           


Q ss_pred             -------------CCHHHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeecc
Q psy2399          79 -------------MTPKEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDP  143 (232)
Q Consensus        79 -------------~~~~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~  143 (232)
                                   .+|.++++++...++++|++||+  +|++.+.|+++.|.+.|+++|.+|+ ++|+||++.+.++|||
T Consensus        98 ~~~~i~~~~i~~~~~~~~~~~~~~~~~~~~~~~lG~s~DW~r~~~T~dp~y~~~v~~~f~~L~-e~G~iy~g~~~v~wcp  176 (938)
T TIGR00395        98 EVHAIPREELLKFTDPEYIVEYFSREAESACKSMGYSIDWRRSFKTTDPYYDRFIEWQMNKLK-ELGLIVKGEHPVRYCP  176 (938)
T ss_pred             hhccCCHHHHHhhcCHHHHHHHHHHHHHHHHHHhCceEECCCCccCCChhHHHHHHHHHHHHH-HCCCEecCCeeEeecC
Confidence                         35677889999999999999998  6777889999999999999999999 9999999999999999


Q ss_pred             CCCcccccceec
Q psy2399         144 IKNIFLPDRYIK  155 (232)
Q Consensus       144 ~~~~~l~~~~v~  155 (232)
                      .|++.|+|.++.
T Consensus       177 ~~~t~lsd~e~~  188 (938)
T TIGR00395       177 KDGNPVEDHDLL  188 (938)
T ss_pred             CCCCCCchhHhc
Confidence            999999998885

The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.

>PTZ00419 valyl-tRNA synthetase-like protein; Provisional

Probab=99.96  E-value=7.1e-30  Score=256.21  Aligned_cols=142  Identities=18%  Similarity=0.222  Sum_probs=130.0

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-----cCCCH-
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-----AGMTP-   81 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-----~g~~~-   81 (232)
                      +.++++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||++++.++++     .|.++ 
T Consensus        56 ~~~~~~f~i~~ppP~~~G~lHiGHa~~~~~~D~~~Ry~rm~G-----~~v~~~~G~D~~Gl~~~~~vE~~l~~~~~~~~~  130 (995)
T PTZ00419         56 LNSGKKFVIVLPPPNVTGYLHIGHALTGAIQDSLIRYHRMKG-----DETLWVPGTDHAGIATQVVVEKKLMKEENKTRH  130 (995)
T ss_pred             cCCCCeEEEEeCCCCCCCCCcHHHHHHHHHHHHHHHHHHhcC-----CcccCCCCCCCCchhhHHHHHHHHHHhcCCChH
Confidence            345678999999999999999999999999999999999999     9999999999999999877655     35443 


Q ss_pred             -----------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcc
Q psy2399          82 -----------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIF  148 (232)
Q Consensus        82 -----------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~  148 (232)
                                 .++++++.+.++++|++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++.++++|||.|+|.
T Consensus       131 ~~~~e~f~~~~~~w~~~~~~~~~~~~~~lG~~~DW~~~~~T~d~~~~~~v~~~F~~l~-~~Gliyr~~~~V~wcp~~~Ta  209 (995)
T PTZ00419        131 DLGREEFLKKVWEWKDKHGNNICNQLRRLGSSLDWSREVFTMDEQRSKAVKEAFVRLY-EDGLIYRDTRLVNWCCYLKTA  209 (995)
T ss_pred             HcCHHHHHHHHHHHHHHHHHHHHHHHHHhCceeeCCCCcCcCCHHHHHHHHHHHHHHH-HCCCEEecceeeecCCCCCCC
Confidence                       35678899999999999997  6668999999999999999999999 999999999999999999999


Q ss_pred             cccceec
Q psy2399         149 LPDRYIK  155 (232)
Q Consensus       149 l~~~~v~  155 (232)
                      |+|.+|+
T Consensus       210 lsd~EVe  216 (995)
T PTZ00419        210 ISDIEVE  216 (995)
T ss_pred             Cchhhcc
Confidence            9999987

>PRK14900 valS valyl-tRNA synthetase; Provisional

Probab=99.96  E-value=7e-30  Score=256.59  Aligned_cols=142  Identities=17%  Similarity=0.172  Sum_probs=129.2

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-c----CCCH--
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-A----GMTP--   81 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~----g~~~--   81 (232)
                      .++++|+|+.||||+||.|||||+++++++|+++||+||+|     ++|.+++|||+||++++.++++ +    |.++  
T Consensus        45 ~~~~~f~i~~pPP~~nG~lHiGH~~~~~~~Di~~Ry~rm~G-----~~vl~~~G~D~~Glp~e~~ve~~l~~~~~~~~~~  119 (1052)
T PRK14900         45 RTRPPFSIVLPPPNVTGSLHLGHALTATLQDVLIRWKRMSG-----FNTLWLPGTDHAGIATQMIVEKELKKTEKKSRHD  119 (1052)
T ss_pred             CCCCCEEEecCCCCCCCcchHHHHHhhHHHHHHHHHHHhcC-----CcccCCCCCCccchHHHHHHHHHhhhccCCChhh
Confidence            45677999999999999999999999999999999999999     9999999999999999998875 2    3333  


Q ss_pred             ----------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccc
Q psy2399          82 ----------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFL  149 (232)
Q Consensus        82 ----------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l  149 (232)
                                .++++++.+.++++|++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++...++|||.|+|+|
T Consensus       120 ~~~e~f~~~~~~~~~~~~~~~~~~~~~lG~s~Dw~~~~~T~d~~~~~~v~~~F~~L~-~~Gliyr~~~~v~wcp~~~T~L  198 (1052)
T PRK14900        120 LGREAFLERVWAWKEQYGSRIGEQHKALGASLDWQRERFTMDEGLSRAVREVFVRLH-EEGLIYREKKLINWCPDCRTAL  198 (1052)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHhchheecCCCcCcCCHHHHHHHHHHHHHHH-HCCCEEeccceeccCCCCCCCc
Confidence                      23678889999999999997  6677888999999999999999999 9999999999999999999999


Q ss_pred             ccceecc
Q psy2399         150 PDRYIKG  156 (232)
Q Consensus       150 ~~~~v~g  156 (232)
                      +|.+|+.
T Consensus       199 sd~Ev~~  205 (1052)
T PRK14900        199 SDLEVEH  205 (1052)
T ss_pred             cHHHhcc
Confidence            9999863

>COG0525 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=1.3e-28  Score=238.43  Aligned_cols=139  Identities=22%  Similarity=0.273  Sum_probs=127.8

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-c---CCCH------
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-A---GMTP------   81 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~---g~~~------   81 (232)
                      ++|.|.+||||+||.||||||+++.+.|+++||+||+|     ++|.++.|+|++|++++.++++ +   |++.      
T Consensus        33 ~~f~I~~PPPNVTG~LHmGHAl~~tl~D~l~RykRM~G-----~~vl~~pG~DhAGIaTq~~VEk~l~~~g~~r~d~gRe  107 (877)
T COG0525          33 PPFSIDTPPPNVTGSLHMGHALNYTLQDILARYKRMRG-----YNVLWPPGTDHAGIATQVVVEKQLAAEGITRHDLGRE  107 (877)
T ss_pred             CCcEEeCCCCCCCCcccchhhhhHHHHHHHHHHHHcCC-----CeeecCCCCCCCCchHHHHHHHHHHHcCCCccccCHH
Confidence            55999999999999999999999999999999999999     9999999999999999999987 2   5432      


Q ss_pred             ------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccce
Q psy2399          82 ------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRY  153 (232)
Q Consensus        82 ------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~  153 (232)
                            .++.+++...|+++|++||+  +|++...|+|+.+.+.|+..|.+|+ ++|+||++++.+.|||.|+|.|||.+
T Consensus       108 ~Fl~~~weWk~e~~~~I~~Q~~rLG~S~DWsrE~fTmD~~~s~av~~~Fv~Ly-~~GlIYr~~~lVNWcP~~~TAiSd~E  186 (877)
T COG0525         108 EFLKKCWEWKEESGGTIREQLRRLGVSVDWSRERFTMDPGLSRAVQEAFVRLY-EKGLIYRGERLVNWCPKCRTAISDIE  186 (877)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCcccccccccCCHHHHHHHHHHHHHHH-HCCceeecCCcccCCCccccchhhhh
Confidence                  34577888999999999998  5667889999999999999999999 99999999999999999999999998


Q ss_pred             ecc
Q psy2399         154 IKG  156 (232)
Q Consensus       154 v~g  156 (232)
                      |+-
T Consensus       187 Ve~  189 (877)
T COG0525         187 VEY  189 (877)
T ss_pred             hcc
Confidence            854

>COG0060 IleS Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=7.6e-29  Score=242.25  Aligned_cols=143  Identities=26%  Similarity=0.378  Sum_probs=133.4

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-cCC------
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-AGM------   79 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~g~------   79 (232)
                      ++++++.|++.++|||+||.+|||||.|-++.|++.||..|+|     ++|.++.|||+||+||+.++++ +|+      
T Consensus        44 ~~~g~~~FvfhDGPPyANG~iHiGHalnKilKDiI~Ry~~m~G-----~~v~~~pGWDcHGLPIE~~vek~lg~~k~~i~  118 (933)
T COG0060          44 RNKGKPKFVLHDGPPYANGNIHIGHALNKILKDIIVRYKTMQG-----YDVPYVPGWDCHGLPIELKVEKKLGIGKKDIE  118 (933)
T ss_pred             HhCCCCcEEEeCCCCCCCCCcchhhhHHHhhhhhhhhhhcccC-----CcCCCCCCCcCCCchHHHHHHHHhCCCcchhh
Confidence            4678899999999999999999999999999999999999999     9999999999999999999877 452      


Q ss_pred             --C-------HHHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcc
Q psy2399          80 --T-------PKEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIF  148 (232)
Q Consensus        80 --~-------~~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~  148 (232)
                        .       +.+++.++.+.+++++++||+  +|++.+.|+++.|.+.++++|.+++ +||+||++.++++||+.|+|.
T Consensus       119 ~~~~~efr~~Cr~~a~~~v~~q~~~f~RLGv~~Dw~npY~Tmd~~ye~~~~~~f~~~~-~kGllyrg~Kpv~wsp~c~Ta  197 (933)
T COG0060         119 SFGVEEFREKCREFALEQVDEQKEQFKRLGVWGDWENPYKTMDPSYEESVWWAFKELY-EKGLLYRGYKPVPWSPRCETA  197 (933)
T ss_pred             hcCHHHHHHHHHHHHHHHHHHHHHHHHhheEeeccCCCeecCCHHHHHHHHHHHHHHH-HCCCeecCCeeeeecCCCCcc
Confidence              2       234577778999999999998  9999999999999999999999999 999999999999999999999


Q ss_pred             cccceec
Q psy2399         149 LPDRYIK  155 (232)
Q Consensus       149 l~~~~v~  155 (232)
                      |++++|+
T Consensus       198 LAeaEve  204 (933)
T COG0060         198 LAEAEVE  204 (933)
T ss_pred             hhhhhhc
Confidence            9999998

>PLN02959 aminoacyl-tRNA ligase

Probab=99.95  E-value=2e-28  Score=246.52  Aligned_cols=140  Identities=20%  Similarity=0.297  Sum_probs=124.1

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-------CCC---
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-------GMT---   80 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-------g~~---   80 (232)
                      +++|+|+.||||+||.|||||+++++++|+++||+||+|     ++|.|++|||+||+||+..|++.       |..   
T Consensus        44 ~~kf~i~~ppPY~NG~lHiGHa~t~t~~D~i~Rykrm~G-----~~vlfp~G~d~tGlPIe~~aek~~~ei~~~g~~~~~  118 (1084)
T PLN02959         44 GEKFFGNFPYPYMNGLLHLGHAFSLSKLEFAAAYHRLRG-----ANVLLPFAFHCTGMPIKASADKLAREIQQYGNPPVF  118 (1084)
T ss_pred             CCcEEEeCCCCCCCCCcchhhHHHHHHHHHHHHHHHcCC-----CccCCCCCcCCCCccHHHHHHHHHHHHHHcCCCccc
Confidence            467999999999999999999999999999999999999     99999999999999999999763       322   


Q ss_pred             ----------------------------------------------------------------HHHHHHHHHHHHHHHH
Q psy2399          81 ----------------------------------------------------------------PKEFINNISSNRKKYL   96 (232)
Q Consensus        81 ----------------------------------------------------------------~~e~~~~~~~~~~~~l   96 (232)
                                                                                      |..+++.+...++++|
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~k~~~k~~~~~~~~~~~~~~~~~~~~i~~f~dp~~~~~yF~~~~~~~~  198 (1084)
T PLN02959        119 PEEDEDEAAAVAAAKAEAEAAAAPPDKFKGKKSKAVAKSGTQKYQWEIMRSFGLPDSEIAKFQDPYHWLSYFPPLAKEDL  198 (1084)
T ss_pred             ccccccccccccccccccccccccHHHHHHHHHHHHHHhCCchHHHHHHhhcCCchhhhhhccCHHHHHHhccHHHHHHH
Confidence                                                                            1113333446778999


Q ss_pred             hccCC--cCCccccCCC--hhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceecc
Q psy2399          97 DGFYI--KFDNWYSTDS--IENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKG  156 (232)
Q Consensus        97 ~~lgI--~~d~~~~t~~--~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g  156 (232)
                      ++||+  +|++.+.|++  +.|..+|++.|.+|+ ++|+||++.+++.|||.|++.|+|.+++.
T Consensus       199 k~lG~~iDW~r~f~T~d~np~y~~~v~wqf~~L~-ekG~I~~g~rpv~wcp~~~t~ladhe~~~  261 (1084)
T PLN02959        199 KAFGLGCDWRRSFITTDVNPYYDAFVRWQFRKLK-KKGKIVKDKRYTIYSPLDGQPCADHDRAS  261 (1084)
T ss_pred             HHhCceEeCCCCcCCCCCChhHHHHHHHHHHHHH-HCCCEEecCeeeeeCCCCCCCchhhHHhc
Confidence            99997  7888888887  899999999999999 99999999999999999999999998853

>TIGR03447 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase

Probab=99.94  E-value=7e-26  Score=206.40  Aligned_cols=127  Identities=16%  Similarity=0.226  Sum_probs=116.9

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      +.-++|||.|.||  +++||||+|++|.+|+++||+|+.|     ++|.|++|+||||+||+.+|++.|++|+++++++.
T Consensus        35 ~~v~~YvCGpTvY--~~~HIGhart~V~~Dvl~R~lr~~G-----~~V~fV~nitD~dDKIi~~A~~~g~t~~ela~~y~  107 (411)
T TIGR03447        35 PEAGMYVCGITPY--DATHLGHAATYLTFDLVNRVWRDAG-----HRVHYVQNVTDVDDPLFERAERDGVDWRELGTSQI  107 (411)
T ss_pred             CcceEEEeCCccC--CCcccccchHHHHHHHHHHHHHhcC-----CceEEeeCCCchhHHHHHHHHHcCCCHHHHHHHHH
Confidence            3455677766655  9999999999999999999999999     99999999999999999999999999999999999


Q ss_pred             HHHHHHHhccCC-cCCccccCCChhHHHHHHHHHHHHHhhcCCEEeccc----ceeeccCCC
Q psy2399          90 SNRKKYLDGFYI-KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKI----NQFFDPIKN  146 (232)
Q Consensus        90 ~~~~~~l~~lgI-~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~----~~~~~~~~~  146 (232)
                      +.|++++++||| .+|.++++++  +.+.++++|++|. ++|++|++..    .+|||++.-
T Consensus       108 ~~f~~d~~~Lni~~~d~~~RaTe--~i~~ii~~i~~L~-~kG~aY~~~~~~~~~VYFdv~~~  166 (411)
T TIGR03447       108 DLFREDMEALRVLPPRDYIGAVE--SIDEVIEMVEKLL-AAGAAYEVEGPEYPDVYFSIEAT  166 (411)
T ss_pred             HHHHHHHHHcCCCCCCcccCCCC--CHHHHHHHHHHHH-HCCCEEecCCCCcCcEEEeccch
Confidence            999999999998 5899999994  6899999999999 9999999886    799998764

Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione.

>PRK12418 cysteinyl-tRNA synthetase; Provisional

Probab=99.93  E-value=1.4e-25  Score=203.42  Aligned_cols=125  Identities=11%  Similarity=0.167  Sum_probs=116.8

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      -++|||.|.  |.+++||||+|++|.+|+++||+|++|     ++|.+++|+||||+||+.+|++.|++|+++++++.+.
T Consensus        10 v~~YvCGpT--vY~~~HIGh~r~~V~~Dvl~R~lr~~G-----~~V~~V~nitD~ddKIi~~A~~~G~~~~e~a~~~~~~   82 (384)
T PRK12418         10 ATMYVCGIT--PYDATHLGHAATYLAFDLVNRVWRDAG-----HDVHYVQNVTDVDDPLLERAARDGVDWRDLAEREIAL   82 (384)
T ss_pred             eEEEecCCC--CCCCCccchhHHHHHHHHHHHHHHHcC-----CceEEEEecCCcchHHHHHHHHcCCCHHHHHHHHHHH
Confidence            356777655  559999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCC-cCCccccCCChhHHHHHHHHHHHHHhhcCCEEeccc----ceeeccCCC
Q psy2399          92 RKKYLDGFYI-KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKI----NQFFDPIKN  146 (232)
Q Consensus        92 ~~~~l~~lgI-~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~----~~~~~~~~~  146 (232)
                      |.+++++||| ++|.++++++  +.+.+++++++|. ++|++|+++.    .+|||+..-
T Consensus        83 f~~d~~~Lni~~~~~~~raTe--~i~~~~~~i~~L~-~kG~aY~~~~~~~~~VYFdv~~~  139 (384)
T PRK12418         83 FREDMEALRVLPPRDYVGAVE--SIPEVVELVEKLL-ASGAAYVVDDEEYPDVYFSVDAT  139 (384)
T ss_pred             HHHHHHHhCCCCCCccccCCC--CHHHHHHHHHHHH-HCCCEEEeCCCCCccEEEecCch
Confidence            9999999997 8999999995  6999999999999 9999999998    899998774

>PRK00260 cysS cysteinyl-tRNA synthetase; Validated

Probab=99.93  E-value=1.8e-25  Score=208.22  Aligned_cols=126  Identities=17%  Similarity=0.206  Sum_probs=116.8

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      ..+++||  .|||+|++||||+|++|.+|+++||+|++|     ++|.|++|+||+|++|...|++.|++|.++++++.+
T Consensus        23 ~v~~yvc--gPtvy~~~HiGHar~~v~~Dvl~R~lr~~G-----~~V~~v~~~tD~ddki~~~A~~~g~~~~e~~~~~~~   95 (463)
T PRK00260         23 KVKMYVC--GPTVYDYAHIGHARSFVVFDVLRRYLRYLG-----YKVTYVRNITDIDDKIIKRANEEGESIKELTERYIA   95 (463)
T ss_pred             cceEEEe--CCccCCCcccccchhHHHHHHHHHHHHhcC-----CceEEeecCCCCcHHHHHHHHHcCCCHHHHHHHHHH
Confidence            3455666  567889999999999999999999999999     999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCC-cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCC
Q psy2399          91 NRKKYLDGFYI-KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKN  146 (232)
Q Consensus        91 ~~~~~l~~lgI-~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~  146 (232)
                      .|+++|++||| .+|.+.+++  .|...+++++.+|. ++|++|+++++++||+..-
T Consensus        96 ~f~~~~~~Lgi~~~d~~~r~t--~~~~~~~~~i~~L~-~kG~aY~~~~~Vyfdv~~~  149 (463)
T PRK00260         96 AFHEDMDALNVLPPDIEPRAT--EHIPEIIELIERLI-DKGHAYEADGDVYFDVRKF  149 (463)
T ss_pred             HHHHHHHHcCCCCCCcccccc--ccHHHHHHHHHHHH-HCCCEEEecCeEEEecccc
Confidence            99999999999 678888887  59999999999999 9999999999999998864

>cd00671 ArgRS_core catalytic core domain of arginyl-tRNA synthetases

Probab=99.93  E-value=2.3e-25  Score=187.93  Aligned_cols=134  Identities=18%  Similarity=0.215  Sum_probs=123.9

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      +++|..++|||||+|||||+|+++++|+++|++++.|     ++|.++.++||+|.+|...|++.+. +.++++.+.+.+
T Consensus         1 ~v~ve~~spN~~~~~HiGH~R~~vigD~l~R~l~~~G-----~~V~~~~~~~D~G~qi~~~a~~~~~-~~~~~~~~~~~~   74 (212)
T cd00671           1 KILVEFVSANPTGPLHVGHLRNAIIGDSLARILEFLG-----YDVTREYYINDWGRQIGLLILSLEK-WRKLVEESIKAD   74 (212)
T ss_pred             CeEEEecCCCCCCCccccccHHHHHHHHHHHHHHHCC-----CcEEEEeccCCcHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence            4788999999999999999999999999999999999     9999999999999999999987755 899999999999


Q ss_pred             HHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceec
Q psy2399          93 KKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIK  155 (232)
Q Consensus        93 ~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~  155 (232)
                      ++++++|||.+|.|.++++  +...++++++.|. ++|++|+.++.+|+++.+...+++..+.
T Consensus        75 ~~~~~~L~i~~d~~~~es~--~~~~~~~~i~~L~-~~g~~~~~~g~~~~~~~~~~~~~d~vl~  134 (212)
T cd00671          75 LETYGRLDVRFDVWFGESS--YLGLMGKVVELLE-ELGLLYEEDGALWLDLTEFGDDKDRVLV  134 (212)
T ss_pred             HHHHHHhCCcCceecchhh--hhhHHHHHHHHHH-HCCCEEEeCCcEEEechhhCCCCCeEEE
Confidence            9999999999999999995  4889999999999 9999999999999998776666676665

Arginyl tRNA synthetase (ArgRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. There are at least three subgroups of ArgRS. One type contains both characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The second subtype lacks the KMSKS motif; however, it has a lysine N-terminal to the HIGH motif, which serves as the functional counterpart to the second lysine of the KMSKS motif. A third group, which is found primarily in archaea and a few bacteria, lacks both the KMSKS motif and the HIGH loop lysine.

>TIGR00435 cysS cysteinyl-tRNA synthetase

Probab=99.93  E-value=4.5e-25  Score=205.53  Aligned_cols=127  Identities=17%  Similarity=0.165  Sum_probs=116.6

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      ++.++|++  .|||+|.+||||+|++|.+|+++||+|++|     ++|.+++|+||+|++|+..|++.|++|.++++++.
T Consensus        20 ~~v~~yvc--gptvy~~~HiGhar~~v~~Dvl~R~lr~~G-----~~V~~v~n~tD~ddkIi~~A~~~g~~~~e~a~~~~   92 (465)
T TIGR00435        20 GKVKMYVC--GPTVYDYCHIGHARTAIVFDVLRRYLRYLG-----YKVQYVQNITDIDDKIIKRARENGESVYEVSERFI   92 (465)
T ss_pred             CcceEEEe--cCccCCCcccccchHHHHHHHHHHHHHHcC-----CcEEEEEeeCCccHHHHHHHHHcCCCHHHHHHHHH
Confidence            34455666  558889999999999999999999999999     99999999999999999999999999999999999


Q ss_pred             HHHHHHHhccCCcCCcc-ccCCChhHHHHHHHHHHHHHhhcCCEEecc-cceeeccCCC
Q psy2399          90 SNRKKYLDGFYIKFDNW-YSTDSIENIDLVQKIYDTLYNKAKLIINKK-INQFFDPIKN  146 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~~-~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~-~~~~~~~~~~  146 (232)
                      +.|++++++|||++|.+ .+++  .|...+++++++|. ++|++|+.+ +.+|||+.+-
T Consensus        93 ~~f~~dl~~LgI~~d~~~~raT--~hi~~i~~~i~~L~-ekG~aY~~~~g~vyfdv~~~  148 (465)
T TIGR00435        93 EAYFEDMKALNVLPPDLEPRAT--EHIDEIIEFIEQLI-EKGYAYVSDNGDVYFDVSKF  148 (465)
T ss_pred             HHHHHHHHHhCCCCCcCCcccc--ccHHHHHHHHHHHH-HCCCEEEecCCcEEEecccc
Confidence            99999999999998886 4555  79999999999999 999999998 9999998773

This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).

>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase

Probab=99.92  E-value=2.1e-25  Score=200.35  Aligned_cols=175  Identities=18%  Similarity=0.242  Sum_probs=142.5

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChh------------------hHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAH------------------GAAIMI   72 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~------------------G~~i~~   72 (232)
                      +.+++|++++ +|||.+||||+++++.+|+++|++|++|     ++|.|++|+|+|                  |.|+..
T Consensus        18 ~~~~~v~tgi-~psG~~HIG~~~e~i~~D~i~R~lr~~G-----~~v~~v~~~Dd~d~lrKvp~~l~~~~~~~~G~pi~~   91 (353)
T cd00674          18 KEKYVVASGI-SPSGHIHIGNFREVITADLVARALRDLG-----FEVRLIYSWDDYDRLRKVPPNVPESYEQYIGMPLSS   91 (353)
T ss_pred             CCeEEEecCC-CCCCCcccCccHHHHHHHHHHHHHHHcC-----CCEEEEEEEcCCCcccccccchhhHHHHhcCccchh
Confidence            3568888888 5999999999999999999999999999     999999999999                  889999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEE------ec--ccceeeccC
Q psy2399          73 AAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLII------NK--KINQFFDPI  144 (232)
Q Consensus        73 ~a~~~g~~~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy------~~--~~~~~~~~~  144 (232)
                      .++..|+.+ ++++++.+.|++.|+.|||++|.+.+|....+....+.++..|. +++.|.      ++  ....||   
T Consensus        92 ip~p~g~~~-~~~d~~~~~f~~~l~~lgi~~d~~~~T~~y~~g~~~~~i~~~L~-~~~~I~~i~~~~~~~~~~~~~~---  166 (353)
T cd00674          92 VPDPFGCCE-SYAEHFERPFEESLEKLGIEVEFISQSQMYKSGLYDENILIALE-KRDEIMAILNEYRGRELQETWY---  166 (353)
T ss_pred             chhhcCCCH-HHHHHHHHHHHHHHHHcCCeeeeeecCCchhhchHHHHHHHHHH-HCChHHHHHHHhcCCccCCCce---
Confidence            999999977 99999999999999999999996666666566688889999999 998873      22  223444   


Q ss_pred             CCcccccceeccCCCCCCccccCCCcCccCCCCCCCc-------cccCCcccCCCCccEEEEccceeEecCChhhHHHHH
Q psy2399         145 KNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPT-------KLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLR  217 (232)
Q Consensus       145 ~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~-------~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~  217 (232)
                                           ++..+|++||+..++.       .-+.++|. ||+..+..-... --||  .|-.||..
T Consensus       167 ---------------------P~~p~c~~cg~~~~~v~~~d~~~~~v~y~c~-cG~~g~~~~~~g-~~KL--~Wr~dW~~  221 (353)
T cd00674         167 ---------------------PFMPYCEKCGKDTTTVEAYDAKAGTVTYKCE-CGHEETVDIRTG-RGKL--TWRVDWPM  221 (353)
T ss_pred             ---------------------eeeeecCCcCcceeEEEEEeCCCCeEEEEcC-CCCEEEEeecCC-Cccc--CCCCCchh
Confidence                                 5778899999654322       12557885 999988644332 2399  89999999


Q ss_pred             hhhh
Q psy2399         218 KWAI  221 (232)
Q Consensus       218 ~~~~  221 (232)
                      .|.+
T Consensus       222 rW~~  225 (353)
T cd00674         222 RWAI  225 (353)
T ss_pred             hhhh
Confidence            9943

Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.

>PLN02946 cysteine-tRNA ligase

Probab=99.92  E-value=1.3e-24  Score=204.51  Aligned_cols=125  Identities=14%  Similarity=0.114  Sum_probs=115.7

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      -++|++  .|||.+.+||||+|++|.+|+++||+++.|     ++|.|++|+||+|++|+..|++.|++|.++++++.+.
T Consensus        81 v~~Y~C--GpTvYd~~HIGhaR~~V~~Dvl~R~Lr~~G-----y~V~~V~niTDiDDKIi~~A~~~g~~~~ela~~y~~~  153 (557)
T PLN02946         81 VGMYVC--GVTAYDLSHIGHARVYVTFDVLYRYLKHLG-----YEVRYVRNFTDVDDKIIARANELGEDPISLSRRYCEE  153 (557)
T ss_pred             eeEEEe--CCccCCCCccccchhhHHHHHHHHHHHhcC-----CcEEEEECCCCccCHHHHHHHHcCCCHHHHHHHHHHH
Confidence            345555  678889999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCC
Q psy2399          92 RKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIK  145 (232)
Q Consensus        92 ~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~  145 (232)
                      |.+++++|||. +.+++|...+|+..+++++++|. ++|++|+.++.+|||+..
T Consensus       154 f~~d~~~LnI~-~p~~~pratehi~~ii~~i~~Li-~kG~aY~~~g~VYFdv~~  205 (557)
T PLN02946        154 FLSDMAYLHCL-PPSVEPRVSDHIPQIIDMIKQIL-DNGCAYRVDGDVYFSVDK  205 (557)
T ss_pred             HHHHHHHCCCC-CCCeecCcchhHHHHHHHHHHHH-HCCCEEEECCeEEEecCc
Confidence            99999999997 55556666699999999999999 999999999999999886

>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional

Probab=99.92  E-value=4.3e-24  Score=198.80  Aligned_cols=126  Identities=15%  Similarity=0.124  Sum_probs=113.5

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEec----------CCChhhHHHHHHHHHcCCCH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFIC----------ADDAHGAAIMIAAEKAGMTP   81 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~----------g~D~~G~~i~~~a~~~g~~~   81 (232)
                      .++-+....|||++++||||+|++|.+|+++||+++.|     ++|.|++          |+|+||.+|...|++.|++|
T Consensus        22 ~~v~mYvCGpTvy~~~HiGhar~~v~~Dvl~R~l~~~G-----~~V~~v~NiTDv~hl~~~~De~ddKii~~A~~~g~~~   96 (490)
T PRK14536         22 GHVRLYGCGPTVYNYAHIGNLRTYVFQDTLRRTLHFLG-----YRVTHVMNITDVGHLTDDADSGEDKMVKSAQEHGKSV   96 (490)
T ss_pred             CceEEEeeCCccCCCcccchhHHHHHHHHHHHHHHhcC-----CceEEEEeeccccccccCCcCCChHHHHHHHHcCCCH
Confidence            34555555789999999999999999999999999999     9999997          77777999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccC
Q psy2399          82 KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPI  144 (232)
Q Consensus        82 ~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~  144 (232)
                      .++++++.+.|++++++|||.++.++.+ ..+|...+++++++|. ++|++|+..+.+|||+.
T Consensus        97 ~e~a~~~~~~f~~d~~~Lni~~~~~~~r-at~hi~~ii~~i~~L~-~kG~aY~~~~~vyFdv~  157 (490)
T PRK14536         97 LEIAAHYTAAFFRDTARLNIERPSIVCN-ATEHIQDMIALIKRLE-ARGHTYCAGGNVYFDIR  157 (490)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCceecC-cccHHHHHHHHHHHHH-HCCCEEEECCeEEEeCC
Confidence            9999999999999999999988665533 2489999999999999 99999999999999984

>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional

Probab=99.91  E-value=1.7e-23  Score=198.90  Aligned_cols=127  Identities=13%  Similarity=0.085  Sum_probs=115.5

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      +++-+....|||.+.+||||+|++|.+|+++||+++.|     ++|.|++|+||||++|..+|++.|+++.++++++.+.
T Consensus       247 ~~V~mYvCGPTVYd~~HIGHaRt~V~~DVL~R~Lr~~G-----y~V~fV~NiTD~DDKII~~A~e~G~sp~ela~~y~~~  321 (699)
T PRK14535        247 ENVRMYVCGMTVYDYCHLGHARVMVVFDMIARWLRECG-----YPLTYVRNITDIDDKIIARAAENGETIGELTARFIQA  321 (699)
T ss_pred             CceEEEecCCcCCCCCcccchhHHHHHHHHHHHHHHcC-----CceEEEeCCcccchHHHHHHHHcCCCHHHHHHHHHHH
Confidence            44445555778889999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecc-cceeeccCC
Q psy2399          92 RKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKK-INQFFDPIK  145 (232)
Q Consensus        92 ~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~-~~~~~~~~~  145 (232)
                      |.+++++|||..+.+..+ ..+|+..+++++++|. ++|++|++. +.+|||+.+
T Consensus       322 F~~d~~~LnI~~p~~~pr-aTeHI~~ii~lI~~Li-dkG~AYe~~~gsVYFdV~~  374 (699)
T PRK14535        322 MHEDADALGVLRPDIEPK-ATENIPQMIAMIETLI-QNGKAYPAANGDVYYAVRE  374 (699)
T ss_pred             HHHHHHHcCCCCCcEeeC-ccchHHHHHHHHHHHH-HCCCEEEeCCCCEEEeccc
Confidence            999999999988876444 4489999999999999 999999874 589999885

>PRK12300 leuS leucyl-tRNA synthetase; Reviewed

Probab=99.90  E-value=3.7e-24  Score=212.91  Aligned_cols=124  Identities=22%  Similarity=0.311  Sum_probs=115.7

Q ss_pred             CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc---------------CC---------CHH
Q psy2399          27 LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA---------------GM---------TPK   82 (232)
Q Consensus        27 lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~---------------g~---------~~~   82 (232)
                      |||||+++++++|+++||+||+|     ++|.+++|||+||+||+..|++.               |+         +|.
T Consensus         1 lHiGH~~~~t~~D~i~Ry~rm~G-----~~Vl~~~G~d~~GlPie~~ae~~~~~~~~~~~~~~~~~gi~~~~i~~f~~~~   75 (897)
T PRK12300          1 LHVGHGRTYTIGDVIARYKRMRG-----YNVLFPMAFHVTGTPILGIAERIARGDPETIELYKSLYGIPEEELEKFKDPE   75 (897)
T ss_pred             CccchhHHHHHHHHHHHHHHcCC-----CcCCCCCCCCCCCcCHHHHHHHhhccchhHHHHHHHHcCCCHHHHHHhcCHH
Confidence            79999999999999999999999     99999999999999999998753               43         456


Q ss_pred             HHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceecc
Q psy2399          83 EFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKG  156 (232)
Q Consensus        83 e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g  156 (232)
                      ++++++.+.+++++++||+  +|++.+.|+++.|.+.++++|.+|+ ++|+||++.+.+.|||.|+|.|+|.++..
T Consensus        76 ~~~~~~~~~~~~~~~~lG~~~DW~r~y~T~dp~y~~~v~w~F~~L~-ekGliyrg~~~v~wcp~~~t~lad~e~~~  150 (897)
T PRK12300         76 YIVEYFSEEAKEDMKRIGYSIDWRREFTTTDPEYSKFIEWQFRKLK-EKGLIVKGSHPVRYCPNDNNPVGDHDLLD  150 (897)
T ss_pred             HHHHHhHHHHHHHHHHhCcEEeCCCCeECCChhHHHHHHHHHHHHH-HCCCEecCCEeeeeCCCCCCCchHHHHhc
Confidence            7888999999999999998  7888899999999999999999999 99999999999999999999999998864

>PTZ00399 cysteinyl-tRNA-synthetase; Provisional

Probab=99.89  E-value=6.9e-23  Score=197.11  Aligned_cols=127  Identities=13%  Similarity=0.168  Sum_probs=116.3

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHH-HcCCCCCCceeEEecCCChhhHHHHHHHHHcCCC-HHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQC-MQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMT-PKEFINNI   88 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr-~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~-~~e~~~~~   88 (232)
                      .-++|||+|.+|  +.+||||||+||.+|+++||++ ..|     |+|.|++|+||+|++|+.+|++.|++ +.++++++
T Consensus        60 ~v~~Y~CGPTvY--d~~HiGhart~v~~Dil~R~l~~~~G-----y~V~~v~nitDidDKIi~~A~~~g~~~~~el~~~~  132 (651)
T PTZ00399         60 QVRWYTCGPTVY--DSSHLGHARTYVTFDIIRRILEDYFG-----YDVFYVMNITDIDDKIIKRAREEKLSIFLELARKW  132 (651)
T ss_pred             eeEEEEeCCCcc--CCcccccchHHHHHHHHHHHHHHhcC-----CceEEEeCCCCcchHHHHHHHHhCCCcHHHHHHHH
Confidence            345677765555  9999999999999999999999 899     99999999999999999999999999 99999999


Q ss_pred             HHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCC
Q psy2399          89 SSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKN  146 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~  146 (232)
                      .+.|.++|++|||..+.++++.. +|...+..++.+|. ++|++|..++.+|||++.=
T Consensus       133 ~~~f~~d~~~Lni~~p~~~~r~t-ehi~~ii~~i~~Li-~~G~aY~~~gsvyFd~~~f  188 (651)
T PTZ00399        133 EKEFFEDMKALNVRPPDVITRVS-EYVPEIVDFIQKII-DNGFAYESNGSVYFDVEAF  188 (651)
T ss_pred             HHHHHHHHHHcCCCCCccccCcC-ccHHHHHHHHHHHH-HCCCEEEECCeEEEEchhc
Confidence            99999999999998877766653 89999999999999 9999999999999998764

>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional

Probab=99.89  E-value=1.2e-22  Score=188.43  Aligned_cols=127  Identities=18%  Similarity=0.193  Sum_probs=115.6

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEe---------cCC-ChhhHHHHHHHHHcCCCH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFI---------CAD-DAHGAAIMIAAEKAGMTP   81 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~---------~g~-D~~G~~i~~~a~~~g~~~   81 (232)
                      .++-+....|||...+||||+|++|.+|+++||++++|     ++|.|+         +|+ |+||.+|...|++.|++|
T Consensus        20 ~~v~mY~CGpTVYd~~HiGh~r~~v~~Dvl~R~l~~~G-----~~V~~v~NiTDIghltg~~D~gddKIi~~A~~~g~~~   94 (481)
T PRK14534         20 SDVKVYACGPTVYNYAHIGNFRTYIFEDLLIKSLRLLK-----YNVNYAMNITDIGHLTGDFDDGEDKVVKAARERGLTV   94 (481)
T ss_pred             CceEEEeCCCCCCCCCCccchhHHHHHHHHHHHHHHcC-----CceEEEEeccccccccCCccCCCcHHHHHHHHcCCCH
Confidence            34555666788999999999999999999999999999     999994         555 445899999999999999


Q ss_pred             HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCC
Q psy2399          82 KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIK  145 (232)
Q Consensus        82 ~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~  145 (232)
                      .++++++.+.|.+++++|||.++.++++. .+|+..+++++++|. ++|++|+....+|||+.+
T Consensus        95 ~e~a~~~~~~f~~d~~~Lni~~~~~~p~a-tehi~~~i~~i~~L~-~kG~aY~~~~~vyFdv~~  156 (481)
T PRK14534         95 YEISRFFTEAFFDDCKKLNIVYPDKVLVA-SEYIPIMIEVVKVLE-ENGFTYFVNGNVYFDTSC  156 (481)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCceecCc-cchHHHHHHHHHHHH-HCCCEEEECCeEEEeccc
Confidence            99999999999999999999999988875 489999999999999 999999999999999887

>cd00672 CysRS_core catalytic core domain of cysteinyl tRNA synthetase

Probab=99.89  E-value=3.4e-23  Score=174.74  Aligned_cols=94  Identities=16%  Similarity=0.167  Sum_probs=87.6

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      +++.+++++.|.  |+|++||||+|++|.+|+++||+|++|     ++|.+++|+|+||+||+.+|++.|++|+++++++
T Consensus        18 ~~~~~~y~~gpt--~y~~~HiGH~r~~v~~Dvl~R~lr~~G-----~~V~~~~g~dd~g~ki~~~A~~~g~~p~e~~~~~   90 (213)
T cd00672          18 PGLVTMYVCGPT--VYDYAHIGHARTYVVFDVLRRYLEDLG-----YKVRYVQNITDIDDKIIKRAREEGLSWKEVADYY   90 (213)
T ss_pred             CCCceEEEeCCc--cCCCcccccchhHHHHHHHHHHHHhcC-----CeeEEEeecCCCCCHHHHHHHHcCCCHHHHHHHH
Confidence            355567777655  558999999999999999999999999     9999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccCCcC-CccccC
Q psy2399          89 SSNRKKYLDGFYIKF-DNWYST  109 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~-d~~~~t  109 (232)
                      .+.|++++++|||++ |.|++|
T Consensus        91 ~~~f~~~~~~l~i~~~d~~~rt  112 (213)
T cd00672          91 TKEFFEDMKALNVLPPDVVPRV  112 (213)
T ss_pred             HHHHHHHHHHcCCCCCCcceee
Confidence            999999999999998 999999

Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.

>PRK01611 argS arginyl-tRNA synthetase; Reviewed

Probab=99.89  E-value=8.5e-23  Score=192.34  Aligned_cols=128  Identities=16%  Similarity=0.223  Sum_probs=120.6

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      .+++++|..++|||||++||||+|+++++|+++|++++.|     ++|.++.++||+|.++...+...+..++++++.+.
T Consensus       109 ~~~~v~Ie~~spnp~g~lHiGH~R~~iigD~laR~lr~~G-----~~V~~~~~i~D~G~qi~~~a~~~~~~~~~~~~~~~  183 (507)
T PRK01611        109 KGKKVVVEYVSANPTGPLHVGHLRSAVIGDALARILEFAG-----YDVTREYYVNDAGTQIGMLIASLELLWRKAVDISL  183 (507)
T ss_pred             CCCEEEEEecCCCCCCCCcCCchHHHHHHHHHHHHHHHcC-----CcEEEEeeeCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999999     99999999999999999999998888899999999


Q ss_pred             HHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEE-ecccceeecc
Q psy2399          90 SNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLII-NKKINQFFDP  143 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy-~~~~~~~~~~  143 (232)
                      +.|+++|++|||.+|.|.++++..+...+++++++|. ++|++| +.++.+|++.
T Consensus       184 ~~~~~~l~~LgI~~D~~~~es~~~~~~~~~~~~~~L~-~~G~~y~~~~Ga~~~~~  237 (507)
T PRK01611        184 DEIKEDLDRLGVHFDVWFSESELYYNGKVDEVVEDLK-EKGLLYVESDGALWVRL  237 (507)
T ss_pred             HHHHHHHHHcCCeeeEEeecCcchhcchHHHHHHHHH-HCCCEEEeeCCcEEEEc
Confidence            9999999999999999999988777889999999999 999999 8788888864

>PF01406 tRNA-synt_1e: tRNA synthetases class I (C) catalytic domain; InterPro: IPR015803 The aminoacyl-tRNA synthetases (6

Probab=99.86  E-value=1.8e-21  Score=170.15  Aligned_cols=126  Identities=17%  Similarity=0.245  Sum_probs=108.3

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      +++-+.+..|||...+||||+|++|..|++.|+|+..|     ++|.++.+++|.+++|..+|++.|+++.++++++.+.
T Consensus         7 ~~v~~Y~CGPTVYd~~HiGhaR~~v~~D~l~R~L~~~g-----~~V~~V~NiTDiDDKii~~A~~~g~~~~ela~~y~~~   81 (300)
T PF01406_consen    7 GKVRMYVCGPTVYDYAHIGHARTYVFFDVLRRYLEYLG-----YDVTYVMNITDIDDKIIKRAREEGVSPQELARRYEEE   81 (300)
T ss_dssp             TEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT------EEEEEEEEB-SSHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCCCCCCCcceeeeeeHHHHHHHHHHcC-----CeEEEEEeccccchHHHHHHHhccCCHHHHHHHHHHH
Confidence            34444444678889999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCC-cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecc-cceeeccCC
Q psy2399          92 RKKYLDGFYI-KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKK-INQFFDPIK  145 (232)
Q Consensus        92 ~~~~l~~lgI-~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~-~~~~~~~~~  145 (232)
                      |.++|++||| .++.+.+.+  +|...+.+++++|. ++|++|... +.+|||+..
T Consensus        82 f~~dm~~Lnv~~p~~~prat--e~i~~ii~~i~~Li-~~G~AY~~~~g~VYFdv~~  134 (300)
T PF01406_consen   82 FFEDMKALNVLPPDHYPRAT--EHIPEIIELIEKLI-DKGHAYESEDGSVYFDVSK  134 (300)
T ss_dssp             HHHHHHHTT----SEEEEGG--GGHHHHHHHHHHHH-HTTSEEEETTSEEEE-CCG
T ss_pred             HHHHHHHcCCCCCccccchh--ccHHHHHHHHHHHH-HCCCeEEcCCCcEEEeecc
Confidence            9999999999 467888888  79999999999999 999999999 999999864

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. Cysteinyl-tRNA synthetase (6.1.1.16 from EC) is an alpha monomer and belongs to class Ia.; GO: 0000166 nucleotide binding, 0004817 cysteine-tRNA ligase activity, 0005524 ATP binding, 0006423 cysteinyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3SP1_B 3TQO_A 3C8Z_B 1LI5_B 1LI7_B 1U0B_B.

>PRK00750 lysK lysyl-tRNA synthetase; Reviewed

Probab=99.86  E-value=1.1e-22  Score=191.42  Aligned_cols=174  Identities=17%  Similarity=0.238  Sum_probs=132.1

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhh--------HHH-HHHHHHcCCC---
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHG--------AAI-MIAAEKAGMT---   80 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G--------~~i-~~~a~~~g~~---   80 (232)
                      .++|++++ +|||.+||||+++++.+|+++|++|++|     ++|.+++|+|+||        .|. +..++..|++   
T Consensus        24 ~~~~~~g~-~psG~~HiG~~~e~~~~d~v~r~lr~~G-----~~v~~i~~~Dd~d~lRkvp~~~p~~~~~~~~~G~pl~~   97 (510)
T PRK00750         24 PVVVETGI-GPSGLPHIGNFREVARTDMVRRALRDLG-----IKTRLIFFSDDMDGLRKVPDNVPNQEMLEEYLGKPLTE   97 (510)
T ss_pred             cEEEEeCC-CCCCCcccccccchhhHHHHHHHHHHcC-----CcEEEEEEEecCCcccccCCCCCchHHHHHhcCccccc
Confidence            47777776 7999999999999999999999999999     9999999999997        232 2344444543   


Q ss_pred             -------HHHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe------c--ccceeeccCC
Q psy2399          81 -------PKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN------K--KINQFFDPIK  145 (232)
Q Consensus        81 -------~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~------~--~~~~~~~~~~  145 (232)
                             ++++++++.+.+++.|+.|||++|.+.+|.........+.+...|. +++.|..      +  ....||    
T Consensus        98 ~p~p~G~~~~~~~~~~~~~~~~~~~~gi~~d~~~~t~~y~~g~~~~~i~~~l~-~~~~i~~il~~~~~~~~~~~~~----  172 (510)
T PRK00750         98 IPDPFGCHESYAEHFNAPLREFLDRFGIEYEFISATECYKSGRYDEAILTALE-NRDEIMEILLPYLGEERQATYS----  172 (510)
T ss_pred             CCCCCCCchHHHHHHHHHHHHHHHHcCCceEEEehhhhhccCchHHHHHHHHH-hHHHHHHHHHHhcCCccCCCee----
Confidence                   8999999999999999999999996655554444456666777777 7776632      1  233344    


Q ss_pred             CcccccceeccCCCCCCccccCCCcCccCCCCCCCcc--------ccCCcccCCCCccEEEEccceeEecCChhhHHHHH
Q psy2399         146 NIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTK--------LINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLR  217 (232)
Q Consensus       146 ~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~--------l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~  217 (232)
                                          ++..+|++||++.+...        -+.+.|. ||+..+..-.. ---||  .|-.||-.
T Consensus       173 --------------------P~~pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~~~~~~~-g~~KL--~Wr~dW~~  228 (510)
T PRK00750        173 --------------------PFLPICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEGEVPVTG-GHGKL--QWKVDWPM  228 (510)
T ss_pred             --------------------eeeeeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEEEEecCC-CCccc--CCCCCcHH
Confidence                                57788999999987331        2456776 99998865444 22489  89999999


Q ss_pred             hhhh
Q psy2399         218 KWAI  221 (232)
Q Consensus       218 ~~~~  221 (232)
                      .|.+
T Consensus       229 rW~~  232 (510)
T PRK00750        229 RWAA  232 (510)
T ss_pred             HHHH
Confidence            9943

>KOG0432|consensus

Probab=99.85  E-value=5.6e-21  Score=182.90  Aligned_cols=141  Identities=20%  Similarity=0.203  Sum_probs=128.0

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-----CC-----
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-----GM-----   79 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-----g~-----   79 (232)
                      ....|+++.|||+++|.||||||.+..+.|+++||.||.|     ++|.++.|+|+.|..++..++|.     |+     
T Consensus        73 ~~~~f~i~~PPPNVTG~LHiGHALt~aiqD~i~R~~rm~G-----~~vlw~PG~DHAGIATQ~VVEK~l~~~~~~~Rh~l  147 (995)
T KOG0432|consen   73 PGGVFVIPLPPPNVTGSLHIGHALTVAIQDALARYNRMHG-----YQVLWVPGTDHAGIATQVVVEKQLAREGGKTRHDL  147 (995)
T ss_pred             CCCcceeecCCCCcccccchhHHHHHHHHHHHHHHHHhcC-----CeeeecCCccccchhHHHHHHHHHHHhcCcchhhc
Confidence            4567999999999999999999999999999999999999     99999999999999999999872     22     


Q ss_pred             CH-------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccc
Q psy2399          80 TP-------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLP  150 (232)
Q Consensus        80 ~~-------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~  150 (232)
                      ..       .++.+++...|.++|++||.  +|++...|+|+...+.|.+.|.+|+ +.|+||+..+.+.||+...+.+|
T Consensus       148 gRe~F~~~vw~Wk~e~g~~I~~Qlk~lGas~DW~re~fTmD~~~s~AV~eAFvrL~-eeglIyR~~rlVNW~~~L~saiS  226 (995)
T KOG0432|consen  148 GREEFLKEVWEWKEEYGGRIYNQLKRLGASLDWDREAFTMDPKLSRAVTEAFVRLH-EEGLIYRANRLVNWCPALRSAIS  226 (995)
T ss_pred             CHHHHHHHHHHHHHHhCccHHHHHHHhcCcccccHhhcccCHHHHHHHHHHHHHHH-hcCceEecCceeeechhHHhhhh
Confidence            22       34566777899999999997  6788889999999999999999999 99999999999999999999999


Q ss_pred             cceecc
Q psy2399         151 DRYIKG  156 (232)
Q Consensus       151 ~~~v~g  156 (232)
                      |.+|+-
T Consensus       227 diEVe~  232 (995)
T KOG0432|consen  227 DIEVES  232 (995)
T ss_pred             hheecc
Confidence            999964

>KOG0433|consensus

Probab=99.82  E-value=5.6e-20  Score=173.40  Aligned_cols=139  Identities=22%  Similarity=0.309  Sum_probs=122.7

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHH-HHHHH------cCCC
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM-IAAEK------AGMT   80 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~-~~a~~------~g~~   80 (232)
                      ++.+..|++.+    +||.||+||+++.|+.|++.|++-+.|     ..+.++.|||+||+||+ .+|-+      ..++
T Consensus        55 ~~q~~~f~L~d----anG~lhlghalnkILkdIinr~~laqg-----~~alyvpGwDchGLPiEs~kalssl~~~~~~~s  125 (937)
T KOG0433|consen   55 DQQRVEFELKD----ANGNLHLGHALNKILKDIINRILLAQG-----KSALYVPGWDCHGLPIESTKALSSLTESEGSRT  125 (937)
T ss_pred             hccCceEEEec----cCCCccchHHHHHHHHHHHHHHHHhcC-----ceeccCCCCCcCCCchHHHHHhhhhhhccccCC
Confidence            34445677776    999999999999999999999999999     99999999999999999 45543      2345


Q ss_pred             HHH-------HHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccccc
Q psy2399          81 PKE-------FINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPD  151 (232)
Q Consensus        81 ~~e-------~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~  151 (232)
                      |.|       +++.-.+.+++.++++||  +|...+-|.++.|.....++|.+|+ +||+||+...++||+|+..|.|+|
T Consensus       126 ~leiR~~Ar~fA~~AIk~Q~e~F~r~gv~aDW~n~Y~T~~~~ye~aQL~iF~~ly-ekgLvyR~~KPVyWSpSSRTALAE  204 (937)
T KOG0433|consen  126 PLEIRAKARIFADEAIKKQMEAFRRWGVTADWENPYVTKSPSYEAAQLDIFAKLY-EKGLVYRSFKPVYWSPSSRTALAE  204 (937)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHheeeccCCCceeecChHHHHHHHHHHHHHH-hccceeccCCcceecCcchhhhhh
Confidence            554       466667888999999999  8999999999999999999999999 999999999999999999999999


Q ss_pred             ceecc
Q psy2399         152 RYIKG  156 (232)
Q Consensus       152 ~~v~g  156 (232)
                      ++++=
T Consensus       205 aELEY  209 (937)
T KOG0433|consen  205 SELEY  209 (937)
T ss_pred             hhccC
Confidence            99874

>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=1.8e-19  Score=165.07  Aligned_cols=124  Identities=19%  Similarity=0.229  Sum_probs=115.8

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      +.|||  .|||....||||+|++|..|++.|||+..|     |.|.|+.+++|.+.||...|.+.|.++.++++++.++|
T Consensus        24 ~mYvC--GpTVYd~~HIGhaRt~V~fDvl~R~L~~~G-----y~V~yV~NiTDIDDKIi~rA~~~g~~~~ev~~~~i~~f   96 (464)
T COG0215          24 KMYVC--GPTVYDYAHIGHARTYVVFDVLRRYLRYLG-----YKVTYVRNITDIDDKIINRAREEGLSIREVAERYIAAF   96 (464)
T ss_pred             EEEec--CCccCCccccccCcceehHHHHHHHHHHhC-----CeEEEEeccccccHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            45555  678889999999999999999999999999     88999999999999999999999999999999999999


Q ss_pred             HHHHhccCC-cCCccccCCChhHHHHHHHHHHHHHhhcCCEEec-ccceeeccCCC
Q psy2399          93 KKYLDGFYI-KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINK-KINQFFDPIKN  146 (232)
Q Consensus        93 ~~~l~~lgI-~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~-~~~~~~~~~~~  146 (232)
                      .+++++||| .+|...+.+  +|+..+.+++++|. +||++|.. .+.++|++..-
T Consensus        97 ~~D~~aL~v~~p~~~PraT--e~I~~iI~~I~~Li-ekG~AY~~~~G~VYFdv~~f  149 (464)
T COG0215          97 FEDMDALNVLPPDIEPRAT--EHIDEIIEFIEKLI-EKGYAYVADDGDVYFDVSKF  149 (464)
T ss_pred             HHHHHHhCCCCCcccCcHh--hCHHHHHHHHHHHH-HCCceEEecCCcEEEecccc
Confidence            999999999 678998988  79999999999999 99999998 68999988754

>KOG0434|consensus

Probab=99.80  E-value=1.6e-19  Score=169.30  Aligned_cols=143  Identities=22%  Similarity=0.226  Sum_probs=130.4

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-cCCC------
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-AGMT------   80 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~g~~------   80 (232)
                      -+++++|...++||.++|.+|-||+..-++.|+.-||..+.|     +.|...+|||+||+||+...++ +|++      
T Consensus        34 sk~rp~ftFyDGPPFATGlPHyGHiLa~TIKDiVtRya~~~G-----~hVeRRFGWD~HGlPVE~eIDKkLgI~g~~dV~  108 (1070)
T KOG0434|consen   34 SKGRPKFTFYDGPPFATGLPHYGHILASTIKDIVTRYATQTG-----HHVERRFGWDTHGLPVEYEIDKKLGITGRDDVM  108 (1070)
T ss_pred             hCCCCceeeccCCccccCCCccchhhhhhHHHHHHHHhhccc-----cceeeecccccCCCccceeechhcCCCCHHHHH
Confidence            466788999999999999999999999999999999999999     9999999999999999988765 5653      


Q ss_pred             ----------HHHHHHHHHHHHHHHHhccC--CcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcc
Q psy2399          81 ----------PKEFINNISSNRKKYLDGFY--IKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIF  148 (232)
Q Consensus        81 ----------~~e~~~~~~~~~~~~l~~lg--I~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~  148 (232)
                                +..++-+|+.+++++..+||  |+||+-+.|+.+.+.+.|+++|.+|+ +||++|++-.-.+||..|.|+
T Consensus       109 kmGI~kYN~ECR~IVmrYssEWe~tv~RlGRWidF~ndYkTmyp~FMESvWwvFkeL~-~kglVYRG~kVMP~STac~TP  187 (1070)
T KOG0434|consen  109 KMGIDKYNNECRKIVMRYSSEWEKTVERLGRWIDFDNDYKTLYPSFMESVWWVFKELH-EKGLVYRGFKVMPYSTACTTP  187 (1070)
T ss_pred             HHhHHhHhHHHHHHHHHHHHHHHHHHHhhccceeccCCcceecHHHHHHHHHHHHHHH-hcCceecceeeeccccccCCc
Confidence                      34467788899999999999  69999999999999999999999999 999999999999999999999


Q ss_pred             cccceecc
Q psy2399         149 LPDRYIKG  156 (232)
Q Consensus       149 l~~~~v~g  156 (232)
                      ||.=+...
T Consensus       188 LSNFEa~Q  195 (1070)
T KOG0434|consen  188 LSNFEAQQ  195 (1070)
T ss_pred             ccchhccc
Confidence            98765543

>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete

Probab=99.79  E-value=3.5e-20  Score=173.87  Aligned_cols=173  Identities=18%  Similarity=0.213  Sum_probs=128.9

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChh------------------hHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAH------------------GAAIMIA   73 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~------------------G~~i~~~   73 (232)
                      .+++|+++.+ |||.+||||+++.+.+|+++|++|++|     .+|.+++++|+|                  |.|+...
T Consensus        18 ~~~~~~tg~~-psG~~HiG~~~e~~~~d~v~r~~r~~g-----~~~~~i~~~Dd~D~lRKvp~~~p~~~~~ylG~Pl~~v   91 (515)
T TIGR00467        18 NLYTVASGIT-PSGHIHIGNFREVITADAIARALRDSG-----SEARFIYIADNYDPLRKVYPFLPEELETYLGMPLTRI   91 (515)
T ss_pred             CeEEEecCCC-CCCCccccchhhhhHHHHHHHHHHHcC-----CCEEEEEEEcCCcccccccccccHHHHHhCCCcceec
Confidence            4688888886 999999999999999999999999999     999999999999                  9999999


Q ss_pred             HHHcCCCHHHHHHHHHHHHHHHHhccCCcCCccccCCC---hhHHHHHHHHHHHHHhhcCCE---Ee--cccceeeccCC
Q psy2399          74 AEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDS---IENIDLVQKIYDTLYNKAKLI---IN--KKINQFFDPIK  145 (232)
Q Consensus        74 a~~~g~~~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~---~~~~~~v~~~~~~L~~~kG~i---y~--~~~~~~~~~~~  145 (232)
                      ++..|+. +.+++++...+.+.|+.|||+++....|..   -.+.+.+..+++.-. +-.-|   |+  .....||    
T Consensus        92 pdp~g~~-~s~~~h~~~~~~~~l~~~gi~~e~~s~te~Y~sG~~~~~i~~~L~~~~-~I~~il~~~~~~~~~~~~~----  165 (515)
T TIGR00467        92 PDPEGCK-TSYAEHFLIPFLESLPVLGINPEFIRASKQYTSGLYASQIKIALDHRK-EISEILNEYRTSKLEENWY----  165 (515)
T ss_pred             CCCCCCc-HHHHHHHHHHHHHHHHHcCCeEEEEEHHHhhhcCChHHHHHHHHHhHH-HHHHHHHHhcCCccCCCce----
Confidence            9999996 999999999999999999998865533321   112222222222111 10000   12  2234455    


Q ss_pred             CcccccceeccCCCCCCccccCCCcCccCCCCCCCc------cccCCcccCCCCccEEEEccceeEecCChhhHHHHHhh
Q psy2399         146 NIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPT------KLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKW  219 (232)
Q Consensus       146 ~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~------~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~  219 (232)
                                          ++..+|++||++.++.      .-+.++|. ||+..+..-...- -||  .|-.||-..|
T Consensus       166 --------------------P~~pic~~cGrv~~~~~~~~~~~~v~Y~c~-cG~~g~~~~~~g~-~KL--~WkvdW~~RW  221 (515)
T TIGR00467       166 --------------------PISVFCENCGRDTTTVNNYDNEYSIEYSCE-CGNQESVDIYTGA-IKL--PWRVDWPARW  221 (515)
T ss_pred             --------------------eeeeecCCcCccCceEEEecCCceEEEEcC-CCCEEEEeecCCC-ccc--CCCCCcHhhH
Confidence                                5778899999997632      12567786 9999987544322 299  8999999999


Q ss_pred             h
Q psy2399         220 A  220 (232)
Q Consensus       220 ~  220 (232)
                      .
T Consensus       222 ~  222 (515)
T TIGR00467       222 K  222 (515)
T ss_pred             h
Confidence            4

This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.

>cd00802 class_I_aaRS_core catalytic core domain of class I amino acyl-tRNA synthetase

Probab=99.72  E-value=2.3e-17  Score=130.71  Aligned_cols=77  Identities=26%  Similarity=0.251  Sum_probs=74.2

Q ss_pred             EEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Q psy2399          16 VTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKY   95 (232)
Q Consensus        16 v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~   95 (232)
                      |++++|||||++||||+|+++++|+++|++|++|     ++|.+++|+||+|.++...|.+.+++++++++++.+.|+++
T Consensus         1 ~~~~~p~~~~~~HlGh~~~~~~~d~~~r~lr~~G-----~~v~~~~~~dd~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   75 (143)
T cd00802           1 TTFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLG-----YKVRCIALIDDAGGLIGDPANKKGENAKAFVERWIERIKED   75 (143)
T ss_pred             CEecCCCCCCCccHhHHHHHHHHHHHHHHHHHcC-----CCeEEEeeeCCCchHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999999999     99999999999999999999999999999999999999998


Q ss_pred             Hh
Q psy2399          96 LD   97 (232)
Q Consensus        96 l~   97 (232)
                      ++
T Consensus        76 ~~   77 (143)
T cd00802          76 VE   77 (143)
T ss_pred             HH
Confidence            87

Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.

>KOG2007|consensus

Probab=99.68  E-value=4.1e-16  Score=142.44  Aligned_cols=125  Identities=16%  Similarity=0.156  Sum_probs=108.3

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHH-HcCCCCCCceeEEecCCChhhHHHHHHHHH--cCCCHHHHHH---
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQC-MQQDNGKSRQVYFICADDAHGAAIMIAAEK--AGMTPKEFIN---   86 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr-~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~--~g~~~~e~~~---   86 (232)
                      .+|++  .||++..-||||||+||..||+.|+|+ ..|     |+|.|++++.|.+++|...|++  .+..|..+.+   
T Consensus        57 ~wY~C--GpTvYD~SHmGHArsYVsfDIlrRiL~dyfg-----y~V~~vmNiTDVDDKII~RAr~~~m~e~~~~l~~~F~  129 (586)
T KOG2007|consen   57 TWYIC--GPTVYDSSHMGHARSYVSFDILRRILRDYFG-----YDVTFVMNITDVDDKIIKRARKEEMGEKPLSLSERFC  129 (586)
T ss_pred             EEEEe--cCcccchhhhhhhhhhhhHHHHHHHHHHHcC-----cceEEEecccchhHHHHHHhhhhhhccchhhHHHHHH
Confidence            44555  678999999999999999999999999 889     9999999999999999999972  3444444433   


Q ss_pred             HHHHHHHHHHhccCC-cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCc
Q psy2399          87 NISSNRKKYLDGFYI-KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNI  147 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI-~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~  147 (232)
                      .|.+.|.++|.+|++ .++...|-+  +|...+..+++++. ++|++|..++++|||+..-.
T Consensus       130 ~~e~eF~~DM~~LnvLpPtv~tRVS--eyvp~II~fIqkII-dnG~aY~~dGsVYFdv~kf~  188 (586)
T KOG2007|consen  130 YYEEEFLQDMAALNVLPPTVQTRVS--EYVPQIIKFIQKII-DNGYAYAVDGSVYFDVDKFP  188 (586)
T ss_pred             HHHHHHHHHHHHhCCCCCcccchhh--hchHHHHHHHHHHH-hCCceeeeCCcEEEeccccc
Confidence            567999999999999 677777777  79999999999999 99999999999999987654

>KOG0437|consensus

Probab=99.62  E-value=1.4e-15  Score=144.09  Aligned_cols=141  Identities=23%  Similarity=0.330  Sum_probs=116.1

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-------CC
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-------GM   79 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-------g~   79 (232)
                      ..+.+++|+++.|.||.||.||+||+++.--.|+.+-|.|++|     ++|+|.+|+.+.|.||...|+++       |.
T Consensus        39 l~~~~~Kff~tfpyPYMNG~LHlGH~FslSK~eFa~~y~rL~G-----k~vLfPfgFHCTGMPI~A~AdKLkrEie~fG~  113 (1080)
T KOG0437|consen   39 LQKSKPKFFVTFPYPYMNGRLHLGHAFSLSKVEFASGYERLQG-----KNVLFPFGFHCTGMPIKASADKLKREIELFGC  113 (1080)
T ss_pred             cccccCceeEeccccccCceeeccceeehhhhHHHHHHHHhcC-----ceEEeecccccCCCccHHhHHHHHHHHHHhCC
Confidence            3566789999999999999999999999999999999999999     99999999999999999999874       22


Q ss_pred             CH---H-----------------------------------------------------------HHHHHHHHHHHHHHh
Q psy2399          80 TP---K-----------------------------------------------------------EFINNISSNRKKYLD   97 (232)
Q Consensus        80 ~~---~-----------------------------------------------------------e~~~~~~~~~~~~l~   97 (232)
                      +|   +                                                           .|...+-..-.++|.
T Consensus       114 ppdf~~e~eeEv~eev~~~~~~~~~k~kgKKsk~aaK~g~~kYQw~IM~slGl~deEI~~F~d~~~WL~yFPpLc~~dlk  193 (1080)
T KOG0437|consen  114 PPDFPEEEEEEVEEEVKTEDAIEDVKFKGKKSKAAAKTGGQKYQWEIMESLGLPDEEIKKFADPKHWLYYFPPLCERDLK  193 (1080)
T ss_pred             CCCCchhhhhhhhhcccccccccccccccchhhHHHhhcccchhHHHHHHcCCCHHHhhcccChhHHHHhCChHHHHHHH
Confidence            11   0                                                           011111134556778


Q ss_pred             ccCC--cCCc-cccCC-ChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccce
Q psy2399          98 GFYI--KFDN-WYSTD-SIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRY  153 (232)
Q Consensus        98 ~lgI--~~d~-~~~t~-~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~  153 (232)
                      ++|.  +|.+ |+.|+ +|.|..+|+|.|.+|. +.|.|..+++..-|||.++++.-|..
T Consensus       194 ~~gl~iDWRRSFITTDvNpYyDsFVRWQ~n~L~-~~gkI~fgkRyTIyspkDgQpCmDHD  252 (1080)
T KOG0437|consen  194 RFGLGIDWRRSFITTDVNPYYDSFVRWQFNKLK-EAGKIKFGKRYTIYSPKDGQPCMDHD  252 (1080)
T ss_pred             HhCCCcceeeeeeecccchhHHHHHHHHHHHHH-hcCCcccCcceeeecCCCCCcccccc
Confidence            7775  6655 66665 6889999999999999 99999999999999999999976643

>PF00750 tRNA-synt_1d: tRNA synthetases class I (R); InterPro: IPR015945 The aminoacyl-tRNA synthetases (6

Probab=99.58  E-value=1.3e-14  Score=131.35  Aligned_cols=132  Identities=20%  Similarity=0.250  Sum_probs=100.5

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc--------C
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA--------G   78 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~--------g   78 (232)
                      ..+.+++++|-...|+|+|+|||||+|+.+++|+|+|.++..|     ++|.-...++|.|.++...+...        .
T Consensus        15 ~~~~~~kv~VE~sSpNp~kplHvGHlR~~iiGd~laril~~~G-----~~V~r~nyigD~G~Q~~~l~~~~~~~~~~~~~   89 (354)
T PF00750_consen   15 EKGKGKKVVVEFSSPNPTKPLHVGHLRNTIIGDSLARILEAAG-----YDVTRENYIGDWGTQIGLLAASYKKFGDEELL   89 (354)
T ss_dssp             -TTTSEEEEEEE---BTTSS-BHHHHHHHHHHHHHHHHHHHTT-----EEEEEEEEEBTTSHHHHHHHHHHHHHHHHHTS
T ss_pred             ccCCCCEEEEEecCCCCCCCCcCCcchhhhhhHHHHHHHHHcC-----CeeeeEEEECCCCHHHHHHHHHHHhhhhhhhc
Confidence            3456788999999999999999999999999999999999999     99999999999987766554210        0


Q ss_pred             -----------------------C------C------------------HHHHHHH-HHHHHHHHHhccCCcCCccccCC
Q psy2399          79 -----------------------M------T------------------PKEFINN-ISSNRKKYLDGFYIKFDNWYSTD  110 (232)
Q Consensus        79 -----------------------~------~------------------~~e~~~~-~~~~~~~~l~~lgI~~d~~~~t~  110 (232)
                                             .      .                  ..++... +.+.++++|++++|.+|.+...+
T Consensus        90 ~~~~~~~l~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~gd~~~~~~~~~~~~~~~k~~l~~l~i~fDv~~~E~  169 (354)
T PF00750_consen   90 EEDPIKHLEDLYVGANKRDEADEIAEKEPEELEEEAREYLKKLEQGDEEFRELWQKYILEWSKETLQRLYIRFDVWFDES  169 (354)
T ss_dssp             HSSCHHHHHHHHHHHHHHHHHTTCSSGCCCCHHHHHHHHHHHHHHCCTTHHHHHHHHHHHHHHHHHHHTT---SEEEEHC
T ss_pred             ccccccchhhhhhhhhhhhhhhhhccccccccccccceeeeecccccHHHHHHHHHHHHHHHHHHHHHHHHHhCcCcccc
Confidence                                   0      0                  0011223 56788899999999999998776


Q ss_pred             ChhHHHHHHHHHHHHHhhcCCEEecccceeeccC
Q psy2399         111 SIENIDLVQKIYDTLYNKAKLIINKKINQFFDPI  144 (232)
Q Consensus       111 ~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~  144 (232)
                      +..+...+..+++.|. ++|++|+.++..|++..
T Consensus       170 Es~~~~~v~~vl~~L~-e~g~~~~~dGa~~i~~~  202 (354)
T PF00750_consen  170 ESFYSGKVDEVLERLK-EKGLLYESDGALWIDLT  202 (354)
T ss_dssp             HHHHTTHHHHHHHHHH-CTTTEEEETTEEEEEGC
T ss_pred             hhhhhhHHHHHHHHHH-hCCcEEecCCcEEEech
Confidence            5567888999999999 99999999999988654

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 represents the core region of arginyl-tRNA synthetase (6.1.1.19 from EC), which has been crystallized and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes is available []. ; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1IQ0_A 1F7V_A 1F7U_A 1BS2_A 3GDZ_B.

>COG0018 ArgS Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.57  E-value=1.5e-14  Score=137.57  Aligned_cols=126  Identities=22%  Similarity=0.235  Sum_probs=104.3

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH--------cC--
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK--------AG--   78 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~--------~g--   78 (232)
                      ..+++++|-...|+|+||+||||+|+.|++|+++|.++..|     |+|.-...++|.|.++-..+..        .+  
T Consensus       114 ~~~~kV~iE~sSaNptkplHiGHlR~aiiGDsLaril~~~G-----y~V~r~~yvnD~G~Q~~~l~~~~~~~~~e~~~~~  188 (577)
T COG0018         114 GKGKKVVIEYSSANPTGPLHIGHLRNAIIGDSLARILEFLG-----YDVTRENYVNDWGTQIGMLALSYEKRGREALGLT  188 (577)
T ss_pred             CCCCEEEEEEeCCCCCCCcccchhhhhHHHHHHHHHHHHcC-----CCeeEEeeECcHHHHHHHHHHHHHHhccccccCC
Confidence            34579999999999999999999999999999999999999     9999988888888766544311        00  


Q ss_pred             -------------------CCHH------------------H------HHHHHHHHHHHHHhccCCcCCccccCCChhHH
Q psy2399          79 -------------------MTPK------------------E------FINNISSNRKKYLDGFYIKFDNWYSTDSIENI  115 (232)
Q Consensus        79 -------------------~~~~------------------e------~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~  115 (232)
                                         .++.                  +      +++...+.++++|++|||.+|.|.+.++..+.
T Consensus       189 ~~~~~~lg~~y~~i~~~~~~~~~~~~~~~~~~~~k~e~~d~~~~lw~~~v~~~l~~~k~~l~~l~V~fD~~~~E~e~~~~  268 (577)
T COG0018         189 PEPDGYLGEYYVKIAKDLEEDPGNDEEEAREEVEKLESGDEEAELWRKFVDLSLEGIKETLDRLGVKFDVYDSEGESFYN  268 (577)
T ss_pred             CCcchHHHHHHHHHHHHHHhCcccchHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhCcccceeeccchhhhc
Confidence                               0111                  1      45566789999999999999999988877778


Q ss_pred             HHHHHHHHHHHhhcCCEEeccccee
Q psy2399         116 DLVQKIYDTLYNKAKLIINKKINQF  140 (232)
Q Consensus       116 ~~v~~~~~~L~~~kG~iy~~~~~~~  140 (232)
                      ..+..+++.|. ++|++|+.++..+
T Consensus       269 ~~~~~vv~~L~-~~~~~~e~~GA~~  292 (577)
T COG0018         269 GKVEKVVEDLE-EKGLLYEDDGALV  292 (577)
T ss_pred             ccHHHHHHHHH-hcCCEeeeCCeEE
Confidence            89999999999 9999999776663

>TIGR00456 argS arginyl-tRNA synthetase

Probab=99.57  E-value=1.7e-14  Score=137.80  Aligned_cols=126  Identities=20%  Similarity=0.240  Sum_probs=102.8

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH---cCC--------
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK---AGM--------   79 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~---~g~--------   79 (232)
                      +++++|..+.|||+|++||||+|+++++|+++|++++.|     ++|.-...+.|.|.++-..+..   .+.        
T Consensus       111 ~~~v~ve~~spn~~~~~hiGh~r~~~~gd~l~r~~~~~g-----~~v~r~~yinD~G~Q~~~l~~~~~~~~~~~~~~~~~  185 (566)
T TIGR00456       111 NKKIIIEFSSANPAGPLHIGHLRNAIIGDSLARILEFLG-----YDVIREYYVNDWGRQFGLLALGVEKFGNEKLNEAVK  185 (566)
T ss_pred             CCeEEEEecCCCCCCCCchhhhHHHHHHHHHHHHHHHCC-----CCeeEEeeecchHHHHHHHHHHHHHhCCccccCccc
Confidence            568999999999999999999999999999999999999     9999888888888766554421   100        


Q ss_pred             -------------------------------------CH------HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHH
Q psy2399          80 -------------------------------------TP------KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENID  116 (232)
Q Consensus        80 -------------------------------------~~------~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~  116 (232)
                                                           ++      +.+++...+.++++|++|||.+|.|.+.++..+..
T Consensus       186 ~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~le~~d~~~~~~w~~~~~~~l~~~~~~~~~l~V~fD~~~~E~e~~~~~  265 (566)
T TIGR00456       186 KPDHGLEGFYVEINKRLEENEELEEEARELFVKLESGDEEAIKLWKRLVEYSLEGIKETLARLNIHFDSFVWEGESVKNG  265 (566)
T ss_pred             CChHHHHHHHHHHHHHHhhCccHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCceeeeeccccccccc
Confidence                                                 01      11234455899999999999999998777667778


Q ss_pred             HHHHHHHHHHhhcCCEEecccceeecc
Q psy2399         117 LVQKIYDTLYNKAKLIINKKINQFFDP  143 (232)
Q Consensus       117 ~v~~~~~~L~~~kG~iy~~~~~~~~~~  143 (232)
                      .+..+++.|. ++|++|++ +..|.+.
T Consensus       266 ~~~~v~~~L~-~~g~~~~~-Ga~~~~~  290 (566)
T TIGR00456       266 MVPKVLEDLK-EKGLVVED-GALWLDL  290 (566)
T ss_pred             cHHHHHHHHH-HCCCEEEc-CCEEEEc
Confidence            8999999999 99999987 8888754

This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori.

>PRK12451 arginyl-tRNA synthetase; Reviewed

Probab=99.56  E-value=3.8e-14  Score=135.17  Aligned_cols=126  Identities=11%  Similarity=0.058  Sum_probs=101.9

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH---cCCC------
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK---AGMT------   80 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~---~g~~------   80 (232)
                      ++++++|-...|+|+|+|||||+|+.+++|+++|.++..|     ++|.-...++|.|.++-..+..   .|..      
T Consensus       111 ~~~~v~vE~sSpNp~kplHvGH~R~aiiGd~l~ril~~~G-----~~V~r~nyinD~G~Q~~~l~~~~~~~~~~~~~~~~  185 (562)
T PRK12451        111 CEKTVVIDYSSPNIAKPFSMGHLRSTMIGNALKHIAEKCG-----YEVVGINYIGDWGTQFGKLITAYKKWGNEAVVKED  185 (562)
T ss_pred             CCCEEEEEecCCCCCCCcccchhhhHHHHHHHHHHHHHCC-----CCeEEEeeecCchHHHHHHHHHHHHhCCccccccC
Confidence            3578999999999999999999999999999999999999     9999999999998766655421   1110      


Q ss_pred             -------------------------------------------HHHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHH
Q psy2399          81 -------------------------------------------PKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDL  117 (232)
Q Consensus        81 -------------------------------------------~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~  117 (232)
                                                                 .+.+++...+.|+++|++|||.||.|...+  .|...
T Consensus       186 ~~~~l~~~Y~~~~~~~~~~~~~~~~~~~~~~~le~gd~~~~~~w~~~~~~~l~~~~~~~~~l~V~fD~~~~es--~~~~~  263 (562)
T PRK12451        186 PIRELFKLYVQFHEEVKDDEELEEEGRAWFKKLEEGDEEAVELWNWFRHESLKEFSRIYELLGVEFTNFQGEA--FYNDL  263 (562)
T ss_pred             chHHHHHHHHHHHHhhccChhHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCceeecchH--hhhhh
Confidence                                                       011234445789999999999999665444  56777


Q ss_pred             HHHHHHHHHhhcCCEEecccceeecc
Q psy2399         118 VQKIYDTLYNKAKLIINKKINQFFDP  143 (232)
Q Consensus       118 v~~~~~~L~~~kG~iy~~~~~~~~~~  143 (232)
                      +..+++.|. ++|++|+.++..|.+.
T Consensus       264 ~~~v~~~L~-~~g~~~e~dGa~~~~~  288 (562)
T PRK12451        264 MEDFIGILE-EHDLLEESEGALVVNL  288 (562)
T ss_pred             HHHHHHHHH-HCCCEEecCCeEEEEe
Confidence            899999999 9999999998888654

>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6

Probab=99.53  E-value=3.4e-16  Score=140.18  Aligned_cols=171  Identities=18%  Similarity=0.245  Sum_probs=101.7

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhH--------HHHHHHHHcCCC--
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGA--------AIMIAAEKAGMT--   80 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~--------~i~~~a~~~g~~--   80 (232)
                      +..+++-++. +|+|.+|||+++..+.+|+++|-++.+|     .+|.+++.+||.+-        |-...++-+|++  
T Consensus        22 ~~~~v~~sG~-sPSG~~HIGn~rEv~~~~~V~~al~~~g-----~~~r~i~~~DD~D~lRKvP~~~p~~~~~~ylg~Plt   95 (360)
T PF01921_consen   22 KEPYVFASGI-SPSGLPHIGNFREVLRADMVARALRDRG-----KDVRLIYFSDDMDPLRKVPPNVPNPELEKYLGKPLT   95 (360)
T ss_dssp             -SEEEEEEEE---SS---HHHHHHHHHHHHHHHHHHTTT------EEEEEEEE-TTSB-----TTS-CC-CCCCTTSBTT
T ss_pred             CccEEEecCC-CCCCCcccccccchhhHHHHHHHHHHcC-----CCEEEEEEeecCCcccCCCCCCChHHHHHhcCCccc
Confidence            4555666554 9999999999999999999999999999     99999999999751        111001112321  


Q ss_pred             --------HHHHHHHHHHHHHHHHhccCCcCCccccCCC---hhH----------HHHHHHHHHHHHhhcCCEEecccce
Q psy2399          81 --------PKEFINNISSNRKKYLDGFYIKFDNWYSTDS---IEN----------IDLVQKIYDTLYNKAKLIINKKINQ  139 (232)
Q Consensus        81 --------~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~---~~~----------~~~v~~~~~~L~~~kG~iy~~~~~~  139 (232)
                              ...+++++...+.+.|+.|||+++....|..   -.+          ...+.+++.... .+     .....
T Consensus        96 ~VPdP~G~~~SyaeH~~~~~~~~L~~~gie~e~~s~te~Y~sG~y~~~i~~aL~~~~~I~~Il~~~~-~~-----~~~~~  169 (360)
T PF01921_consen   96 RVPDPFGCHESYAEHFNAPFEEFLDEFGIEYEFISQTEMYRSGRYDEQIRTALENRDEIREILNEYR-GR-----ERPET  169 (360)
T ss_dssp             TSB-TTSSSSCHHHHHHHHHHHHHHTTT---EEEECCCCCCTTTTHHHHCHHHHTHHHHHHHHHHHH-HH-----T--TT
T ss_pred             cCCCCCCCCccHHHHHHHHHHHHHHHcCCceEEEeHHHhhhCCchHHHHHHHHHhHHHHHHHHHHhc-Cc-----CCCCC
Confidence                    3468999999999999999998865544321   122          233344444443 21     12334


Q ss_pred             eeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCc--------cccCCcccCCCCccEEEEccceeEecCChh
Q psy2399         140 FFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPT--------KLINPYSILSGTKPIIKSSKHFFFKLSDKR  211 (232)
Q Consensus       140 ~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~--------~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~  211 (232)
                      ||                        ++..+|++||++.+..        .-+.++|..||+..+..-...- -||  .|
T Consensus       170 y~------------------------Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~g~-gKL--~W  222 (360)
T PF01921_consen  170 YS------------------------PFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITGGN-GKL--QW  222 (360)
T ss_dssp             --------------------------SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTTT--EEE---H
T ss_pred             ee------------------------eeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCCCc-ccc--cC
Confidence            44                        5667899999976532        3367899889999997666543 799  99


Q ss_pred             hHHHHHhhh
Q psy2399         212 CIDFLRKWA  220 (232)
Q Consensus       212 ~~~~l~~~~  220 (232)
                      -.||...|.
T Consensus       223 kvDW~mRW~  231 (360)
T PF01921_consen  223 KVDWPMRWA  231 (360)
T ss_dssp             HHHHHHHHH
T ss_pred             CCcChhhhh
Confidence            999999994

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. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.

>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]

Probab=99.47  E-value=4.9e-14  Score=129.99  Aligned_cols=169  Identities=20%  Similarity=0.217  Sum_probs=118.8

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhh--------HHHHHHHH-HcCCC--
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHG--------AAIMIAAE-KAGMT--   80 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G--------~~i~~~a~-~~g~~--   80 (232)
                      ..++|-++. +|+|.+|||++|..+.+|+++|-++.+|     .+|.+++-+||++        +|-....+ -+|++  
T Consensus        19 ~~~~v~tGi-sPSG~~HIGn~rEv~t~d~V~ralr~~g-----~~~r~I~~~DD~D~lRkvp~~lp~~~~~e~Ylg~Plt   92 (521)
T COG1384          19 DEYVVATGI-SPSGLIHIGNFREVLTADAVRRALRDRG-----DEVRLIYISDDYDPLRKVPRNLPDPEELEQYLGMPLT   92 (521)
T ss_pred             CcEEEecCc-CCCCCcccccHHHHHHHHHHHHHHHHcC-----CceEEEEEccCCcccccCCCCCCChHHHHHHcCCccc
Confidence            456666665 9999999999999999999999999999     9999999999985        22212222 24542  


Q ss_pred             --------HHHHHHHHHHHHHHHHhccCCcCCccccCCCh---hHHH----------HHHHHHHHHHhhcCCEEecccce
Q psy2399          81 --------PKEFINNISSNRKKYLDGFYIKFDNWYSTDSI---ENID----------LVQKIYDTLYNKAKLIINKKINQ  139 (232)
Q Consensus        81 --------~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~---~~~~----------~v~~~~~~L~~~kG~iy~~~~~~  139 (232)
                              ...+++++.+.|.+.|+.|||+++....|...   .+.+          .+.+++.+.. .+     .....
T Consensus        93 ~IPdP~G~~~Sya~hf~~~f~~~l~~~Gi~~E~~s~se~Yk~G~~~~~i~~ale~rdeI~~il~~~~-~~-----~~~e~  166 (521)
T COG1384          93 EIPDPFGCCDSYAEHFLRPFEEFLDEFGIEVEFVSATELYKSGLYDEAIRIALERRDEIMEILNEYR-GR-----ELEED  166 (521)
T ss_pred             cCCCCccccchHHHHHHHHHHHHHHhcCCceEEEEhHHhhhcccHHHHHHHHHhhHHHHHHHHHHhc-CC-----cccCC
Confidence                    45789999999999999999988765433211   1222          2222222222 11     22445


Q ss_pred             eeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCc-------cccCCcccCCCCccEEEEccceeEecCChhh
Q psy2399         140 FFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPT-------KLINPYSILSGTKPIIKSSKHFFFKLSDKRC  212 (232)
Q Consensus       140 ~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~-------~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~  212 (232)
                      ||                        ++..+|++||++.+..       .-+.++|. ||+..++--+ ..=-||  +|-
T Consensus       167 ~~------------------------P~~piC~kcGri~~t~v~~~d~~~~v~Y~Ce-~Gh~g~v~ir-~g~~KL--~WR  218 (521)
T COG1384         167 WS------------------------PFMPICEKCGRILTTPVIEWDGEGTVEYRCE-CGHEGEVDIR-GGEGKL--PWR  218 (521)
T ss_pred             ce------------------------eccccccccCCcceeEEEEecCCceEEEEec-CCccceeecc-ccCccc--ccC
Confidence            55                        6888999999977644       24678897 7998875332 444599  899


Q ss_pred             HHHHHhhh
Q psy2399         213 IDFLRKWA  220 (232)
Q Consensus       213 ~~~l~~~~  220 (232)
                      .||-..|.
T Consensus       219 vdWp~RW~  226 (521)
T COG1384         219 VDWPMRWA  226 (521)
T ss_pred             cCccchhh
Confidence            99999993

>PLN02286 arginine-tRNA ligase

Probab=99.46  E-value=3.6e-13  Score=128.82  Aligned_cols=125  Identities=14%  Similarity=0.144  Sum_probs=99.5

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc----CC------
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA----GM------   79 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~----g~------   79 (232)
                      .+++++|-...|+|+|++||||+|+.+++|+|+|.++..|     ++|.-...++|.|.++...+...    +-      
T Consensus       115 ~~~~v~VEfsSpNp~kplHvGHlRsaiiGdsLaril~~~G-----~~V~r~nyinD~G~Qi~~l~~~~~~~~~~~~~~~~  189 (576)
T PLN02286        115 PVKRAVVDFSSPNIAKEMHVGHLRSTIIGDTLARMLEFSG-----VEVLRRNHVGDWGTQFGMLIEHLFEKFPNWESVSD  189 (576)
T ss_pred             CCceEEEEecCCCCCCCCccccccchhhHHHHHHHHHHcC-----CceEEEEeecchHHHHHHHHHHHHHhcCcccccCc
Confidence            3478999999999999999999999999999999999999     99999999999998766555221    10      


Q ss_pred             -------------------CH------------------------HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHH
Q psy2399          80 -------------------TP------------------------KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENID  116 (232)
Q Consensus        80 -------------------~~------------------------~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~  116 (232)
                                         ++                        +.+++.....|++++++|||.+|.+  ..+ .|..
T Consensus       190 ~~i~~l~~~Y~~~~~~~~~~~~~~~~~~~~~~~le~gd~~~~~lw~~~~~~~~~~~~~~y~~l~V~fd~~--ges-~y~~  266 (576)
T PLN02286        190 QAIGDLQEFYKAAKKRFDEDEEFKARAQQAVVRLQGGDPEYRAAWAKICEISRREFEKVYQRLRVELEEK--GES-FYNP  266 (576)
T ss_pred             ccHHHHHHHHHHhhhhccCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhCCeeeec--Cch-hhhh
Confidence                               00                        0122333467889999999999873  322 5777


Q ss_pred             HHHHHHHHHHhhcCCEEecccceeecc
Q psy2399         117 LVQKIYDTLYNKAKLIINKKINQFFDP  143 (232)
Q Consensus       117 ~v~~~~~~L~~~kG~iy~~~~~~~~~~  143 (232)
                      .+..+++.|. ++|++|+.++..|.+.
T Consensus       267 ~~~~vi~~L~-~~g~~~e~dGa~~v~l  292 (576)
T PLN02286        267 YIPGVIEELE-SKGLVVESDGARVIFV  292 (576)
T ss_pred             hHHHHHHHHH-HCCCEEeeCCceEeec
Confidence            7899999999 9999999988888643

>cd09287 GluRS_non_core catalytic core domain of non-discriminating glutamyl-tRNA synthetase

Probab=99.34  E-value=2.7e-12  Score=109.80  Aligned_cols=96  Identities=19%  Similarity=0.137  Sum_probs=78.5

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++-.+|+|||.|||||+++++..++++|     +     +++.++.-+||.+.+..           .......+.|.+
T Consensus         2 v~~RfaPsPtG~lHiG~~rtal~~~l~Ar-----~-----~~G~~ilRieDtD~~r~-----------~~~~~~~~~i~~   60 (240)
T cd09287           2 VVMRFAPNPNGPLHLGHARAAILNGEYAK-----M-----YGGKFILRFDDTDPRTK-----------RPDPEAYDMIPE   60 (240)
T ss_pred             ceEeCCCCCCCCccHHHHHHHHHHHHHHH-----H-----cCCEEEEeeCcCCCCcc-----------cchHHHHHHHHH
Confidence            46778899999999999999999999999     4     56677777777654421           134455556899


Q ss_pred             HHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||+.||..++.|  ++.+..++++.+|. ++|++|.
T Consensus        61 dL~wLGl~~d~~~~qS--~r~~~y~~~~~~Li-~~G~aY~   97 (240)
T cd09287          61 DLEWLGVKWDEVVIAS--DRIELYYEYARKLI-EMGGAYV   97 (240)
T ss_pred             HHHHcCCCCCCccchh--ccHHHHHHHHHHHH-HcCCccc
Confidence            9999999999776766  68889999999999 9999996

Non-discriminating Glutamyl-tRNA synthetase (GluRS) cataytic core domain. These enzymes attach Glu to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea and most bacteria lack GlnRS. In these organisms, the "non-discriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme.

>PRK04156 gltX glutamyl-tRNA synthetase; Provisional

Probab=99.25  E-value=2.3e-11  Score=115.27  Aligned_cols=97  Identities=16%  Similarity=0.121  Sum_probs=79.6

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -+++-.+|+|||+||||||+++++.+.+||     .     +...++.-+||.+.++           ......+.+.|+
T Consensus       101 ~V~tRFaPsPtG~LHIGharaalln~~~Ar-----~-----~~G~~iLRidDTDpk~-----------~R~~~e~~~~I~  159 (567)
T PRK04156        101 KVVMRFAPNPSGPLHLGHARAAILNDEYAK-----M-----YGGKFILRFEDTDPRT-----------KRPDPEAYDMIL  159 (567)
T ss_pred             eEEEEeCCCCCCCccHHHHHHHHHHHHHHH-----H-----cCCEEEEeEccCCCCc-----------ccchHHHHHHHH
Confidence            477888999999999999999999999999     2     4556666667654322           223445558899


Q ss_pred             HHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      ++|++||+.||..+.+|  .+.+...++..+|. ++|++|.
T Consensus       160 edL~wLGl~wD~~~~qS--dr~~~y~~~a~~Li-~~G~AY~  197 (567)
T PRK04156        160 EDLKWLGVKWDEVVIQS--DRLEIYYEYARKLI-EMGGAYV  197 (567)
T ss_pred             HHHHHcCCCCCCccCcc--cCHHHHHHHHHHHH-HcCCCcc
Confidence            99999999999887777  58899999999999 9999986

>TIGR00463 gltX_arch glutamyl-tRNA synthetase, archaeal and eukaryotic family

Probab=99.21  E-value=3.2e-11  Score=114.22  Aligned_cols=96  Identities=19%  Similarity=0.131  Sum_probs=79.7

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      .-+++-.+|.|||.||||||+++++.+.+||-          +...++.-+||..             |..-...+.+.|
T Consensus        92 ~~vvtRFaPsPtG~LHiGharaalln~~~Ar~----------~~G~~iLRidDTD-------------p~R~~~e~~~~I  148 (560)
T TIGR00463        92 GEVVMRFAPNPSGPLHIGHARAAILNQYFAKK----------YKGKLIIRFDDTD-------------PRRVKPEAYDMI  148 (560)
T ss_pred             CeeEEEeCCCCCCCccHHHHHHHHHHHHHHHh----------cCCEEEEEeCcCC-------------cccccHHHHHHH
Confidence            34889999999999999999999999999972          3445555556543             334455688899


Q ss_pred             HHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          93 KKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        93 ~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      .++|++|||.||..+++|  .|.+...+++.+|. ++|++|.
T Consensus       149 ~edL~wLGi~~d~~~~qS--d~~~~y~~~a~~Li-~~G~AY~  187 (560)
T TIGR00463       149 LEDLDWLGVKGDEVVYQS--DRIEEYYDYCRKLI-EMGKAYV  187 (560)
T ss_pred             HHHHHHcCCCCCcccccc--ccHHHHHHHHHHHH-HcCCcee
Confidence            999999999999888887  58899999999999 9999996

The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This alignment models just the eukaryotic cytosolic and archaeal forms of the enzyme. In some eukaryotes, the glutamyl-tRNA synthetase is part of a longer, multifunctional aminoacyl-tRNA ligase. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases may act on both tRNA(gln) and tRNA(glu).

>cd00807 GlnRS_core catalytic core domain of glutaminyl-tRNA synthetase

Probab=99.14  E-value=1.4e-10  Score=99.13  Aligned_cols=94  Identities=20%  Similarity=0.116  Sum_probs=76.7

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++-.+|.|||+|||||+++++++..+||-  ..|     .   ++.-+||             .++......+.+.|.+
T Consensus         2 v~~RFAPsPtG~lHlG~~~~al~~~l~Ar~--~~G-----~---~iLRieD-------------tD~~R~~~~~~~~I~~   58 (238)
T cd00807           2 VVTRFPPEPNGYLHIGHAKAILLNFGYAKK--YGG-----R---CNLRFDD-------------TNPEKEEEEYVDSIKE   58 (238)
T ss_pred             ceEecCCCCCCcccHHHHHHHHHHHHHHHH--hCC-----E---EEEEecC-------------CCCcccchHHHHHHHH
Confidence            567789999999999999999999999984  345     3   3333343             3455667788899999


Q ss_pred             HHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||++||..+..|  ++.+..++.+.+|. ++|++|.
T Consensus        59 dL~wlGl~wD~~~~QS--~r~~~Y~~~~~~L~-~~g~aY~   95 (238)
T cd00807          59 DVKWLGIKPYKVTYAS--DYFDQLYEYAEQLI-KKGKAYV   95 (238)
T ss_pred             HHHHcCCCCCCceecc--cCHHHHHHHHHHHH-HcCCeec
Confidence            9999999999665555  57888999999999 9999998

Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Gln to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. GlnRS contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea and most bacteria lack GlnRS. In these organisms, the "non-discriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme.

>PRK12558 glutamyl-tRNA synthetase; Provisional

Probab=99.13  E-value=1.6e-10  Score=106.99  Aligned_cols=94  Identities=17%  Similarity=0.177  Sum_probs=76.0

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.|||||+|+++....+||-  ..|        .|+.-+||.+             ++...+.+.+.|++
T Consensus         3 vr~RFAPSPTG~lHiG~artAL~n~l~Ar~--~gG--------~fiLRIEDTD-------------~~Rs~~~~~~~I~e   59 (445)
T PRK12558          3 VITRFAPSPTGYLHVGNARTALLNWLYARK--HGG--------KFILRIDDTD-------------LERSKQEYADAIAE   59 (445)
T ss_pred             eeEEeCCCCCCcccHHHHHHHHHHHHHHHH--hCC--------EEEEEeccCC-------------cccchHHHHHHHHH
Confidence            567778999999999999999999999874  334        4444445433             44556888999999


Q ss_pred             HHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||.+++.++  ..+.+++++++|. ++|++|.
T Consensus        60 ~L~wLGI~~De~y~QSe--r~~~y~~~~e~L~-e~G~AY~   96 (445)
T PRK12558         60 DLKWLGINWDRTFRQSD--RFDRYDEAAEKLK-AAGRLYP   96 (445)
T ss_pred             HHHHcCCCCCccccHHH--HHHHHHHHHHHHH-HCCCEEE
Confidence            99999999999887774  4468899999999 9999985

>PLN03233 putative glutamate-tRNA ligase; Provisional

Probab=99.11  E-value=1.7e-10  Score=108.35  Aligned_cols=95  Identities=23%  Similarity=0.206  Sum_probs=78.8

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -+++--+|.|||.||||||+++++...+||-  ..|     .   ++.=+||             .+|+.-...+.+.|.
T Consensus        11 ~v~tRFAPsPtG~LHiGharaAlln~l~Ar~--~gG-----~---~iLRiED-------------TDp~R~~~e~~~~I~   67 (523)
T PLN03233         11 QIVTRFPPEPSGYLHIGHAKAALLNDYYARR--YKG-----R---LILRFDD-------------TNPSKEKAEFEESII   67 (523)
T ss_pred             eEEEeeCCCCCCcccHHHHHHHHHHHHHHHH--hCC-----E---EEEEECC-------------CCCCccchHHHHHHH
Confidence            4889999999999999999999999999984  345     3   3333344             345666778889999


Q ss_pred             HHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      ++|++||++||..+.+|  .+.+...+...+|. ++|++|.
T Consensus        68 ~dL~WLGl~wD~~~~qS--dr~~~y~~~a~~Li-~~G~AY~  105 (523)
T PLN03233         68 EDLGKIEIKPDSVSFTS--DYFEPIRCYAIILI-EEGLAYM  105 (523)
T ss_pred             HHHHHhCCCCCCCcccc--ccHHHHHHHHHHHH-HcCCeEe
Confidence            99999999999877777  57888999999999 9999996

>COG0008 GlnS Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]

Probab=99.09  E-value=2.3e-10  Score=106.68  Aligned_cols=94  Identities=18%  Similarity=0.214  Sum_probs=77.7

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      |++--+|.|||.|||||||+.+....+||.  ..|     .-++-+   ||             .+|+.-...+.+.|.+
T Consensus        10 v~tRFAPsPtG~LHiG~artAl~N~~~Ar~--~~G-----~fiLRi---ED-------------TD~~R~~~e~~~~I~~   66 (472)
T COG0008          10 VRTRFAPSPTGYLHIGHARTALLNYLYARK--YGG-----KFILRI---ED-------------TDPERETPEAEDAILE   66 (472)
T ss_pred             eEEEECcCCCCccchHHHHHHHHHHHHHHH--hCC-----EEEEEe---cC-------------CCCCCCCHHHHHHHHH
Confidence            889999999999999999999999999984  344     344444   33             3355566778889999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||++||. .++.|  ++.+...+...+|. ++|++|.
T Consensus        67 ~L~WLGl~wde~~~~QS--~r~~~Y~~~~~~Li-~~G~AY~  104 (472)
T COG0008          67 DLEWLGLDWDEGPYYQS--ERFDIYYEYAEKLI-EKGKAYV  104 (472)
T ss_pred             HHHhcCCCCCCceeehh--hhHHHHHHHHHHHH-HCCCeEE
Confidence            99999999999 56777  68888999999999 9999986

>PTZ00402 glutamyl-tRNA synthetase; Provisional

Probab=99.08  E-value=2.7e-10  Score=108.22  Aligned_cols=95  Identities=20%  Similarity=0.189  Sum_probs=78.0

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -+++--+|.|||.||||||+++++...+||-  ..|        .++.=+||             .+|......+.+.|+
T Consensus        52 ~v~tRFAPsPtGyLHIGharaAllN~l~Ar~--~gG--------~~iLRiED-------------TDp~R~~~e~~d~Il  108 (601)
T PTZ00402         52 KVVTRFPPEASGFLHIGHAKAALINSMLADK--YKG--------KLVFRFDD-------------TNPSKEKEHFEQAIL  108 (601)
T ss_pred             eeEEeeCCCCCCcccHHHHHHHHHHHHHHHH--hCC--------EEEEEEcC-------------CCCcccCHHHHHHHH
Confidence            4889999999999999999999999999984  344        33333344             346667778899999


Q ss_pred             HHHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      ++|++||++||. .+.+|  .+.+...++..+|. ++|++|.
T Consensus       109 eDL~WLGl~wDe~~~~QS--dr~d~y~e~a~~Li-~~G~AY~  147 (601)
T PTZ00402        109 DDLATLGVSWDVGPTYSS--DYMDLMYEKAEELI-KKGLAYC  147 (601)
T ss_pred             HHHHHCCCCCCCceeecc--ccHHHHHHHHHHHH-HcCCEEE
Confidence            999999999996 55666  57889999999999 9999993

>TIGR03838 queuosine_YadB glutamyl-queuosine tRNA(Asp) synthetase

Probab=99.08  E-value=2.4e-10  Score=99.72  Aligned_cols=93  Identities=18%  Similarity=0.229  Sum_probs=72.8

Q ss_pred             EEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Q psy2399          16 VTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKY   95 (232)
Q Consensus        16 v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~   95 (232)
                      ++--.|.|||.|||||+++++++..+||  +..|     .-++.+   ||.             ++......+.+.|.++
T Consensus         2 ~~RFAPSPtG~lHiG~~rtAL~n~l~Ar--~~gG-----~~iLRi---EDt-------------D~~R~~~~~~~~I~~d   58 (272)
T TIGR03838         2 RGRFAPSPSGPLHFGSLVAALGSYLDAR--AHGG-----RWLVRI---EDL-------------DPPREVPGAADDILRT   58 (272)
T ss_pred             eeeeCCCCCCcccHHHHHHHHHHHHHHH--HhCC-----EEEEEe---CcC-------------CCCCCChHHHHHHHHH
Confidence            4667899999999999999999999998  4455     333344   432             2344456778889999


Q ss_pred             HhccCCcCCcc-ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          96 LDGFYIKFDNW-YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        96 l~~lgI~~d~~-~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      |++|||+||.- +..|  ++.+...+.+.+|. ++|++|.
T Consensus        59 L~wLGl~wDe~~~~QS--~r~~~Y~~~~~~L~-~~G~aY~   95 (272)
T TIGR03838        59 LEAYGLHWDGEVVYQS--QRHALYQAALDRLL-AAGLAYP   95 (272)
T ss_pred             HHHcCCCCCCCeeeee--CCHHHHHHHHHHHH-HcCCEEe
Confidence            99999999964 3555  57788899999999 9999985

This protein resembles a shortened glutamyl-tRNA ligase, but its purpose is to modify tRNA(Asp) at a queuosine position in the anticodon rather than to charge a tRNA with its cognate amino acid.

>PTZ00437 glutaminyl-tRNA synthetase; Provisional

Probab=99.05  E-value=6e-10  Score=105.20  Aligned_cols=94  Identities=17%  Similarity=-0.027  Sum_probs=75.7

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      ++|--+|.|||.||||||+++++...+||.  ..|        .++.-+||             .+|......+.+.|.+
T Consensus        52 v~tRFaPsPtG~LHiGharaalln~~~Ar~--~gG--------~~iLRiED-------------TDp~r~~~e~~~~I~~  108 (574)
T PTZ00437         52 PYFRFPPEPNGFLHIGHAKSMNLNFGSARA--HGG--------KCYLRYDD-------------TNPETEEQVYIDAIME  108 (574)
T ss_pred             EEEEeCCCCCCcccHHHHHHHHHHHHHHHH--hCC--------EEEEEECC-------------CCccccChHHHHHHHH
Confidence            788889999999999999999999999984  334        33333444             3466667788999999


Q ss_pred             HHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||..+.++  .|.+...+...+|. ++|++|.
T Consensus       109 dL~wLGi~~D~~~~qS--~y~~~~ye~A~~Li-~~G~AY~  145 (574)
T PTZ00437        109 MVKWMGWKPDWVTFSS--DYFDQLHEFAVQLI-KDGKAYV  145 (574)
T ss_pred             HHHHcCCCCCCCCcCc--hhHHHHHHHHHHHH-HcCCEEE
Confidence            9999999999876665  46666668888999 9999986

>PRK05710 glutamyl-Q tRNA(Asp) synthetase; Reviewed

Probab=99.05  E-value=4.6e-10  Score=99.12  Aligned_cols=94  Identities=14%  Similarity=0.196  Sum_probs=74.2

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--.|.|||.|||||+++++++..+||-  ..|        .|+.=+||             .++......+.+.|.+
T Consensus         6 v~~RFAPSPTG~LHlG~~rtAL~n~l~Ar~--~~G--------~~iLRiED-------------tD~~R~~~~~~~~I~~   62 (299)
T PRK05710          6 YIGRFAPSPSGPLHFGSLVAALGSWLDARA--HGG--------RWLLRIED-------------IDPPREVPGAADAILA   62 (299)
T ss_pred             eeEEeCcCCCCcccHHHHHHHHHHHHHHHH--cCC--------EEEEEECc-------------CCCCccchHHHHHHHH
Confidence            678889999999999999999999999984  234        33333343             2344556677889999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||. .+..|  ++.+..+++..+|. ++|++|.
T Consensus        63 dL~wlGl~wDe~~~~QS--~r~~~Y~~~~~~L~-~~G~aY~  100 (299)
T PRK05710         63 DLEWLGLHWDGPVLYQS--QRHDAYRAALDRLR-AQGLVYP  100 (299)
T ss_pred             HHHHCCCCCCCCceEee--ccHHHHHHHHHHHH-HCCCcee
Confidence            99999999995 44555  57788899999999 9999985

>PF00749 tRNA-synt_1c: tRNA synthetases class I (E and Q), catalytic domain; InterPro: IPR020058 The aminoacyl-tRNA synthetases (6

Probab=99.03  E-value=5.1e-10  Score=99.80  Aligned_cols=94  Identities=17%  Similarity=0.221  Sum_probs=67.5

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      |++--+|.|||.|||||+++++++..+||  +..|     .-++.+   ||             .++......+.+.|.+
T Consensus         2 v~tRFAPsPtG~lHiG~~r~al~n~~~Ar--~~~G-----~~iLRi---eD-------------tD~~R~~~~~~~~i~~   58 (314)
T PF00749_consen    2 VRTRFAPSPTGYLHIGHARTALLNYLFAR--KYGG-----KFILRI---ED-------------TDPERCRPEFYDAILE   58 (314)
T ss_dssp             -EEEE---SSSS-BHHHHHHHHHHHHHHH--HTTS-----EEEEEE---ET-------------SSTTTCHHHHHHHHHH
T ss_pred             eeEeeCCCCCCCcccchhHHHHHHHHHHh--ccCc-----eEEEec---cc-------------cccccchhhHHHHHHh
Confidence            56777899999999999999999999998  4445     344444   33             2344456677888999


Q ss_pred             HHhccCCcCC-ccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFD-NWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d-~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||.|| ..+..|  .+.+..++++++|. ++|++|.
T Consensus        59 ~L~wlGl~~D~~~~~QS--~r~~~Y~~~~~~L~-~~g~aY~   96 (314)
T PF00749_consen   59 DLRWLGLEWDYGPYYQS--DRLEIYQEAAEKLI-DKGKAYP   96 (314)
T ss_dssp             HHHHHT---STCEEEGG--GGHHHHHHHHHHHH-HTTSEEE
T ss_pred             heeEEEEecCCeEEeHH--HHHHHHHHHHHHHh-hcCCCcc
Confidence            9999999998 455555  68889999999999 9999986

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. Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure []. ; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016876 ligase activity, forming aminoacyl-tRNA and related compounds, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 2HZ7_A 2CFO_A 4A91_A 1NZJ_A 1N78_A 1G59_C 2CV2_A 2CV1_A 2CV0_B 1GLN_A ....

>PLN02907 glutamate-tRNA ligase

Probab=99.03  E-value=5.3e-10  Score=109.23  Aligned_cols=96  Identities=21%  Similarity=0.225  Sum_probs=79.3

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      .-++|--+|.|||.||||||+++++...+||  +..|        .++.-+||             .+|..-...+.+.|
T Consensus       212 ~~v~tRFaPsPtG~LHiG~ar~al~n~~~Ar--~~~G--------~~iLR~eD-------------Tdp~r~~~e~~~~I  268 (722)
T PLN02907        212 GKVCTRFPPEPSGYLHIGHAKAALLNQYFAR--RYKG--------KLIVRFDD-------------TNPSKESDEFVENI  268 (722)
T ss_pred             CceEEeeCCCCCCcccHHHHHHHHHHHHHHH--HhCC--------EEEEEecC-------------CCCCcCChHHHHHH
Confidence            3488999999999999999999999999998  3445        33333444             33556667888999


Q ss_pred             HHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          93 KKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        93 ~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      .++|++||++||..+.+|  .+.+...+...+|. ++|++|.
T Consensus       269 ~~dl~wLG~~~d~~~~qS--~r~~~y~~~a~~Li-~~G~aY~  307 (722)
T PLN02907        269 LKDIETLGIKYDAVTYTS--DYFPQLMEMAEKLI-KEGKAYV  307 (722)
T ss_pred             HHHHHHcCCCCCCccccc--ccHHHHHHHHHHHH-HcCCeee
Confidence            999999999999887777  57888999999999 9999996

>TIGR00440 glnS glutaminyl-tRNA synthetase

Probab=98.97  E-value=1.3e-09  Score=102.46  Aligned_cols=94  Identities=18%  Similarity=0.130  Sum_probs=73.2

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.||||||+++++...+||  +..|        .++.-+||             .+|..-...+.+.|.+
T Consensus         1 V~tRFaPsPtG~LHiG~ar~al~n~~~A~--~~~G--------~~iLRieD-------------Td~~r~~~e~~~~I~~   57 (522)
T TIGR00440         1 VHTRFPPEPNGYLHIGHAKSICLNFGYAK--YYNG--------TCNLRFDD-------------TNPVKEDPEYVESIKR   57 (522)
T ss_pred             CeEecCCCCCCcccHHHHHHHHHHHHHHH--HhCC--------EEEEEEcC-------------CCcccCChHHHHHHHH
Confidence            46778999999999999999999999998  3344        33333444             3355667788899999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||+.||. .+.+|  .+.+...+...+|. ++|++|.
T Consensus        58 dL~wLG~~~d~~~~~qS--~~~~~~~~~a~~Li-~~G~AY~   95 (522)
T TIGR00440        58 DVEWLGFKWEGKIRYSS--DYFDELYRYAEELI-KKGLAYV   95 (522)
T ss_pred             HHHHcCCCCCCCceEcc--ccHHHHHHHHHHHH-HcCCEEe
Confidence            99999999964 44555  46676777889999 9999996

This protein is a relatively rare aminoacyl-tRNA synthetase, found in the cytosolic compartment of eukaryotes, in E. coli and a number of other Gram-negative Bacteria, and in Deinococcus radiodurans. In contrast, the pathway to Gln-tRNA in mitochondria, Archaea, Gram-positive Bacteria, and a number of other lineages is by misacylation with Glu followed by transamidation to correct the aminoacylation to Gln. This enzyme is a class I tRNA synthetase (hit by the pfam model tRNA-synt_1c) and is quite closely related to glutamyl-tRNA synthetases.

>cd00418 GlxRS_core catalytic core domain of glutamyl-tRNA and glutaminyl-tRNA synthetase

Probab=98.97  E-value=1.2e-09  Score=93.10  Aligned_cols=90  Identities=22%  Similarity=0.246  Sum_probs=70.9

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++-.+|.|||+|||||++++++...+||-  ..|        .++.-+||.             ++......+.+.|.+
T Consensus         2 v~~RFAPsPtG~lHlG~~r~al~n~l~Ar~--~~G--------~~iLRieDt-------------D~~R~~~~~~~~I~~   58 (230)
T cd00418           2 VVTRFAPSPTGYLHIGHARTALFNFAFARK--YGG--------KFILRIEDT-------------DPERSRPEYVESILE   58 (230)
T ss_pred             ceEEeCCCCCCcccHHHHHHHHHHHHHHHH--cCC--------eEEEEeCcC-------------CCCCCChHHHHHHHH
Confidence            467778999999999999999999999984  344        333334442             344556678889999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcC
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAK  130 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG  130 (232)
                      +|++||+.||. .+..|  .+.+..++.+.+|. ++|
T Consensus        59 dL~wlGl~wd~~~~~QS--~r~~~y~~~~~~L~-~~g   92 (230)
T cd00418          59 DLKWLGLDWDEGPYRQS--DRFDLYRAYAEELI-KKG   92 (230)
T ss_pred             HHHHcCCCCCCCeeehh--cCHHHHHHHHHHHH-HcC
Confidence            99999999997 55555  57788889999999 988

Glutamyl-tRNA synthetase(GluRS)/Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Glu or Gln, respectively, to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea, cellular organelles, and some bacteria lack GlnRS. In these cases, the "non-discriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme. The discriminating form of GluRS differs from GlnRS and the non-discriminating form of GluRS in their C-terminal anti-codon bind

>PRK05347 glutaminyl-tRNA synthetase; Provisional

Probab=98.96  E-value=1.5e-09  Score=102.39  Aligned_cols=95  Identities=16%  Similarity=0.023  Sum_probs=74.0

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -+++--+|.|||.||||||+++++...+||-  ..|        .++.-+||             .+|......+.+.|.
T Consensus        29 ~v~tRFaPsPtG~LHiG~ar~al~n~~~Ar~--~~G--------~~iLRieD-------------Td~~r~~~e~~~~I~   85 (554)
T PRK05347         29 RVHTRFPPEPNGYLHIGHAKSICLNFGLAQD--YGG--------KCNLRFDD-------------TNPEKEDQEYVDSIK   85 (554)
T ss_pred             ceEEEeCCCCCCcccHHHHHHHHHHHHHHHH--hCC--------EEEEEECC-------------CCCCcCChHHHHHHH
Confidence            4788899999999999999999999999984  344        33333344             345566778889999


Q ss_pred             HHHhccCCcCC-ccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFD-NWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d-~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      ++|++||+.|| ..+.+|  .+.+...+...+|. ++|++|.
T Consensus        86 ~dL~wLGi~~d~~~~~qS--~r~~~~y~~a~~Li-~~G~AY~  124 (554)
T PRK05347         86 EDVRWLGFDWSGELRYAS--DYFDQLYEYAVELI-KKGKAYV  124 (554)
T ss_pred             HHHHHcCCCCCCCceeee--cCHHHHHHHHHHHH-HcCCEee
Confidence            99999999995 445555  45666667778999 9999996

>TIGR00464 gltX_bact glutamyl-tRNA synthetase, bacterial family

Probab=98.94  E-value=1.9e-09  Score=100.99  Aligned_cols=94  Identities=19%  Similarity=0.210  Sum_probs=73.0

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.|||||+|+++....+||  ...|     .   |+.-+||.             ++......+.+.|.+
T Consensus         2 v~~RfAPsPtG~lHiG~~rtal~n~l~Ar--~~~G-----~---~iLRieDt-------------D~~R~~~~~~~~i~~   58 (470)
T TIGR00464         2 VRTRFAPSPTGYLHIGGARTALFNYLFAK--HTGG-----E---FILRIEDT-------------DLERNIEEAEEAILE   58 (470)
T ss_pred             ceEeeCCCCCCcccHHHHHHHHHHHHHHH--HcCC-----E---EEEEeCcC-------------CCccCChHHHHHHHH
Confidence            46777899999999999999999999998  3344     3   33334442             344556678888999


Q ss_pred             HHhccCCcCC-ccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFD-NWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d-~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+|| -.++.|  ++.+...++..+|. ++|++|.
T Consensus        59 ~L~wlGl~~de~~~~QS--~r~~~y~~~~~~L~-~~g~aY~   96 (470)
T TIGR00464        59 GLKWLGISWDEGPYYQS--QRLDIYKKYAKELL-EEGLAYR   96 (470)
T ss_pred             HHHHCCCCCCCCeeehh--CCHHHHHHHHHHHH-HcCCEEe
Confidence            9999999999 445555  46677788999999 9999985

The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This alignment models just the bacterial and mitochondrial forms of the enzyme. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases may act on both tRNA(gln) and tRNA(glu). This model is highly specific. Proteins with positive scores below the trusted cutoff may be fragments rather than full-length sequences.

>PRK12410 glutamylglutaminyl-tRNA synthetase; Provisional

Probab=98.93  E-value=2.8e-09  Score=98.49  Aligned_cols=91  Identities=19%  Similarity=0.256  Sum_probs=72.1

Q ss_pred             cCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Q psy2399          18 TALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLD   97 (232)
Q Consensus        18 ~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~   97 (232)
                      --.|.|||.|||||+|+++....+||-  ..|     .-++.+   ||.             ++......+.+.|.++|+
T Consensus         3 RFAPSPTG~LHiG~artAL~n~l~Ar~--~gG-----~fiLRi---EDT-------------D~~R~~~e~~~~I~~~L~   59 (433)
T PRK12410          3 RFAPSPTGDMHIGNLRAAIFNYIVAKQ--QNE-----DFLIRI---EDT-------------DKERNIEGKDKEILEILN   59 (433)
T ss_pred             ccCCCCCCcccHHHHHHHHHHHHHHHH--cCC-----EEEEEe---CcC-------------CCCcCChHHHHHHHHHHH
Confidence            347899999999999999999999983  444     333333   442             244556677888999999


Q ss_pred             ccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          98 GFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        98 ~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|||+||..+..|  ++.+...++.++|. ++|.+|.
T Consensus        60 WlGl~wDe~y~QS--eR~~~Y~~~a~~Li-~~G~AY~   93 (433)
T PRK12410         60 LFGISWDKLVYQS--ENLKFHRQMAEKLL-SEKKAFA   93 (433)
T ss_pred             HcCCCCCCCeehh--ccHHHHHHHHHHHH-HcCCeee
Confidence            9999999877777  56778889999999 9999984

>PRK14895 gltX glutamyl-tRNA synthetase; Provisional

Probab=98.92  E-value=4.6e-09  Score=98.64  Aligned_cols=94  Identities=13%  Similarity=0.094  Sum_probs=74.2

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--.|.|||.|||||+|+++....+||  +..|     .-++.+   ||.             ++......+.+.+.+
T Consensus         5 vrtRFAPSPTG~lHiG~artAL~n~l~Ar--~~gG-----~fiLRI---EDT-------------D~~R~~~~~~~~i~~   61 (513)
T PRK14895          5 VITRFAPSPTGFLHIGSARTALFNYLFAR--HHNG-----KFLLRI---EDT-------------DKERSTKEAVEAIFS   61 (513)
T ss_pred             eeEeeCCCCCCCccHHHHHHHHHHHHHHH--HcCC-----EEEEEE---CCC-------------CccccChHHHHHHHH
Confidence            56777899999999999999999999998  4455     344444   332             345566788888999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||++||. .++.|  +..+...+...+|. ++|++|.
T Consensus        62 ~L~WLGl~wDe~py~QS--eR~~~Y~~~a~~Li-~~G~AY~   99 (513)
T PRK14895         62 GLKWLGLDWNGEVIFQS--KRNNLYKEAALKLL-QNGKAYY   99 (513)
T ss_pred             HHHHcCCCCCCCceeEe--CcHHHHHHHHHHHH-HcCCeEE
Confidence            99999999993 45555  45678889999999 9999985

>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional

Probab=98.91  E-value=2.2e-09  Score=105.11  Aligned_cols=95  Identities=19%  Similarity=0.115  Sum_probs=76.9

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -++|-.+|.|||.|||||++++++...+||-  ..|        .++.-+||             .+|..-...+.+.|.
T Consensus        31 ~v~tRFaPsPtG~lHiGhar~alln~~~A~~--~~G--------~~~LR~eD-------------Td~~r~~~e~~~~I~   87 (771)
T PRK14703         31 RVVTRFPPEPNGYLHIGHAKSILLNFGIARD--YGG--------RCHLRMDD-------------TNPETEDTEYVEAIK   87 (771)
T ss_pred             ceEEEeCcCCCCcccHHHHHHHHHHHHHHHH--hCC--------EEEEEeCC-------------CCCCcCChHHHHHHH
Confidence            3889999999999999999999999999983  334        34444444             345566778889999


Q ss_pred             HHHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      ++|++||++||. .+.+|  .+.+...+...+|. ++|++|.
T Consensus        88 ~dl~wLG~~wd~~~~~qS--~~~~~y~~~a~~Li-~~G~aY~  126 (771)
T PRK14703         88 DDVRWLGFDWGEHLYYAS--DYFERMYAYAEQLI-KMGLAYV  126 (771)
T ss_pred             HHHHHcCCCCCCCceEee--cCHHHHHHHHHHHH-HcCCccc
Confidence            999999999985 35566  57888889999999 9999985

>PLN02859 glutamine-tRNA ligase

Probab=98.89  E-value=5.2e-09  Score=102.02  Aligned_cols=94  Identities=14%  Similarity=0.004  Sum_probs=73.1

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++..+|.|||.||||||++.++...+||.  ..|        .++.-+||             .+|..-...+.+.|.+
T Consensus       265 V~tRFaPsPtG~LHiGharaallN~~~Ar~--~~G--------~~~LRieD-------------Tdp~r~~~e~~~~I~e  321 (788)
T PLN02859        265 VYTRFPPEPNGYLHIGHAKAMFVDFGLAKE--RGG--------CCYLRFDD-------------TNPEAEKKEYIDHIEE  321 (788)
T ss_pred             eEEEeCCCCCCcccHHHHHHHHHHHHHHHH--hCC--------EEEEEecC-------------CCCCccchHHHHHHHH
Confidence            778889999999999999999999999985  344        33333344             3466667788899999


Q ss_pred             HHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||++||..+.+|+  |.+...+...+|. ++|++|.
T Consensus       322 dL~WLG~~~d~~~~qSd--~f~~~Y~~A~~Li-~~G~AY~  358 (788)
T PLN02859        322 IVEWMGWEPFKITYTSD--YFQELYELAVELI-RRGHAYV  358 (788)
T ss_pred             HHHHcCCCCCCcccccH--hHHHHHHHHHHHH-HcCCeEe
Confidence            99999999987766663  4433444567799 9999986

>PRK01406 gltX glutamyl-tRNA synthetase; Reviewed

Probab=98.89  E-value=5.6e-09  Score=97.98  Aligned_cols=94  Identities=17%  Similarity=0.182  Sum_probs=74.9

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.|||||+|+++....+||-  ..|        .|+.-+||.             ++......+.+.+.+
T Consensus         5 v~~RfAPSPtG~lHiG~~rtal~n~l~Ar~--~~G--------~fiLRieDt-------------D~~R~~~~~~~~i~~   61 (476)
T PRK01406          5 VRTRFAPSPTGYLHIGGARTALFNWLFARH--HGG--------KFILRIEDT-------------DQERSTEEAEEAILE   61 (476)
T ss_pred             eeEEeCCCCCCcccHHHHHHHHHHHHHHHH--cCC--------EEEEEeCcC-------------CCCCCChHHHHHHHH
Confidence            677888999999999999999999999984  344        344434442             345667778889999


Q ss_pred             HHhccCCcCCcc--------ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNW--------YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~--------~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||.-        ++.|  ++.+...++..+|. ++|++|.
T Consensus        62 ~L~wlGl~~De~p~~~~~gpy~QS--~r~~~y~~~~~~L~-~~g~aY~  106 (476)
T PRK01406         62 GLKWLGLDWDEGPDGGPYGPYRQS--ERLDIYKEYAEQLL-EEGKAYY  106 (476)
T ss_pred             HHHHCCCCCCCCCccCCCCceehh--cCHHHHHHHHHHHH-HcCCeee
Confidence            999999999964        4555  46688889999999 9999985

>PLN02627 glutamyl-tRNA synthetase

Probab=98.87  E-value=8.9e-09  Score=97.02  Aligned_cols=94  Identities=14%  Similarity=0.174  Sum_probs=74.2

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--.|.|||.|||||+|+++....+||  +..|     .-++.+   ||             .++......+.+.|.+
T Consensus        46 vr~RFAPSPTG~LHiG~aRtAL~n~l~Ar--~~gG-----~fiLRI---ED-------------TD~~R~~~e~~~~I~~  102 (535)
T PLN02627         46 VRVRFAPSPTGNLHVGGARTALFNYLFAR--SKGG-----KFVLRI---ED-------------TDLARSTKESEEAVLR  102 (535)
T ss_pred             eEEEeCCCCCCCccHHHHHHHHHHHHHHH--HhCC-----EEEEEe---Cc-------------CCCCCCChHHHHHHHH
Confidence            77777889999999999999999999998  4445     344444   33             2344566778889999


Q ss_pred             HHhccCCcCCcc---------ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNW---------YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~---------~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||.-         ++.|  ++.+...++..+|. ++|++|.
T Consensus       103 ~L~WLGl~wDegp~~gg~~gpy~QS--eR~~~Y~~~a~~Li-~~G~AY~  148 (535)
T PLN02627        103 DLKWLGLDWDEGPDVGGEYGPYRQS--ERNAIYKQYAEKLL-ESGHVYP  148 (535)
T ss_pred             HHHHcCCCCCcCcccCCCCCCeeee--ccHHHHHHHHHHHH-HcCCeee
Confidence            999999999963         3444  46778889999999 9999985

>cd00808 GluRS_core catalytic core domain of discriminating glutamyl-tRNA synthetase

Probab=98.86  E-value=4.7e-09  Score=90.07  Aligned_cols=90  Identities=18%  Similarity=0.209  Sum_probs=68.5

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.|||||++++++...++|-  ..|        .++.-+||             .++..-...+.+.+.+
T Consensus         2 v~~RfAPsPtG~LHlG~~~~al~n~l~ar~--~~G--------~~ilRieD-------------td~~r~~~~~~~~i~~   58 (239)
T cd00808           2 VRTRFAPSPTGFLHIGGARTALFNYLFARK--HGG--------KFILRIED-------------TDQERSVPEAEEAILE   58 (239)
T ss_pred             ceEEeCCCCCCcccHHHHHHHHHHHHHHHH--cCC--------eEEEEECc-------------CCCCCCchHHHHHHHH
Confidence            467778999999999999999999999983  334        33333444             2233445677788889


Q ss_pred             HHhccCCcCCc---------cccCCChhHHHHHHHHHHHHHhhcC
Q psy2399          95 YLDGFYIKFDN---------WYSTDSIENIDLVQKIYDTLYNKAK  130 (232)
Q Consensus        95 ~l~~lgI~~d~---------~~~t~~~~~~~~v~~~~~~L~~~kG  130 (232)
                      +|++|||+||.         .+..|  .+.+...+++.+|. ++|
T Consensus        59 dL~wlGl~~d~~~~~~g~~~~~~QS--~r~~~y~~~~~~L~-~~g  100 (239)
T cd00808          59 ALKWLGLDWDEGPDVGGPYGPYRQS--ERLEIYRKYAEKLL-EKG  100 (239)
T ss_pred             HHHHcCCCCCcCCccCCCCCCEeee--CCHHHHHHHHHHHH-HcC
Confidence            99999999998         55555  46778888899999 888

Discriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain . The discriminating form of GluRS is only found in bacteria and cellular organelles. GluRS is a monomer that attaches Glu to the appropriate tRNA. Like other class I tRNA synthetases, GluRS aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.

>KOG1147|consensus

Probab=98.54  E-value=3.1e-07  Score=85.51  Aligned_cols=98  Identities=21%  Similarity=0.143  Sum_probs=78.4

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -+|+..||-|+|.||||||...++..-++-  +        ++-.++.-+||             ..|..-.+++.+.|+
T Consensus       200 kVv~RFPPEpSGyLHIGHAKAALLNqYfa~--~--------~~G~LIvRFDD-------------TNPaKE~~eFe~~Il  256 (712)
T KOG1147|consen  200 KVVTRFPPEPSGYLHIGHAKAALLNQYFAQ--A--------YQGKLIVRFDD-------------TNPAKENEEFEDVIL  256 (712)
T ss_pred             ceEEecCCCCCceeehhhHHHHHHHHHHHH--h--------cCceEEEEecC-------------CCcchhhHHHHHHHH
Confidence            477888999999999999998776655543  2        23345555565             357777888999999


Q ss_pred             HHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEeccc
Q psy2399          94 KYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKI  137 (232)
Q Consensus        94 ~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~  137 (232)
                      +++..|||.+|.+..||  .|-+.+.....+|. +.|.+|..+.
T Consensus       257 eDl~~LgIkpd~~TyTS--DyF~~i~dycv~li-keGKAYvDDT  297 (712)
T KOG1147|consen  257 EDLSLLGIKPDRVTYTS--DYFDEIMDYCVKLI-KEGKAYVDDT  297 (712)
T ss_pred             HHHHHhCcCcceeeech--hhHHHHHHHHHHHH-hcCcccccCC
Confidence            99999999999998888  58888889999999 9999997554

>KOG4426|consensus

Probab=98.39  E-value=3.1e-06  Score=77.35  Aligned_cols=130  Identities=18%  Similarity=0.200  Sum_probs=96.2

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhH----HHHHHHHHc----CC---
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGA----AIMIAAEKA----GM---   79 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~----~i~~~a~~~----g~---   79 (232)
                      .++.+|....|+.-..+|+||+|+.|++|.++|.+...|     ++|+.+.-+.|.|+    -|+...++.    ..   
T Consensus       187 ~KrvlVDFSSPNIAKeMHVGHLRSTIIGdsl~RllE~~~-----~dVlR~NHvGDWGTQFGMLIahL~dkFPd~l~vsp~  261 (656)
T KOG4426|consen  187 VKRVLVDFSSPNIAKEMHVGHLRSTIIGDSLCRLLEFSG-----VDVLRRNHVGDWGTQFGMLIAHLFDKFPDYLSVSPP  261 (656)
T ss_pred             eeeEEEecCCCcHHHHhhhhhhhhhhHhHHHHHHHHhcC-----cceEeeccccchHHHHHHHHHHHHHhCCchhccCCC
Confidence            478999999999999999999999999999999999999     99998877777654    344333331    11   


Q ss_pred             -----------------------------------CH------HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHH
Q psy2399          80 -----------------------------------TP------KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLV  118 (232)
Q Consensus        80 -----------------------------------~~------~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v  118 (232)
                                                         +|      ..+++--.+.+...+++|.|+...- .+|  .|...+
T Consensus       262 IgDLQvFYkeSKkrFD~deeFKkrAyq~VV~LQggdp~~~kAW~~ICdvSr~ef~kvY~rLdi~l~e~-GES--FYq~~m  338 (656)
T KOG4426|consen  262 IGDLQVFYKESKKRFDEDEEFKKRAYQAVVRLQGGDPDIRKAWALICDVSRKEFQKVYNRLDISLKER-GES--FYQDRM  338 (656)
T ss_pred             chhHHHHHHHHHhccCcCHHHHHHHHHHeeecccCCChHHHHHHHHHHhhHHHHHHHHHHhcchHhhc-chh--hhhhHH
Confidence                                               11      1124445578888899999875322 122  688889


Q ss_pred             HHHHHHHHhhcCCEEecc-cceeeccCCCccc
Q psy2399         119 QKIYDTLYNKAKLIINKK-INQFFDPIKNIFL  149 (232)
Q Consensus       119 ~~~~~~L~~~kG~iy~~~-~~~~~~~~~~~~l  149 (232)
                      .++++.|. .+|++.+.+ ..+-|-+.|+.+|
T Consensus       339 ~~vveel~-~kglvee~~Gr~i~f~~g~~IPL  369 (656)
T KOG4426|consen  339 AEVVEELK-SKGLVEEDDGRRIMFPEGCDIPL  369 (656)
T ss_pred             HHHHHHHh-cCCceeecCCceEeccCCCCcce
Confidence            99999999 999998876 4556655555544

>KOG1195|consensus

Probab=98.24  E-value=7.3e-06  Score=76.06  Aligned_cols=128  Identities=18%  Similarity=0.178  Sum_probs=95.3

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHH---HcC--------
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAE---KAG--------   78 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~---~~g--------   78 (232)
                      +.++++|....|+.+.+.|+||+|+.+++-+++...+..|     ++|.-+...-|.|..+-..|.   +.|        
T Consensus       108 ~~k~iVVefSSPNIAK~FHvGhLRsTiiG~flanl~e~~G-----~~Vtr~NYLGDWGkQFgll~~g~~~~g~e~~L~~~  182 (567)
T KOG1195|consen  108 SGKKIVVEFSSPNIAKPFHVGHLRSTIIGNFLANLHEALG-----WEVTRVNYLGDWGKQFGLLALGFQLYGDEEELQLN  182 (567)
T ss_pred             cCceEEEEecCCCcccccccchhhhhhhhhHhhhhHHhhC-----CceeehhhhhHHHHHhhHHhccHHhhCchhhhccc
Confidence            3588999999999999999999999999999999999999     999987777776643332221   011        


Q ss_pred             -------------------CCH----HH------------------HHHHHHHHHHHHHhccCCcCCccccCCChhHHHH
Q psy2399          79 -------------------MTP----KE------------------FINNISSNRKKYLDGFYIKFDNWYSTDSIENIDL  117 (232)
Q Consensus        79 -------------------~~~----~e------------------~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~  117 (232)
                                         .+.    .+                  +.+--+....+.+.+|||.||.|...+. .+.+.
T Consensus       183 pI~hL~dvYVk~nk~~~~~~~~~~~are~f~rlE~~d~e~~k~Wqrfr~lsIe~l~~~Y~Rl~v~FD~y~gESq-v~~e~  261 (567)
T KOG1195|consen  183 PIKHLFDVYVKINKDAEKDPDTAEEAREFFKRLEDGDEEHLKLWQRFRDLSIEKLIKTYNRLNVKFDEYSGESQ-VSNEK  261 (567)
T ss_pred             hHHHHHHHHHHhhhhhhhCcchHHHHHHHHHHHhcccHHHHHHHHHhhhhhHHHHHHHHHHhceeeeeccchHH-HHHHH
Confidence                               000    01                  1111235677788999999999988875 67888


Q ss_pred             HHHHHHHHHhhcCCEEecccceeeccC
Q psy2399         118 VQKIYDTLYNKAKLIINKKINQFFDPI  144 (232)
Q Consensus       118 v~~~~~~L~~~kG~iy~~~~~~~~~~~  144 (232)
                      .+.+.+.+. .+|++...++..-++..
T Consensus       262 ~~~~~d~~r-s~~l~~e~dG~~vidL~  287 (567)
T KOG1195|consen  262 MQEALDLLR-SANLTEEIDGTIVIDLS  287 (567)
T ss_pred             HHHHHHHHH-hcCCcccCCCcEEEEec
Confidence            999999999 99977666666655443

>KOG1148|consensus

Probab=97.63  E-value=0.00014  Score=68.75  Aligned_cols=95  Identities=19%  Similarity=0.118  Sum_probs=65.8

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -++|..||-|||-|||||+-..-+.=-+|+   ..|      -|-++. .||             ..|+.-.++|-..|+
T Consensus       248 kV~TRFPPEPNG~LHIGHaKAInvNFgyAk---~~~------G~cyLR-fDD-------------TNPEkEee~yf~sI~  304 (764)
T KOG1148|consen  248 KVVTRFPPEPNGILHIGHAKAINVNFGYAK---AHG------GVCYLR-FDD-------------TNPEKEEEEYFESIK  304 (764)
T ss_pred             eeEEeCCCCCCceeeecchhheeechhhhh---hhC------CeEEEe-cCC-------------CCcchhhHHHHHHHH
Confidence            388999999999999999975433322333   233      222332 122             358888889999999


Q ss_pred             HHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +.-.+||..+-..  |.+..|-...-++-..|+ ++|++|.
T Consensus       305 e~V~WLG~~P~kv--TysSDyFdqLy~~av~LI-rkG~AYV  342 (764)
T KOG1148|consen  305 EMVAWLGFEPYKV--TYSSDYFDQLYELAVELI-RKGKAYV  342 (764)
T ss_pred             HHHHHhCCCceee--ecchhHHHHHHHHHHHHH-hcCceeE
Confidence            9999999976444  433356666666667888 9999985

>KOG1149|consensus

Probab=97.61  E-value=0.00022  Score=65.43  Aligned_cols=96  Identities=16%  Similarity=0.170  Sum_probs=69.6

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      |=+...|.|+|.||||-+|+++..-++||  +..|     .-+..+-.+|                ...++..-...+.+
T Consensus        34 VRvRFAPSPTGfLHlGgLRTALfNYLfAr--k~gG-----kFiLRiEDTD----------------q~R~v~gs~e~i~~   90 (524)
T KOG1149|consen   34 VRVRFAPSPTGFLHLGGLRTALFNYLFAR--KKGG-----KFILRIEDTD----------------QKRLIRGSEEAIYE   90 (524)
T ss_pred             eEEeecCCCCcceehhhHHHHHHHHHHHH--hcCC-----eEEEEecccc----------------ccccccchHHHHHH
Confidence            44555689999999999999988888887  3334     4555554443                33455556677889


Q ss_pred             HHhccCCcCCccccCCC---h----hHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNWYSTDS---I----ENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~~~t~~---~----~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|.++||+||.=.+...   |    +..+..+...++|. +.|.+|+
T Consensus        91 ~L~w~nl~~DEgP~~gG~~GPY~QS~R~eiY~kyae~Ll-~sG~AYr  136 (524)
T KOG1149|consen   91 DLKWANLDWDEGPGVGGPFGPYEQSERLEIYKKYAEKLL-ESGHAYR  136 (524)
T ss_pred             HHHhcCCCcccCCCcCCCCCchhhHHHHHHHHHHHHHHH-hcCCeeE
Confidence            99999999997442221   1    34566778888999 9999996

>PRK12285 tryptophanyl-tRNA synthetase; Reviewed

Probab=96.83  E-value=0.011  Score=54.02  Aligned_cols=78  Identities=24%  Similarity=0.209  Sum_probs=50.0

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      +++++.|.++. -|+|.+||||+.   ....+.+++. .|     +++.+..+ |.|..-     .+ +.+++++. ++.
T Consensus        63 ~~~~~~iytG~-~PSG~lHLGh~~---~~~~~~~lQ~-~g-----~~~~i~Ia-D~ha~~-----~~-~~~~e~~~-~~~  124 (368)
T PRK12285         63 NGKPFAVYTGF-MPSGPMHIGHKM---VFDELKWHQE-FG-----ANVYIPIA-DDEAYA-----AR-GLSWEETR-EWA  124 (368)
T ss_pred             cCCCeEEEEcc-CCCCCccHHHHH---HHHHHHHHHh-cC-----CCEEEEec-chHHHh-----cC-CCCHHHHH-HHH
Confidence            35677777765 778999999964   3445555555 78     78766654 444321     11 45666554 444


Q ss_pred             HHHHHHHhccCCcCCc
Q psy2399          90 SNRKKYLDGFYIKFDN  105 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~  105 (232)
                      ..+..++.++|++++.
T Consensus       125 ~~~~~~~lA~G~Dp~k  140 (368)
T PRK12285        125 YEYILDLIALGFDPDK  140 (368)
T ss_pred             HHHHHHHHHhCCCccc
Confidence            4466788899998874

>PLN02486 aminoacyl-tRNA ligase

Probab=96.72  E-value=0.024  Score=52.06  Aligned_cols=85  Identities=12%  Similarity=0.117  Sum_probs=52.1

Q ss_pred             CCCCcEEEEcCCCCCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINN   87 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~   87 (232)
                      ..+++++|.++. -|+| .+||||+.   ....+..+++..|     ..+.+.. +|+     +.... .+.+.+++ .+
T Consensus        69 e~~~~~~vYtG~-~PSg~~lHlGHlv---~~~~~~~lQ~~~~-----~~~~I~i-aD~-----e~~~~-~~~~~e~i-~~  131 (383)
T PLN02486         69 EKGEKFYLYTGR-GPSSEALHLGHLI---PFMFTKYLQDAFK-----VPLVIQL-TDD-----EKFLW-KNLSVEES-QR  131 (383)
T ss_pred             hcCCCeEEEeCC-CCCCccccHHHHH---HHHHHHHHHHhCC-----CeEEEEe-cCH-----HHHhh-cCCCHHHH-HH
Confidence            345678888775 8999 59999954   4445554444556     6666553 354     22222 25666554 45


Q ss_pred             HHHHHHHHHhccCCcCCc-cccCC
Q psy2399          88 ISSNRKKYLDGFYIKFDN-WYSTD  110 (232)
Q Consensus        88 ~~~~~~~~l~~lgI~~d~-~~~t~  110 (232)
                      +.....+++.++|++++. ++...
T Consensus       132 ~~~en~~~iiA~G~dp~kt~I~s~  155 (383)
T PLN02486        132 LARENAKDIIACGFDVERTFIFSD  155 (383)
T ss_pred             HHHHHHHHHHHhCCCCcceEEEec
Confidence            555667777889998864 44433

>COG0180 TrpS Tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=96.25  E-value=0.044  Score=48.95  Aligned_cols=91  Identities=12%  Similarity=0.224  Sum_probs=55.5

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCc-eeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSR-QVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~-~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      .++.|+++. -|+|.|||||..+++..    +++-..+     + ++. ++=.|.|-..+      .+.++++-..+...
T Consensus         4 ~~~~vlSG~-~PSG~lHLGny~ga~~~----~v~~q~~-----~~~~f-~~IaDlha~t~------~~~~~~~~l~~~~~   66 (314)
T COG0180           4 KKFRVLSGI-QPSGKLHLGNYLGAIRN----WVLLQEE-----YYECF-FFIADLHAITV------RQDPTEEDLRQATR   66 (314)
T ss_pred             CCceEEecC-CCCCCcchhHhHHHHHH----HHHHhcc-----cCceE-EEEecHHHhhc------CCCChHHHHHHHHH
Confidence            445566655 78899999999887543    3333334     3 444 33456654432      22334455666667


Q ss_pred             HHHHHHhccCCcCCc---cccCCChhHHHHHH
Q psy2399          91 NRKKYLDGFYIKFDN---WYSTDSIENIDLVQ  119 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~---~~~t~~~~~~~~v~  119 (232)
                      ....++-++||+++.   |..+.-++|.+..+
T Consensus        67 e~~a~~LA~GiDP~k~~if~QS~v~e~~eLa~   98 (314)
T COG0180          67 EVAADYLAVGLDPEKSTIFLQSEVPEHAELAW   98 (314)
T ss_pred             HHHHHHHHhccCccccEEEEccCchHHHHHHH
Confidence            777888899998875   44555566655444

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=96.24  E-value=0.0071  Score=62.07  Aligned_cols=96  Identities=11%  Similarity=0.078  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHH---HhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCC
Q psy2399         115 IDLVQKIYDTL---YNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS  191 (232)
Q Consensus       115 ~~~v~~~~~~L---~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~  191 (232)
                      .+.+.+.....   . +++-...-+.....||+|++..+.    ..||.||+...--..|.+||....+++-....|+-|
T Consensus       641 qR~I~kAa~~a~~~~-d~~G~ieVEV~~rkCPkCG~~t~~----~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~C  715 (1337)
T PRK14714        641 QRDVAKAAKHAPDMS-DEGGVIEVEVGRRRCPSCGTETYE----NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRC  715 (1337)
T ss_pred             cccHHHHHHhhhhcc-ccCCeEEEEEEEEECCCCCCcccc----ccCcccCCcCCCceeCccCCCccCCCccccccCCCC
Confidence            34455555433   2 344455666678899999998764    399999998754557999999776554446689999


Q ss_pred             CCccEEEEccceeEecCChhhHHHHHh
Q psy2399         192 GTKPIIKSSKHFFFKLSDKRCIDFLRK  218 (232)
Q Consensus       192 g~~~~~~~~~~~f~~L~~~~~~~~l~~  218 (232)
                      |.++.-....  -++|. +.|+..|.+
T Consensus       716 Gtplv~~~~~--~i~~~-~~~~~A~~~  739 (1337)
T PRK14714        716 DVELTPYQRR--TINVK-EEYRSALEN  739 (1337)
T ss_pred             CCcccccceE--EecHH-HHHHHHHHH
Confidence            9887643332  34662 234444443

>PRK12284 tryptophanyl-tRNA synthetase; Reviewed

Probab=95.95  E-value=0.038  Score=51.38  Aligned_cols=94  Identities=13%  Similarity=0.115  Sum_probs=56.9

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      .|.+++ .|+|.|||||..+.+-.  ..+.+...|     +++.+.. .|-|-.-       ...+|+++.+... .+..
T Consensus         4 rvlSGi-qPTG~lHLGNylGaik~--~v~lq~q~~-----~~~~~~I-ADlHAlT-------~~~dp~~lr~~~~-e~aa   66 (431)
T PRK12284          4 RVLTGI-TTTGTPHLGNYAGAIRP--AIAASRQPG-----VESFYFL-ADYHALI-------KCDDPARIQRSTL-EIAA   66 (431)
T ss_pred             EEEEEe-cCCCcchHHHHHHHHHH--HHHHHHhCC-----CcEEEEe-echhhcc-------CCCCHHHHHHHHH-HHHH
Confidence            355555 78899999997776543  333444458     7776543 3444432       1246776665544 4678


Q ss_pred             HHhccCCcCCc--cccCC-ChhHHHHHHHHHHHHH
Q psy2399          95 YLDGFYIKFDN--WYSTD-SIENIDLVQKIYDTLY  126 (232)
Q Consensus        95 ~l~~lgI~~d~--~~~t~-~~~~~~~v~~~~~~L~  126 (232)
                      ++-++||+++.  ++.-| -++|.+. .|++..+.
T Consensus        67 ~~LA~GlDPek~~if~QSdvpeh~EL-~wiL~~it  100 (431)
T PRK12284         67 TWLAAGLDPERVTFYRQSDIPEIPEL-TWLLTCVA  100 (431)
T ss_pred             HHHHhCCCccceEEEECCcchhHHHH-HHHHHhhh
Confidence            88899999874  44455 4555444 44554343

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=95.87  E-value=0.013  Score=47.33  Aligned_cols=122  Identities=15%  Similarity=0.098  Sum_probs=59.7

Q ss_pred             HHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHH
Q psy2399          40 IWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQ  119 (232)
Q Consensus        40 vl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~  119 (232)
                      -||||||+.|     |++.+..  +..+..|...+.+.|.=   +.-+=...+++.  ++|+. ..++.++  ...+++.
T Consensus        17 ~LARwLRllG-----ydt~~~~--~~~d~~i~~i~~~e~rI---llTRDr~L~~r~--k~g~~-~i~i~~~--s~~~Ql~   81 (165)
T COG1656          17 KLARWLRLLG-----YDTVYSS--NESDDEIILIAKKEGRI---LLTRDRELYKRA--KLGIK-AILIRSD--SIEEQLA   81 (165)
T ss_pred             HHHHHHHHcC-----Cceeeec--cCCcHHHHHHHhcCCeE---EEeccHHHHHHh--hccCc-eEEEeCC--CHHHHHH
Confidence            3799999999     9999996  22234555555554310   000001111221  34442 2355555  4667777


Q ss_pred             HHHHHHHhhcCCEEecccceeeccCCCcc---cccceeccCCCCC-CccccCCCcCccCCCCCCC
Q psy2399         120 KIYDTLYNKAKLIINKKINQFFDPIKNIF---LPDRYIKGECPIC-NAKDQYGDFCECCSSIYTP  180 (232)
Q Consensus       120 ~~~~~L~~~kG~iy~~~~~~~~~~~~~~~---l~~~~v~g~cp~c-~~~~~~g~~Ce~Cg~~~~~  180 (232)
                      +++.+|- .++.+.....   =||.|+..   ++..+|++.-|-= ......-..|++||++|-+
T Consensus        82 e~~~~~~-l~~~~~~e~~---RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~  142 (165)
T COG1656          82 EFLARLG-LKPRLFPEFS---RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK  142 (165)
T ss_pred             HHHHHhc-cchhcccccc---cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence            7877777 5552222122   24444443   3445555444411 0000111237777777654

>TIGR00233 trpS tryptophanyl-tRNA synthetase

Probab=95.84  E-value=0.044  Score=49.35  Aligned_cols=90  Identities=16%  Similarity=0.249  Sum_probs=51.4

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      ++.|.++. -|+|.+||||..+.+..-+..    ..|     +++.+..+ |.|-.-.    . .+-+++.+ ......+
T Consensus         2 ~~~v~~G~-~PTG~~HlG~~l~~~~~~~~~----q~~-----~~~~i~Ia-D~ha~t~----~-~~~~~~~~-~~~~~~~   64 (328)
T TIGR00233         2 KFRVLTGI-QPSGKMHLGHYLGAIQTKWLQ----QFG-----VELFICIA-DLHAITV----K-DNTDPDAL-RKAREEL   64 (328)
T ss_pred             CCEEEEee-CCCcHhHHHHHHHHHHHHHHH----hCC-----CCEEEEee-cchhhcC----C-CCCCHHHH-HHHHHHH
Confidence            34556655 788999999977765543332    568     78766643 3333221    0 11134333 4444555


Q ss_pred             HHHHhccCCcCCc--cccCC-ChhHHHHHH
Q psy2399          93 KKYLDGFYIKFDN--WYSTD-SIENIDLVQ  119 (232)
Q Consensus        93 ~~~l~~lgI~~d~--~~~t~-~~~~~~~v~  119 (232)
                      ..++.++|++++.  +++.| -++|.+.++
T Consensus        65 ~~~~lA~GlDp~k~~if~qS~~~e~~el~~   94 (328)
T TIGR00233        65 AADILAVGLDPKKTFIFLQSDYPEHYELAW   94 (328)
T ss_pred             HHHHHHhCcChhheEEEEcCCcHHHHHHHH
Confidence            6777799998874  33444 345555444

This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this model.

>PRK08560 tyrosyl-tRNA synthetase; Validated

Probab=95.72  E-value=0.061  Score=48.40  Aligned_cols=82  Identities=16%  Similarity=0.175  Sum_probs=49.0

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      ++++.|.++. -|+|.+||||+.   ..-.++++++ .|     +++.+..+ |.|..-..      ..+++ .+.++..
T Consensus        28 ~~~~~v~~G~-~PTG~lHLG~~~---~~~~~~~lq~-~g-----~~~~i~Ia-D~ha~~~~------~~~~~-~i~~~~~   89 (329)
T PRK08560         28 KEEPKAYIGF-EPSGKIHLGHLL---TMNKLADLQK-AG-----FKVTVLLA-DWHAYLND------KGDLE-EIRKVAE   89 (329)
T ss_pred             CCCCEEEEcc-CCCCcchhhhhH---HHHHHHHHHH-CC-----CeEEEEEc-cchhhcCC------CCCHH-HHHHHHH
Confidence            3555555554 788999999854   3333555555 48     77766543 33332211      13444 4455556


Q ss_pred             HHHHHHhccCCcCCc--cccCC
Q psy2399          91 NRKKYLDGFYIKFDN--WYSTD  110 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~--~~~t~  110 (232)
                      .+..++.++|++++.  ++..+
T Consensus        90 ~~~~~~~A~G~dp~k~~i~~qS  111 (329)
T PRK08560         90 YNKKVFEALGLDPDKTEFVLGS  111 (329)
T ss_pred             HHHHHHHHcCCChhheEEEecc
Confidence            788889999998763  44444

>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed

Probab=95.72  E-value=0.022  Score=58.31  Aligned_cols=70  Identities=16%  Similarity=0.171  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCC
Q psy2399         114 NIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGT  193 (232)
Q Consensus       114 ~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~  193 (232)
                      ..+.-..+++.|. ++|++.......                                           -.-|.|..||.
T Consensus       361 v~eA~~~Ii~~L~-~~g~l~~~~~~~-------------------------------------------h~~p~c~R~g~  396 (975)
T PRK06039        361 VKDADKEIIRDLK-ERGLLFKAETYE-------------------------------------------HSYPHCWRCDT  396 (975)
T ss_pred             HHHhhHHHHHHHH-hCCCEeeeeeec-------------------------------------------CCCCEeCCCCC
Confidence            3455667889999 999987654211                                           12378889999


Q ss_pred             ccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCCC
Q psy2399         194 KPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI  230 (232)
Q Consensus       194 ~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~~  230 (232)
                      +++.+.++|||+++  +++++++.++ ++.-.+.|+.
T Consensus       397 pv~~~~~~qWFi~~--~~~k~~ll~~-~~~i~~~P~~  430 (975)
T PRK06039        397 PLIYYATESWFIRV--TKIKDRMLEL-NQKINWYPEH  430 (975)
T ss_pred             EEEEEecCeeeEec--HHHHHHHHHh-hCCeEEECcc
Confidence            99999999999999  9999999999 5543355553

>cd00806 TrpRS_core catalytic core domain of tryptophanyl-tRNA synthetase

Probab=95.34  E-value=0.091  Score=46.22  Aligned_cols=68  Identities=18%  Similarity=0.358  Sum_probs=42.5

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|+|.|||||+.+.+..  + +++...|     +++.+..+ |.|..-.      ...+++ -+.++...+.+++.++|+
T Consensus         7 ~PTG~lHLG~~~~al~~--~-~~lQ~ag-----~~~~~~Ia-D~ha~t~------~~~~~~-~~~~~~~~~~~~~lA~G~   70 (280)
T cd00806           7 QPSGSLHLGHYLGAFRF--W-VWLQEAG-----YELFFFIA-DLHALTV------KQLDPE-ELRQNTRENAKDYLACGL   70 (280)
T ss_pred             CCCchhhHHHHHHHHHH--H-HHHHhCC-----CCEEEEec-chHHHhC------CCCCHH-HHHHHHHHHHHHHHHcCC
Confidence            68899999998874432  2 2223348     78776653 4444321      113454 455566667888889999


Q ss_pred             cCCc
Q psy2399         102 KFDN  105 (232)
Q Consensus       102 ~~d~  105 (232)
                      +++.
T Consensus        71 dp~k   74 (280)
T cd00806          71 DPEK   74 (280)
T ss_pred             Cccc
Confidence            8853

Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding

>PF12773 DZR: Double zinc ribbon

Probab=94.73  E-value=0.031  Score=35.89  Aligned_cols=37  Identities=22%  Similarity=0.576  Sum_probs=19.7

Q ss_pred             CCCCCccccC-CCcCccCCCCCCCccccCCcccCCCCc
Q psy2399         158 CPICNAKDQY-GDFCECCSSIYTPTKLINPYSILSGTK  194 (232)
Q Consensus       158 cp~c~~~~~~-g~~Ce~Cg~~~~~~~l~~~~~~~~g~~  194 (232)
                      ||.|+..... ..+|..||..+...+.....|..||..
T Consensus         1 Cp~Cg~~~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~   38 (50)
T PF12773_consen    1 CPHCGTPNPDDAKFCPHCGTPLPPPDQSKKICPNCGAE   38 (50)
T ss_pred             CCCcCCcCCccccCChhhcCChhhccCCCCCCcCCcCC
Confidence            5555555333 355666666665333334456666654

>PRK04023 DNA polymerase II large subunit; Validated

Probab=94.72  E-value=0.042  Score=55.43  Aligned_cols=73  Identities=18%  Similarity=0.159  Sum_probs=52.0

Q ss_pred             HHHHHhh-cCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEEEEc
Q psy2399         122 YDTLYNK-AKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSS  200 (232)
Q Consensus       122 ~~~L~~~-kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~  200 (232)
                      +.+-. + +|.+ .-+....+|++|++..    +...||.||+...-...|..||....+     +.|+-||..+.-.. 
T Consensus       610 i~~A~-~~~g~~-eVEVg~RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~~~~~-----y~CPKCG~El~~~s-  677 (1121)
T PRK04023        610 INKAA-KYKGTI-EVEIGRRKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGIEVEE-----DECEKCGREPTPYS-  677 (1121)
T ss_pred             HHHHH-hcCCce-eecccCccCCCCCCcC----CcccCCCCCCCCCcceeCccccCcCCC-----CcCCCCCCCCCccc-
Confidence            34444 4 5655 4456667999999985    668999999986666789999986543     56999998776333 


Q ss_pred             cceeEec
Q psy2399         201 KHFFFKL  207 (232)
Q Consensus       201 ~~~f~~L  207 (232)
                       ..-++|
T Consensus       678 -~~~i~l  683 (1121)
T PRK04023        678 -KRKIDL  683 (1121)
T ss_pred             -eEEecH
Confidence             333566

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=94.69  E-value=0.02  Score=31.03  Aligned_cols=21  Identities=33%  Similarity=0.822  Sum_probs=12.9

Q ss_pred             CCCCCCccccCC-CcCccCCCC
Q psy2399         157 ECPICNAKDQYG-DFCECCSSI  177 (232)
Q Consensus       157 ~cp~c~~~~~~g-~~Ce~Cg~~  177 (232)
                      .||.||.+...+ .+|..||..
T Consensus         1 ~Cp~CG~~~~~~~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCPNCGAEIEDDAKFCPNCGTP   22 (23)
T ss_pred             CCcccCCCCCCcCcchhhhCCc
Confidence            377777765444 457666653

>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function

Probab=94.57  E-value=0.16  Score=40.30  Aligned_cols=31  Identities=16%  Similarity=0.193  Sum_probs=23.2

Q ss_pred             HHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcC
Q psy2399          41 WVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAG   78 (232)
Q Consensus        41 l~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g   78 (232)
                      ++||||+.|     +++.+..+.+|  ..|...|.+.+
T Consensus        12 Lar~LR~lG-----~Dt~~~~~~~D--~~il~~A~~e~   42 (147)
T PF01927_consen   12 LARWLRLLG-----YDTLYSRDIDD--DEILELAREEG   42 (147)
T ss_pred             HHHHHHHCC-----CcEEEeCCCCh--HHHHHHhhhCC
Confidence            789999999     99999986654  44555565544

The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.

>PRK14900 valS valyl-tRNA synthetase; Provisional

Probab=94.34  E-value=0.085  Score=54.51  Aligned_cols=69  Identities=14%  Similarity=0.058  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCC
Q psy2399         114 NIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGT  193 (232)
Q Consensus       114 ~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~  193 (232)
                      ..+.-..+++.|. ++|++...+...                                           ...|.|..||.
T Consensus       330 ~~ear~~Ii~~L~-~~g~l~~~~~~~-------------------------------------------h~~~~c~R~~~  365 (1052)
T PRK14900        330 RFEARKEVKRLLA-EQGLDRGAKPHV-------------------------------------------LPLGRCQRSAT  365 (1052)
T ss_pred             HHHHHHHHHHHHH-hCCCeecceeee-------------------------------------------ccCceeCCCCc
Confidence            3455667888999 999987653211                                           12377888999


Q ss_pred             ccEEEEccceeEecCChhhHHHHHhhhhcC--CCCCCC
Q psy2399         194 KPIIKSSKHFFFKLSDKRCIDFLRKWAIHD--KRLQPE  229 (232)
Q Consensus       194 ~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~--~~~~p~  229 (232)
                      +++.+..+||||+|  +.+++++.++ ++.  ..+.|+
T Consensus       366 ~ie~~~s~qWFi~l--~~~k~~~~~~-v~~~~~~~~P~  400 (1052)
T PRK14900        366 ILEPLLSDQWYVRI--EPLARPAIEA-VEQGRTRFIPE  400 (1052)
T ss_pred             eEEEEeccceeeeh--HHHHHHHHHH-HhcCCcEEECh
Confidence            99999999999999  9999999999 543  345554

>PTZ00126 tyrosyl-tRNA synthetase; Provisional

Probab=94.31  E-value=0.068  Score=49.17  Aligned_cols=80  Identities=15%  Similarity=0.127  Sum_probs=46.9

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      +++..|.++. -|+|.+||||  ..+..--+..+ ...|     ++|.+..+ |-|..-.    .+.|.+++++ .+...
T Consensus        64 ~~~~~v~~G~-~PTG~lHLG~--g~i~~~~~~~l-q~~G-----~~v~~~Ia-D~hA~~~----~~~g~~l~~i-~~~~~  128 (383)
T PTZ00126         64 KERPICYDGF-EPSGRMHIAQ--GILKAINVNKL-TKAG-----CVFVFWVA-DWFALLN----NKMGGDLEKI-RKVGE  128 (383)
T ss_pred             CCCCEEEEEE-CCCCcccccc--hHhHhHHHHHH-HhCC-----CeEEEEEc-cceeecC----CCCCCCHHHH-HHHHH
Confidence            3445555554 6889999999  22222233333 4558     88876653 2222110    1234455554 55666


Q ss_pred             HHHHHHhccCCcCCc
Q psy2399          91 NRKKYLDGFYIKFDN  105 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~  105 (232)
                      .+...+.++|++++.
T Consensus       129 ~~~~~~~A~GlDp~k  143 (383)
T PTZ00126        129 YFIEVWKAAGMDMDN  143 (383)
T ss_pred             HHHHHHHHhCCCccc
Confidence            677889999998764

>PLN02886 aminoacyl-tRNA ligase

Probab=94.26  E-value=0.42  Score=44.06  Aligned_cols=83  Identities=19%  Similarity=0.377  Sum_probs=49.9

Q ss_pred             EEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Q psy2399          16 VTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKY   95 (232)
Q Consensus        16 v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~   95 (232)
                      |.++. -|+|.+||||..+.+  .-+..+++  |     +++.+ +=.|.|-..+       .-+++++.+.. ..+..+
T Consensus        49 v~sGi-qPSG~lHLGnylGai--~~~v~lQ~--~-----~~~~~-~IADlHAlt~-------~~~~~~lr~~~-~~~~a~  109 (389)
T PLN02886         49 VVSGV-QPTGSIHLGNYLGAI--KNWVALQE--T-----YDTFF-CVVDLHAITL-------PHDPRELGKAT-RSTAAI  109 (389)
T ss_pred             EEEEE-CCCCccHHHHHHHHH--HHHHHHhc--c-----CCEEE-EEecHHHhhC-------CCCHHHHHHHH-HHHHHH
Confidence            44444 677999999977765  23333333  7     77654 3456655431       23666655444 456788


Q ss_pred             HhccCCcCCc---cccCCChhHHHH
Q psy2399          96 LDGFYIKFDN---WYSTDSIENIDL  117 (232)
Q Consensus        96 l~~lgI~~d~---~~~t~~~~~~~~  117 (232)
                      +.++|++++.   |..+.-++|.+.
T Consensus       110 ~lA~GlDP~ks~if~QS~v~e~~eL  134 (389)
T PLN02886        110 YLACGIDPSKASVFVQSHVPAHAEL  134 (389)
T ss_pred             HHHcCcCccceEEEEeCCCchhHHH
Confidence            8899999873   434444555443

>cd00395 Tyr_Trp_RS_core catalytic core domain of tyrosinyl-tRNA and tryptophanyl-tRNA synthetase

Probab=94.25  E-value=0.18  Score=44.25  Aligned_cols=71  Identities=20%  Similarity=0.199  Sum_probs=41.3

Q ss_pred             CCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChh--hHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhc
Q psy2399          22 YANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAH--GAAIMIAAEKAGMTPKEFINNISSNRKKYLDG   98 (232)
Q Consensus        22 ~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~--G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~   98 (232)
                      -|+| .|||||+.+   -..+.+++ ..|     +++.++.|-.+.  |.+.-...++.-.++ +.+.++...+.+++.+
T Consensus         7 ~PTg~~lHlGh~~~---l~~~~~lq-~~g-----~~~~~~I~d~~a~~~d~sg~~~~r~~~~~-~~i~~n~~~~~~~~~a   76 (273)
T cd00395           7 DPTADSLHIGHLIG---LLTFRRFQ-HAG-----HRPIFLIGGQTGIIGDPSGKKSERTLNDP-EEVRQNIRRIAAQYLA   76 (273)
T ss_pred             cCCCCCccHHHHHH---HHHHHHHH-HCC-----CCEEEEEecCceeeCCCCCccccccCCCH-HHHHHHHHHHHHHHHH
Confidence            5789 699999776   33444444 468     888776652211  111101111122244 4455557788889999


Q ss_pred             cCCc
Q psy2399          99 FYIK  102 (232)
Q Consensus        99 lgI~  102 (232)
                      +|++
T Consensus        77 ~g~d   80 (273)
T cd00395          77 VGIF   80 (273)
T ss_pred             hcCc
Confidence            9997

Tyrosinyl-tRNA synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. These enzymes attach Tyr or Trp, respectively, to the appropriate tRNA. These class I enzymes are homodimers, which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.

>PF00579 tRNA-synt_1b: tRNA synthetases class I (W and Y); InterPro: IPR002305 The aminoacyl-tRNA synthetases (6

Probab=94.15  E-value=0.092  Score=46.19  Aligned_cols=79  Identities=16%  Similarity=0.210  Sum_probs=42.8

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      ++++.|.++. -|+|.+||||+....   .+.++++ .|     .+|.++.|-. |..-    ..+.+. ..+.+.....
T Consensus         3 ~~~~~~y~G~-~PTg~lHlG~l~~~~---~~~~lq~-~g-----~~~~i~iaD~-~a~~----~~~~~~-~~~~~~~~~~   66 (292)
T PF00579_consen    3 NKPFRVYTGI-DPTGDLHLGHLVPIM---KLIWLQK-AG-----FKVIILIADL-HALL----GDPSKG-DERKIRSRAE   66 (292)
T ss_dssp             HSSEEEEEEE-ESSSS-BHHHHHHHH---HHHHHHH-TT-----SEEEEEEEHH-HHHH----TTTTGS-SHHHHHHHHH
T ss_pred             CCCcEEEEeE-CCCCcccchHHHHHH---HHHHHHh-cC-----CccceEecch-hhcc----cCcccc-cHHHHHHHHH
Confidence            4556666655 688999999887653   3333333 88     8888876532 2211    011111 2333333444


Q ss_pred             HHHHH--HhccCCcCCc
Q psy2399          91 NRKKY--LDGFYIKFDN  105 (232)
Q Consensus        91 ~~~~~--l~~lgI~~d~  105 (232)
                      .+.+.  +-++|++++.
T Consensus        67 ~~~~~~~~la~g~d~~k   83 (292)
T PF00579_consen   67 YNINDKAILALGLDPEK   83 (292)
T ss_dssp             HHHHHHHHHHTTSHTTT
T ss_pred             HHHHHHHHHHhccCccc
Confidence            44444  6689997753

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. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2JAN_A 3P0J_B 3P0I_B 3P0H_B 1YID_C 2A4M_C 1YIA_C 1YI8_C 2EL7_A 3PRH_A ....

>PRK05912 tyrosyl-tRNA synthetase; Validated

Probab=94.09  E-value=0.19  Score=46.61  Aligned_cols=77  Identities=18%  Similarity=0.252  Sum_probs=44.0

Q ss_pred             CcEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCC------ChhhHHHHHHHHHcCCCHHHH
Q psy2399          12 RRIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICAD------DAHGAAIMIAAEKAGMTPKEF   84 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~------D~~G~~i~~~a~~~g~~~~e~   84 (232)
                      +++.|.++. -|+|+ |||||+..   -..+.+++ ..|     +++.++.|-      |..|...    ++...+. +.
T Consensus        32 ~~~~vy~G~-dPTg~slHlGhlv~---l~~l~~lQ-~~G-----~~~~~ligd~ta~igDpsgk~~----~r~~l~~-e~   96 (408)
T PRK05912         32 EPLRIYLGF-DPTAPSLHLGHLVP---LLKLRRFQ-DAG-----HKPIALIGGFTGMIGDPSGKSE----TRKLLTR-EQ   96 (408)
T ss_pred             CCCEEEEee-cCCCCCccHHhHHH---HHHHHHHH-HCC-----CcEEEEEcCceeEcCCCCCCch----hhccCCH-HH
Confidence            456666655 78895 99999774   34455554 468     787776543      2333221    2223333 34


Q ss_pred             HHHHHHHHHHHHhccCCcCC
Q psy2399          85 INNISSNRKKYLDGFYIKFD  104 (232)
Q Consensus        85 ~~~~~~~~~~~l~~lgI~~d  104 (232)
                      +.++.+.+++++ +.+++++
T Consensus        97 i~~n~~~i~~ql-~~~ld~~  115 (408)
T PRK05912         97 VAENAETIKEQL-FKFLDFE  115 (408)
T ss_pred             HHHHHHHHHHHH-HHhcCcC
Confidence            445556677766 5566654

>TIGR00392 ileS isoleucyl-tRNA synthetase

Probab=94.00  E-value=0.11  Score=52.60  Aligned_cols=41  Identities=24%  Similarity=0.327  Sum_probs=34.2

Q ss_pred             CcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         186 PYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       186 ~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                      |.|..||.+++.+.++|||+++  +++++++.++ ++.-.+.|+
T Consensus       407 p~~~R~~~~v~~~~~~QWFi~~--~~~k~~~l~~-~~~i~~~P~  447 (861)
T TIGR00392       407 PHCWRTKTPVIYRATEQWFIKT--KDIKDQMLEQ-IKKVNWVPE  447 (861)
T ss_pred             CccCCCCCEEEEecCccccEEc--HHHHHHHHHH-hCCcEEECc
Confidence            6788899999999999999999  9999999999 553333344

The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms.

>PRK00927 tryptophanyl-tRNA synthetase; Reviewed

Probab=93.62  E-value=0.41  Score=43.18  Aligned_cols=66  Identities=21%  Similarity=0.379  Sum_probs=40.6

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|+|.+||||..+.+..  +.+++.  +     +++.++. .|.|-.-.       ..+++++. .+...+..++.++|+
T Consensus         9 ~PTG~lHLG~~~g~~~~--~~~lQ~--~-----~~~~~~I-aD~ha~t~-------~~~~~~i~-~~~~~~~~~~lA~Gl   70 (333)
T PRK00927          9 QPTGKLHLGNYLGAIKN--WVELQD--E-----YECFFCI-ADLHALTV-------PQDPEELR-ENTRELAADYLACGI   70 (333)
T ss_pred             CCCccchHHhHHHHHHH--HHHHHh--c-----CCeEEEE-ecHHHHhC-------CCCHHHHH-HHHHHHHHHHHeEcc
Confidence            67899999998877532  333433  3     4666554 34443321       22555444 445567788889999


Q ss_pred             cCCc
Q psy2399         102 KFDN  105 (232)
Q Consensus       102 ~~d~  105 (232)
                      +++.
T Consensus        71 Dp~k   74 (333)
T PRK00927         71 DPEK   74 (333)
T ss_pred             Chhh
Confidence            8863

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=93.61  E-value=0.043  Score=30.55  Aligned_cols=20  Identities=35%  Similarity=0.868  Sum_probs=11.6

Q ss_pred             CCCCCCccccC-CCcCccCCC
Q psy2399         157 ECPICNAKDQY-GDFCECCSS  176 (232)
Q Consensus       157 ~cp~c~~~~~~-g~~Ce~Cg~  176 (232)
                      .||.|+..... ..+|..||.
T Consensus         4 ~Cp~Cg~~~~~~~~fC~~CG~   24 (26)
T PF13248_consen    4 FCPNCGAEIDPDAKFCPNCGA   24 (26)
T ss_pred             CCcccCCcCCcccccChhhCC
Confidence            57777765322 345666665

>PRK13354 tyrosyl-tRNA synthetase; Provisional

Probab=93.56  E-value=0.24  Score=46.01  Aligned_cols=82  Identities=11%  Similarity=0.081  Sum_probs=45.7

Q ss_pred             CCCcEEEEcCCCCCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCCh--hhHHHHHHHHHcCCCHHHHHH
Q psy2399          10 DVRRIFVTTALPYANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDA--HGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~--~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      .++++.|.++. -|+| .|||||+...   -.+. ++...|     +++.++.|-.+  .|.|.-...++...+.+++. 
T Consensus        30 ~~~~~~iy~G~-dPT~~sLHlGhlv~l---~~l~-~lq~~G-----~~~~~ligd~ta~igDpsgk~~~R~~l~~e~i~-   98 (410)
T PRK13354         30 EGKPLTLYLGF-DPTAPSLHIGHLVPL---MKLK-RFQDAG-----HRPVILIGGFTGKIGDPSGKSKERKLLTDEQVQ-   98 (410)
T ss_pred             cCCCcEEEEcc-cCCCCCcchhhHHHH---HHHH-HHHHcC-----CeEEEEEcccccccCCCCcccccccCCCHHHHH-
Confidence            34566666665 7888 4999995543   3344 445578     88887775443  33332122222344444444 


Q ss_pred             HHHHHHHHHHhccCCcC
Q psy2399          87 NISSNRKKYLDGFYIKF  103 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI~~  103 (232)
                      ++...+.+++.+ ++++
T Consensus        99 ~n~~~i~~q~~~-~ld~  114 (410)
T PRK13354         99 HNAKTYTEQIFK-LFDF  114 (410)
T ss_pred             HHHHHHHHHHHH-hcCc
Confidence            445566665554 4444

>PRK12556 tryptophanyl-tRNA synthetase; Provisional

Probab=93.05  E-value=0.65  Score=41.94  Aligned_cols=86  Identities=14%  Similarity=0.214  Sum_probs=48.3

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|+|.+||||..+.+..  ..+.+...|     .++.+.. .|.|-.-     .  .-+++++.+ +......++-++|+
T Consensus        11 qPTG~~HLGnylga~k~--~~~lq~~~~-----~~~~~~I-ADlHalt-----~--~~~~~~l~~-~~~~~~~~~lA~Gl   74 (332)
T PRK12556         11 KPTGYPHLGNYIGAIKP--ALQMAKNYE-----GKALYFI-ADYHALN-----A--VHDPEQFRS-YTREVAATWLSLGL   74 (332)
T ss_pred             CCCCcchHHHHHHHHHH--HHHHHHhcC-----CeEEEEE-echhhcc-----C--CCCHHHHHH-HHHHHHHHHhheee
Confidence            57799999997765443  222333445     5555543 4544431     0  126666544 44456677889999


Q ss_pred             cCCc--cccCC-ChhHHHHHHHHHHH
Q psy2399         102 KFDN--WYSTD-SIENIDLVQKIYDT  124 (232)
Q Consensus       102 ~~d~--~~~t~-~~~~~~~v~~~~~~  124 (232)
                      +++.  ++.-| -++|.+..+ ++..
T Consensus        75 DP~k~~if~qS~v~~~~eL~~-il~~   99 (332)
T PRK12556         75 DPEDVIFYRQSDVPEIFELAW-ILSC   99 (332)
T ss_pred             cccceEEEECCCchHHHHHHH-HHHc
Confidence            9874  33444 355654333 4443

>PLN02882 aminoacyl-tRNA ligase

Probab=92.91  E-value=0.097  Score=54.58  Aligned_cols=55  Identities=16%  Similarity=0.231  Sum_probs=42.9

Q ss_pred             cCCCCCCCccccC--CcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCCC
Q psy2399         173 CCSSIYTPTKLIN--PYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI  230 (232)
Q Consensus       173 ~Cg~~~~~~~l~~--~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~~  230 (232)
                      .+|..+..+++..  |.|..||.+++.+..++||+++  +++++++.+. .+.-.|.|+.
T Consensus       395 ~~g~L~~~~~~~Hsyp~cwR~~tpli~~a~~qWFi~~--~~~k~~~l~~-~~~i~w~P~~  451 (1159)
T PLN02882        395 AKGRLVKSGSITHSYPFCWRSDTPLIYRAVPSWFVKV--EEIKDRLLEN-NKQTYWVPDY  451 (1159)
T ss_pred             HCCCccceeeeecCCCEeeCCCCEEEEEecceeEEEc--HHHHHHHHHh-hCCcEEECCc
Confidence            3455555555554  9999999999999999999999  9999999997 5444455653

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=92.85  E-value=0.061  Score=36.00  Aligned_cols=49  Identities=18%  Similarity=0.078  Sum_probs=36.0

Q ss_pred             eeeccCCCccccc--ceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCc
Q psy2399         139 QFFDPIKNIFLPD--RYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTK  194 (232)
Q Consensus       139 ~~~~~~~~~~l~~--~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~  194 (232)
                      ...|.+++..|++  ..++..||.||+..  -.-|+.|.+.-     ..++|+.||..
T Consensus         7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~--I~RC~~CRk~~-----~~Y~CP~CGF~   57 (59)
T PRK14890          7 PPKCTSCGIEIAPREKAVKFLCPNCGEVI--IYRCEKCRKQS-----NPYTCPKCGFE   57 (59)
T ss_pred             CccccCCCCcccCCCccCEeeCCCCCCee--EeechhHHhcC-----CceECCCCCCc
Confidence            3468899998884  46999999999861  12388888754     45788888853

>PRK12283 tryptophanyl-tRNA synthetase; Reviewed

Probab=92.84  E-value=0.51  Score=43.57  Aligned_cols=82  Identities=13%  Similarity=0.178  Sum_probs=48.3

Q ss_pred             EEcCCCCCCCcCCchHHHhHHHHHHHHHHHHH-cCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          16 VTTALPYANGELHIGHIMEYIQADIWVRFQCM-QQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        16 v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~-~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      |.++. -|+|.+||||..+.+.     .|..+ .+     +++. ++=.|.|-.-+      ...+++++. +....+..
T Consensus         5 v~sGi-qPSG~~HLGnylG~ik-----~wv~lq~~-----~~~~-~~IADlHAlt~------~~~d~~~ir-~~~~~~~a   65 (398)
T PRK12283          5 VLSGM-RPTGRLHLGHYHGVLK-----NWVKLQHE-----YECF-FFVADWHALTT------HYETPEVIE-KNVWDMVI   65 (398)
T ss_pred             EEEEe-CCCCcchHHHHHHHHH-----HHHHHhcC-----CcEE-EEeecHHHHhC------CCCCHHHHH-HHHHHHHH
Confidence            34433 6789999999888543     44443 36     6654 33455554321      112565554 44455788


Q ss_pred             HHhccCCcCCc--cc-cCCChhHHH
Q psy2399          95 YLDGFYIKFDN--WY-STDSIENID  116 (232)
Q Consensus        95 ~l~~lgI~~d~--~~-~t~~~~~~~  116 (232)
                      ++.++|++++.  ++ .+.-++|.+
T Consensus        66 ~~lA~GlDP~k~~if~QS~v~eh~e   90 (398)
T PRK12283         66 DWLAAGVDPAQATLFIQSKVPEHAE   90 (398)
T ss_pred             HHHHcCCCccceEEEECCCchHHHH
Confidence            89999998863  33 344455533

>PTZ00348 tyrosyl-tRNA synthetase; Provisional

Probab=92.81  E-value=0.55  Score=46.32  Aligned_cols=85  Identities=14%  Similarity=0.096  Sum_probs=46.7

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      +++.|.++. -|||.+||||.   ++.=+-.+-+...|     +++.+..+ |-|..-    ..+.|.+.+++.. ....
T Consensus        31 ~~~rv~sGi-~PTG~lHLGng---~~~aik~~~~~q~g-----~~~~~lIA-D~HAlt----~~~~~~~l~~i~~-~~~~   95 (682)
T PTZ00348         31 PLIRCYDGF-EPSGRMHIAQG---IFKAVNVNKCTQAG-----CEFVFWVA-DWFALM----NDKVGGELEKIRI-VGRY   95 (682)
T ss_pred             CCCEEEEee-CCCCcCeeccH---HHHHHHHHHHHhCC-----CeEEEEEc-chhhhc----CCCCCCCHHHHHH-HHHH
Confidence            445566654 78899999993   22211111123468     78766542 333221    1233444554433 2345


Q ss_pred             HHHHHhccCCcCCc--cccCCC
Q psy2399          92 RKKYLDGFYIKFDN--WYSTDS  111 (232)
Q Consensus        92 ~~~~l~~lgI~~d~--~~~t~~  111 (232)
                      +.+.+.++|++++.  |+..|+
T Consensus        96 ~~~~~lA~GlDpeK~~~~~qSd  117 (682)
T PTZ00348         96 LIEVWKAAGMDMDKVLFLWSSE  117 (682)
T ss_pred             HHHHHHHcCCCccceEEEECcH
Confidence            67788999998873  555443

>PTZ00419 valyl-tRNA synthetase-like protein; Provisional

Probab=92.25  E-value=0.27  Score=50.62  Aligned_cols=41  Identities=12%  Similarity=0.108  Sum_probs=34.6

Q ss_pred             CcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcC--CCCCCC
Q psy2399         186 PYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHD--KRLQPE  229 (232)
Q Consensus       186 ~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~--~~~~p~  229 (232)
                      |.|..||.+++.+.+++||+++  +.+++++.++ +++  -.+.|+
T Consensus       387 p~~~R~~~~ie~~~~~QWFi~~--~~~~~~al~~-v~~~~i~~~P~  429 (995)
T PTZ00419        387 PRCSRSGDIVEPMLIPQWYVNC--KDMAKRAVEA-VRNGELKIIPS  429 (995)
T ss_pred             CEeCCCCCEEEEEecCeeeEec--HHHHHHHHHH-hhcCCeEEECh
Confidence            6778899999999999999999  9999999999 542  256665

>cd00805 TyrRS_core catalytic core domain of tyrosinyl-tRNA synthetase

Probab=92.21  E-value=0.16  Score=44.43  Aligned_cols=71  Identities=20%  Similarity=0.198  Sum_probs=42.7

Q ss_pred             CCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChh--hHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhc
Q psy2399          22 YANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAH--GAAIMIAAEKAGMTPKEFINNISSNRKKYLDG   98 (232)
Q Consensus        22 ~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~--G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~   98 (232)
                      -|+| .+||||..+.   -.+.++++. |     +++.++.|-.+.  |.+.-...++.+.++++ +.++...+.+++.+
T Consensus         8 ~PTg~~lHLG~~~~~---~~~~~lq~~-g-----~~~~ilI~D~~a~~~~~~~~~~~r~~~~~~~-i~~~~~~~~~~~~a   77 (269)
T cd00805           8 DPTAPSLHLGHLVPL---MKLRDFQQA-G-----HEVIVLIGDATAMIGDPSGKSEERKLLDLEL-IRENAKYYKKQLKA   77 (269)
T ss_pred             CCCCCcccHHHHHHH---HHHHHHHHC-C-----CeEEEEECCCeeecCCCCCccccccCCCHHH-HHHHHHHHHHHHHH
Confidence            6789 8999997753   356666664 8     888776654321  11211112223355554 45555667888888


Q ss_pred             cCCc
Q psy2399          99 FYIK  102 (232)
Q Consensus        99 lgI~  102 (232)
                      +|++
T Consensus        78 ~g~~   81 (269)
T cd00805          78 ILDF   81 (269)
T ss_pred             HHcc
Confidence            8875

Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.

>PRK12282 tryptophanyl-tRNA synthetase II; Reviewed

Probab=91.40  E-value=1.2  Score=40.30  Aligned_cols=67  Identities=12%  Similarity=0.110  Sum_probs=40.6

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|+|.+||||..+.+..-   +++...|     . +. ++=.|.|..-.      ...+++++.+ +......++.++|+
T Consensus        10 ~PTG~~HLGn~l~~~~~~---~~lQ~~~-----~-~~-i~IaD~ha~~~------~~~~~~~i~~-~~~~~~~~~lA~G~   72 (333)
T PRK12282         10 RPTGKLHLGHYVGSLKNR---VALQNEH-----E-QF-VLIADQQALTD------NAKNPEKIRR-NILEVALDYLAVGI   72 (333)
T ss_pred             CCCCcchHHHHHHHHHHH---HHHHhCC-----C-EE-EEEccchhHhC------CCCCHHHHHH-HHHHHHHHHHHhCc
Confidence            567999999987754332   2334456     4 53 33366664321      1345665554 44556677889999


Q ss_pred             cCCc
Q psy2399         102 KFDN  105 (232)
Q Consensus       102 ~~d~  105 (232)
                      +++.
T Consensus        73 dp~k   76 (333)
T PRK12282         73 DPAK   76 (333)
T ss_pred             ChhH
Confidence            8873

>PTZ00427 isoleucine-tRNA ligase, putative; Provisional

Probab=91.40  E-value=0.45  Score=49.90  Aligned_cols=69  Identities=14%  Similarity=0.139  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCc
Q psy2399         115 IDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTK  194 (232)
Q Consensus       115 ~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~  194 (232)
                      .+.-..+++.|. ++|++...+....                                           .-|.|..||.+
T Consensus       487 ~dA~~~Ii~~Lk-~~g~L~~~e~~~H-------------------------------------------~yP~cwR~~tp  522 (1205)
T PTZ00427        487 KEADNVIKKKLK-NENRLLSNNTIVH-------------------------------------------SYPFCWRSDTP  522 (1205)
T ss_pred             HHhHHHHHHHHH-hCCCeeeeeeeec-------------------------------------------cCCEeCCCCCE
Confidence            445567888999 9999876543211                                           23778889999


Q ss_pred             cEEEEccceeEecCChhhHHHHHhhhhcCCCCCCCC
Q psy2399         195 PIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI  230 (232)
Q Consensus       195 ~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~~  230 (232)
                      ++.+..++||+++  +.+++.+.+. .+.-.|.|+.
T Consensus       523 li~~a~~QWFI~~--~~~k~~~l~~-~~~i~w~P~~  555 (1205)
T PTZ00427        523 LIYRAIPAWFIRV--SNSTNELVKN-NETTYWIPAH  555 (1205)
T ss_pred             EEEEecceeEEeC--cHHHHHHHHc-CCccEEeCch
Confidence            9999999999999  8899988887 4444455653

>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed

Probab=91.17  E-value=0.41  Score=48.88  Aligned_cols=34  Identities=15%  Similarity=0.247  Sum_probs=30.2

Q ss_pred             CcccCCCCccEEEEccceeEecCChh--hHHHHHhhhhc
Q psy2399         186 PYSILSGTKPIIKSSKHFFFKLSDKR--CIDFLRKWAIH  222 (232)
Q Consensus       186 ~~~~~~g~~~~~~~~~~~f~~L~~~~--~~~~l~~~~~~  222 (232)
                      |.|..||.+++.+.++|||+++  ++  +++.+.+. ++
T Consensus       396 p~~wR~~~pvi~r~~~QWFi~~--~~~~~k~~~l~~-~~  431 (912)
T PRK05743        396 PHCWRTKKPVIFRATPQWFISM--DKKGLREQALKA-IE  431 (912)
T ss_pred             CeecCCCCEEEEEecCcccEeC--ChHHHHHHHHHH-Hc
Confidence            6788899999999999999999  76  99998888 44

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=90.98  E-value=0.98  Score=35.42  Aligned_cols=62  Identities=8%  Similarity=-0.064  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHhccCCc----CCccccCCChhHHHHHHHHHHHHHhhcCCEEec-------ccceeeccCCCc
Q psy2399          84 FINNISSNRKKYLDGFYIK----FDNWYSTDSIENIDLVQKIYDTLYNKAKLIINK-------KINQFFDPIKNI  147 (232)
Q Consensus        84 ~~~~~~~~~~~~l~~lgI~----~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~-------~~~~~~~~~~~~  147 (232)
                      ++....+.+.+..+.-|..    .-..+...+..+.+..+..|..+.  +|-+..+       ....|+|..|+.
T Consensus         6 i~~~i~~~v~~~A~~~g~~~V~~V~l~IG~ls~V~pe~L~fafe~l~--~gt~~ega~L~i~~~p~~~~C~~CG~   78 (135)
T PRK03824          6 LAEAIVRTVIDYAQKEGASKVKALKVVLGELQDVDKEIVEFALNELL--KGTILEGAEIIFEEEEAVLKCRNCGN   78 (135)
T ss_pred             HHHHHHHHHHHHHHHcCCchhHhHHhhHhhhhhhhHHHHHHHHHHHH--cCCcccCCEEEEEecceEEECCCCCC
Confidence            3444444444444444441    112333444467778888888765  4444333       235566555553

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=90.85  E-value=0.16  Score=52.60  Aligned_cols=37  Identities=19%  Similarity=0.363  Sum_probs=29.7

Q ss_pred             cCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEE
Q psy2399         156 GECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPII  197 (232)
Q Consensus       156 g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~  197 (232)
                      -.||.||.... ...|..||....+    .+.|+.||..+..
T Consensus       668 rkCPkCG~~t~-~~fCP~CGs~te~----vy~CPsCGaev~~  704 (1337)
T PRK14714        668 RRCPSCGTETY-ENRCPDCGTHTEP----VYVCPDCGAEVPP  704 (1337)
T ss_pred             EECCCCCCccc-cccCcccCCcCCC----ceeCccCCCccCC
Confidence            48999999874 4699999998754    3589999997653

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=90.71  E-value=0.18  Score=49.48  Aligned_cols=37  Identities=19%  Similarity=0.353  Sum_probs=26.5

Q ss_pred             eeeccCCCcccccceeccCCCCCCccccCC-CcCccCCCCCC
Q psy2399         139 QFFDPIKNIFLPDRYIKGECPICNAKDQYG-DFCECCSSIYT  179 (232)
Q Consensus       139 ~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g-~~Ce~Cg~~~~  179 (232)
                      .-||+.|++.|..    ..||.||+..+.+ .+|.+||....
T Consensus        15 akFC~~CG~~l~~----~~Cp~CG~~~~~~~~fC~~CG~~~~   52 (645)
T PRK14559         15 NRFCQKCGTSLTH----KPCPQCGTEVPVDEAHCPNCGAETG   52 (645)
T ss_pred             CccccccCCCCCC----CcCCCCCCCCCcccccccccCCccc
Confidence            3478888887753    4688888876555 66888887654

>TIGR00395 leuS_arch leucyl-tRNA synthetase, archaeal and cytosolic family

Probab=90.67  E-value=1.2  Score=45.58  Aligned_cols=43  Identities=28%  Similarity=0.473  Sum_probs=32.3

Q ss_pred             CcccCCCCccEEE-EccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         186 PYSILSGTKPIIK-SSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       186 ~~~~~~g~~~~~~-~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                      ++|..||.+++++ ..+|||++++++++++++.++ ++.-.+.|+
T Consensus       428 ~v~~R~g~~~vv~~~~~QWFi~~~~~~~k~~~~~~-l~~~~~~P~  471 (938)
T TIGR00395       428 PVICRCGTDCIVKVVEDQWFVKYSDESWKELAHEC-LEGMRIIPE  471 (938)
T ss_pred             CcEecCCCeEEEeccCCCCeEEcCcHHHHHHHHHH-HhcCEEeCH
Confidence            4455789999987 999999999333699999999 554444443

The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=90.04  E-value=0.22  Score=31.48  Aligned_cols=33  Identities=12%  Similarity=0.165  Sum_probs=21.9

Q ss_pred             CccCCCCCCCcccc-CCcccCCCCccEEEEccce
Q psy2399         171 CECCSSIYTPTKLI-NPYSILSGTKPIIKSSKHF  203 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~-~~~~~~~g~~~~~~~~~~~  203 (232)
                      |.+||..++..+.. ..+|+.||++.........
T Consensus         6 C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~~   39 (46)
T PRK00398          6 CARCGREVELDEYGTGVRCPYCGYRILFKERPPV   39 (46)
T ss_pred             CCCCCCEEEECCCCCceECCCCCCeEEEccCCCc
Confidence            67777766544433 6788889988876555543

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=89.88  E-value=0.29  Score=37.27  Aligned_cols=50  Identities=18%  Similarity=0.282  Sum_probs=36.7

Q ss_pred             CccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCC
Q psy2399         171 CECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDK  224 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~  224 (232)
                      |+-||..+..+.   ..|..||..++=+=+..||..|+ +.-.+++..|+..++
T Consensus         1 CPvCg~~l~vt~---l~C~~C~t~i~G~F~l~~~~~L~-~E~~~Fi~~Fi~~rG   50 (113)
T PF09862_consen    1 CPVCGGELVVTR---LKCPSCGTEIEGEFELPWFARLS-PEQLEFIKLFIKNRG   50 (113)
T ss_pred             CCCCCCceEEEE---EEcCCCCCEEEeeeccchhhcCC-HHHHHHHHHHHHhcC
Confidence            444555444444   47999999998888889999997 578888888855444

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=89.86  E-value=0.27  Score=48.21  Aligned_cols=50  Identities=14%  Similarity=0.173  Sum_probs=32.1

Q ss_pred             eccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccE
Q psy2399         141 FDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPI  196 (232)
Q Consensus       141 ~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~  196 (232)
                      .||.|+...++.-  ..|+.||.+-.. ..|.+||..+.+.   ...|..||.++.
T Consensus         3 ~Cp~Cg~~n~~~a--kFC~~CG~~l~~-~~Cp~CG~~~~~~---~~fC~~CG~~~~   52 (645)
T PRK14559          3 ICPQCQFENPNNN--RFCQKCGTSLTH-KPCPQCGTEVPVD---EAHCPNCGAETG   52 (645)
T ss_pred             cCCCCCCcCCCCC--ccccccCCCCCC-CcCCCCCCCCCcc---cccccccCCccc
Confidence            4677777665442  368888776432 3588888776554   346888887653

>PF12773 DZR: Double zinc ribbon

Probab=89.40  E-value=0.27  Score=31.41  Aligned_cols=37  Identities=24%  Similarity=0.466  Sum_probs=18.9

Q ss_pred             cCCCcccccceeccCCCCCCcccc----CCCcCccCCCCCCCc
Q psy2399         143 PIKNIFLPDRYIKGECPICNAKDQ----YGDFCECCSSIYTPT  181 (232)
Q Consensus       143 ~~~~~~l~~~~v~g~cp~c~~~~~----~g~~Ce~Cg~~~~~~  181 (232)
                      +.+++.+++.  .-.||.||.+-.    ...+|..||..+.+.
T Consensus         2 p~Cg~~~~~~--~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~   42 (50)
T PF12773_consen    2 PHCGTPNPDD--AKFCPHCGTPLPPPDQSKKICPNCGAENPPN   42 (50)
T ss_pred             CCcCCcCCcc--ccCChhhcCChhhccCCCCCCcCCcCCCcCC
Confidence            3444444433  335666666544    123577777765443

>PF00133 tRNA-synt_1: tRNA synthetases class I (I, L, M and V); InterPro: IPR002300 The aminoacyl-tRNA synthetases (6

Probab=89.29  E-value=1.2  Score=43.45  Aligned_cols=69  Identities=19%  Similarity=0.221  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCC
Q psy2399         114 NIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGT  193 (232)
Q Consensus       114 ~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~  193 (232)
                      ..+.-..+++.|. ++|++.......                                           -.-|.|..||.
T Consensus       333 v~~ar~~ii~~L~-~~g~l~~~~~~~-------------------------------------------~~~p~c~R~~~  368 (601)
T PF00133_consen  333 VFEAREKIIEDLK-EKGLLLKIEEIE-------------------------------------------HSYPHCWRSGT  368 (601)
T ss_dssp             HHHHHHHHHHHHH-HTTSEEEEEEEE-------------------------------------------EEEEEETTTSC
T ss_pred             eeeccHHHHHHHH-Hhhhhccccccc-------------------------------------------cccceecCCCC
Confidence            3566778899999 999986533211                                           01256778999


Q ss_pred             ccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         194 KPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       194 ~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                      +++.+..+|||+++  +.+++.+.+. ++.-.+.|+
T Consensus       369 ~ii~~~~~QWFi~~--~~~k~~~l~~-~~~i~~~P~  401 (601)
T PF00133_consen  369 PIIPRLTDQWFIKY--DDWKKKALEA-LEKIKFYPE  401 (601)
T ss_dssp             BEEEEEEEEEEEEH--HHHHHHHHHH-HHTSEESSS
T ss_pred             EEEecccceeEEec--HHhHHHHHhh-cccceEEcc
Confidence            99999999999999  9999999999 554444454

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. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1OBC_A 2AJH_B 4ARI_A 2AJG_B 4AQ7_D 2AJI_B 4ARC_A 4AS1_A 1QU3_A 1QU2_A ....

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=88.45  E-value=0.4  Score=26.73  Aligned_cols=21  Identities=33%  Similarity=0.790  Sum_probs=10.9

Q ss_pred             CCCCCCccccCC-CcCccCCCC
Q psy2399         157 ECPICNAKDQYG-DFCECCSSI  177 (232)
Q Consensus       157 ~cp~c~~~~~~g-~~Ce~Cg~~  177 (232)
                      .||.|++.-... ..|+.||..
T Consensus         2 ~CP~C~~~V~~~~~~Cp~CG~~   23 (26)
T PF10571_consen    2 TCPECGAEVPESAKFCPHCGYD   23 (26)
T ss_pred             cCCCCcCCchhhcCcCCCCCCC
Confidence            467666654332 335555543

Several members are annotated as putative helicases.

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.45  E-value=0.24  Score=30.85  Aligned_cols=25  Identities=28%  Similarity=0.902  Sum_probs=13.0

Q ss_pred             CCCCCCccc-----cCCC-cCccCCCCCCCc
Q psy2399         157 ECPICNAKD-----QYGD-FCECCSSIYTPT  181 (232)
Q Consensus       157 ~cp~c~~~~-----~~g~-~Ce~Cg~~~~~~  181 (232)
                      .||.|++..     ..|. .|..||.++...
T Consensus         2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~   32 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPERGELVCPNCGLVLEEN   32 (43)
T ss_dssp             SBTTTSSSEEEEETTTTEEEETTT-BBEE-T
T ss_pred             CCcCCcCCceEEcCCCCeEECCCCCCEeecc
Confidence            578887753     1232 466666655443

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>TIGR00234 tyrS tyrosyl-tRNA synthetase

Probab=88.41  E-value=1.2  Score=40.99  Aligned_cols=40  Identities=20%  Similarity=0.317  Sum_probs=26.3

Q ss_pred             cEEEEcCCCCCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecC
Q psy2399          13 RIFVTTALPYANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICA   62 (232)
Q Consensus        13 ~~~v~~~~P~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g   62 (232)
                      ++.+.++. -|+| .|||||+.+   .-.+.+++ ..|     +++.++.|
T Consensus        30 ~~~vy~G~-dPTg~~lHlGh~v~---l~~l~~lq-~~G-----~~~~ilig   70 (377)
T TIGR00234        30 KIKLYVGF-DPTAPSLHLGHLVP---LLKLRDFQ-QAG-----HEVIVLLG   70 (377)
T ss_pred             CCEEEEee-CCCCCCccHHHHHH---HHHHHHHH-HCC-----CcEEEEEe
Confidence            44555544 7889 899999764   33345554 478     88877654

This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.

>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=87.87  E-value=0.49  Score=31.35  Aligned_cols=27  Identities=22%  Similarity=0.635  Sum_probs=20.3

Q ss_pred             cCCCCCCccccCCCcCccCCCCCCCccc
Q psy2399         156 GECPICNAKDQYGDFCECCSSIYTPTKL  183 (232)
Q Consensus       156 g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l  183 (232)
                      ..||.||+....--.|.+|| +|...++
T Consensus        27 ~~c~~cg~~~~~H~vc~~cG-~y~~r~v   53 (56)
T PF01783_consen   27 VKCPNCGEPKLPHRVCPSCG-YYKGRQV   53 (56)
T ss_dssp             EESSSSSSEESTTSBCTTTB-BSSSSSS
T ss_pred             eeeccCCCEecccEeeCCCC-eECCEEE
Confidence            46999999888888899998 4444443

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=87.40  E-value=0.19  Score=30.31  Aligned_cols=29  Identities=17%  Similarity=0.346  Sum_probs=19.9

Q ss_pred             cCccCCCCCCCc---cccCCcccCCCCccEEE
Q psy2399         170 FCECCSSIYTPT---KLINPYSILSGTKPIIK  198 (232)
Q Consensus       170 ~Ce~Cg~~~~~~---~l~~~~~~~~g~~~~~~  198 (232)
                      .|+.||++|...   -..+.+|..||.++..|
T Consensus         3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~qR   34 (36)
T PF05191_consen    3 ICPKCGRIYHIEFNPPKVEGVCDNCGGELVQR   34 (36)
T ss_dssp             EETTTTEEEETTTB--SSTTBCTTTTEBEBEE
T ss_pred             CcCCCCCccccccCCCCCCCccCCCCCeeEeC
Confidence            377888776432   34678999999876655

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=87.18  E-value=0.59  Score=29.46  Aligned_cols=33  Identities=12%  Similarity=0.081  Sum_probs=25.6

Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEEccc
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKSSKH  202 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~  202 (232)
                      .|.+||..++....-.-+|+.||+.+..++.+.
T Consensus         4 ~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~R~~   36 (44)
T smart00659        4 ICGECGRENEIKSKDVVRCRECGYRILYKKRTK   36 (44)
T ss_pred             ECCCCCCEeecCCCCceECCCCCceEEEEeCCC
Confidence            488888877766555679999999998776655

present in RNA polymerase I, II and III

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=87.01  E-value=0.34  Score=32.46  Aligned_cols=48  Identities=15%  Similarity=0.119  Sum_probs=33.7

Q ss_pred             eeeccCCCccc--ccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCC
Q psy2399         139 QFFDPIKNIFL--PDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGT  193 (232)
Q Consensus       139 ~~~~~~~~~~l--~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~  193 (232)
                      ...|.+++..|  -+..|+..||.||...  -.-|..|-+.-.     .++|+-||.
T Consensus         9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~--I~Rc~~CRk~g~-----~Y~Cp~CGF   58 (61)
T COG2888           9 PPVCTSCGREIAPGETAVKFPCPNCGEVE--IYRCAKCRKLGN-----PYRCPKCGF   58 (61)
T ss_pred             CceeccCCCEeccCCceeEeeCCCCCcee--eehhhhHHHcCC-----ceECCCcCc
Confidence            45788899887  4578999999999543  234777766543     367777774

>COG0060 IleS Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=86.87  E-value=1.3  Score=45.27  Aligned_cols=41  Identities=20%  Similarity=0.260  Sum_probs=33.1

Q ss_pred             CCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCC
Q psy2399         185 NPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQP  228 (232)
Q Consensus       185 ~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p  228 (232)
                      -|.|..|+.|+..|.+++||..+  +.+++++.+- ++.-.+.|
T Consensus       400 YPhcWR~ktPlIyRAt~QWFi~v--~~~r~~~l~~-i~~v~w~P  440 (933)
T COG0060         400 YPHCWRTKTPLIYRATPQWFVSV--DKLRDKMLKE-INKVNWVP  440 (933)
T ss_pred             CCcccCCCCeeEEeecchheeEH--HHHHHHHHHH-HhcceEEC
Confidence            37789999999999999999999  9999999955 33333444

>KOG2713|consensus

Probab=86.86  E-value=4.8  Score=35.70  Aligned_cols=88  Identities=17%  Similarity=0.206  Sum_probs=52.2

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      .|.+++ -|+|.+|||+..+.+-..+--.-....|     -.|.|. -.|.|-..       ..-+|.++... .-....
T Consensus        15 rvfSGI-QPTG~~HLGNYLGai~~Wv~LQ~~~d~~-----~~~~f~-vvDlHaIT-------vp~dp~~lrq~-~~dm~A   79 (347)
T KOG2713|consen   15 RVFSGI-QPTGIPHLGNYLGAIKPWVQLQNEYDKN-----ILVLFS-VVDLHAIT-------VPQDPAELRQA-THDMAA   79 (347)
T ss_pred             eeEecc-CCCCCchhhhhhhhhhHHHHHHHHhcCC-----ceEEEE-Eeeceeec-------CCCChHHHHHH-HHHHHH
Confidence            344444 6789999999999877666554444555     444443 34555432       45566654444 444456


Q ss_pred             HHhccCCcCCc---cccCCChhHHHH
Q psy2399          95 YLDGFYIKFDN---WYSTDSIENIDL  117 (232)
Q Consensus        95 ~l~~lgI~~d~---~~~t~~~~~~~~  117 (232)
                      .|-+.||++..   |....-++|.+.
T Consensus        80 ~lLAcGIdp~Ks~lF~QS~Vpqh~el  105 (347)
T KOG2713|consen   80 SLLACGIDPEKSSLFVQSDVPQHAEL  105 (347)
T ss_pred             HHHHhccCcccceeeeeccchHHHHH
Confidence            67789998764   444444555443

>PRK05978 hypothetical protein; Provisional

Probab=86.11  E-value=0.49  Score=37.75  Aligned_cols=14  Identities=29%  Similarity=0.826  Sum_probs=10.4

Q ss_pred             eeccCCCCCCcccc
Q psy2399         153 YIKGECPICNAKDQ  166 (232)
Q Consensus       153 ~v~g~cp~c~~~~~  166 (232)
                      -..|+||.|++..-
T Consensus        31 Gl~grCP~CG~G~L   44 (148)
T PRK05978         31 GFRGRCPACGEGKL   44 (148)
T ss_pred             HHcCcCCCCCCCcc
Confidence            34679999988654

>PLN02843 isoleucyl-tRNA synthetase

Probab=85.91  E-value=1.5  Score=45.18  Aligned_cols=42  Identities=14%  Similarity=0.267  Sum_probs=34.7

Q ss_pred             CCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         185 NPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       185 ~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                      -|.|..|+.+++.|..++||+++  +.+++.+.+. ++.-.+.|+
T Consensus       412 yp~cwR~~~pvi~r~t~QWFi~~--~~~k~~al~~-~~~v~~~P~  453 (974)
T PLN02843        412 YPYDWRTKKPTIFRATEQWFASV--EGFRQAALDA-IDKVKWIPA  453 (974)
T ss_pred             CCccCCCCCeEEEEecCceeEeC--HHHHHHHHHH-HhccEEECh
Confidence            37888999999999999999999  9999999998 554444444

>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=85.73  E-value=1.2  Score=41.32  Aligned_cols=33  Identities=18%  Similarity=0.227  Sum_probs=23.2

Q ss_pred             CCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCC
Q psy2399          22 YANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICAD   63 (232)
Q Consensus        22 ~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~   63 (232)
                      =|+| .|||||+-..   -.++| +...|     ++|.++.|-
T Consensus        40 DPTa~slHlGhlv~l---~kL~~-fQ~aG-----h~~ivLigd   73 (401)
T COG0162          40 DPTAPSLHLGHLVPL---MKLRR-FQDAG-----HKPIVLIGD   73 (401)
T ss_pred             CCCCCccchhhHHHH---HHHHH-HHHCC-----CeEEEEecc
Confidence            5778 8999998753   33444 46678     898877654

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=85.26  E-value=0.65  Score=27.23  Aligned_cols=25  Identities=20%  Similarity=0.401  Sum_probs=18.8

Q ss_pred             cCccCCCCCCCccccCCcccCCCCcc
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKP  195 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~  195 (232)
                      +|..||-++++.+ .+.+|+.||.+-
T Consensus         3 ~C~~CGy~y~~~~-~~~~CP~Cg~~~   27 (33)
T cd00350           3 VCPVCGYIYDGEE-APWVCPVCGAPK   27 (33)
T ss_pred             ECCCCCCEECCCc-CCCcCcCCCCcH
Confidence            4888888887654 567999998753

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=84.49  E-value=0.85  Score=37.49  Aligned_cols=47  Identities=17%  Similarity=0.134  Sum_probs=26.3

Q ss_pred             CccCCCCCCCcccc--CCcccCCCCccEEEEccceeEecCChhhHHHHHhh
Q psy2399         171 CECCSSIYTPTKLI--NPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKW  219 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~--~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~  219 (232)
                      |++|+.-++..+..  +-.|+.||+.++........=.|  .+-.+.|.+.
T Consensus       120 Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~dn~~~~~~l--~~~I~~l~~~  168 (178)
T PRK06266        120 CPNCHIRFTFDEAMEYGFRCPQCGEMLEEYDNSELIKEL--KEQIKELEEE  168 (178)
T ss_pred             CCCCCcEEeHHHHhhcCCcCCCCCCCCeecccHHHHHHH--HHHHHHHHHH
Confidence            66666666544442  46888888888764444433334  3344444444

>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional

Probab=84.40  E-value=1.7  Score=44.77  Aligned_cols=41  Identities=20%  Similarity=0.279  Sum_probs=32.3

Q ss_pred             CCcccCCCCccEEEEccceeEecCChh-------hHHHHHhhhhcCCCCCC
Q psy2399         185 NPYSILSGTKPIIKSSKHFFFKLSDKR-------CIDFLRKWAIHDKRLQP  228 (232)
Q Consensus       185 ~~~~~~~g~~~~~~~~~~~f~~L~~~~-------~~~~l~~~~~~~~~~~p  228 (232)
                      -|.|..||.+++.+..+|||+++  +.       +++.+.+. ++.-.+.|
T Consensus       426 yp~~wR~~~pii~r~t~QWFi~~--~~~~~~~~~~k~~al~~-i~~v~~~P  473 (961)
T PRK13804        426 YPHSWRSKKPVIFRNTPQWFISM--DKDLGDGTTLRSRALDA-IDKTRFVP  473 (961)
T ss_pred             CCccCCCCCeEEEeccccccEEc--CCcccchHHHHHHHHHH-HhccEEEC
Confidence            36788899999999999999999  66       88888887 44333444

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=84.37  E-value=0.73  Score=25.23  Aligned_cols=20  Identities=15%  Similarity=0.218  Sum_probs=7.7

Q ss_pred             cCCCCCCCcc-ccCCcccCCC
Q psy2399         173 CCSSIYTPTK-LINPYSILSG  192 (232)
Q Consensus       173 ~Cg~~~~~~~-l~~~~~~~~g  192 (232)
                      .||..+.+.+ -....|+-||
T Consensus         3 sC~~~i~~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    3 SCGRPIAPREQAVPFPCPNCG   23 (24)
T ss_pred             cCCCcccCcccCceEeCCCCC
Confidence            3444444333 2333444443

It is likely to bind zinc via its four well-conserved cysteine residues.

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=83.99  E-value=0.61  Score=41.60  Aligned_cols=33  Identities=21%  Similarity=0.443  Sum_probs=21.7

Q ss_pred             ccceeccCCCCCCccc-----cCC-CcCccCCCCCCCcc
Q psy2399         150 PDRYIKGECPICNAKD-----QYG-DFCECCSSIYTPTK  182 (232)
Q Consensus       150 ~~~~v~g~cp~c~~~~-----~~g-~~Ce~Cg~~~~~~~  182 (232)
                      .+..-...||.|+...     ..| -.|.+||.++...-
T Consensus         6 ~~~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~~   44 (310)
T PRK00423          6 LEEEEKLVCPECGSDKLIYDYERGEIVCADCGLVIEENI   44 (310)
T ss_pred             hhcccCCcCcCCCCCCeeEECCCCeEeecccCCcccccc
Confidence            4445556799998722     234 45999999887543

>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.68  E-value=0.51  Score=36.23  Aligned_cols=28  Identities=32%  Similarity=0.784  Sum_probs=18.0

Q ss_pred             ceeccCCCCCCccccC------CCcCccCCCCCC
Q psy2399         152 RYIKGECPICNAKDQY------GDFCECCSSIYT  179 (232)
Q Consensus       152 ~~v~g~cp~c~~~~~~------g~~Ce~Cg~~~~  179 (232)
                      +-..|+||.||+..-+      .+-|+.||.-+.
T Consensus        18 ~Gl~grCP~CGeGrLF~gFLK~~p~C~aCG~dyg   51 (126)
T COG5349          18 RGLRGRCPRCGEGRLFRGFLKVVPACEACGLDYG   51 (126)
T ss_pred             HHhcCCCCCCCCchhhhhhcccCchhhhcccccc
Confidence            3467899999875422      245777776554

>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus

Probab=83.21  E-value=0.36  Score=48.16  Aligned_cols=51  Identities=14%  Similarity=0.141  Sum_probs=0.0

Q ss_pred             ceeeccCCCcccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEE
Q psy2399         138 NQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPII  197 (232)
Q Consensus       138 ~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~  197 (232)
                      ....|++|+..-    ..-+||.||....--..|..||....+     ..|+.||..+.-
T Consensus       654 ~~r~Cp~Cg~~t----~~~~Cp~CG~~T~~~~~Cp~C~~~~~~-----~~C~~C~~~~~~  704 (900)
T PF03833_consen  654 GRRRCPKCGKET----FYNRCPECGSHTEPVYVCPDCGIEVEE-----DECPKCGRETTS  704 (900)
T ss_dssp             ------------------------------------------------------------
T ss_pred             ecccCcccCCcc----hhhcCcccCCccccceeccccccccCc-----cccccccccCcc
Confidence            334556665542    233566666665555556666664433     377777766543

The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=82.90  E-value=7.7  Score=29.42  Aligned_cols=79  Identities=8%  Similarity=0.073  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHhccCCc-CC---ccccCCChhHHHHHHHHHHHHHhhcCC------EEecccceeeccCCCcccccce
Q psy2399          84 FINNISSNRKKYLDGFYIK-FD---NWYSTDSIENIDLVQKIYDTLYNKAKL------IINKKINQFFDPIKNIFLPDRY  153 (232)
Q Consensus        84 ~~~~~~~~~~~~l~~lgI~-~d---~~~~t~~~~~~~~v~~~~~~L~~~kG~------iy~~~~~~~~~~~~~~~l~~~~  153 (232)
                      ++..+.+...+..++-|.. ..   .-+...+---.+..+..|..+. +...      .........+|..|+...+...
T Consensus         6 i~~~iv~~v~~~a~~~~~~~V~~V~l~iG~ls~V~p~~L~f~f~~~~-~~t~~egA~L~i~~~p~~~~C~~Cg~~~~~~~   84 (114)
T PRK03681          6 LCQRALELIEQQAAKHGAKRVTGVWLKIGAFSCVETSSLAFCFDLVC-RGTVAEGCKLHLEEQEAECWCETCQQYVTLLT   84 (114)
T ss_pred             HHHHHHHHHHHHHHHcCCCeEEEEEEEEcCccccCHHHHHHHHHHHh-CCCccCCCEEEEEeeCcEEEcccCCCeeecCC
Confidence            4455555555555555542 11   2223333234455666666655 3222      2233345566666665443322


Q ss_pred             ec-cCCCCCCc
Q psy2399         154 IK-GECPICNA  163 (232)
Q Consensus       154 v~-g~cp~c~~  163 (232)
                      .. ..||.||+
T Consensus        85 ~~~~~CP~Cgs   95 (114)
T PRK03681         85 QRVRRCPQCHG   95 (114)
T ss_pred             ccCCcCcCcCC
Confidence            21 33555544

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=82.55  E-value=0.88  Score=29.36  Aligned_cols=34  Identities=12%  Similarity=0.185  Sum_probs=25.2

Q ss_pred             CcCccCCCCCC-CccccCCcccCCCCccEEEEccc
Q psy2399         169 DFCECCSSIYT-PTKLINPYSILSGTKPIIKSSKH  202 (232)
Q Consensus       169 ~~Ce~Cg~~~~-~~~l~~~~~~~~g~~~~~~~~~~  202 (232)
                      ..|-.||+.++ ......-+|+.||+.+.+++...
T Consensus         7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R~~   41 (49)
T COG1996           7 YKCARCGREVELDQETRGIRCPYCGSRILVKERPK   41 (49)
T ss_pred             EEhhhcCCeeehhhccCceeCCCCCcEEEEeccCC
Confidence            34889998886 33555679999999888766554

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=81.61  E-value=9  Score=29.05  Aligned_cols=43  Identities=9%  Similarity=-0.035  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHhccCCc----CCccccCCChhHHHHHHHHHHHHH
Q psy2399          84 FINNISSNRKKYLDGFYIK----FDNWYSTDSIENIDLVQKIYDTLY  126 (232)
Q Consensus        84 ~~~~~~~~~~~~l~~lgI~----~d~~~~t~~~~~~~~v~~~~~~L~  126 (232)
                      ++....+...+..+.-|..    ...-+...+---.+..+..|..+.
T Consensus         6 ia~~iv~~v~~~a~~~~~~~V~~V~l~iG~ls~V~p~~L~faf~~~~   52 (115)
T TIGR00100         6 LAEAMLEIVEEQAEKHQAKKVTRVTLEIGELSCVNPSQLQFAFEVVR   52 (115)
T ss_pred             HHHHHHHHHHHHHHHhCCCeEEEEEEEEccccccCHHHHHHHHHHHh
Confidence            3444555555555555542    112223333334556666776665

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=81.35  E-value=0.92  Score=29.92  Aligned_cols=20  Identities=10%  Similarity=-0.011  Sum_probs=16.2

Q ss_pred             cccCCCCccEEEEccceeEe
Q psy2399         187 YSILSGTKPIIKSSKHFFFK  206 (232)
Q Consensus       187 ~~~~~g~~~~~~~~~~~f~~  206 (232)
                      .|..||...++++....-|+
T Consensus        24 ~Cp~CGaeleVv~~~p~~L~   43 (54)
T TIGR01206        24 ICDECGAELEVVSLDPLRLE   43 (54)
T ss_pred             eCCCCCCEEEEEeCCCCEEE
Confidence            79999999999988884333

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=80.98  E-value=1.5  Score=25.72  Aligned_cols=30  Identities=13%  Similarity=0.092  Sum_probs=18.1

Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEE
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKS  199 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~  199 (232)
                      .|-+||...+-...-.-+|..||+.+..++
T Consensus         2 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   31 (32)
T PF03604_consen    2 ICGECGAEVELKPGDPIRCPECGHRILYKK   31 (32)
T ss_dssp             BESSSSSSE-BSTSSTSSBSSSS-SEEBE-
T ss_pred             CCCcCCCeeEcCCCCcEECCcCCCeEEEec
Confidence            367777776644444458999998876543

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PRK12496 hypothetical protein; Provisional

Probab=80.66  E-value=0.93  Score=36.75  Aligned_cols=29  Identities=17%  Similarity=0.309  Sum_probs=17.2

Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEE
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKS  199 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~  199 (232)
                      .|.+||+.+.... ....|+.||+++..+.
T Consensus       129 ~C~gC~~~~~~~~-~~~~C~~CG~~~~r~~  157 (164)
T PRK12496        129 VCKGCKKKYPEDY-PDDVCEICGSPVKRKM  157 (164)
T ss_pred             ECCCCCccccCCC-CCCcCCCCCChhhhcc
Confidence            3777777664321 2236888887775443

>PRK12300 leuS leucyl-tRNA synthetase; Reviewed

Probab=80.57  E-value=4  Score=41.74  Aligned_cols=36  Identities=22%  Similarity=0.384  Sum_probs=27.5

Q ss_pred             CcccCCCCccEEEE-ccceeEecCChhhHHHHHhhhhc
Q psy2399         186 PYSILSGTKPIIKS-SKHFFFKLSDKRCIDFLRKWAIH  222 (232)
Q Consensus       186 ~~~~~~g~~~~~~~-~~~~f~~L~~~~~~~~l~~~~~~  222 (232)
                      |.|..||.+++.+. .+|||++++++++++.+.++ ++
T Consensus       381 ~~~~R~~~~~i~~~~~~QWFi~~~~~~~k~~~~~~-~~  417 (897)
T PRK12300        381 PVYCRCGTECVVKVVKDQWFIDYSDPEWKELAHKA-LD  417 (897)
T ss_pred             CcCcCCCCEEEEEecCCceEEEcCcHHHHHHHHHH-Hc
Confidence            44557999999876 49999999433788888888 44

>PRK00420 hypothetical protein; Validated

Probab=80.43  E-value=1  Score=34.21  Aligned_cols=24  Identities=21%  Similarity=0.545  Sum_probs=12.5

Q ss_pred             cCCCCCCccccC----CCcCccCCCCCC
Q psy2399         156 GECPICNAKDQY----GDFCECCSSIYT  179 (232)
Q Consensus       156 g~cp~c~~~~~~----g~~Ce~Cg~~~~  179 (232)
                      .+||.||.+-..    -.+|+.||..+.
T Consensus        24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         24 KHCPVCGLPLFELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             CCCCCCCCcceecCCCceECCCCCCeee
Confidence            456666654321    134666666544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	232
1f4l_A	551	Crystal Structure Of The E.Coli Methionyl-Trna Synt		1e-53
1qqt_A	551	Methionyl-Trna Synthetase From Escherichia Coli Len		1e-53
1p7p_A	551	Methionyl-trna Synthetase From Escherichia Coli Com		2e-53
3h9c_A	547	Structure Of Methionyl-Trna Synthetase: Crystal For		2e-53
3h97_A	560	Structure Of A Mutant Methionyl-trna Synthetase Wit		9e-53
1rqg_A	722	Methionyl-Trna Synthetase From Pyrococcus Abyssi Le		9e-28
4dlp_A	536	Crystal Structure Of Methionyl-Trna Synthetase Metr		4e-10
1woy_A	500	Crystal Structure Of Methionyl Trna Synthetase Y225		4e-10
1a8h_A	500	Methionyl-Trna Synthetase From Thermus Thermophilus		5e-10
2d54_A	502	Crystal Structure Of Methionyl Trna Synthetase Y225		5e-10
2csx_A	497	Crystal Structure Of Aquifex Aeolicus Methionyl-Trn		2e-09
3kfl_A	564	Leishmania Major Methionyl-Trna Synthetase In Compl		1e-07
2x1l_A	524	Crystal Structure Of Mycobacterium Smegmatis Methio		5e-07
3tun_A	542	Trypanosoma Brucei Methionyl-Trna Synthetase In Com		2e-05
4eg5_A	542	Trypanosoma Brucei Methionyl-Trna Synthetase In Com		3e-05
4eg1_A	542	Trypanosoma Brucei Methionyl-Trna Synthetase In Com		3e-05
2v0c_A	878	Leucyl-Trna Synthetase From Thermus Thermophilus Co		9e-05
1obh_A	878	Leucyl-Trna Synthetase From Thermus Thermophilus Co		9e-05
1mea_A	28	Methionyl-Trna Synthetase Zinc Binding Domain. 3d S		2e-04
1wkb_A	810	Crystal Structure Of Leucyl-Trna Synthetase From Th		4e-04
1wz2_A	967	The Crystal Structure Of Leucyl-Trna Synthetase And		4e-04
4aq7_A	880	Ternary Complex Of E. Coli Leucyl-Trna Synthetase,		5e-04

>pdb|1F4L|A Chain A, Crystal Structure Of The E.Coli Methionyl-Trna Synthetase Complexed With Methionine Length = 551

Iteration: 1
 Score =  205 bits (522), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 93/197 (47%), Positives = 130/197 (65%), Gaps = 6/197 (3%)
Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            ++I VT ALPYANG +H+GH++E+IQAD+WVR+Q M     +  +V FICADDAHG  I
Sbjct: 5   AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRM-----RGHEVNFICADDAHGTPI 59
Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXX 130
           M+ A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + IY  L     
Sbjct: 60  MLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRL-KENG 118
Query: 131 XXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
                   Q +DP K +FLPDR++KG CP C + DQYGD CE C + Y+PT+LI P S++
Sbjct: 119 FIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKSVV 178
Query: 191 SGTKPIIKSSKHFFFKL 207
           SG  P+++ S+HFFF L
Sbjct: 179 SGATPVMRDSEHFFFDL 195

>pdb|1QQT|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli Length = 551

Iteration: 1
 Score =  205 bits (522), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 93/197 (47%), Positives = 130/197 (65%), Gaps = 6/197 (3%)
Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            ++I VT ALPYANG +H+GH++E+IQAD+WVR+Q M     +  +V FICADDAHG  I
Sbjct: 4   AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRM-----RGHEVNFICADDAHGTPI 58
Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXX 130
           M+ A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + IY  L     
Sbjct: 59  MLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRL-KENG 117
Query: 131 XXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
                   Q +DP K +FLPDR++KG CP C + DQYGD CE C + Y+PT+LI P S++
Sbjct: 118 FIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKSVV 177
Query: 191 SGTKPIIKSSKHFFFKL 207
           SG  P+++ S+HFFF L
Sbjct: 178 SGATPVMRDSEHFFFDL 194

>pdb|1P7P|A Chain A, Methionyl-trna Synthetase From Escherichia Coli Complexed With Methionine Phosphonate Length = 551

Iteration: 1
 Score =  205 bits (522), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 93/197 (47%), Positives = 130/197 (65%), Gaps = 6/197 (3%)
Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            ++I VT ALPYANG +H+GH++E+IQAD+WVR+Q M     +  +V FICADDAHG  I
Sbjct: 4   AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRM-----RGHEVNFICADDAHGTPI 58
Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXX 130
           M+ A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + IY  L     
Sbjct: 59  MLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRL-KENG 117
Query: 131 XXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
                   Q +DP K +FLPDR++KG CP C + DQYGD CE C + Y+PT+LI P S++
Sbjct: 118 FIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKSVV 177
Query: 191 SGTKPIIKSSKHFFFKL 207
           SG  P+++ S+HFFF L
Sbjct: 178 SGATPVMRDSEHFFFDL 194

>pdb|3H9C|A Chain A, Structure Of Methionyl-Trna Synthetase: Crystal Form 2 Length = 547

Iteration: 1
 Score =  205 bits (521), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 93/197 (47%), Positives = 130/197 (65%), Gaps = 6/197 (3%)
Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            ++I VT ALPYANG +H+GH++E+IQAD+WVR+Q M     +  +V FICADDAHG  I
Sbjct: 4   AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRM-----RGHEVNFICADDAHGTPI 58
Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXX 130
           M+ A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + IY  L     
Sbjct: 59  MLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRL-KENG 117
Query: 131 XXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
                   Q +DP K +FLPDR++KG CP C + DQYGD CE C + Y+PT+LI P S++
Sbjct: 118 FIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKSVV 177
Query: 191 SGTKPIIKSSKHFFFKL 207
           SG  P+++ S+HFFF L
Sbjct: 178 SGATPVMRDSEHFFFDL 194

>pdb|3H97|A Chain A, Structure Of A Mutant Methionyl-trna Synthetase With Modified Specificity Length = 560

Iteration: 1
 Score =  202 bits (515), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 92/197 (46%), Positives = 129/197 (65%), Gaps = 6/197 (3%)
Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            ++I VT A PYANG +H+GH++E+IQAD+WVR+Q M     +  +V FICADDAHG  I
Sbjct: 17  AKKILVTCASPYANGSIHLGHMLEHIQADVWVRYQRM-----RGHEVNFICADDAHGTPI 71
Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXX 130
           M+ A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + IY  L     
Sbjct: 72  MLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRL-KENG 130
Query: 131 XXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
                   Q +DP K +FLPDR++KG CP C + DQYGD CE C + Y+PT+LI P S++
Sbjct: 131 FIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKSVV 190
Query: 191 SGTKPIIKSSKHFFFKL 207
           SG  P+++ S+HFFF L
Sbjct: 191 SGATPVMRDSEHFFFDL 207

>pdb|1RQG|A Chain A, Methionyl-Trna Synthetase From Pyrococcus Abyssi Length = 722

Iteration: 1
 Score =  120 bits (300), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 74/219 (33%), Positives = 107/219 (48%), Gaps = 10/219 (4%)
Query: 13  RIFVTTALPYANGELHIGHIM-EYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R  VT+ALPYANG +H GH+   Y+ ADI+VR+  +     K   V FIC  D HG  I 
Sbjct: 3   RYMVTSALPYANGPIHAGHLAGAYLPADIFVRYLRL-----KGEDVVFICGTDEHGTPIS 57
Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXX 131
             A K G +P+E ++      K       I FD +  T+   +  L Q+ +   Y     
Sbjct: 58  FRALKEGRSPREIVDEFHEQIKITFQRAKISFDFFGRTELPIHYKLSQEFFLKAYENGHL 117
Query: 132 XXXXXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
                   + +  K +FLPDR++ G CP C A+DQ GD CE C    TP  LINP   + 
Sbjct: 118 VKKVTKQAYCEHDK-MFLPDRFVIGTCPYCGAEDQKGDQCEVCGRPLTPEILINPRCAIC 176
Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           G     + S H++ K+ D    + L++W I  +  +P +
Sbjct: 177 GRPISFRDSAHYYIKMQD--FAERLKRW-IEKQPWKPNV 212

>pdb|4DLP|A Chain A, Crystal Structure Of Methionyl-Trna Synthetase Metrs From Brucella Melitensis Bound To Selenomethionine Length = 536

Iteration: 1
 Score = 61.2 bits (147), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 56/111 (50%), Gaps = 5/111 (4%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           ++TTA+ Y NG+ HIGH  E I  D   RFQ +   NG    VYF+   D HG  ++ +A
Sbjct: 28  YITTAIAYPNGKPHIGHAYELIATDAMARFQRL---NGMD--VYFLTGTDEHGIKMLQSA 82
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTL 125
            K G+TP++  +  +S  ++  +      D++  T    +    Q I+  +
Sbjct: 83  RKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAM 133

>pdb|1WOY|A Chain A, Crystal Structure Of Methionyl Trna Synthetase Y225f Mutant From Thermus Thermophilus Length = 500

Iteration: 1
 Score = 61.2 bits (147), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 43/197 (21%), Positives = 75/197 (38%), Gaps = 35/197 (17%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           +VTT + Y N E H+GH    + AD   R+  +        + +F+   D HG  +  AA
Sbjct: 6   YVTTPIYYVNAEPHLGHAYTTVVADFLARWHRLD-----GYRTFFLTGTDEHGETVYRAA 60
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXXXXX 134
           + AG  PK F++ +S   K+  D   I +D++  T    +  +VQ +   +Y        
Sbjct: 61  QAAGEDPKAFVDRVSGRFKRAWDLLGIAYDDFIRTTEERHKKVVQLVLKKVY-------- 112
Query: 135 XXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTK 194
                                 E       +  G +C  C   YT  +L+     + G  
Sbjct: 113 ----------------------EAGDIYYGEYEGLYCVSCERFYTEKELVEGLCPIHGRP 150
Query: 195 PIIKSSKHFFFKLSDKR 211
              +   ++FF++   R
Sbjct: 151 VERRKEGNYFFRMEKYR 167

>pdb|1A8H|A Chain A, Methionyl-Trna Synthetase From Thermus Thermophilus Length = 500

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 43/197 (21%), Positives = 75/197 (38%), Gaps = 35/197 (17%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           +VTT + Y N E H+GH    + AD   R+  +        + +F+   D HG  +  AA
Sbjct: 6   YVTTPIYYVNAEPHLGHAYTTVVADFLARWHRLD-----GYRTFFLTGTDEHGETVYRAA 60
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXXXXX 134
           + AG  PK F++ +S   K+  D   I +D++  T    +  +VQ +   +Y        
Sbjct: 61  QAAGEDPKAFVDRVSGRFKRAWDLLGIAYDDFIRTTEERHKKVVQLVLKKVY-------- 112
Query: 135 XXXXQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTK 194
                                 E       +  G +C  C   YT  +L+     + G  
Sbjct: 113 ----------------------EAGDIYYGEYEGLYCVSCERFYTEKELVEGLCPIHGRP 150
Query: 195 PIIKSSKHFFFKLSDKR 211
              +   ++FF++   R
Sbjct: 151 VERRKEGNYFFRMEKYR 167

>pdb|2D54|A Chain A, Crystal Structure Of Methionyl Trna Synthetase Y225a Mutant From Thermus Thermophilus Length = 502

Iteration: 1
 Score = 60.8 bits (146), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 36/146 (24%), Positives = 63/146 (43%), Gaps = 5/146 (3%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           +VTT + Y N E H+GH    + AD   R+  +        + +F+   D HG  +  AA
Sbjct: 6   YVTTPIYYVNAEPHLGHAYTTVVADFLARWHRLD-----GYRTFFLTGTDEHGETVYRAA 60
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYXXXXXXXX 134
           + AG  PK F++ +S   K+  D   I +D++  T    +  +VQ +   +Y        
Sbjct: 61  QAAGEDPKAFVDRVSGRFKRAWDLLGIAYDDFIRTTEERHKKVVQLVLKKVYEAGDIYYG 120
Query: 135 XXXXQFFDPIKNIFLPDRYIKGECPI 160
                +    +  +     ++G CPI
Sbjct: 121 EYEGLYCVSCERFYTEKELVEGLCPI 146

>pdb|2CSX|A Chain A, Crystal Structure Of Aquifex Aeolicus Methionyl-Trna Synthetase Complexed With Trna(Met) Length = 497

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 58/116 (50%), Gaps = 5/116 (4%)
Query: 11  VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
           +++ +VTT + Y N   H+GH    I AD   R+  +     +   V+F+   D HG  I
Sbjct: 4   MKKFYVTTPIYYVNDVPHLGHAYTTIAADTIARYYRL-----RDYDVFFLTGTDEHGLKI 58
Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLY 126
              AE+ G++PKE ++  +   KK  +   I++  +  T    ++  VQK+++  Y
Sbjct: 59  QKKAEELGISPKELVDRNAERFKKLWEFLKIEYTKFIRTTDPYHVKFVQKVFEECY 114

>pdb|3KFL|A Chain A, Leishmania Major Methionyl-Trna Synthetase In Complex With Methionyladenylate And Pyrophosphate Length = 564

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/120 (26%), Positives = 54/120 (45%), Gaps = 5/120 (4%)
Query: 6   SEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDA 65
              K  +  F TT + Y N   HIGH+   +  D+  R+  +     K  +V+ +   D 
Sbjct: 20  GSMKKQKVFFATTPIYYVNASPHIGHVYSTLIVDVLGRYHRV-----KGEEVFVMTGTDE 74
Query: 66  HGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTL 125
           HG  +  AA K G++P +F  ++SS  K+         + +  T +  +  LVQ I+  L
Sbjct: 75  HGQKVAEAAAKQGVSPMDFTTSVSSEFKQCFQEMNYDMNYFIRTTNPTHEKLVQDIWKKL 134

>pdb|2X1L|A Chain A, Crystal Structure Of Mycobacterium Smegmatis Methionyl-Trna Synthetase In Complex With Methionine And Adenosine Length = 524

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 48/108 (44%), Gaps = 5/108 (4%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           ++TTA+ Y NG  HIGH  EYI  D   RF+ +         V ++   D HG  +   A
Sbjct: 15  YITTAIAYPNGVPHIGHAYEYIATDAIARFKRLD-----GYDVRYLTGTDVHGQKMAETA 69
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIY 122
            K G+   E     S   ++  +   I FD +  T   ++ +  + I+
Sbjct: 70  AKEGIPAAELARRNSDVFQRLQEKLNISFDRFIRTSDADHYEASKAIW 117

>pdb|3TUN|A Chain A, Trypanosoma Brucei Methionyl-Trna Synthetase In Complex With Inhibitor Chem 1356 Length = 542

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/111 (23%), Positives = 54/111 (48%), Gaps = 5/111 (4%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           FVT+ + Y N   HIGH+   +  D+  R+  +     K  +V+ +   D HG  +  AA
Sbjct: 12  FVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRV-----KGERVFALTGTDEHGQKVAEAA 66
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTL 125
           ++  ++P +F   ++   KK  +      D +  T + ++  +V++++  L
Sbjct: 67  KQKQVSPYDFTTAVAGEFKKXFEQMDYSIDYFIRTTNEQHKAVVKELWTKL 117

>pdb|4EG5|A Chain A, Trypanosoma Brucei Methionyl-Trna Synthetase In Complex With Inhibitor Chem 1312 Length = 542

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/111 (23%), Positives = 54/111 (48%), Gaps = 5/111 (4%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           FVT+ + Y N   HIGH+   +  D+  R+  +     K  +V+ +   D HG  +  AA
Sbjct: 12  FVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRV-----KGERVFALTGTDEHGQKVAEAA 66
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTL 125
           ++  ++P +F   ++   KK  +      D +  T + ++  +V++++  L
Sbjct: 67  KQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKL 117

>pdb|4EG1|A Chain A, Trypanosoma Brucei Methionyl-Trna Synthetase In Complex With Substrate Methionine Length = 542

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/111 (23%), Positives = 54/111 (48%), Gaps = 5/111 (4%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           FVT+ + Y N   HIGH+   +  D+  R+  +     K  +V+ +   D HG  +  AA
Sbjct: 12  FVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRV-----KGERVFALTGTDEHGQKVAEAA 66
Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTL 125
           ++  ++P +F   ++   KK  +      D +  T + ++  +V++++  L
Sbjct: 67  KQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKL 117

>pdb|2V0C|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed With A Sulphamoyl Analogue Of Leucyl-Adenylate In The Synthetic Site And An Adduct Of Amp With 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (An2690) In The Editing Site Length = 878

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           +V    PY +G+LH+GH+  Y   D+  RF+ MQ       +V      DA G     AA
Sbjct: 36  YVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQ-----GYEVLHPMGWDAFGLPAENAA 90
Query: 75  EKAGMTPKEF 84
            K G+ PK++
Sbjct: 91  LKFGVHPKDW 100

>pdb|1OBH|A Chain A, Leucyl-Trna Synthetase From Thermus Thermophilus Complexed With A Pre-Transfer Editing Substrate Analogue In Both Synthetic Active Site And Editing Site Length = 878

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           +V    PY +G+LH+GH+  Y   D+  RF+ MQ       +V      DA G     AA
Sbjct: 36  YVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQ-----GYEVLHPMGWDAFGLPAENAA 90
Query: 75  EKAGMTPKEF 84
            K G+ PK++
Sbjct: 91  LKFGVHPKDW 100

>pdb|1MEA|A Chain A, Methionyl-Trna Synthetase Zinc Binding Domain. 3d Structure And Homology With Rubredoxin And Gag Retroviral Proteins Length = 28

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/26 (57%), Positives = 19/26 (73%)
Query: 151 DRYIKGECPICNAKDQYGDFCECCSS 176
           DR++KG CP C + DQYGD CE C +
Sbjct: 3   DRFVKGTCPKCKSPDQYGDNCEVCGA 28

>pdb|1WKB|A Chain A, Crystal Structure Of Leucyl-Trna Synthetase From The Archaeon Pyrococcus Horikoshii Reveals A Novel Editing Domain Orientation Length = 810

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
          ++ ++T A PY +G LH+GH   Y   D+  RF+ MQ  N     V F  A    G+ I+
Sbjct: 34 KKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQGYN-----VLFPMAWHITGSPIV 88
Query: 72 IAAEK 76
            AE+
Sbjct: 89 GIAER 93

>pdb|1WZ2|A Chain A, The Crystal Structure Of Leucyl-Trna Synthetase And Trna(Leucine) Complex Length = 967

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
          ++ ++T A PY +G LH+GH   Y   D+  RF+ MQ  N     V F  A    G+ I+
Sbjct: 34 KKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQGYN-----VLFPMAWHITGSPIV 88
Query: 72 IAAEK 76
            AE+
Sbjct: 89 GIAER 93

>pdb|4AQ7|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase, Trna(Leu) And Leucyl-Adenylate Analogue In The Aminoacylation Conformation Length = 880

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 41/162 (25%), Positives = 65/162 (40%), Gaps = 9/162 (5%)
Query: 6   SEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDA 65
           +E +   + +  + LPY +G LH+GH+  Y   D+  R+Q M   N     V      DA
Sbjct: 47  TEDESKEKYYCLSMLPYPSGRLHMGHVRNYTIGDVIARYQRMLGKN-----VLQPIGWDA 101
Query: 66  HGAAIMIAAEKAGMTPKEFI-NNIS--SNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIY 122
            G     AA K    P  +  +NI+   N+ K L GF   +    +T + E     QK +
Sbjct: 102 FGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKML-GFGYDWSRELATCTPEYYRWEQKFF 160
Query: 123 DTLYXXXXXXXXXXXXQFFDPIKNIFLPDRYIKGECPICNAK 164
             LY             +    + +   ++ I G C  C+ K
Sbjct: 161 TELYKKGLVYKKTSAVNWCPNDQTVLANEQVIDGCCWRCDTK 202

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	232
3h99_A	560	Methionyl-tRNA synthetase; rossmann fold, aminoacy	1e-102
1rqg_A	722	Methionyl-tRNA synthetase; translation, dimerizati	2e-92
3tun_A	542	Methionyl-tRNA synthetase; aminoacyl-tRNA syntheta	2e-23
2d5b_A	500	Methionyl-tRNA synthetase; rossmann fold, class 1A	3e-23
2x1l_A	524	Methionyl-tRNA synthetase; nucleotide-binding, pro	3e-22
2csx_A	497	Methionyl-tRNA synthetase; ligase, riken structura	6e-22
4dlp_A	536	Aminoacyl-tRNA synthetase, class I:aminoacyl-tRNA	2e-21
3kfl_A	564	Methionyl-tRNA synthetase; parasite, aminoacyl-tRN	2e-19
1wz2_A	967	Leucyl-tRNA synthetase; ligase, riken structural g	4e-12
1wkb_A	810	Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, e	2e-11
1ffy_A	917	Isoleucyl-tRNA synthetase; protein-RNA complex, me	6e-06
1ile_A	821	Ilers, isoleucyl-tRNA synthetase; aminoacyl-tRNA s	7e-06

>3h99_A Methionyl-tRNA synthetase; rossmann fold, aminoacyl-tRNA synthetase, ATP-binding, ligas binding, nucleotide-binding, protein biosynthesis; HET: CIT; 1.40A {Escherichia coli} PDB: 3h97_A* 3h9b_A* 1f4l_A 3h9c_A* 1pfv_A* 1pfu_A 1p7p_A* 1pfw_A* 1pfy_A* 1pg0_A* 1pg2_A* 1qqt_A 1mea_A 1med_A Length = 560

 Score =  306 bits (785), Expect = e-102
 Identities = 101/229 (44%), Positives = 144/229 (62%), Gaps = 9/229 (3%)

Query: 2   KKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFIC 61
             H S  +  ++I VT A PYANG +H+GH++E+IQAD+WVR+Q M+        V FIC
Sbjct: 8   HHHGSMTQVAKKILVTCASPYANGSIHLGHMLEHIQADVWVRYQRMRGHE-----VNFIC 62

Query: 62  ADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKI 121
           ADDAHG  IM+ A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + I
Sbjct: 63  ADDAHGTPIMLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELI 122

Query: 122 YDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPT 181
           Y  L      I N+ I+Q +DP K +FLPDR++KG CP C + DQYGD CE C + Y+PT
Sbjct: 123 YSRLKEN-GFIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQYGDNCEVCGATYSPT 181

Query: 182 KLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
           +LI P S++SG  P+++ S+HFFF L      + L+ W      LQ ++
Sbjct: 182 ELIEPKSVVSGATPVMRDSEHFFFDLP--SFSEMLQAW-TRSGALQEQV 227

>1rqg_A Methionyl-tRNA synthetase; translation, dimerization, ligase; 2.90A {Pyrococcus abyssi} SCOP: a.27.1.1 c.26.1.1 g.41.1.1 Length = 722

 Score =  285 bits (730), Expect = 2e-92
 Identities = 73/220 (33%), Positives = 110/220 (50%), Gaps = 10/220 (4%)

Query: 12  RRIFVTTALPYANGELHIGHIM-EYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI 70
            R  VT+ALPYANG +H GH+   Y+ ADI+VR+  ++ ++     V FIC  D HG  I
Sbjct: 2   VRYMVTSALPYANGPIHAGHLAGAYLPADIFVRYLRLKGED-----VVFICGTDEHGTPI 56

Query: 71  MIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAK 130
              A K G +P+E ++      K       I FD +  T+   +  L Q+ +   Y    
Sbjct: 57  SFRALKEGRSPREIVDEFHEQIKITFQRAKISFDFFGRTELPIHYKLSQEFFLKAYEN-G 115

Query: 131 LIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSIL 190
            ++ K   Q +     +FLPDR++ G CP C A+DQ GD CE C    TP  LINP   +
Sbjct: 116 HLVKKVTKQAYCEHDKMFLPDRFVIGTCPYCGAEDQKGDQCEVCGRPLTPEILINPRCAI 175

Query: 191 SGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEI 230
            G     + S H++ K+      + L++W I  +  +P +
Sbjct: 176 CGRPISFRDSAHYYIKMQ--DFAERLKRW-IEKQPWKPNV 212

>3tun_A Methionyl-tRNA synthetase; aminoacyl-tRNA synthetase, AARS, metrs, parasite, protein-IN complex, translation, nucleotide binding; HET: C13; 2.55A {Trypanosoma brucei} Length = 542

 Score = 96.6 bits (240), Expect = 2e-23
 Identities = 39/217 (17%), Positives = 85/217 (39%), Gaps = 31/217 (14%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           FVT+ + Y N   HIGH+   +  D+  R+  ++ +      V+ +   D HG  +  AA
Sbjct: 12  FVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGER-----VFALTGTDEHGQKVAEAA 66

Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN 134
           ++  ++P +F   ++   KK  +      D +  T + ++  +V++++  L  K  + + 
Sbjct: 67  KQKQVSPYDFTTAVAGEFKKXFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLG 126

Query: 135 KKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTK 194
           +    +    ++   P     G     N                         S+ SG  
Sbjct: 127 RYEGWYSISDESFLTPQNITDGVDKDGNPC---------------------KVSLESGHV 165

Query: 195 PIIKSSKHFFFKLSD--KRCIDFLRKWAIHDKRLQPE 229
               S +++ F+LS   +R +++      +   + PE
Sbjct: 166 VTWVSEENYMFRLSAFRERLLEWYHA---NPGCIVPE 199

>2d5b_A Methionyl-tRNA synthetase; rossmann fold, class 1A AARS, isomerase, structural genomics, NPPSFA; 1.80A {Thermus thermophilus} SCOP: a.27.1.1 c.26.1.1 PDB: 1woy_A 1a8h_A 2d54_A Length = 500

 Score = 96.1 bits (240), Expect = 3e-23
 Identities = 46/218 (21%), Positives = 85/218 (38%), Gaps = 42/218 (19%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           +VTT + Y N E H+GH    + AD   R+  +          +F+   D HG  +  AA
Sbjct: 6   YVTTPIYYVNAEPHLGHAYTTVVADFLARWHRLDGYR-----TFFLTGTDEHGETVYRAA 60

Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN 134
           + AG  PK F++ +S   K+  D   I +D++  T    +  +VQ +   +Y        
Sbjct: 61  QAAGEDPKAFVDRVSGRFKRAWDLLGIAYDDFIRTTEERHKKVVQLVLKKVYEAG----- 115

Query: 135 KKINQFFDPIKNIFLPDRYIKGECPICNAKDQY-GDFCECCSSIYTPTKLINPYSILSGT 193
                           D Y            +Y G +C  C   YT  +L+     + G 
Sbjct: 116 ----------------DIY----------YGEYEGLYCVSCERFYTEKELVEGLCPIHGR 149

Query: 194 KPIIKSSKHFFFKLSD--KRCIDFLRKWAIHDKRLQPE 229
               +   ++FF++        +++++   +   ++PE
Sbjct: 150 PVERRKEGNYFFRMEKYRPWLQEYIQE---NPDLIRPE 184

>2x1l_A Methionyl-tRNA synthetase; nucleotide-binding, protein biosynthesis, ligase, aminoacyl- synthetase; HET: ADN CXS; 2.30A {Mycobacterium smegmatis} PDB: 2x1m_A* Length = 524

 Score = 93.5 bits (233), Expect = 3e-22
 Identities = 46/237 (19%), Positives = 80/237 (33%), Gaps = 47/237 (19%)

Query: 1   MKKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFI 60
           M  H          ++TTA+ Y NG  HIGH  EYI  D   RF+ +   +     V ++
Sbjct: 1   MAHHHHHHGGSEPFYITTAIAYPNGVPHIGHAYEYIATDAIARFKRLDGYD-----VRYL 55

Query: 61  CADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQK 120
              D HG  +   A K G+   E     S   ++  +   I FD +  T   ++ +  + 
Sbjct: 56  TGTDVHGQKMAETAAKEGIPAAELARRNSDVFQRLQEKLNISFDRFIRTSDADHYEASKA 115

Query: 121 IYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQY-GDFCECCSSIYT 179
           I+  + +                       D Y           D Y G +       +T
Sbjct: 116 IWKRMADAG---------------------DIY----------LDAYKGWYSIRDERFFT 144

Query: 180 PTKLI-----NPYSILSGTKPIIKSSKHFFFKLSD--KRCIDFLRKWAIHDKRLQPE 229
             +          +  +G        + +FF+LS    R +    +   H + + P+
Sbjct: 145 ENETTEQPDGTRIATETGAPVTWTEEQTYFFRLSAYTDRLLALYEE---HPEFIGPD 198

>2csx_A Methionyl-tRNA synthetase; ligase, riken structural genomics/proteomics initiative, RSGI, structural genomics, ligase/RNA complex; 2.70A {Aquifex aeolicus} PDB: 2ct8_A* Length = 497

 Score = 92.3 bits (230), Expect = 6e-22
 Identities = 47/222 (21%), Positives = 89/222 (40%), Gaps = 43/222 (19%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           ++ +VTT + Y N   H+GH    I AD   R+  ++  +     V+F+   D HG  I 
Sbjct: 5   KKFYVTTPIYYVNDVPHLGHAYTTIAADTIARYYRLRDYD-----VFFLTGTDEHGLKIQ 59

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
             AE+ G++PKE ++  +   KK  +   I++  +  T    ++  VQK+++  Y +   
Sbjct: 60  KKAEELGISPKELVDRNAERFKKLWEFLKIEYTKFIRTTDPYHVKFVQKVFEECYKRG-- 117

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQY-GDFCECCSSIYTPTKLI-NPYSI 189
                              D Y            +Y G +C  C    +  +L  +    
Sbjct: 118 -------------------DIY----------LGEYEGWYCVGCEEFKSEAELAEDHTCP 148

Query: 190 LSGTKPIIKSSKHFFFKLSD--KRCIDFLRKWAIHDKRLQPE 229
           +   K        +FF+LS    + ++   K   + + +QP+
Sbjct: 149 IHQKKCEYIKEPSYFFRLSKYQDKLLELYEK---NPEFIQPD 187

>4dlp_A Aminoacyl-tRNA synthetase, class I:aminoacyl-tRNA synthetase, class IA:methionyl-tRNA...; structural genomics; 2.65A {Brucella melitensis biovar abortus 230ORGANISM_TAXID} Length = 536

 Score = 90.8 bits (226), Expect = 2e-21
 Identities = 46/222 (20%), Positives = 79/222 (35%), Gaps = 46/222 (20%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           ++TTA+ Y NG+ HIGH  E I  D   RFQ +   +     VYF+   D HG  ++ +A
Sbjct: 28  YITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMD-----VYFLTGTDEHGIKMLQSA 82

Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN 134
            K G+TP++  +  +S  ++  +      D++  T    +    Q I+  +         
Sbjct: 83  RKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANG----- 137

Query: 135 KKINQFFDPIKNIFLPDRYIKGECPICNAKDQY-GDFCECCSSIYTPTKLI----NPYSI 189
                           D Y          K  Y G +     + Y   +           
Sbjct: 138 ----------------DIY----------KGGYAGWYSVRDEAYYGEEETEVRADGVRYG 171

Query: 190 LSGTKPIIKSSKHFFFKLSD--KRCIDFLRKWAIHDKRLQPE 229
             GT       + +FF+LS    + +D       +   + P 
Sbjct: 172 PQGTPVEWVEEESYFFRLSAYQDKLLDLYEN---NPGFIMPA 210

>3kfl_A Methionyl-tRNA synthetase; parasite, aminoacyl-tRNA synthetase, tRNA ligase metrs, methionine, translation, ATP-binding; HET: ME8; 2.00A {Leishmania major} Length = 564

 Score = 85.0 bits (211), Expect = 2e-19
 Identities = 46/227 (20%), Positives = 79/227 (34%), Gaps = 51/227 (22%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           F TT + Y N   HIGH+   +  D+  R+  ++ +      V+ +   D HG  +  AA
Sbjct: 29  FATTPIYYVNASPHIGHVYSTLIVDVLGRYHRVKGEE-----VFVMTGTDEHGQKVAEAA 83

Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN 134
            K G++P +F  ++SS  K+         + +  T +  +  LVQ I+  L  K      
Sbjct: 84  AKQGVSPMDFTTSVSSEFKQCFQEMNYDMNYFIRTTNPTHEKLVQDIWKKLAAKG----- 138

Query: 135 KKINQFFDPIKNIFLPDRYIKGECPICNAKDQY-GDFCECCSSIYTPTKLINPYSILSGT 193
                           D Y            +Y G +     S  T   + +        
Sbjct: 139 ----------------DIY----------LGKYEGWYSVSDESFLTAQNVADGVDRDGKP 172

Query: 194 KPIIKSSKH---------FFFKLSD--KRCIDFLRKWAIHDKRLQPE 229
             +   S H         + F+LS   +R + +      H   + PE
Sbjct: 173 CKVSLESGHVVTWVEEENYMFRLSAFRERLLKYFHD---HPNCIVPE 216

>1wz2_A Leucyl-tRNA synthetase; ligase, riken structural genomics/proteomics initiativ structural genomics, ligase-RNA complex; 3.21A {Pyrococcus horikoshii} Length = 967

 Score = 64.2 bits (156), Expect = 4e-12
 Identities = 26/96 (27%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           ++T A PY +G LH+GH   Y   D+  RF+ MQ   G    V F  A    G+ I+  A
Sbjct: 37  YITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQ---GY--NVLFPMAWHITGSPIVGIA 91

Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTD 110
           E+      + I       K   +  +   D      
Sbjct: 92  ERIKNRDPKTIWIYRDVYKVPEEILWTFEDPINIVK 127

>1wkb_A Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, editing, amino acid, aminoacylation, trnaLeu, structural genomics; 2.05A {Pyrococcus horikoshii} Length = 810

 Score = 62.3 bits (151), Expect = 2e-11
 Identities = 26/96 (27%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           ++T A PY +G LH+GH   Y   D+  RF+ MQ   G    V F  A    G+ I+  A
Sbjct: 37  YITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQ---GY--NVLFPMAWHITGSPIVGIA 91

Query: 75  EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTD 110
           E+      + I       K   +  +   D      
Sbjct: 92  ERIKNRDPKTIWIYRDVYKVPEEILWTFEDPINIVK 127

>1ffy_A Isoleucyl-tRNA synthetase; protein-RNA complex, metal IONS, editing tRNA synthetase, double-sieve, ligase/RNA, mupiroci; HET: MRC; 2.20A {Staphylococcus aureus} SCOP: a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1qu2_A* 1qu3_A* Length = 917

 Score = 45.6 bits (109), Expect = 6e-06
 Identities = 26/69 (37%), Positives = 33/69 (47%), Gaps = 10/69 (14%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAG-- 78
           PYANG LH+GH +  I  D  VR++ MQ   G      ++   D HG  I  A  K G  
Sbjct: 57  PYANGNLHMGHALNKILKDFIVRYKTMQ---GF--YAPYVPGWDTHGLPIEQALTKKGVD 111

Query: 79  ---MTPKEF 84
              M+  EF
Sbjct: 112 RKKMSTAEF 120

>1ile_A Ilers, isoleucyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken structural genomics/proteom initiative, RSGI, structural genomics; 2.50A {Thermus thermophilus} SCOP: a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1jzq_A* 1jzs_A* Length = 821

 Score = 45.2 bits (108), Expect = 7e-06
 Identities = 25/127 (19%), Positives = 46/127 (36%), Gaps = 24/127 (18%)

Query: 21  PYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-GM 79
           P ANG  H+GH       D++ R++ M+   G           D HG  + +  EK  G+
Sbjct: 47  PTANGLPHVGHAQARSYKDLFPRYKTMR---GY--YAPRRAGWDTHGLPVELEVEKKLGL 101

Query: 80  TPKEFINNISS---NRK------KYLD---------GFYIKFDNWYSTDSIENIDLVQKI 121
             K  I        N+        Y            +++  ++ Y+T     I+ +   
Sbjct: 102 KSKREIEAYGIERFNQACRESVFTYEKEWEAFTERIAYWVDLEDAYATLEPTYIESIWWS 161

Query: 122 YDTLYNK 128
              L+++
Sbjct: 162 LKNLFDR 168

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	232
1rqg_A	722	Methionyl-tRNA synthetase; translation, dimerizati	100.0
3h99_A	560	Methionyl-tRNA synthetase; rossmann fold, aminoacy	100.0
3u1f_A	542	Methionyl-tRNA synthetase; aminoacyl-tRNA syntheta	100.0
3kfl_A	564	Methionyl-tRNA synthetase; parasite, aminoacyl-tRN	100.0
2x1l_A	524	Methionyl-tRNA synthetase; nucleotide-binding, pro	100.0
4dlp_A	536	Aminoacyl-tRNA synthetase, class I:aminoacyl-tRNA	100.0
4arc_A	880	Leucine--tRNA ligase; ligase-RNA complex, nucleoti	100.0
1ile_A	821	Ilers, isoleucyl-tRNA synthetase; aminoacyl-tRNA s	100.0
2d5b_A	500	Methionyl-tRNA synthetase; rossmann fold, class 1A	100.0
2csx_A	497	Methionyl-tRNA synthetase; ligase, riken structura	100.0
2v0c_A	878	Aminoacyl-tRNA synthetase; ligase, nucleotide-bind	100.0
1gax_A	862	Valrs, valyl-tRNA synthetase; protein-RNA complex,	100.0
1ffy_A	917	Isoleucyl-tRNA synthetase; protein-RNA complex, me	100.0
1wkb_A	810	Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, e	100.0
1wz2_A	967	Leucyl-tRNA synthetase; ligase, riken structural g	100.0
3c8z_A	414	Cysteinyl-tRNA synthetase; cysteine ligase, rossma	99.94
3tqo_A	462	Cysteinyl-tRNA synthetase; protein synthesis, liga	99.93
3sp1_A	501	Cysteinyl-tRNA synthetase; structural genomics, se	99.93
1li5_A	461	Cysrs, cysteinyl-tRNA synthetase, transfer RNA-Cys	99.92
2zue_A	629	Arginyl-tRNA synthetase; aminoacyl-tRNA synthetase	99.82
1iq0_A	592	Arginyl-tRNA synthetase; riken structural genomics	99.8
1irx_A	523	Lysyl-tRNA synthetase; beta sandwitch, zinc-bindin	99.78
1f7u_A	607	Arginyl-tRNA synthetase; RNA-protein complex, amin	99.76
3fnr_A	464	Arginyl-tRNA synthetase; transferase, PSI-2, NYSGX	99.65
1nzj_A	298	Hypothetical protein YADB; Zn cluster, glutamyl T-	99.23
3aii_A	553	Glutamyl-tRNA synthetase; amino-acyl tRNA syntheta	99.19
1qtq_A	553	GLNRS, protein (glutaminyl-tRNA synthetase); gluta	99.14
2o5r_A	481	Glutamyl-tRNA synthetase 1; TM1351, EC 6.1.1.17, g	99.11
2hz7_A	851	Glutaminyl-tRNA synthetase; rossmann fold, GLNRS c	99.06
4g6z_A	490	Glutamate-tRNA ligase; aminoacyl-tRNA synthetase,	99.05
3al0_C	592	Glutamyl-tRNA(Gln) amidotransferase subunit C, GL	99.03
2cfo_A	492	Glutamyl-tRNA synthetase; ligase, aminoacyl-tRNA s	99.03
3afh_A	488	Glutamyl-tRNA synthetase 2; protein-substrate comp	98.99
4gri_A	512	Glutamate--tRNA ligase; structural genomics, seatt	98.95
1j09_A	468	Glutamyl-tRNA synthetase; glurs-ATP-Glu complex, r	98.94
2ja2_A	498	Glutamyl-tRNA synthetase; non-discriminating gluta	98.86
3jxe_A	392	Tryptophanyl-tRNA synthetase; adenosine triphospha	96.72
2cyb_A	323	Tyrosyl-tRNA synthetase; rossmann-fold, structural	96.34
3a04_A	372	Tryptophanyl-tRNA synthetase; ligase, aminoacyl-tR	96.29
3hzr_A	386	Tryptophanyl-tRNA synthetase; APO tRNA-ligase, str	96.13
2g36_A	340	Tryptophanyl-tRNA synthetase; TM0492, structural g	95.95
2dlc_X	394	Tyrosyl-tRNA synthetase, cytoplasmic; tyrrs, ligas	95.94
2zp1_A	314	Tyrosyl-tRNA synthetase; tRNA synthetases class I,	95.87
3tzl_A	322	Tryptophanyl-tRNA synthetase; structural genomics,	95.87
3prh_A	388	Tryptophanyl-tRNA synthetase; TRPRS, protein biosy	95.77
2cya_A	364	Tyrosyl-tRNA synthetase; tyrrs, aminoacylation, st	95.76
1i6k_A	328	TRPRS, tryptophanyl-tRNA synthetase; class I tRNA	95.73
1n3l_A	372	Tyrosyl-tRNA synthetase; rossmann fold AS catalyti	95.58
3tze_A	406	Tryptophanyl-tRNA synthetase; structural genomics,	95.41
3hv0_A	393	Tryptophanyl-tRNA synthetase; tRNA-ligase, ATP-bin	95.35
2ip1_A	432	Tryptophanyl-tRNA synthetase; rossmann fold, struc	95.31
2j5b_A	348	Tyrosyl-tRNA synthetase; ligase, protein biosynthe	95.23
1r6t_A	477	Tryptophanyl-tRNA synthetase; class IC tRNA synthe	95.13
3foc_A	451	Tryptophanyl-tRNA synthetase; structural genomics,	95.1
1yi8_B	351	Tryptophanyl-tRNA synthetase; ligase; HET: TRP; 2.	95.09
2yy5_A	348	Tryptophanyl-tRNA synthetase; aminoaccyl tRNA synt	95.0
3vgj_A	373	Tyrosyl-tRNA synthetase, putative; tyrrs, ligase;	94.91
3i05_A	395	Tryptophanyl-tRNA synthetase; APO tRNA-ligase, ATP	94.85
1r6u_A	437	Tryptophanyl-tRNA synthetase; class IC tRNA synthe	94.8
3p0j_A	690	Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase	94.77
3sz3_A	341	Tryptophanyl-tRNA synthetase; structural genomics,	94.66
2cyc_A	375	Tyrosyl-tRNA synthetase; tyrosine, tyrrs, aminoacy	94.37
3n9i_A	346	Tryptophanyl-tRNA synthetase; tryptophan-tRNA liga	93.82
2el7_A	337	Tryptophanyl-tRNA synthetase; aminoacyl-tRNA synth	93.67
1jil_A	420	Tyrrs, tyrosyl-tRNA synthetase; truncation, based	90.28
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	90.0
1h3f_A	432	Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy	89.65
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	89.4
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	88.88
2pid_A	356	Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase	88.65
2ts1_A	419	Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30	88.51
2yxn_A	322	Tyrosyl-tRNA synthetase; tRNA synthetases class I,	87.91
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	87.27
1y42_X	392	Tyrosyl-tRNA synthetase, mitochondrial; CYT-18, tR	86.91
3p0j_A	690	Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase	86.6
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	85.81
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	85.77
2jan_A	432	Tyrosyl-tRNA synthetase; protein biosynthesis, ami	85.09
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	84.94
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	84.18
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	83.64
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	82.54
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	81.9
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	81.84
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	81.76
3v2d_5	60	50S ribosomal protein L32; ribosome associated inh	81.0
2zjr_Z	60	50S ribosomal protein L32; ribosome, large ribosom	80.81

>1rqg_A Methionyl-tRNA synthetase; translation, dimerization, ligase; 2.90A {Pyrococcus abyssi} SCOP: a.27.1.1 c.26.1.1 g.41.1.1

Probab=100.00  E-value=1.1e-53  Score=414.45  Aligned_cols=208  Identities=35%  Similarity=0.678  Sum_probs=201.1

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHh-HHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIME-YIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~-~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      ++|+||+|||||||.|||||+++ ++++|+++||+||+|     ++|.|++|+|+||+||+.+|++.|++|+++++++.+
T Consensus         2 ~~~~itt~~Py~nG~lHiGHa~~~~i~~DiiaRy~rm~G-----~~V~~v~G~D~hG~pie~~A~k~G~~p~e~~~~~~~   76 (722)
T 1rqg_A            2 VRYMVTSALPYANGPIHAGHLAGAYLPADIFVRYLRLKG-----EDVVFICGTDEHGTPISFRALKEGRSPREIVDEFHE   76 (722)
T ss_dssp             CEEEEEECCCBTTSCCBHHHHHHHTHHHHHHHHHHHHTT-----CEEEEEEEEBCCSHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCEEEecCCCCCCCchhhchhhccHHHHHHHHHHHHhcC-----CceEecceeCCCCHHHHHHHHHcCCCHHHHHHHHHH
Confidence            67999999999999999999998 999999999999999     999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCc
Q psy2399          91 NRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDF  170 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~  170 (232)
                      .|+++|++|||++|.|++|+++.|.+.++++|.+|+ ++|+||++.+.+|||+.|++||+|++|+|+||.|+.++++|++
T Consensus        77 ~~~~~~~~lgis~D~~~rT~d~~~~~~v~~~f~~L~-~kG~iY~~~~~v~y~~~~~tfl~d~~v~gtcP~c~~~~~~Gd~  155 (722)
T 1rqg_A           77 QIKITFQRAKISFDFFGRTELPIHYKLSQEFFLKAY-ENGHLVKKVTKQAYCEHDKMFLPDRFVIGTCPYCGAEDQKGDQ  155 (722)
T ss_dssp             HHHHHHHHHTCCCSEEEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEBTTTTBCCCGGGCCSBCSSSCCSCCCTTT
T ss_pred             HHHHHHHHhCCCCCCCeeCCCHHHHHHHHHHHHHHH-HCCCEEecceeeeecCCCCcCcchhhcccccCccCCccCCcch
Confidence            999999999999999999999999999999999999 9999999999999999999999999999999999999999999


Q ss_pred             CccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCC
Q psy2399         171 CECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQP  228 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p  228 (232)
                      |+.||+.+++.+|++|+|..||.+++++.++||||+|  ++|+++|.+| ++...++|
T Consensus       156 c~~~G~~l~~~~l~~p~~~r~g~~v~~~~~~qwF~~l--~~~~~~l~~~-~~~~~wp~  210 (722)
T 1rqg_A          156 CEVCGRPLTPEILINPRCAICGRPISFRDSAHYYIKM--QDFAERLKRW-IEKQPWKP  210 (722)
T ss_dssp             CSSSCCCCCTTSSBSCBCTTTCCBCEEEEEEEEEECG--GGTHHHHHHH-HHSSCCCH
T ss_pred             hhhcccccChhhccCCcccCCCcEeEEEEeccEEEEh--HHHHHHHHHH-HHhCCCCH
Confidence            9999999999999999999999999999999999999  9999999999 54333443

>3h99_A Methionyl-tRNA synthetase; rossmann fold, aminoacyl-tRNA synthetase, ATP-binding, ligas binding, nucleotide-binding, protein biosynthesis; HET: CIT; 1.40A {Escherichia coli} PDB: 3h97_A* 3h9b_A* 1f4l_A 3h9c_A* 1pfv_A* 1pfu_A 1p7p_A* 1pfw_A* 1pfy_A* 1pg0_A* 1pg2_A* 1qqt_A 1mea_A 1med_A

Probab=100.00  E-value=8.2e-53  Score=398.50  Aligned_cols=214  Identities=46%  Similarity=0.906  Sum_probs=204.9

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      .+.++++++|++|||||||+|||||+|+++++|+++||+|++|     ++|.+++|+|+||++|+..|++.|++++++++
T Consensus        13 ~~~~~~~~~v~~~~py~ng~lHiGH~r~~v~~D~laR~~r~~G-----~~V~~~~g~D~~G~~i~~~a~~~g~~~~~~~~   87 (560)
T 3h99_A           13 MTQVAKKILVTCASPYANGSIHLGHMLEHIQADVWVRYQRMRG-----HEVNFICADDAHGTPIMLKAQQLGITPEQMIG   87 (560)
T ss_dssp             ----CCEEEEEECCCBTTSCCBHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEEBCCSHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCcEEEeCCCCCCCCCcchhhHHHHHHHHHHHHHHHHcC-----CeEEEeeeecCcCcHHHHHHHHhCCCHHHHHH
Confidence            3567789999999999999999999999999999999999999     99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcccc
Q psy2399          87 NISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQ  166 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~  166 (232)
                      ++.+.|+++|++|||++|.|++|+++.|.+.++++|.+|. ++|+||++++.+|||+.++++|++++|+|+||.|+..++
T Consensus        88 ~~~~~~~~~~~~lgi~~d~~~~t~~~~~~~~v~~~~~~L~-~~G~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~  166 (560)
T 3h99_A           88 EMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRLK-ENGFIKNRTISQLYDPEKGMFLPDRFVKGTCPKCKSPDQ  166 (560)
T ss_dssp             HHHHHHHHHHHHTTCCCSEEEESSSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEECCGGGEEEECTTTCCSSE
T ss_pred             HHHHHHHHHHHHcCCCCCCceeCCCHHHHHHHHHHHHHHH-HCCCEEEeeeeEeecCccCceecchhcCCCCCCCCCccc
Confidence            9999999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             CCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCCC
Q psy2399         167 YGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPE  229 (232)
Q Consensus       167 ~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p~  229 (232)
                      +|++||+||+.+++.+|++|+|..||++++++.+++|||+|  ++|+++|.+| +++++++|+
T Consensus       167 ~gd~ce~cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~l--~~~~~~l~~~-~~~~~~~~~  226 (560)
T 3h99_A          167 YGDNCEVCGATYSPTELIEPKSVVSGATPVMRDSEHFFFDL--PSFSEMLQAW-TRSGALQEQ  226 (560)
T ss_dssp             ETTBCTTTCCBCCGGGCEEEEETTTCCCCEEEEEEEEEECG--GGGHHHHHHH-HHTSCSCHH
T ss_pred             ccchhhhccccCChhhhcCCccccCCCCceEEecceEEEEH--HHHHHHHHHH-HHhCCCCHH
Confidence            99999999999999999999999999999999999999999  9999999999 666667664

>3u1f_A Methionyl-tRNA synthetase; aminoacyl-tRNA synthetase, AARS, metrs, parasite, protein-IN complex, rossmann-fold, translation; HET: 392; 2.20A {Trypanosoma brucei} PDB: 3u1e_A* 3u1g_A* 3u20_A* 4eg1_A 4eg3_A* 4eg6_A* 4eg8_A* 4eg5_A* 3tun_A* 3u1z_A* 4eg4_A* 4eg7_A* 4ega_A*

Probab=100.00  E-value=4.7e-47  Score=357.37  Aligned_cols=194  Identities=21%  Similarity=0.371  Sum_probs=179.4

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHH
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINN   87 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~   87 (232)
                      .+..++|+||+|+|||||.||||||++++++|+++||+||+|     ++|.+++|+|+||+||+.+|++.|++|++++++
T Consensus         5 ~~~~k~f~Ittp~pY~nG~lHiGHa~~~~~~Dii~Ry~r~~G-----~~v~~v~G~D~hG~~ie~~a~k~g~~~~e~~~~   79 (542)
T 3u1f_A            5 MKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKG-----ERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTA   79 (542)
T ss_dssp             --CCCCEEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHTT-----CCEEEEEEEECCSHHHHHHHHHTTSCHHHHHHH
T ss_pred             CCCCCCEEEeCCCCCCCCchhhHHHHHHHHHHHHHHHHHhcC-----CCccccCccCcChHHHHHHHHHcCCCHHHHHHH
Confidence            456688999999999999999999999999999999999999     999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccC
Q psy2399          88 ISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQY  167 (232)
Q Consensus        88 ~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~  167 (232)
                      +++.|++++++|||++|.|++|+++.|.+.|+++|.+|+ ++|+||++.+.++||+.|++||+|++|++.|+.||     
T Consensus        80 ~~~~~~~~~~~lgi~~D~~~~T~~~~~~~~v~~~f~~L~-~~G~iy~~~~~v~~~~~~~~~l~d~~v~~~~~~~g-----  153 (542)
T 3u1f_A           80 VAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLE-QKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDG-----  153 (542)
T ss_dssp             HHHHHHHHHHHHTCCCSEEEETTCHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEEECGGGEEEEECTTS-----
T ss_pred             HHHHHHHHHHHhCCccCcCccCCCHHHHHHHHHHHHHHh-hcCcEEecceeEEeeccCcccchhhhhhccccccC-----
Confidence            999999999999999999999999999999999999999 99999999999999999999999999999888764     


Q ss_pred             CCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCCC
Q psy2399         168 GDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQPE  229 (232)
Q Consensus       168 g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p~  229 (232)
                       +.|+              .|..||++++++.++||||+|  ++++++|.+|+.. +.++.|+
T Consensus       154 -~~~~--------------~~~~sg~~ve~~~~~~~f~~l--~~~~~~l~~~~~~~~~~~~P~  199 (542)
T 3u1f_A          154 -NPCK--------------VSLESGHVVTWVSEENYMFRL--SAFRERLLEWYHANPGCIVPE  199 (542)
T ss_dssp             -CEEE--------------EETTTCCBEEEEEEEEEEECG--GGGHHHHHHHHHHCTTSEESH
T ss_pred             -cccc--------------ccCCCCCcceeeccccceecc--hhHHHHHHHHHhhcccccCCc
Confidence             3453              455689999999999999999  9999999999443 4566664

>3kfl_A Methionyl-tRNA synthetase; parasite, aminoacyl-tRNA synthetase, tRNA ligase metrs, methionine, translation, ATP-binding; HET: ME8; 2.00A {Leishmania major}

Probab=100.00  E-value=3.8e-42  Score=325.76  Aligned_cols=193  Identities=24%  Similarity=0.395  Sum_probs=176.0

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      +++++++||+|+|||||+|||||+|++|++|+++||+|++|     ++|.+++|+|+||++|+.+|++.|++|+++++++
T Consensus        23 ~~~~~~~i~~~~py~ng~lHiGH~r~~v~~D~laR~~r~~G-----~~V~~~~g~dd~G~ki~~~a~~~g~~p~~~~~~~   97 (564)
T 3kfl_A           23 KKQKVFFATTPIYYVNASPHIGHVYSTLIVDVLGRYHRVKG-----EEVFVMTGTDEHGQKVAEAAAKQGVSPMDFTTSV   97 (564)
T ss_dssp             -CCCCEEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHT-----CCEEEEEEEECCSHHHHHHHHHTTCCHHHHHHHH
T ss_pred             cCCCCEEEeCCCCCCCCCCCcchhHHHHHHHHHHHHHHHcC-----CcEEEecCcCCCCcHHHHHHHHcCCCHHHHHHHH
Confidence            45678999999999999999999999999999999999999     9999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCC
Q psy2399          89 SSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYG  168 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g  168 (232)
                      .+.|+++|++|||++|.|++|+++.|.+.++++|.+|. ++|+||++++.+|||+.|++|++++++...|+.+      |
T Consensus        98 ~~~~~~~~~~lgi~~D~~~~t~~~~~~~~v~~~~~~L~-~~G~iy~~~~~~~y~~~~~~~l~~~~~~~~~~~~------g  170 (564)
T 3kfl_A           98 SSEFKQCFQEMNYDMNYFIRTTNPTHEKLVQDIWKKLA-AKGDIYLGKYEGWYSVSDESFLTAQNVADGVDRD------G  170 (564)
T ss_dssp             HHHHHHHHHHTTCCCSEEEETTSHHHHHHHHHHHHHHH-HHTCEEEEEEEEEEETTTTEEECGGGEEEEECTT------S
T ss_pred             HHHHHHHHHHcCCCCCccccCCCHHHHHHHHHHHHHHH-HCCCEEEeeeeEEecCCcCCCCCHHHhccCcCCC------C
Confidence            99999999999999999999999999999999999999 9999999999999999999999999998877543      3


Q ss_pred             CcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCCC
Q psy2399         169 DFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQPE  229 (232)
Q Consensus       169 ~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p~  229 (232)
                      ..|..              +..||.+++++.+++|||+|  ++|+++|.+|+.+ +.++.|+
T Consensus       171 ~~c~~--------------~~~~g~~~~~~~~~~~f~~l--~~~~~~l~~~~~~~~~~i~P~  216 (564)
T 3kfl_A          171 KPCKV--------------SLESGHVVTWVEEENYMFRL--SAFRERLLKYFHDHPNCIVPE  216 (564)
T ss_dssp             CEEEE--------------ETTTSCBCEEEEEEEEEECG--GGGHHHHHHHHHHCTTSEESH
T ss_pred             CEecc--------------ccCCCCccEEEecceeEEEH--HHHHHHHHHHHHhCCCccCCH
Confidence            33421              12479999999999999999  9999999999432 4567774

>2x1l_A Methionyl-tRNA synthetase; nucleotide-binding, protein biosynthesis, ligase, aminoacyl- synthetase; HET: ADN CXS; 2.30A {Mycobacterium smegmatis} PDB: 2x1m_A*

Probab=100.00  E-value=3.1e-40  Score=310.02  Aligned_cols=194  Identities=22%  Similarity=0.358  Sum_probs=170.3

Q ss_pred             CCCCCccCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCC
Q psy2399           1 MKKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMT   80 (232)
Q Consensus         1 ~~~~~~~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~   80 (232)
                      |.-+.---.+++.++|+||+|||||+|||||+++++++|+++||+|++|     ++|.+++|+|+||++|+.+|++.|++
T Consensus         1 ~~~~~~~~~~~~~~~i~t~~P~~ng~lHiGHa~~~i~~D~l~R~~r~~G-----~~V~~~~g~D~~G~~i~~~a~~~g~~   75 (524)
T 2x1l_A            1 MAHHHHHHGGSEPFYITTAIAYPNGVPHIGHAYEYIATDAIARFKRLDG-----YDVRYLTGTDVHGQKMAETAAKEGIP   75 (524)
T ss_dssp             ----------CCEEEEEECCBCCSSCCCHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEECCCSHHHHHHHHHHTSC
T ss_pred             CCccccccCCCCCEEEeeCCCCCCCCcccchhHHHHHHHHHHHHHHhcC-----CceeeeCCcCcccHHHHHHHHHcCCC
Confidence            3344444567788999999999999999999999999999999999999     99999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceec-cCCC
Q psy2399          81 PKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIK-GECP  159 (232)
Q Consensus        81 ~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~-g~cp  159 (232)
                      |+++++++.+.|++++++|||++|.|++|+++.|.+.++++|.+|+ ++|+||++++.+|||+.|++++++++|+ |.  
T Consensus        76 ~~~~~~~~~~~~~~~~~~lgi~~d~~~~t~~~~~~~~v~~~~~~L~-~~G~iY~~~~~v~~~~~~~t~l~~~ev~~g~--  152 (524)
T 2x1l_A           76 AAELARRNSDVFQRLQEKLNISFDRFIRTSDADHYEASKAIWKRMA-DAGDIYLDAYKGWYSIRDERFFTENETTEQP--  152 (524)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCCSEEEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEEECGGGEEECT--
T ss_pred             HHHHHHHHHHHHHHHHHHcCCcCCCCeecCCHHHHHHHHHHHHHHH-HCCCEEeeeeeeeccCccCccccHHHhccCC--
Confidence            9999999999999999999999999999999999999999999999 9999999999999999999999999985 32  


Q ss_pred             CCCccccCCCcCccCCCCCCCccccCCccc-CCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCC
Q psy2399         160 ICNAKDQYGDFCECCSSIYTPTKLINPYSI-LSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQP  228 (232)
Q Consensus       160 ~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~-~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p  228 (232)
                                    ||          +.|. .||.+++++.+++|||+|  ++|+++|.+++-+ +.++.|
T Consensus       153 --------------~G----------~~c~~~~g~~v~~~~~~qwF~~l--~~~~~~l~~~~~~~~~~i~p  197 (524)
T 2x1l_A          153 --------------DG----------TRIATETGAPVTWTEEQTYFFRL--SAYTDRLLALYEEHPEFIGP  197 (524)
T ss_dssp             --------------TS----------CEEETTTCCBEEEEEEEEEEECG--GGSHHHHHHHHHHCGGGEES
T ss_pred             --------------CC----------CccccccCCcceEEecCCeEeeH--HHHHHHHHHHHHhCCCeeCC
Confidence                          22          2577 899999999999999999  9999999999332 234544

>4dlp_A Aminoacyl-tRNA synthetase, class I:aminoacyl-tRNA synthetase, class IA:methionyl-tRNA...; structural genomics; 2.65A {Brucella melitensis biovar abortus 230ORGANISM_TAXID}

Probab=100.00  E-value=4.8e-40  Score=309.63  Aligned_cols=186  Identities=23%  Similarity=0.358  Sum_probs=171.1

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      +++++||+|+|||||+|||||+|++|++|+++||+|++|     ++|.+++|+|+||++|+..|++.|++|+++++++.+
T Consensus        24 ~~~~~i~~p~pypng~lHiGH~r~~v~~D~laR~lr~~G-----~~V~~~~g~dd~g~ki~~~a~~~g~~~~~~~~~~~~   98 (536)
T 4dlp_A           24 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNG-----MDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTS   98 (536)
T ss_dssp             CCEEEEEECCBCCSSCCCHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEECCCSHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCEEEeCCCCCCCCCcCcchhHHHHHHHHHHHHHHhcC-----CcEEEecCcCCcchHHHHHHHHcCCCHHHHHHHHHH
Confidence            468999999999999999999999999999999999999     999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCc
Q psy2399          91 NRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDF  170 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~  170 (232)
                      .|+++|++|||++|.|++|+++.|.+.++++|.+|. ++|+||++++.+|||+.|+++++++++...        ..|. 
T Consensus        99 ~~~~~l~~lgi~~d~~~~t~~~~~~~~v~~~~~~L~-~~G~iY~~~~~~~~~~~~~~~l~~~~~~~~--------~~g~-  168 (536)
T 4dlp_A           99 AFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMV-ANGDIYKGGYAGWYSVRDEAYYGEEETEVR--------ADGV-  168 (536)
T ss_dssp             HHHHHHHHTTCCCSEEEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEEECGGGCEEC--------TTSC-
T ss_pred             HHHHHHHHcCCCCCcceeCCCHHHHHHHHHHHHHHH-HCCCEEEeceeeeecCCcCcccCHHHhhcC--------CCCC-
Confidence            999999999999999999999999999999999999 999999999999999999999999988631        1122 


Q ss_pred             CccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCCC
Q psy2399         171 CECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQPE  229 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p~  229 (232)
                                      .|..||.+++++.+++|||+|  ++++++|.+|+.+ +.++.|+
T Consensus       169 ----------------~c~~~g~~~e~~~~~~~f~~l--~~~~~~l~~~~~~~~~~i~P~  210 (536)
T 4dlp_A          169 ----------------RYGPQGTPVEWVEEESYFFRL--SAYQDKLLDLYENNPGFIMPA  210 (536)
T ss_dssp             ----------------EECTTSSBCEEEEEEEEEECG--GGGHHHHHHHHHHCTTSEESH
T ss_pred             ----------------cccCCCCcceEEeccceEEec--HHHHHHHHHHHHhCCCccCcH
Confidence                            355688999999999999999  9999999999433 3466664

>4arc_A Leucine--tRNA ligase; ligase-RNA complex, nucleotide-binding, protein biosynthesis I aminoacyl-tRNA synthetase, ATP-binding; 2.00A {Escherichia coli} PDB: 4aq7_A 4ari_A* 4as1_A*

Probab=100.00  E-value=4.4e-40  Score=323.57  Aligned_cols=175  Identities=25%  Similarity=0.306  Sum_probs=140.1

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      .++++|+|+++||||||.|||||+++++++|+++||+||+|     ++|.+++|+|+||+||+..|++.|++|.++++++
T Consensus        50 ~~~~~~~v~~~~PypnG~lHiGHa~~~~~~DvlaRy~rm~G-----~~V~~~~G~D~~Glpie~~a~~~g~~p~~~~~~~  124 (880)
T 4arc_A           50 ESKEKYYCLSMLPYPSGRLHMGHVRNYTIGDVIARYQRMLG-----KNVLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDN  124 (880)
T ss_dssp             TTSCEEEEEECCCCCCSSCCHHHHHHHHHHHHHHHHHHHTT-----CEEECCCEECCCSTHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCCCCEEEEcCCCCCCCCcchhhhHHHHHHHHHHHHHHHcC-----CceEEecCccccCcHHHHHHHHcCCCHHHHHHHH
Confidence            45678999999999999999999999999999999999999     9999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccCCcCC--ccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcccc
Q psy2399          89 SSNRKKYLDGFYIKFD--NWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQ  166 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d--~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~  166 (232)
                      .+.|+++|++||+++|  ++++|+++.|.+.++++|.+|+ ++|+||++.+.+|||+.|+++|++.+|            
T Consensus       125 i~~~~~~l~~LGis~Dw~~~~~T~d~~~~~~v~~~f~~L~-ekGliY~~~~~v~wcp~~~t~La~~ev------------  191 (880)
T 4arc_A          125 IAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELY-KKGLVYKKTSAVNWCPNDQTVLANEQV------------  191 (880)
T ss_dssp             HHHHHHHHHHTTCCCCGGGCEETTSHHHHHHHHHHHHHHH-HTTCEEEEEECC---------------------------
T ss_pred             HHHHHHHHHHhCCCcCCCCCEEcCCHHHHHHHHHHHHHHH-HCCCEEEeceeEeecCCcCCEecchhh------------
Confidence            9999999999999655  8999999999999999999999 999999999999998888888776655            


Q ss_pred             CCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhh
Q psy2399         167 YGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWA  220 (232)
Q Consensus       167 ~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~  220 (232)
                                       ++++|..||.+++.+++++|||+|  ++|+++|.++|
T Consensus       192 -----------------~~g~~~~~g~~ve~~~~~~~f~~i--~~y~~~Ll~~l  226 (880)
T 4arc_A          192 -----------------IDGCCWRCDTKVERKEIPQWFIKI--TAYADELLNDL  226 (880)
T ss_dssp             --------------------------------CEEEEEECG--GGGHHHHHHHG
T ss_pred             -----------------hcCcCcCCCCccEEEEccceEEee--chhHHHHHHHH
Confidence                             445677788999999999999999  99999999994

>1ile_A Ilers, isoleucyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken structural genomics/proteom initiative, RSGI, structural genomics; 2.50A {Thermus thermophilus} SCOP: a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1jzq_A* 1jzs_A*

Probab=100.00  E-value=8.8e-41  Score=328.30  Aligned_cols=140  Identities=19%  Similarity=0.252  Sum_probs=132.9

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-CCCH------
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-GMTP------   81 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-g~~~------   81 (232)
                      +++++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|+|+||+||+.+|++. |+++      
T Consensus        35 ~~~~~f~i~~~pPy~nG~lHiGH~~~~~~~D~i~R~~rm~G-----~~v~~~~G~D~~Glpie~~a~k~l~~~~~~~~~~  109 (821)
T 1ile_A           35 KGGPRYTVYEGPPTANGLPHVGHAQARSYKDLFPRYKTMRG-----YYAPRRAGWDTHGLPVELEVEKKLGLKSKREIEA  109 (821)
T ss_dssp             TTSCBCCBCCCCCCTTSCCCTTHHHHHHHHHHHHHHHHHTT-----CBCCCEEEECCCHHHHHHHHHHHTTCCSHHHHHH
T ss_pred             CCCCcEEEecCCCCCCCCCchhhhHhHHHHHHHHHHHHhcC-----CcccccccccCCCchHHHHHHHHhcccccchHhh
Confidence            46688999999999999999999999999999999999999     99999999999999999999985 8764      


Q ss_pred             ----------HHHHHHHHHHHHHHHhccC--CcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCccc
Q psy2399          82 ----------KEFINNISSNRKKYLDGFY--IKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFL  149 (232)
Q Consensus        82 ----------~e~~~~~~~~~~~~l~~lg--I~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l  149 (232)
                                .++++++.+.++++|++||  ++||++++|+++.|.+.++++|.+|+ ++|+||++.+.++|||.|+|+|
T Consensus       110 ~g~~~f~~~~~~~~~~~~~~~~~~~~~lg~~~dwd~~~~T~d~~~~~~v~~~f~~L~-~~Gliy~~~~~v~wcp~~~t~L  188 (821)
T 1ile_A          110 YGIERFNQACRESVFTYEKEWEAFTERIAYWVDLEDAYATLEPTYIESIWWSLKNLF-DRGLLYRDHKVVPYCPRCGTPL  188 (821)
T ss_dssp             HCHHHHHHHHHHHTTTTHHHHTTHHHHTTCCCEEEEEEETTSHHHHHHHHHHHHHHH-HTTCEEEECCEEEEETTTTEEC
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHhCCeEccCCCeEECCHHHHHHHHHHHHHHH-HcCCeeecCcceEecCCCCCcc
Confidence                      4567788899999999999  79999999999999999999999999 9999999999999999999999


Q ss_pred             cccee
Q psy2399         150 PDRYI  154 (232)
Q Consensus       150 ~~~~v  154 (232)
                      +|++|
T Consensus       189 ad~ev  193 (821)
T 1ile_A          189 SSHEV  193 (821)
T ss_dssp             CHHHH
T ss_pred             cHhHh
Confidence            99999

>2d5b_A Methionyl-tRNA synthetase; rossmann fold, class 1A AARS, isomerase, structural genomics, NPPSFA; 1.80A {Thermus thermophilus} SCOP: a.27.1.1 c.26.1.1 PDB: 1woy_A 1a8h_A 2d54_A

Probab=100.00  E-value=3.2e-39  Score=301.35  Aligned_cols=180  Identities=22%  Similarity=0.439  Sum_probs=165.6

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++++|++|+|||||+|||||+|+++++|+++||+|++|     ++|.+++|+|+||++|+.+|++.|+++.++++++.+.
T Consensus         3 ~~~~i~~p~py~~g~lHiGH~r~~~~~D~~~R~~r~~G-----~~V~~~~g~D~~G~~i~~~a~~~g~~~~~~~~~~~~~   77 (500)
T 2d5b_A            3 KVFYVTTPIYYVNAEPHLGHAYTTVVADFLARWHRLDG-----YRTFFLTGTDEHGETVYRAAQAAGEDPKAFVDRVSGR   77 (500)
T ss_dssp             CEEEEECCCEETTSCCCHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEEECCSHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CcEEEecCCCCCCCCcchhhHHHHHHHHHHHHHHHcCC-----CceeeecccCCchHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCcC
Q psy2399          92 RKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFC  171 (232)
Q Consensus        92 ~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~C  171 (232)
                      |+++|++|||++|.+++|+++.|.+.++++|.+|+ ++|+||++++.++||+.|+++++++++                 
T Consensus        78 ~~~~~~~lgi~~d~~~~t~~~~~~~~~~~~~~~L~-~~G~iy~~~~~~~~~~~~~~~~~~~~l-----------------  139 (500)
T 2d5b_A           78 FKRAWDLLGIAYDDFIRTTEERHKKVVQLVLKKVY-EAGDIYYGEYEGLYCVSCERFYTEKEL-----------------  139 (500)
T ss_dssp             HHHHHHHTTCCCSEEEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEECCTTTS-----------------
T ss_pred             HHHHHHHhCCcCCCCcccCCHHHHHHHHHHHHHHH-HCCCEEecceEEecCCCcCcccCchhc-----------------
Confidence            99999999999999999999999999999999999 999999999999998888888876654                 


Q ss_pred             ccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCC
Q psy2399         172 ECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQP  228 (232)
Q Consensus       172 e~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p  228 (232)
                                  +++.|+.||.+++.+.+++|||+|  ++|+++|.+++-+ +.++.|
T Consensus       140 ------------~~g~c~~~~~~v~~~~~~~wf~~l--~~~~~~l~~~~~~~~~~~~p  183 (500)
T 2d5b_A          140 ------------VEGLCPIHGRPVERRKEGNYFFRM--EKYRPWLQEYIQENPDLIRP  183 (500)
T ss_dssp             ------------BTTBCTTTCSBCEEEEEEEEEECG--GGGHHHHHHHHHTCTTSEES
T ss_pred             ------------cCCcCCCCCCeeeEEecCceEEEc--HHHHHHHHHHHHhCCCeeCC
Confidence                        334567788899999999999999  9999999999433 345544

>2csx_A Methionyl-tRNA synthetase; ligase, riken structural genomics/proteomics initiative, RSGI, structural genomics, ligase/RNA complex; 2.70A {Aquifex aeolicus} PDB: 2ct8_A*

Probab=100.00  E-value=1.2e-39  Score=304.28  Aligned_cols=183  Identities=23%  Similarity=0.387  Sum_probs=142.2

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      +++++|++|+|||||+|||||+++++++|+++||+|++|     ++|.++.|+|+||++|+.+|++.|++|+++++++.+
T Consensus         4 ~~~~~i~~p~py~ng~lHiGH~~~~~~~D~~~R~~r~~G-----~~V~~~~g~D~~G~~i~~~a~~~g~~~~~~~~~~~~   78 (497)
T 2csx_A            4 MKKFYVTTPIYYVNDVPHLGHAYTTIAADTIARYYRLRD-----YDVFFLTGTDEHGLKIQKKAEELGISPKELVDRNAE   78 (497)
T ss_dssp             SCEEEEEEEEEETTSCCCHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEEECCSHHHHTHHHHSSSCHHHHHHHHHH
T ss_pred             CCcEEEecCCCCCCCccchhhHHHHHHHHHHHHHHHhcC-----CceeeecccCCCcHHHHHHHHHcCCCHHHHHHHHHH
Confidence            478999999999999999999999999999999999999     999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCc
Q psy2399          91 NRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDF  170 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~  170 (232)
                      .|+++|++|||++|.+++|+++.|.+.++++|.+|+ ++|+||++++.++||+.++++++++++..              
T Consensus        79 ~~~~~~~~lgi~~d~~~~t~~~~~~~~~~~~~~~L~-~~G~iY~~~~~~~~~~~~~~~~~~~~~~~--------------  143 (497)
T 2csx_A           79 RFKKLWEFLKIEYTKFIRTTDPYHVKFVQKVFEECY-KRGDIYLGEYEGWYCVGCEEFKSEAELAE--------------  143 (497)
T ss_dssp             HHHHHHHHTTCCCSEEEETTSHHHHHHHHHHHHHHH-HTTCEEEEEC---------------------------------
T ss_pred             HHHHHHHHhCCcCCCCccCCCHHHHHHHHHHHHHHH-HCCCEEecceeeccCcccCeEccHHHhcc--------------
Confidence            999999999999999999999999999999999999 99999999999999999999988887742              


Q ss_pred             CccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCCC
Q psy2399         171 CECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQPE  229 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p~  229 (232)
                                    .+.|..||.+++.+.+++|||+|  ++|+++|.+++-+ +.++.|+
T Consensus       144 --------------~~~c~~~~~~~~~~~~~~wf~~l--~~~~~~l~~~~~~~~~~~~p~  187 (497)
T 2csx_A          144 --------------DHTCPIHQKKCEYIKEPSYFFRL--SKYQDKLLELYEKNPEFIQPD  187 (497)
T ss_dssp             ----------------------------CCEEEEECT--TSSHHHHHHHHHHCTTSBCSH
T ss_pred             --------------CCCCCCCCCCCeEEecCceEEEc--HHHHHHHHHHHHhCCCeeCcH
Confidence                          04466677788999999999999  9999999999433 3466664

>2v0c_A Aminoacyl-tRNA synthetase; ligase, nucleotide-binding, protein biosynthesis; HET: LMS ANZ; 1.85A {Thermus thermophilus} PDB: 1h3n_A* 1obc_A* 1obh_A* 2bte_A* 2byt_A 2v0g_A*

Probab=100.00  E-value=7.3e-39  Score=315.92  Aligned_cols=175  Identities=22%  Similarity=0.258  Sum_probs=161.8

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      +++++++|+++||||||.|||||+++++++|+++||+||+|     ++|.+++|+|+||+||+.+|++.|++|.++++++
T Consensus        30 ~~~~k~~v~~~~Py~nG~lHiGHa~~~~~~Dvl~Ry~rm~G-----~~V~~~~G~D~~Glpie~~a~k~g~~~~~~~~~~  104 (878)
T 2v0c_A           30 GGRGKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQG-----YEVLHPMGWDAFGLPAENAALKFGVHPKDWTYAN  104 (878)
T ss_dssp             C---EEEEEECCCCCSSCCBHHHHHHHHHHHHHHHHHHHHT-----CEEECCCCBCCSSHHHHHHHHHTTCCHHHHHHHH
T ss_pred             CCCCCEEEECCCCCCCCCcchhhhHHHHHHHHHHHHHHhcC-----CceEeecccCcccHHHHHHHHHcCCCHHHHHHHH
Confidence            45677999999999999999999999999999999999999     9999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccCCcCC--ccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcccc
Q psy2399          89 SSNRKKYLDGFYIKFD--NWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQ  166 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d--~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~  166 (232)
                      .+.|+++|++|||++|  ++++|+++.|.+.++++|.+|+ ++|+||++.+.++||+.|+++|++.+|+           
T Consensus       105 ~~~~~~~~~~LGi~~Dw~~~~~T~d~~~~~~v~~~f~~L~-~kGliY~~~~~v~w~p~~~t~La~~ev~-----------  172 (878)
T 2v0c_A          105 IRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMW-EKGLAYRAKGLVNWCPKCQTVLANEQVV-----------  172 (878)
T ss_dssp             HHHHHHHHHHTTCCCCGGGCCBTTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEEECGGGEE-----------
T ss_pred             HHHHHHHHHHhCCccCcCCCeecCCHHHHHHHHHHHHHHH-HCCCEEEcceeEEEeCCCCCCcCHHHHh-----------
Confidence            9999999999999655  8999999999999999999999 9999999999999999999999998884           


Q ss_pred             CCCcCccCCCCCCCccccCCcccC-CCCccEEEEccceeEecCChhhHHHHHhhh
Q psy2399         167 YGDFCECCSSIYTPTKLINPYSIL-SGTKPIIKSSKHFFFKLSDKRCIDFLRKWA  220 (232)
Q Consensus       167 ~g~~Ce~Cg~~~~~~~l~~~~~~~-~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~  220 (232)
                                        ++.|.. ||++++.+++++|||+|  ++|+++|.+++
T Consensus       173 ------------------~g~~~~~~~~~~~~~~~~~~f~~l--~~~~~~L~~~l  207 (878)
T 2v0c_A          173 ------------------EGRCWRHEDTPVEKRELEQWYLRI--TAYAERLLKDL  207 (878)
T ss_dssp             ------------------TTEESSCTTCBCEEEEEEEEEECG--GGGHHHHHHTT
T ss_pred             ------------------cCCCcccCCCceEEEecceeeEec--chhHHHHHHHh
Confidence                              223445 78899999999999999  99999999994

>1gax_A Valrs, valyl-tRNA synthetase; protein-RNA complex, rossmann fold, coiled coil, riken structural genomics/proteomics initiative, RSGI; HET: VAA; 2.90A {Thermus thermophilus} SCOP: a.2.7.3 a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1ivs_A* 1iyw_A

Probab=100.00  E-value=1.2e-38  Score=313.70  Aligned_cols=213  Identities=16%  Similarity=0.180  Sum_probs=181.6

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH----cCCCHH--
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK----AGMTPK--   82 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~----~g~~~~--   82 (232)
                      +++++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||++++.++++    .|+++.  
T Consensus        31 ~~~~~f~i~~ppPy~nG~lHiGHa~~~~l~Dii~Ry~rm~G-----~~vl~~~G~D~~Glp~e~~vek~l~~~g~~~~~~  105 (862)
T 1gax_A           31 SGKPPFVIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRG-----FEAVWLPGTDHAGIATQVVVERLLLKEGKTRHDL  105 (862)
T ss_dssp             CCSCEEEEECCCCBSSSCCCHHHHHHHHHHHHHHHHHHTTT-----SEEEEECEEBCCTHHHHHHHHTTTTTTTSCCSCC
T ss_pred             CCCCcEEEEcCCCCCCCCcchhhhHHHHHHHHHHHHHHhCC-----CccccccccCCCCcHHHHHHHHHHHHcCCChHHc
Confidence            45678999999999999999999999999999999999999     9999999999999999999985    466543  


Q ss_pred             ----------HHHHHHHHHHHHHHhccCCcCC--ccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccc
Q psy2399          83 ----------EFINNISSNRKKYLDGFYIKFD--NWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLP  150 (232)
Q Consensus        83 ----------e~~~~~~~~~~~~l~~lgI~~d--~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~  150 (232)
                                ++++++.+.++++|++||+++|  +.+.|+++.|.+.|+++|.+|+ ++|+||++.+.++|||.|+|+|+
T Consensus       106 ~~~~f~~~~~~~~~~~~~~~~~q~~rlG~s~Dw~r~~~T~d~~~~~~v~~~F~~L~-~kGliYrg~~~v~wcp~~~T~Ls  184 (862)
T 1gax_A          106 GREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYY-HEGLAYRAPRLVNWCPRCETTLS  184 (862)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHHTTCCCCGGGCEETTSHHHHHHHHHHHHHHH-TTSSEEEECCEEEEETTTTEEEC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCcccCCHHHHHHHHHHHHHHH-HCCCEEecccccccCCCcCcccc
Confidence                      5689999999999999998555  5556999999999999999999 99999999999999999999999


Q ss_pred             cceec-----c------------------------------------------------CCCCCCcc-------------
Q psy2399         151 DRYIK-----G------------------------------------------------ECPICNAK-------------  164 (232)
Q Consensus       151 ~~~v~-----g------------------------------------------------~cp~c~~~-------------  164 (232)
                      |.+|+     |                                                .||.|+..             
T Consensus       185 d~EV~~~e~~g~~~~v~f~~~~~~~l~v~TTrPeTl~g~~avav~P~~~ry~~l~G~~~~~P~~~~~ipii~~~~V~~~~  264 (862)
T 1gax_A          185 DLEVETEPTPGKLYTLRYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEVWIPILADPAVEKDF  264 (862)
T ss_dssp             GGGEEECCEEEEEEEEECCCSSSCCCEEEESCSGGGTTCCCEEECSSCCTTCSCTTCCCBCTTCCCBCCEEECTTCCTTS
T ss_pred             ccccccccccceEEEEEEEecCCCEEEEEeCCccccccceEEEECCCccHHHHHcCCEEECCCCCCeeeEEeccccccCC
Confidence            99986     1                                                38888753             


Q ss_pred             ------------------------------ccCCCcCccC--CCCC------------------------CCccccCCcc
Q psy2399         165 ------------------------------DQYGDFCECC--SSIY------------------------TPTKLINPYS  188 (232)
Q Consensus       165 ------------------------------~~~g~~Ce~C--g~~~------------------------~~~~l~~~~~  188 (232)
                                                    +..|..|++|  |.+.                        .+.....|.|
T Consensus       265 GTG~V~~~Pahd~~D~~~~~~~~L~~~~~id~~G~~~~~~~~g~~~Gl~~~~a~~~iv~~L~~~g~l~~~~~~~h~~p~c  344 (862)
T 1gax_A          265 GTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRMEGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATC  344 (862)
T ss_dssp             SSSEEECCGGGCHHHHHHHHHTTCCCCCSBCTTSBBCSSSSCTTTSSSBSSHHHHHHHHHHHTTTCEEEEEEEEECCEEE
T ss_pred             CCcceEecCCCCchHHHHHHHcCCCccceeCCCCccccccCCcccCCcCHHHHHHHHHHHHHhCCCeeeeccccccCCee
Confidence                                          2457788888  6422                        1112356899


Q ss_pred             cCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCCCC
Q psy2399         189 ILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQPE  229 (232)
Q Consensus       189 ~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~p~  229 (232)
                      ..||.+++.+.++|||+++  +++++++.+++.+ ...+.|+
T Consensus       345 ~R~~~~i~~~~~~qWFv~~--~~~~~~~l~~v~~~~~~~~P~  384 (862)
T 1gax_A          345 SRCGTPIEYAIFPQWWLRM--RPLAEEVLKGLRRGDIAFVPE  384 (862)
T ss_dssp             TTTCSBCCEEECCEEEECH--HHHHHHHHHHHHHTCCEESSS
T ss_pred             cCCCCeEEEEecceEEEEh--HHHHHHHHHHHHcCCceEcCH
Confidence            9999999999999999999  9999999999422 2244554

>1ffy_A Isoleucyl-tRNA synthetase; protein-RNA complex, metal IONS, editing tRNA synthetase, double-sieve, ligase/RNA, mupiroci; HET: MRC; 2.20A {Staphylococcus aureus} SCOP: a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1qu2_A* 1qu3_A*

Probab=100.00  E-value=1.5e-38  Score=314.84  Aligned_cols=142  Identities=27%  Similarity=0.363  Sum_probs=135.7

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCH------
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTP------   81 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~------   81 (232)
                      ++++++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+.+|++.|+++      
T Consensus        44 ~~~~~~f~i~~~pPY~nG~lHiGHa~n~~~~Dii~Ry~rm~G-----~~v~~~~GwD~hGlpiE~~a~k~G~~~~~~~~~  118 (917)
T 1ffy_A           44 NKGNETFILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQG-----FYAPYVPGWDTHGLPIEQALTKKGVDRKKMSTA  118 (917)
T ss_dssp             TTTSCBCCEECCCCBSSSCCCHHHHHHHHHHHHHHHHHHTTT-----CBCCCCCEEBCCSHHHHHHHHHHTCCSTTTCHH
T ss_pred             ccCCCceeeCCCCCCCCCcchHHHHHHHHHHHHHHHHHHhCC-----CCCCCcccCchhhHHHHHHHHHcCCCchhCCHH
Confidence            356778999999999999999999999999999999999999     999999999999999999999999875      


Q ss_pred             ------HHHHHHHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccce
Q psy2399          82 ------KEFINNISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRY  153 (232)
Q Consensus        82 ------~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~  153 (232)
                            .++++++.+.++++|++||+  +||++++|+++.|.+.++++|.+|+ ++|+||++.++++|||.|+|+|+|++
T Consensus       119 ~f~~~~~~~~~~~~~~~~~~~~rlG~~~Dwd~~~~T~d~~~~~~v~~~F~~l~-~kGliYr~~~~v~wcp~~~T~Lae~e  197 (917)
T 1ffy_A          119 EFREKCKEFALEQIELQKKDFRRLGVRGDFNDPYITLKPEYEAAQIRIFGEMA-DKGLIYKGKKPVYWSPSSESSLAEAE  197 (917)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTTCCSCTTSCEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEECCGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCeEEccCCCeEcCCHHHHHHHHHHHHHHH-HcCCeEecccceeccCCCCcCcchhh
Confidence                  56888999999999999999  6889999999999999999999999 99999999999999999999999999


Q ss_pred             ec
Q psy2399         154 IK  155 (232)
Q Consensus       154 v~  155 (232)
                      |+
T Consensus       198 Ve  199 (917)
T 1ffy_A          198 IE  199 (917)
T ss_dssp             EE
T ss_pred             hh
Confidence            96

>1wkb_A Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, editing, amino acid, aminoacylation, trnaLeu, structural genomics; 2.05A {Pyrococcus horikoshii}

Probab=100.00  E-value=1.6e-34  Score=283.66  Aligned_cols=142  Identities=23%  Similarity=0.308  Sum_probs=131.5

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc-----------
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA-----------   77 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~-----------   77 (232)
                      +++++|+|++|||||||+|||||+++++++|+++||+||+|     ++|.+++|+|+||+||+..|++.           
T Consensus        31 ~~~~~~~i~~~~Py~nG~lHiGH~~~~~~~D~i~R~~rm~G-----~~V~~~~G~D~~G~pie~~a~~~~~~~~~~~~~~  105 (810)
T 1wkb_A           31 PKEKKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQG-----YNVLFPMAWHITGSPIVGIAERIKNRDPKTIWIY  105 (810)
T ss_dssp             CGGGEEEEEECCCBTTSCCBHHHHHHHHHHHHHHHHHHHHT-----CEEECCCCBBCCBSHHHHHHHHHHTTCHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCCCccccchhHHHHHHHHHHHHcCC-----CccCcCCccCCCCChHHHHHHHhcccCchHHHHH
Confidence            34678999999999999999999999999999999999999     99999999999999999888642           


Q ss_pred             -------------CCCHHHHHHHHHHHHHHHHhccCCcCC--ccccCCC--hhHHHHHHHHHHHHHhhcCCEEeccccee
Q psy2399          78 -------------GMTPKEFINNISSNRKKYLDGFYIKFD--NWYSTDS--IENIDLVQKIYDTLYNKAKLIINKKINQF  140 (232)
Q Consensus        78 -------------g~~~~e~~~~~~~~~~~~l~~lgI~~d--~~~~t~~--~~~~~~v~~~~~~L~~~kG~iy~~~~~~~  140 (232)
                                   +.++.++++++.+.++++|++|||++|  ++++|++  +.|.+.++++|.+|+ ++|+||++.+.+|
T Consensus       106 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lgi~~Dw~~~~~T~d~~~~~~~~v~~~f~~L~-~~Gliy~~~~~v~  184 (810)
T 1wkb_A          106 RDVYKVPEEILWTFEDPINIVKYFMKAAKETFIRAGFSVDWSREFYTTSLFPPFSKFIEWQFWKLK-EKGYIVKGAHRVR  184 (810)
T ss_dssp             HHTSCCCHHHHHGGGSHHHHHHHHHHHHHHHHHHTTCCCCGGGCCBCSTTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEE
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCeEEecCCceEecCCchHHHHHHHHHHHHHH-HCCCEEECCeeee
Confidence                         246788999999999999999999666  7788999  999999999999999 9999999999999


Q ss_pred             eccCCCcccccceecc
Q psy2399         141 FDPIKNIFLPDRYIKG  156 (232)
Q Consensus       141 ~~~~~~~~l~~~~v~g  156 (232)
                      |||.|+|+|++.+|+.
T Consensus       185 ~~~~~~t~La~~ev~~  200 (810)
T 1wkb_A          185 WDPVVGTPLGDHDLME  200 (810)
T ss_dssp             EETTTTEECCTTCCSB
T ss_pred             ccCCcCCCccHHHHhc
Confidence            9999999999998853

>1wz2_A Leucyl-tRNA synthetase; ligase, riken structural genomics/proteomics initiativ structural genomics, ligase-RNA complex; 3.21A {Pyrococcus horikoshii}

Probab=100.00  E-value=2.9e-34  Score=285.96  Aligned_cols=139  Identities=23%  Similarity=0.329  Sum_probs=130.1

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc--------------
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA--------------   77 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~--------------   77 (232)
                      ++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|||+||+||+.+|++.              
T Consensus        34 ~kf~i~~~pPy~nG~lHiGH~~~~~~~Dii~Ry~rm~G-----~~Vl~~~GwD~~GlPie~~a~~~~~~~~~~~~~~~~~  108 (967)
T 1wz2_A           34 KKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQG-----YNVLFPMAWHITGSPIVGIAERIKNRDPKTIWIYRDV  108 (967)
T ss_dssp             GCCBEEECCCBCSSCCBHHHHHHHHHHHHHHHHHHHTT-----CCCBCCCCBBCCSSHHHHHHHHHHTTCHHHHHHHHTT
T ss_pred             CcEEEEeCCCCCCCCcchhhhHHHHHHHHHHHHHHcCC-----CccCCCCcCCCCCcHHHHHHHHhhccchhHHHHHHHh
Confidence            78999999999999999999999999999999999999     99999999999999999988752              


Q ss_pred             -C---------CCHHHHHHHHHHHHHHHHhccCC--cCCccccCCC--hhHHHHHHHHHHHHHhhcCCEEecccceeecc
Q psy2399          78 -G---------MTPKEFINNISSNRKKYLDGFYI--KFDNWYSTDS--IENIDLVQKIYDTLYNKAKLIINKKINQFFDP  143 (232)
Q Consensus        78 -g---------~~~~e~~~~~~~~~~~~l~~lgI--~~d~~~~t~~--~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~  143 (232)
                       |         .+|.++++++.+.++++|++||+  +|++.+.|++  +.|.+.++++|.+|+ ++|+||++.+.++|||
T Consensus       109 ~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~lG~~~Dw~r~~~T~d~np~y~~~v~~~F~~L~-~kGliyr~~~~v~wcp  187 (967)
T 1wz2_A          109 YKVPEEILWTFEDPINIVKYFMKAAKETFIRAGFSVDWSREFYTTSLFPPFSKFIEWQFWKLK-EKGYIVKGAHRVRWDP  187 (967)
T ss_dssp             SCCCHHHHHGGGSHHHHHHHHHHHHHHHHHTTTCCCCTTSCCBCSTTSHHHHHHHHHHHHHTT-TTTCEEECCCCCEECT
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCceEecCCCeEECCCChhHHHHHHHHHHHHH-HCCCEEEeceEecccC
Confidence             3         35788899999999999999998  5667889999  999999999999999 9999999999999999


Q ss_pred             CCCcccccceecc
Q psy2399         144 IKNIFLPDRYIKG  156 (232)
Q Consensus       144 ~~~~~l~~~~v~g  156 (232)
                      .|+|+|+|.+|+.
T Consensus       188 ~~~T~Lad~Ev~~  200 (967)
T 1wz2_A          188 VVGTPLGDHDLME  200 (967)
T ss_dssp             TTSCBCCSSSCSS
T ss_pred             CCCCCcchhhhcc
Confidence            9999999998753

>3c8z_A Cysteinyl-tRNA synthetase; cysteine ligase, rossmann fold, Cys-SA inhibitor, zinc binding, ATP-binding, aminoacyl-tRNA synthetase; HET: 5CA 1PE EPE; 1.60A {Mycobacterium smegmatis}

Probab=99.94  E-value=2.9e-26  Score=209.66  Aligned_cols=126  Identities=11%  Similarity=0.126  Sum_probs=116.1

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      .+..+....|||||++||||+|++|++|+++||+|++|     ++|.+++|+|+||++|+.+|++.|+++.++++++.+.
T Consensus        38 ~~v~~y~~gPt~yg~~HiGHar~~v~~DvlaR~lr~~G-----~~V~~~~~~dd~g~ki~~~A~~~g~~~~~~~~~~~~~  112 (414)
T 3c8z_A           38 PTATMYVCGITPYDATHLGHAATYLTFDLVHRLWLDAG-----HTVQYVQNVTDVDDPLFERAERDGIDWRTLGDRETQL  112 (414)
T ss_dssp             SEEEEEECCCCTTSCCBHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEECCSCHHHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCceEEeCCCcCCCCcCccccHHHHHHHHHHHHHHHcC-----CCEEeCCCCCCccHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            33444444678899999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCc-CCccccCCChhHHHHHHHHHHHHHhhcCCEEecc----cceeeccCC
Q psy2399          92 RKKYLDGFYIK-FDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKK----INQFFDPIK  145 (232)
Q Consensus        92 ~~~~l~~lgI~-~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~----~~~~~~~~~  145 (232)
                      |+++|++|||. +|.|++|++  |...++++|.+|. ++|++|+++    ..+||+.+.
T Consensus       113 ~~~~~~~Lgi~~~d~~~r~t~--~~~~~~~~~~~L~-~kG~~Y~~~~~~e~~~~f~~~~  168 (414)
T 3c8z_A          113 FREDMAALRVLPPHDYVAATD--AIAEVVEMVEKLL-ASGAAYIVEDAEYPDVYFRADA  168 (414)
T ss_dssp             HHHHHHHTTCCCCSEEEEGGG--CHHHHHHHHHHHH-HHTSEEECSCSSCCCEEECTTS
T ss_pred             HHHHHHHcCCCCCcceecccc--hHHHHHHHHHHHH-HCCCEEeccCCcCCCEEEEchh
Confidence            99999999998 999999984  8899999999999 999999988    788987664

>3tqo_A Cysteinyl-tRNA synthetase; protein synthesis, ligase; 2.30A {Coxiella burnetii}

Probab=99.93  E-value=3.6e-26  Score=210.94  Aligned_cols=128  Identities=15%  Similarity=0.146  Sum_probs=118.1

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      ++++.+...+|||+|.+||||+|++|++|+++||+|++|     ++|.++.|+||+|+||+.+|++.|+++.++++++.+
T Consensus        23 ~~~v~~YvcGPtvy~~~HIGHaR~~v~~Dvl~R~lr~~G-----y~V~~v~n~dD~ddKIi~~A~~~g~~~~e~a~~~~~   97 (462)
T 3tqo_A           23 SGKVKLYVCGMTVYDYMHIGHGRSWIIFDMVVRYLRMRG-----YEVTFVRNITDIDDKIIKRAGENKESPAALAERFIQ   97 (462)
T ss_dssp             TTEEEEEECCCBTTSCCBHHHHHHHHHHHHHHHHHHHTT-----CEEEEEECBBCCCHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CCeEEEEeCCCcCCCCCchhhhHHHHHHHHHHHHHHHcC-----CceEEecCcCCCCcHHHHHHHHcCCCHHHHHHHHHH
Confidence            345556666789999999999999999999999999999     999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCcCCccc-cCCChhHHHHHHHHHHHHHhhcCCEEec-ccceeeccCCC
Q psy2399          91 NRKKYLDGFYIKFDNWY-STDSIENIDLVQKIYDTLYNKAKLIINK-KINQFFDPIKN  146 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~~~-~t~~~~~~~~v~~~~~~L~~~kG~iy~~-~~~~~~~~~~~  146 (232)
                      .|++++++|||.++.+. +++  +|...++++|.+|. ++|++|+. .+.+|||+.+-
T Consensus        98 ~f~~d~~~LgI~~d~~~praT--e~i~~i~~~i~~L~-ekG~aY~~~~g~Vyfdv~~~  152 (462)
T 3tqo_A           98 ILHEDEKALRVLSPDQEPRAT--QYVPEIIKLIQKLL-DNQYAYTGQNGDVFFDVRRF  152 (462)
T ss_dssp             HHHHHHHHHTCCCCSBCCBGG--GCHHHHHHHHHHHH-HHTSEEECTTSCEEECTTTC
T ss_pred             HHHHHHHHcCCCCCccccChh--hHHHHHHHHHHHHH-HCCCEEEecCCcEEeccccc
Confidence            99999999999987665 666  79999999999999 99999998 68999998764

>3sp1_A Cysteinyl-tRNA synthetase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, LYME disease; HET: AMP; 2.55A {Borrelia burgdorferi}

Probab=99.93  E-value=1e-25  Score=209.21  Aligned_cols=125  Identities=17%  Similarity=0.216  Sum_probs=99.8

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecC---------C-ChhhHHHHHHHHHcCCCH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICA---------D-DAHGAAIMIAAEKAGMTP   81 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g---------~-D~~G~~i~~~a~~~g~~~   81 (232)
                      .++||+  +|||+|.+||||+|++|++|+++||+|++|     ++|.|+.|         + |+||+||+.+|++.|++|
T Consensus        43 v~~Yvc--gPTvYg~~HIGHar~~v~~Dvl~R~lr~~G-----y~V~~v~niTDvGhltG~~DehddKI~~~A~~~g~~~  115 (501)
T 3sp1_A           43 VKVYAC--GPTVYNYAHIGNFRTYIFGDLLIKTLRFLG-----YKVNYAMNITDIGHLTGDLDDGEDKVAKTAREKGLTV  115 (501)
T ss_dssp             EEEEEC--CCBCSSCCCHHHHHHHHHHHHHHHHHHHHT-----CCEEEEEEEBCSCCC-------------------CCH
T ss_pred             ceEEeC--CCcCCCCcchhhhHHHHHHHHHHHHHHHcC-----CceeEEeeecccccccCCCCCCCcHHHHHHHHcCCCH
Confidence            345555  567779999999999999999999999999     99999954         4 677999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCC
Q psy2399          82 KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIK  145 (232)
Q Consensus        82 ~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~  145 (232)
                      .++++++.+.|++++++|||.+|.+.++ ..+|...++++|.+|+ ++|++|++++.+|||+.+
T Consensus       116 ~e~a~~~~~~f~~d~~~Lgi~~d~~~~~-~t~hi~~v~~~i~~L~-~kG~aY~~~g~Vyf~v~~  177 (501)
T 3sp1_A          116 YEISEFFTEAFFNDCRKLNIVYPDKVLV-ASKHIPIMIEVVKILE-EKKITYFSNGNVYFDTSC  177 (501)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCSEEEE-GGGCHHHHHHHHHHHH-HTTCEEEETTEEEECGGG
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCCcccC-cchHHHHHHHHHHHHH-HCCCEEEeCCcEEecCCc
Confidence            9999999999999999999999988765 4689999999999999 999999999999999987

>1li5_A Cysrs, cysteinyl-tRNA synthetase, transfer RNA-Cys; cysteine, E.coli, ligase; 2.30A {Escherichia coli} SCOP: a.27.1.1 c.26.1.1 PDB: 1li7_A 1u0b_B

Probab=99.92  E-value=4.2e-25  Score=204.41  Aligned_cols=124  Identities=15%  Similarity=0.145  Sum_probs=115.5

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      .+++|+  .|+|+|++||||+|++|++|+++||+|++|     ++|.++.++||+|.+|..+|++.|.+++++++++.+.
T Consensus        23 v~~yv~--gPt~y~~~HiGHar~~v~~D~l~R~lr~~G-----~~V~~v~~~tD~d~ki~~~A~~~g~~~~~~~~~~~~~   95 (461)
T 1li5_A           23 VGMYVC--GITVYDLCHIGHGRTFVAFDVVARYLRFLG-----YKLKYVRNITDIDDKIIKRANENGESFVAMVDRMIAE   95 (461)
T ss_dssp             EEEEEC--CCBSSSCCBHHHHHHHHHHHHHHHHHHHHT-----CEEEEEECBBCCSHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             eeEEEc--CCcCCCCCcccccHHHHHHHHHHHHHHHcC-----CCEEEeecCCCCcHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            345555  566779999999999999999999999999     9999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCcC-CccccCCChhHHHHHHHHHHHHHhhcCCEEec-ccceeeccCC
Q psy2399          92 RKKYLDGFYIKF-DNWYSTDSIENIDLVQKIYDTLYNKAKLIINK-KINQFFDPIK  145 (232)
Q Consensus        92 ~~~~l~~lgI~~-d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~-~~~~~~~~~~  145 (232)
                      |++++++|||.+ |.+++++  +|.+.+++++++|. ++|++|+. ++.+|||+.+
T Consensus        96 f~~~~~~LgI~~~d~~~r~t--~~~~~~~~~i~~L~-~~G~aY~~~~g~v~f~~~~  148 (461)
T 1li5_A           96 MHKDFDALNILRPDMEPRAT--HHIAEIIELTEQLI-AKGHAYVADNGDVMFDVPT  148 (461)
T ss_dssp             HHHHHHHTTCCCCSBCCBGG--GCHHHHHHHHHHHH-HTTSEEECTTSCEEECGGG
T ss_pred             HHHHHHHcCCCCCccccccc--chHHHHHHHHHHHH-HCCCEEEecCCCEEEeccc
Confidence            999999999997 8888988  48999999999999 99999999 8999998875

>2zue_A Arginyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase, nucleotide-binding, protein biosynthesis, ligase/RNA complex; HET: ANP; 2.00A {Pyrococcus horikoshii} PDB: 2zuf_A

Probab=99.82  E-value=1.2e-20  Score=180.40  Aligned_cols=134  Identities=15%  Similarity=0.114  Sum_probs=111.4

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHH-------------------
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAA-------------------   69 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~-------------------   69 (232)
                      ..+++++|....|||||++||||+|++|++|+++|+++..|     ++|.++..++|+|.+                   
T Consensus       116 ~~~~~V~ve~~spN~~~~~HiGH~Rs~iigD~laR~l~~~G-----~~V~~~~~i~D~G~Q~~~l~~~~~~~g~~~~~~~  190 (629)
T 2zue_A          116 GKGKKVIVEHTSVNPTKPLHMGHARNAILGDVMARILRFLG-----YEVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIM  190 (629)
T ss_dssp             TTTCEEEEECCCCCTTSCCBHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEECTTSHHHHHHHHHHHHCHHHHHHHH
T ss_pred             CCCCEEEEEeeCCCCCCCCccchhHHHHHHHHHHHHHHHcC-----CCceEEecccchhHHHHHHHHHHHHhCCcchhhh
Confidence            35678999999999999999999999999999999999999     999999988887665                   


Q ss_pred             --------------------HHHHHHHcCCCH--------------------HHHHHHHHHHHHHHHhccCCcCCccccC
Q psy2399          70 --------------------IMIAAEKAGMTP--------------------KEFINNISSNRKKYLDGFYIKFDNWYST  109 (232)
Q Consensus        70 --------------------i~~~a~~~g~~~--------------------~e~~~~~~~~~~~~l~~lgI~~d~~~~t  109 (232)
                                          +...+++.+.+|                    +++++.+.+.|++++++|||++|.|+++
T Consensus       191 ~~~~~~~~~~~~~d~~~g~~y~~~a~~~~~~~~~~~~~~~~~~~~e~gd~~~~~~~~~~~~~f~~~~~~L~I~~D~~~~e  270 (629)
T 2zue_A          191 NELRERGLKDNPIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGELYGRKLAEEVVRAQMVTTYKLGVKYDLLVWE  270 (629)
T ss_dssp             HHHHHHTSCSCCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHHTCCCSEEEEH
T ss_pred             hhhcccccccCcchhhHHHHHHHHHHHHhcCchHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHcCCccccccCc
Confidence                                334444444444                    7889999999999999999999999999


Q ss_pred             CChhHHHHHHHHHHHHHhhcCCEEe---cccceeeccCCCcc
Q psy2399         110 DSIENIDLVQKIYDTLYNKAKLIIN---KKINQFFDPIKNIF  148 (232)
Q Consensus       110 ~~~~~~~~v~~~~~~L~~~kG~iy~---~~~~~~~~~~~~~~  148 (232)
                      ++..|...++.++++|. ++|++|+   ++..++|+..+..|
T Consensus       271 s~~~~~~~v~~vi~~L~-~kG~~y~~~~ge~~Ga~~v~~~~~  311 (629)
T 2zue_A          271 SDIVRRKLFEIALELLS-KNENFYIPSDGKYRGAFVMDLRKL  311 (629)
T ss_dssp             HHHHHTTHHHHHHHHHH-TSTTEECCSSSTTTTCEEEECTTT
T ss_pred             CccccchhHHHHHHHHH-HCCCccccccCCcCCcEEEECccc
Confidence            97667899999999999 9999992   34445544444444

>1iq0_A Arginyl-tRNA synthetase; riken structural genomics/proteomics initiative, RSGI, structural genomics, ligase; 2.30A {Thermus thermophilus} SCOP: a.27.1.1 c.26.1.1 d.67.2.1

Probab=99.80  E-value=1.4e-19  Score=172.01  Aligned_cols=115  Identities=20%  Similarity=0.233  Sum_probs=99.8

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHH--------------------
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMI--------------------   72 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~--------------------   72 (232)
                      +++|..+.|||||++||||+|++|++|+++|++++.|     ++|.++..++|.|.++..                    
T Consensus       104 ~v~ve~~spn~~~~~HiGH~R~~iigD~laR~l~~~G-----~~V~~~~~i~D~G~q~~~li~~~~~~g~d~~~~~~~d~  178 (592)
T 1iq0_A          104 VVLVEHTSVNPNKELHVGHLRNIALGDAIARILAYAG-----REVLVLNYIDDTGRQAAETLFALRHYGLTWDGKEKYDH  178 (592)
T ss_dssp             EEEEECCCCCTTSCCBHHHHHHHHHHHHHHHHHHHTT-----EEEEEEEEECTTSHHHHHHHHHHHHTTCCCCSSSCHHH
T ss_pred             eEEEEeeCCCCCCCCcchHHHHHHHHHHHHHHHHHcC-----CceEEEeccCCcchHHHHHHHHHHHhCCcccCCCCcch
Confidence            6899999999999999999999999999999999999     999998777777643321                    


Q ss_pred             --------HH------------------HHcCCCHHHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHH
Q psy2399          73 --------AA------------------EKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLY  126 (232)
Q Consensus        73 --------~a------------------~~~g~~~~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~  126 (232)
                              .+                  .+.|. .+++++.+.+.|+++|++|||++|.|.+|++..|...+++++++|.
T Consensus       179 ~~g~~y~~~~~~~~~~~~~~~a~~~~~~~e~g~-~~~~~~~~~~~~~~~~~~LgI~~D~~~~es~~~~~~~v~~~~~~L~  257 (592)
T 1iq0_A          179 FAGRAYVRLHQDPEYERLQPAIEEVLHALERGE-LREEVNRILLAQMATMHALNARYDLLVWESDIVRAGLLQKALALLE  257 (592)
T ss_dssp             HHHHHHHHHHHCTTTGGGHHHHHHHHHHHHTTT-THHHHHHHHHHHHHHHHHTTCCCSEEEEHHHHHHTTHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhhhHHHHHHHHHHhCCchH-HHHHHHHHHHHHHHHHHHcCCEeEEeccCCcccccchHHHHHHHHH
Confidence                    11                  22343 3889999999999999999999999999997667899999999999


Q ss_pred             hhcCCEEe
Q psy2399         127 NKAKLIIN  134 (232)
Q Consensus       127 ~~kG~iy~  134 (232)
                       ++|++|+
T Consensus       258 -~kG~~y~  264 (592)
T 1iq0_A          258 -QSPHVFR  264 (592)
T ss_dssp             -TSTTEEC
T ss_pred             -HCCCccc
Confidence             9999993

>1irx_A Lysyl-tRNA synthetase; beta sandwitch, zinc-binding structure, rossmann fold, alpha-helix CAGE; 2.60A {Pyrococcus horikoshii} SCOP: a.97.1.2 c.26.1.1

Probab=99.78  E-value=1.6e-20  Score=176.18  Aligned_cols=112  Identities=14%  Similarity=0.119  Sum_probs=98.3

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhh--HHH---HHHHHHc--CCCH-----
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHG--AAI---MIAAEKA--GMTP-----   81 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G--~~i---~~~a~~~--g~~~-----   81 (232)
                      .+|+.+.|||||+|||||+|+++.+|+++||++++|     ++|.|+.++||+|  .+|   ...|.+.  |+++     
T Consensus        21 ~yv~~tgPsPtG~lHIGhaR~al~~D~laR~l~~~g-----~~v~fi~~idD~d~~rkip~~~~~a~~~~~G~~~~~~p~   95 (523)
T 1irx_A           21 KYVVESGITPSGYVHVGNFRELFTAYIVGHALRDKG-----YEVRHIHMWDDYDRFRKVPRNVPQEWKDYLGMPISEVPD   95 (523)
T ss_dssp             EEEEEEEECCSSCCCHHHHHHHHHHHHHHHHHHTTT-----CEEEEEEEECTTSBCCCCCSSSCGGGGGGTTSBGGGSCC
T ss_pred             eEEECCCCCCCCCcccCCcHHHHHHHHHHHHHHHcC-----CCEEEEEeeCCcchhhhhhhHHHHHHHHHcCCCcccCCc
Confidence            566666789999999999999999999999999999     9999999999999  666   4444444  8887     


Q ss_pred             -----HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHH-HHHHHHHHHHhhcC-CEE
Q psy2399          82 -----KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENID-LVQKIYDTLYNKAK-LII  133 (232)
Q Consensus        82 -----~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~-~v~~~~~~L~~~kG-~iy  133 (232)
                           +++++++.+.|+++|++|||++|.+ ++++. |.. .+++++.+|. ++| .||
T Consensus        96 p~~~~~~~~~~~~~~~~~~l~~Lgi~~D~~-~~se~-~~~g~~~~~i~~L~-~~G~~iy  151 (523)
T 1irx_A           96 PWGCHESYAEHFMRKFEEEVEKLGIEVDLL-YASEL-YKRGEYSEEIRLAF-EKRDKIM  151 (523)
T ss_dssp             TTSSSSSHHHHHHHHHHHHHHTTTCCCEEE-EHHHH-HHTTTTHHHHHHHH-HTHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHHcCCCceEE-echhh-ccchHHHHHHHHHH-HchHHHH
Confidence                 8899999999999999999999988 77632 777 8999999999 999 665

>1f7u_A Arginyl-tRNA synthetase; RNA-protein complex, aminoacylation; HET: PSU 1MG 2MG H2U M2G 5MC 5MU 1MA ARG; 2.20A {Saccharomyces cerevisiae} SCOP: a.27.1.1 c.26.1.1 d.67.2.1 PDB: 1bs2_A* 1f7v_A*

Probab=99.76  E-value=1.6e-18  Score=165.00  Aligned_cols=129  Identities=15%  Similarity=0.117  Sum_probs=109.5

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHH------------------
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAI------------------   70 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i------------------   70 (232)
                      ..+++++|....|||+|++||||+|++|++|+++|+++..|     ++|..+..++|+|.++                  
T Consensus       140 ~~~~~V~ve~~spN~~~plHvGHlRs~iiGD~laRil~~~G-----~~V~~~~~i~D~G~Q~~~l~~~~~~~g~~~~~~~  214 (607)
T 1f7u_A          140 VENKKVIIEFSSPNIAKPFHAGHLRSTIIGGFLANLYEKLG-----WEVIRMNYLGDWGKQFGLLAVGFERYGNEEALVK  214 (607)
T ss_dssp             SSCCEEEEECCCCBTTSCCBGGGHHHHHHHHHHHHHHHHTT-----CEEEEEEEEBCCSHHHHHHHHHHHHHCCHHHHHH
T ss_pred             cCCCeEEEEecCCCCCCCCccchHHHHHHHHHHHHHHHHcC-----CCeeEEEeecCcchHHHHHHHHHHHhCchhhccC
Confidence            35678999999999999999999999999999999999999     9999999988876654                  


Q ss_pred             ------------------------------HHHHHH------cCCC-----HHHHHHHHHHHHHHHHhccCCcCCccccC
Q psy2399          71 ------------------------------MIAAEK------AGMT-----PKEFINNISSNRKKYLDGFYIKFDNWYST  109 (232)
Q Consensus        71 ------------------------------~~~a~~------~g~~-----~~e~~~~~~~~~~~~l~~lgI~~d~~~~t  109 (232)
                                                    ...|++      .|.+     .+++++...+.|++++++|||.+|.|.++
T Consensus       215 ~~i~~l~~~Y~~~~~~~~~~~e~g~~~~~i~~~A~~~~~~le~gd~e~~~~w~~~~~~~~~~~~~~~~~L~V~fD~~~~E  294 (607)
T 1f7u_A          215 DPIHHLFDVYVRINKDIEEEGDSIPLEQSTNGKAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYARLNIKYDVYSGE  294 (607)
T ss_dssp             CHHHHHHHHHHHHHHHHHHSTTSSCHHHHSSHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSEEEEG
T ss_pred             CChHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCcceeecCc
Confidence                                          222333      2443     35678889999999999999999999988


Q ss_pred             CChhHHHHHHHHHHHHHhhcCCEEecccceeeccC
Q psy2399         110 DSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPI  144 (232)
Q Consensus       110 ~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~  144 (232)
                      ++ .+...+..+++.|. ++|++|+.++.+|++..
T Consensus       295 S~-~~~~~~~~vi~~L~-~kG~~ye~dGa~~~~~~  327 (607)
T 1f7u_A          295 SQ-VSKESMLKAIDLFK-EKGLTHEDKGAVLIDLT  327 (607)
T ss_dssp             GG-CCHHHHHHHHHHHH-HTTCEEEETTEEEEEGG
T ss_pred             ch-hhhhHHHHHHHHHH-hCCCEEEECCcEEEEec
Confidence            85 23378899999999 99999999999998654

>3fnr_A Arginyl-tRNA synthetase; transferase, PSI-2, NYSGXRC, struc genomics, protein structure initiative; 2.20A {Campylobacter jejuni}

Probab=99.65  E-value=8e-16  Score=142.21  Aligned_cols=127  Identities=17%  Similarity=0.161  Sum_probs=104.1

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHH-------HH--cCCC
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA-------EK--AGMT   80 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a-------~~--~g~~   80 (232)
                      .+++++|...+|||+|++||||+|+++++|+++|++++.|     ++|.-...+.|.|.++...+       .+  .|.+
T Consensus        28 ~~~~v~vE~ss~n~~~~~h~gh~r~~~~gd~~~r~~~~~G-----~~v~r~nyi~D~G~Q~g~l~~~~~~~y~~~~~~~~  102 (464)
T 3fnr_A           28 KQESFLLEYVSANPTGPLHIGHARGAVFGDTLTRLARHLG-----YKFNTEYYVNDAGNQIYLLGLSILLSVKESILHEN  102 (464)
T ss_dssp             CSCEEEEECCCCCSSSSCBGGGHHHHHHHHHHHHHHHHTT-----CEEEEEEEECCCHHHHHHHHHHHHHHHHHHTSCCC
T ss_pred             CCCEEEEEeCCCCCCCCCccchhHHHHHHHHHHHHHHHcC-----CceEEEeeeCCccHHHHHHHHHHHHHHHHHhcCCC
Confidence            5578999999999999999999999999999999999999     99999999999998874332       11  1211


Q ss_pred             ---H-------------H---------------------HHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHH
Q psy2399          81 ---P-------------K---------------------EFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYD  123 (232)
Q Consensus        81 ---~-------------~---------------------e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~  123 (232)
                         |             +                     ...+...+.+++++++|||.+|.|..+++. |. .+.++++
T Consensus       103 ~~~p~~~y~g~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~V~fD~~~~Ess~-~~-~~~~vv~  180 (464)
T 3fnr_A          103 VEYPEQYYKGEYIVDLAKEAFEKFGKEFFSEENIPSLADWAKDKMLVLIKQNLEQAKIKIDSYVSERSY-YD-ALNATLE  180 (464)
T ss_dssp             CCCCSSCCCSHHHHHHHHHHHHHHCGGGCSGGGHHHHHHHHHHHHHHHHHHHHHHTTCCCSCEEEGGGG-ST-THHHHHH
T ss_pred             CCCchhhcCccHHHHHHHHHHHhcchhhcCcHHHHHHHHHHHHHHHHHHHHHHHHhCCCceeecCHHHH-HH-HHHHHHH
Confidence               0             0                     112334568999999999999999888653 44 8999999


Q ss_pred             HHHhhcCCEEecccceeeccC
Q psy2399         124 TLYNKAKLIINKKINQFFDPI  144 (232)
Q Consensus       124 ~L~~~kG~iy~~~~~~~~~~~  144 (232)
                      .|. ++|++|++++..|++..
T Consensus       181 ~L~-~~g~~~e~dGa~~~~~~  200 (464)
T 3fnr_A          181 SLK-EHKGIYEQEGKIWLASS  200 (464)
T ss_dssp             HHH-HTTCEEEETTEEEECGG
T ss_pred             HHH-HCCCEEEeCCeEEEEec
Confidence            999 99999999999998654

>1nzj_A Hypothetical protein YADB; Zn cluster, glutamyl T-RNA synthetase, structural genomics, unknown function; 1.50A {Escherichia coli} SCOP: c.26.1.1 PDB: 2zlz_A* 4a91_A*

Probab=99.23  E-value=4.5e-12  Score=110.92  Aligned_cols=94  Identities=16%  Similarity=0.247  Sum_probs=73.5

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|+|||.|||||+|+++....++|     +     +.+.|+.-+||.+             ++.-...+.+.|.+
T Consensus         6 v~~RFAPsPtG~LHiG~~rtal~n~l~Ar-----~-----~~g~~ilRieDtD-------------~~R~~~~~~~~I~~   62 (298)
T 1nzj_A            6 YIGRFAPSPSGELHFGSLIAALGSYLQAR-----A-----RQGRWLVRIEDID-------------PPREVPGAAETILR   62 (298)
T ss_dssp             CEEEECCCTTSCCCHHHHHHHHHHHHHHH-----H-----TTCEEEEEECCSC-------------GGGSCTTHHHHHHH
T ss_pred             eEEEECcCCCCCccHHHHHHHHHHHHHHH-----h-----cCCeEEEEEecCC-------------chhhHHHHHHHHHH
Confidence            67778899999999999999996666665     3     4445555555533             22334678899999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||. .++.|  ++.+..++++++|. ++|++|.
T Consensus        63 dL~~LGl~~D~~~~~qS--er~~~y~~~~~~L~-~~G~aY~  100 (298)
T 1nzj_A           63 QLEHYGLHWDGDVLWQS--QRHDAYREALAWLH-EQGLSYY  100 (298)
T ss_dssp             HHHHTTCCCSSCCEEGG--GCHHHHHHHHHHHH-HTTCEEE
T ss_pred             HHHHcCCCCCCCCeeee--CCHHHHHHHHHHHH-HcCCccc
Confidence            99999999997 55666  57789999999999 9999997

>3aii_A Glutamyl-tRNA synthetase; amino-acyl tRNA synthetase, ligase; 1.65A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=99.19  E-value=1.2e-11  Score=115.86  Aligned_cols=94  Identities=16%  Similarity=0.163  Sum_probs=77.8

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|+|||.||||||+++++.+.++|     +     +.+.++.-+||.+             ++.-...+.+.|.+
T Consensus        97 v~tRFaPsPtG~LHIGhaRtal~n~l~Ar-----~-----~~G~~iLRieDtD-------------~~R~~~e~~~~I~e  153 (553)
T 3aii_A           97 VVLRFAPNPSGPLHIGHARAAILNHEYAR-----K-----YDGRLILRIEDTD-------------PRRVDPEAYDMIPA  153 (553)
T ss_dssp             CEEEECCCSSSSCBHHHHHHHHHHHHHHH-----H-----TTCEEEEEECCCC-------------GGGCCTTHHHHHHH
T ss_pred             eEEEeCCCCCCCccHHHHHHHHHHHHHHH-----H-----cCCEEEEEECcCC-------------cccccHHHHHHHHH
Confidence            77888999999999999999999777776     3     4555666666543             22335678899999


Q ss_pred             HHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||+.||..++.|  +|.+...+++.+|. ++|++|.
T Consensus       154 dL~wLGl~wd~~~~qS--dr~~~y~~~~~~Li-~~G~AY~  190 (553)
T 3aii_A          154 DLEWLGVEWDETVIQS--DRMETYYEYTEKLI-ERGGAYV  190 (553)
T ss_dssp             HHHHHTCCCSEEEEGG--GGHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHcCCCCCCCcccc--cCHHHHHHHHHHHH-HcCCcee
Confidence            9999999999887887  68999999999999 9999996

>1qtq_A GLNRS, protein (glutaminyl-tRNA synthetase); glutamine, trnaGln, E. coli, complex, ligase/RNA complex; HET: QSI; 2.25A {Escherichia coli} SCOP: b.53.1.2 c.26.1.1 PDB: 1gsg_P* 1gts_A* 1gtr_A* 1zjw_A* 1o0b_A* 1o0c_A* 1qru_A* 1qrs_A* 1qrt_A* 1euy_A* 1euq_A* 1exd_A* 2rd2_A* 2re8_A* 1nyl_A

Probab=99.14  E-value=4.7e-11  Score=111.75  Aligned_cols=94  Identities=17%  Similarity=0.032  Sum_probs=74.1

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|+|||.|||||||++++.+.+||-          +...++.-+||.+             +......+.+.|.+
T Consensus        27 v~tRFaPSPtG~LHIGhaRtal~n~l~Ar~----------~gG~fiLRieDTD-------------~~R~~~e~~~~I~e   83 (553)
T 1qtq_A           27 VHTRFPPEPNGYLHIGHAKSICLNFGIAQD----------YKGQCNLRFDDTN-------------PVKEDIEYVESIKN   83 (553)
T ss_dssp             CEEEECCCTTSCCBHHHHHHHHHHHHHHHH----------TTCEEEEEECCCC-------------GGGCCHHHHHHHHH
T ss_pred             eEEEeCCCCCCCccHHHHHHHHHHHHHHHH----------cCCEEEEEECCCC-------------chhcCHHHHHHHHH
Confidence            678889999999999999999998888872          3344554455432             23346788899999


Q ss_pred             HHhccCCcCC-ccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFD-NWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d-~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+|| ..++.|  +|.....+...+|. ++|++|.
T Consensus        84 dL~wLGl~wde~~~~qS--er~~~~~~~a~~Li-~~G~AY~  121 (553)
T 1qtq_A           84 DVEWLGFHWSGNVRYSS--DYFDQLHAYAIELI-NKGLAYV  121 (553)
T ss_dssp             HHHHTTCCCSSSCEEGG--GGHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHcCCCCCCCCeehc--ccHHHHHHHHHHHH-HCCCcee
Confidence            9999999995 455666  57777778889999 9999996

>2o5r_A Glutamyl-tRNA synthetase 1; TM1351, EC 6.1.1.17, glutamate-T ligase 1, glurs 1, structural genomics, joint center for ST genomics, JCSG; 2.34A {Thermotoga maritima}

Probab=99.11  E-value=7.4e-11  Score=109.45  Aligned_cols=96  Identities=15%  Similarity=0.150  Sum_probs=76.4

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      .++++...|+|||+|||||+|+.+.+|.+||.  ..|     .-++-+-.+|                ++...+.+.+.|
T Consensus        12 ~vv~~RfaPsPTG~LHiG~aRtAl~n~~~Ar~--~~G-----~~iLRieDtD----------------~~r~~~~~~~~I   68 (481)
T 2o5r_A           12 HMVRVRFAPSPTGFLHVGGARTALFNFLFARK--EKG-----KFILRIEDTD----------------LERSEREYEEKL   68 (481)
T ss_dssp             -CCEEEECCCCCSCCBHHHHHHHHHHHHHHHH--HTC-----EEEECBCCSS----------------CCSGGGHHHHHH
T ss_pred             eEEEEEECCCCCCCcCHHHHHHHHHHHHHHHH--cCC-----eEEEEEecCC----------------ccccHHHHHHHH
Confidence            46788889999999999999999999999997  567     6665554333                334456677778


Q ss_pred             HHHHhccCCcCCcc---------ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          93 KKYLDGFYIKFDNW---------YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        93 ~~~l~~lgI~~d~~---------~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      .++|++||++||..         ++.|  ++.+..++++.+|. ++|.+|.
T Consensus        69 ~~~l~wlGl~~de~p~~gg~~g~y~QS--~r~~~y~~~a~~L~-~~G~aY~  116 (481)
T 2o5r_A           69 MESLRWLGLLWDEGPDVGGDHGPYRQS--ERVEIYREHAERLV-KEGKAYY  116 (481)
T ss_dssp             HHHHHHHTCCCSBBTTTBCTTCCCBGG--GGHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHHHcCCCCCCCcccCCCCCceeee--ccHHHHHHHHHHHH-HCCCeeE
Confidence            89999999999963         3444  57888999999999 9999984

>2hz7_A Glutaminyl-tRNA synthetase; rossmann fold, GLNRS core, class I aminoacyl-tRNA synthetase, ligase; 2.30A {Deinococcus radiodurans}

Probab=99.06  E-value=1.2e-10  Score=113.55  Aligned_cols=94  Identities=16%  Similarity=0.128  Sum_probs=75.8

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|+|||.|||||||++++...++|-          +.+.|+.-+||.+             ++.....+.+.|.+
T Consensus        67 v~tRFaPSPtG~LHIGhARtAL~n~l~Ar~----------~gG~fiLRIEDTD-------------~~R~~~e~~~~Ile  123 (851)
T 2hz7_A           67 VVTRFPPDPSGYAHLGHVFASLLDFNTARQ----------YGGQFNLRMDDTN-------------PELARQEYVDSIAD  123 (851)
T ss_dssp             CEEEECCCSSSCCBHHHHHHHHHHHHHHHH----------TTCEEEEEECCCC-------------TTTCCHHHHHHHHH
T ss_pred             eEEEeCCCCCCCccHHHHHHHHHHHHHHHH----------cCCEEEEEECcCC-------------cccccHHHHHHHHH
Confidence            778889999999999999999998777773          4445555555543             22336688899999


Q ss_pred             HHhccCCcCC-ccccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFD-NWYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d-~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+|| ..++.|  +|.....+++.+|. ++|++|.
T Consensus       124 dL~wLGl~wde~~~~qS--er~d~y~e~a~~LI-~~G~AY~  161 (851)
T 2hz7_A          124 DLKWLGLDWGEHFYYAS--DYFDRYYAYAEQLI-RQGDAYV  161 (851)
T ss_dssp             HHHHHTCCCTTCEEEGG--GGHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHcCCCCCCCcccHh--hhHHHHHHHHHHHH-HCCCcEe
Confidence            9999999995 456666  68999999999999 9999996

>4g6z_A Glutamate-tRNA ligase; aminoacyl-tRNA synthetase, AARS, class 1B AARS, ATP-dependen charging, protein synthesis, structural genomics; HET: GLU; 2.05A {Burkholderia thailandensis}

Probab=99.05  E-value=1.7e-10  Score=106.82  Aligned_cols=94  Identities=16%  Similarity=0.182  Sum_probs=74.7

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|+|||.|||||+|+++..+.++|.  ..|     .-++-+-.+|.                +.....+.+.|.+
T Consensus        26 v~~RFAPSPTG~lHiG~~rtal~n~l~Ar~--~~G-----~filRieDtD~----------------~R~~~~~~~~i~~   82 (490)
T 4g6z_A           26 VRTRFAPSPTGFIHLGNIRSALYPWAFARK--MKG-----TFVLRIEDTDV----------------ERSSQEAVDAILE   82 (490)
T ss_dssp             CEEEECCCCCSCCBHHHHHHHHHHHHHHHH--TTC-----EEEEEECCCCG----------------GGCCHHHHHHHHH
T ss_pred             ceEEeCCCCCCCccHHHHHHHHHHHHHHHh--cCC-----eEEEEeCCCCc----------------ccccHHHHHHHHH
Confidence            667778999999999999999999988884  344     44544444442                2335678899999


Q ss_pred             HHhccCCcCCcc-ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNW-YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~-~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||.- ++.|  ++.+..++++.+|. ++|++|.
T Consensus        83 dl~wlGl~~d~~~~~qS--~r~~~y~~~~~~Li-~~G~aY~  120 (490)
T 4g6z_A           83 GMAWLGLDYDEGPYYQM--QRMDRYREVLAQMQ-EKGLVYP  120 (490)
T ss_dssp             HHHHTTCCCSEEEEEGG--GCHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHcCCCCCCCCcccc--cCHHHHHHHHHHHH-HCCCEEe
Confidence            999999999973 5555  58888999999999 9999985

>3al0_C Glutamyl-tRNA(Gln) amidotransferase subunit C, GL tRNA synthetase 2; protein-RNA complex, ligase-RNA complex; HET: GSU; 3.37A {Thermotoga maritima}

Probab=99.03  E-value=2.1e-10  Score=108.69  Aligned_cols=94  Identities=15%  Similarity=0.180  Sum_probs=73.1

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|+|||+|||||+|+.+..+.+||.  ..|     .   |+.-+||.             ++..-...+.+.|.+
T Consensus       130 v~~RFaPsPTG~LHiG~artAl~n~l~Ar~--~~G-----~---~ilRieDt-------------D~~r~~~~~~~~I~~  186 (592)
T 3al0_C          130 VRVRFAPSPTGHLHVGGARTALFNWMFARK--EGG-----K---FILRIEDT-------------DTERSSREYEQQILE  186 (592)
T ss_dssp             CEEEECCCSSSCCBHHHHHHHHHHHHHHHH--HTC-----E---EEECBCCC-------------CSSSCCHHHHHHHHH
T ss_pred             EEEEECCCCCCCccHHHHHHHHHHHHHHHh--cCC-----c---EEEEecCc-------------ChhhccHHHHHHHHH
Confidence            445555999999999999999999999985  445     3   33334442             233446677888999


Q ss_pred             HHhccCCcCCcc---------ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNW---------YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~---------~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||.-         ++.|  ++.+..++++.+|. ++|++|.
T Consensus       187 dL~wlGl~~D~~~~~gG~~gp~~qS--er~~~y~~~~~~L~-~~G~aY~  232 (592)
T 3al0_C          187 SLRWCGLDWDEGPDIGGDFGPYRQS--ERLEIYREYAEKLV-EDKRAYY  232 (592)
T ss_dssp             HHHHTTCCCSBBTTTBCTTCCCBST--TCHHHHHHHHHHHH-HTTTEEE
T ss_pred             HHHHcCCCCCCCCCcCCCCCCeeee--CCHHHHHHHHHHHH-HcCCceE
Confidence            999999999983         4555  46688999999999 9999997

>2cfo_A Glutamyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase, ATP-binding, nucleotide-B; HET: GLU; 2.45A {Synechococcus elongatus}

Probab=99.03  E-value=1.6e-10  Score=107.44  Aligned_cols=94  Identities=20%  Similarity=0.229  Sum_probs=73.2

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|+|||.|||||+|+++....++|-          +.+.|+.-+||.+             +......+.+.|.+
T Consensus         2 v~~RFAPSPtG~lHiG~artal~n~l~Ar~----------~~G~filRieDtD-------------~~R~~~~~~~~i~~   58 (492)
T 2cfo_A            2 VRVRLAPSPTGNLHIGTARTAVFNWLYARH----------RGGKFILRIEDTD-------------RERSRPEYTENILE   58 (492)
T ss_dssp             CEEEECCCTTSCCBHHHHHHHHHHHHHHHH----------TTCEEEEEECCCS-------------SSSCCHHHHHHHHH
T ss_pred             ceEEeCCCCCCCccHHHHHHHHHHHHHHHh----------cCCeEEEEEeeCC-------------ccccchHHHHHHHH
Confidence            456778999999999999999997777763          3344555455433             12224677889999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||. .++.|  ++.+...+++.+|. ++|++|.
T Consensus        59 dL~wLGl~wde~~~~QS--~r~~~y~~~~~~Li-~~G~AY~   96 (492)
T 2cfo_A           59 GLQWLGLTWDEGPYFQS--DRLDLYRQAIQTLL-DKGLAYY   96 (492)
T ss_dssp             HHHHTTCCCSEEEEEGG--GCHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHcCCCCCCCCcccc--CCHHHHHHHHHHHH-HCCCceE
Confidence            99999999997 66666  57889999999999 9999996

>3afh_A Glutamyl-tRNA synthetase 2; protein-substrate complex, aminoacyl-tRNA synthetase, ATP-binding, ligase, nucleotide-binding; HET: GSU; 2.00A {Thermotoga maritima} PDB: 3akz_B*

Probab=98.99  E-value=4.9e-10  Score=104.02  Aligned_cols=94  Identities=15%  Similarity=0.163  Sum_probs=74.9

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.|||||+|+.+....+||-  ..|        .|+.-+||.             ++......+.+.|.+
T Consensus        26 v~~RFAPsPtG~LHiG~~rtal~n~l~Ar~--~~G--------~filRieDt-------------D~~R~~~~~~~~I~~   82 (488)
T 3afh_A           26 VRVRFAPSPTGHLHVGGARTALFNWMFARK--EGG--------KFILRIEDT-------------DTERSSREYEQQILE   82 (488)
T ss_dssp             CEEEECCCCSSSCBHHHHHHHHHHHHHHHH--HTC--------EEEECBCCC-------------CTTTCCHHHHHHHHH
T ss_pred             ceEEECCCCCCCccHHHHHHHHHHHHHHHH--cCC--------EEEEEEeeC-------------CcccccHHHHHHHHH
Confidence            677788999999999999999999999884  344        344444443             334446678888999


Q ss_pred             HHhccCCcCCcc---------ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNW---------YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~---------~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||.-         ++.|  ++.+..++.+.+|. ++|++|.
T Consensus        83 dL~wlGl~wDe~~~~gG~~gp~~QS--er~~~y~~~~~~L~-~~G~aY~  128 (488)
T 3afh_A           83 SLRWCGLDWDEGPDIGGDFGPYRQS--ERLEIYREYAEKLV-EDKRAYY  128 (488)
T ss_dssp             HHHHTTCCCSBBTTTBCTTCCCBGG--GCHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHcCCCCCcCCCCCCCCCCeeee--CCHHHHHHHHHHHH-HcCCeEe
Confidence            999999999984         4555  56788999999999 9999996

>4gri_A Glutamate--tRNA ligase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, aminoacyl-tRNA synthetase; HET: GLU; 2.60A {Borrelia burgdorferi}

Probab=98.95  E-value=6.9e-10  Score=103.72  Aligned_cols=95  Identities=13%  Similarity=0.089  Sum_probs=72.9

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -|.|--+|.|||.|||||||++++...+||-  ..|        .|+.-+||.             ++......+.+.|.
T Consensus        24 ~vrtRFAPsPtG~LHiG~artAl~n~~~Ar~--~~G--------~fiLRieDt-------------D~~R~~~~~~~~I~   80 (512)
T 4gri_A           24 STRVRYAPSPTGLQHIGGIRTALFNYFFAKS--CGG--------KFLLRIEDT-------------DQSRYSPEAENDLY   80 (512)
T ss_dssp             CCEEEECCCSSSCCBHHHHHHHHHHHHHHHH--TTC--------EEEECBCCC-------------CTTSCCHHHHHHHH
T ss_pred             ceeEEeCcCCCCcccHHHHHHHHHHHHHHHH--cCC--------EEEEEeCcC-------------CCCcCCHHHHHHHH
Confidence            3667889999999999999999999999973  344        344444442             34444567788889


Q ss_pred             HHHhccCCcCCccc---------cCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFDNWY---------STDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d~~~---------~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      ++|++|||+||.-.         +.|  ++.+..++.+.+|. ++|++|.
T Consensus        81 ~~L~wlGl~wDe~p~~~g~~~py~QS--~r~~~Y~~~~~~L~-~~G~aY~  127 (512)
T 4gri_A           81 SSLKWLGISFDEGPVVGGDYAPYVQS--QRSAIYKQYAKYLI-ESGHAYY  127 (512)
T ss_dssp             HHHHHHTCCCSBBTTTBCTTCCCBGG--GCHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHHcCCCCCcCCccCCCCCCcccc--chHHHHHHHHHHHH-HcCCccc
Confidence            99999999999632         223  46677888999999 9999985

>1j09_A Glutamyl-tRNA synthetase; glurs-ATP-Glu complex, riken structural genomics/proteomics initiative, RSGI, structural genomics, ligase; HET: GLU ATP; 1.80A {Thermus thermophilus} SCOP: a.97.1.1 c.26.1.1 PDB: 1n75_A* 1n77_A* 1n78_A* 2cuz_A* 2cv0_A* 2cv1_A* 2cv2_A* 2dxi_A* 1g59_A 1gln_A

Probab=98.94  E-value=6.1e-10  Score=102.93  Aligned_cols=94  Identities=20%  Similarity=0.269  Sum_probs=74.2

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.|||||+++.+....+||-  ..|        .|+.-+||.             ++......+.+.|.+
T Consensus         2 v~~RFaPsPtG~LHiG~~rtal~n~l~Ar~--~~G--------~filRieDt-------------D~~R~~~~~~~~I~~   58 (468)
T 1j09_A            2 VVTRIAPSPTGDPHVGTAYIALFNYAWARR--NGG--------RFIVRIEDT-------------DRARYVPGAEERILA   58 (468)
T ss_dssp             CEEEECCCCSSSCBHHHHHHHHHHHHHHHH--TTC--------EEEECBCCC-------------CTTSCCTTHHHHHHH
T ss_pred             ceEEeCCCCCCCccHHHHHHHHHHHHHHHH--cCC--------EEEEEeCcC-------------CCcccChHHHHHHHH
Confidence            456778999999999999999999999883  334        354445543             233445677888899


Q ss_pred             HHhccCCcCCcc---------ccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDNW---------YSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~~---------~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||++||.-         ++.|  ++.+..++++.+|. ++|++|.
T Consensus        59 dl~wlGl~wd~~~~~gG~~gp~~QS--~r~~~y~~~~~~L~-~~G~aY~  104 (468)
T 1j09_A           59 ALKWLGLSYDEGPDVGGPHGPYRQS--ERLPLYQKYAEELL-KRGWAYR  104 (468)
T ss_dssp             HHHHTTCCCSBBTTTBCTTCCCBGG--GCHHHHHHHHHHHH-HHTSEEE
T ss_pred             HHHHcCCCCCCCCCCCCCCCCeecc--CCHHHHHHHHHHHH-HcCCeEE
Confidence            999999999975         4555  67888999999999 9999995

>2ja2_A Glutamyl-tRNA synthetase; non-discriminating glutamyl-tRNA aminoacylation, protein biosynthesis, aminoacyl-tRNA synthetase, ligase; 1.65A {Mycobacterium tuberculosis} PDB: 3pny_A 3pnv_A

Probab=98.86  E-value=2.9e-09  Score=98.93  Aligned_cols=94  Identities=12%  Similarity=0.128  Sum_probs=75.0

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +++--+|.|||.|||||+++.+....+||-  ..|     .   |+.-+||.             ++......+.+.|.+
T Consensus         7 vr~RFAPsPTG~LHiG~~rtAL~n~l~Ar~--~gG-----~---fiLRieDt-------------D~~R~~~~~~~~I~~   63 (498)
T 2ja2_A            7 VRVRFCPSPTGTPHVGLVRTALFNWAYARH--TGG-----T---FVFRIEDT-------------DAQRDSEESYLALLD   63 (498)
T ss_dssp             CEEEECCCSSSSCBHHHHHHHHHHHHHHHH--HTC-----E---EEECBCCC-------------CTTTCCHHHHHHHHH
T ss_pred             eeEEECcCCCCCccHHHHHHHHHHHHHHHH--cCC-----E---EEEEECcC-------------CCcccChHHHHHHHH
Confidence            567778999999999999999999999983  445     3   33333432             345556678888999


Q ss_pred             HHhccCCcCCc---------cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN---------WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~---------~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++|||+||.         .++.|  ++.+..++.+.+|. ++|++|.
T Consensus        64 ~L~wlGl~wDegp~~gG~~~~~~QS--~r~~~y~~~~~~L~-~~g~aY~  109 (498)
T 2ja2_A           64 ALRWLGLDWDEGPEVGGPYGPYRQS--QRAEIYRDVLARLL-AAGEAYH  109 (498)
T ss_dssp             HHHHHTCCCSBBTTTBCTTCCCBGG--GCHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHcCCCcCCCcCcCCCCCCeeee--cCHHHHHHHHHHHH-HcCCeEE
Confidence            99999999997         45555  57888899999999 9999995

>3jxe_A Tryptophanyl-tRNA synthetase; adenosine triphosphate, rossmann fold, crystallography, X-RAY, P. horikoshii, aminoacyl-tRNA synthetase; HET: TYM; 3.00A {Pyrococcus horikoshii}

Probab=96.72  E-value=0.0057  Score=55.08  Aligned_cols=93  Identities=15%  Similarity=0.202  Sum_probs=55.7

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHH-cCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCM-QQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~-~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      .++++.|.++. -|+|.|||||..+.+.    .||+.. .|     .++.+..+ |.|..-.     ..+.+++++. ++
T Consensus        70 ~~~p~~i~sG~-~PTG~lHLGh~v~~~~----~~~lQ~~~g-----~~~~i~Ia-D~ha~~~-----~~~~~~e~i~-~~  132 (392)
T 3jxe_A           70 EGRGFFLYTGR-GPSGPMHIGHIIPFFA----TKWLQEKFG-----VNLYIQIT-DDEKFLF-----KENLTFDDTK-RW  132 (392)
T ss_dssp             TTCCCEEEEEE-CCSSCCBHHHHHHHHH----HHHHHHHHC-----CEEEEEEC-HHHHHHH-----CSSCCHHHHH-HH
T ss_pred             cCCCeEEEecc-CCCCchhHHHHHHHHH----HHHHHHhcC-----CceEEEec-chHHhhc-----CCCCCHHHHH-HH
Confidence            34566666655 5679999999886642    233443 68     88888776 5554321     1135665554 44


Q ss_pred             HHHHHHHHhccCCcCCc--cccCC-ChhHHHHHH
Q psy2399          89 SSNRKKYLDGFYIKFDN--WYSTD-SIENIDLVQ  119 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~--~~~t~-~~~~~~~v~  119 (232)
                      .....+++.++|++++.  ++.-| -+.|.+.++
T Consensus       133 ~~~~~~~~lA~GlDp~kt~i~~qS~~~~~~~~~~  166 (392)
T 3jxe_A          133 AYDNILDIIAVGFDPDKTFIFQNSEFTKIYEMAI  166 (392)
T ss_dssp             HHHHHHHHHTTCCCTTSEEEEETTTSTHHHHHHH
T ss_pred             HHHHHHHHHHhCcCccceEEEECchhHHHHHHHH
Confidence            44666778889998874  33333 244554444

>2cyb_A Tyrosyl-tRNA synthetase; rossmann-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: TYR; 1.80A {Archaeoglobus fulgidus}

Probab=96.34  E-value=0.0062  Score=53.28  Aligned_cols=76  Identities=21%  Similarity=0.256  Sum_probs=46.6

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++..|.++. -|||+|||||+.. +.  .+.++ +..|     +++.+..| |.|+.-.    .  ..++++ +.++...
T Consensus        31 ~~~~vy~G~-~PTg~lHlG~l~~-l~--~~~~l-q~~g-----~~~~~~i~-D~~a~~~----d--~~~~~~-i~~~~~~   92 (323)
T 2cyb_A           31 EKPRAYVGY-EPSGEIHLGHMMT-VQ--KLMDL-QEAG-----FEIIVLLA-DIHAYLN----E--KGTFEE-IAEVADY   92 (323)
T ss_dssp             SCCEEEEEE-CCCSCCBHHHHHH-HH--HHHHH-HHTT-----CEEEEEEC-HHHHHHT----T--CCCHHH-HHHHHHH
T ss_pred             CCCEEEECc-CCCCcchHHHHHH-HH--HHHHH-HHCC-----CcEEEEEC-CceeEcC----C--CCCHHH-HHHHHHH
Confidence            344555554 6789999999633 22  33344 4458     78766653 3333221    1  125554 5667788


Q ss_pred             HHHHHhccCCcCCc
Q psy2399          92 RKKYLDGFYIKFDN  105 (232)
Q Consensus        92 ~~~~l~~lgI~~d~  105 (232)
                      +.+++.++|++++.
T Consensus        93 ~~~~~~a~Gldp~k  106 (323)
T 2cyb_A           93 NKKVFIALGLDESR  106 (323)
T ss_dssp             HHHHHHHTTCCTTT
T ss_pred             HHHHHHHhCCCccc
Confidence            88899999999875

>3a04_A Tryptophanyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, nucleotide-binding, protein biosynthesis; 1.97A {Aeropyrum pernix} PDB: 3a05_A*

Probab=96.29  E-value=0.0051  Score=55.01  Aligned_cols=80  Identities=15%  Similarity=0.179  Sum_probs=51.7

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      ..+++++|.++. -|+|.|||||..+.+    -.+++...|     +++.+.. .|.|-.-.      ......+.....
T Consensus        66 e~gk~~~v~sG~-~PTG~lHLGhyv~~~----~~~~lq~~~-----~~~~~~I-aD~ha~t~------~~~~~~e~~r~~  128 (372)
T 3a04_A           66 ARGERVAVLTGF-MPSGKFHFGHKLTVD----QLIYLQKNG-----FKVFVAI-ADAEAFAV------RRIGREEAVRIA  128 (372)
T ss_dssp             HTTCCCEEEEEE-CCCSCCBHHHHHHHH----HHHHHHHTT-----CEEEEEE-CHHHHHHT------TCCCHHHHHHHH
T ss_pred             HcCCCCEEEeCc-CCCcHhHHHHHHHHH----HHHHHHhCC-----CeEEEEE-ecchhhcc------CCCCCHHHHHHH
Confidence            345777887776 788999999977442    234455568     8887654 45554321      123344555566


Q ss_pred             HHHHHHHHhccCCcCCc
Q psy2399          89 SSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~  105 (232)
                      ......++-++|++++.
T Consensus       129 ~~~~~~~~lA~GlDP~k  145 (372)
T 3a04_A          129 VEEYIANMIALGLDPKD  145 (372)
T ss_dssp             HHTTHHHHHHHTCCTTT
T ss_pred             HHHHHHHHHHcCCChHH
Confidence            66667777889998764

>3hzr_A Tryptophanyl-tRNA synthetase; APO tRNA-ligase, structural genomics, medical structural GEN pathogenic protozoa, MSGPP, ligase; 3.00A {Entamoeba histolytica}

Probab=96.13  E-value=0.013  Score=52.61  Aligned_cols=79  Identities=16%  Similarity=0.114  Sum_probs=47.2

Q ss_pred             CCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      +++++.|.++. -|+|+|||||..+.   ..+.++++.-|     ..+.++.+ |.+      +......+++++.+...
T Consensus        79 ~~~~~~vysG~-~PTG~lHLGh~v~~---~~~~~lQ~~~g-----~~v~i~I~-D~~------a~~~r~~~~e~i~~~~~  142 (386)
T 3hzr_A           79 AKKPTFIFIQK-YPQKEVALEEYITL---EFARYLQDAFN-----IQVIIQIL-DDI------KVLNREATINEASKMSN  142 (386)
T ss_dssp             TTCCEEEEEEE-CCCSSCBGGGHHHH---HHHHHHHHHHC-----CEEEEEEC-HHH------HHHTTSCCHHHHHHHHH
T ss_pred             cCCCeEEEecc-CCCCCccHHHHHHH---HHHHHHHHhcC-----CeEEEEeC-chH------HhhcCCCCHHHHHHHHH
Confidence            34667777765 78899999996654   33433444457     77777633 221      11111256666554444


Q ss_pred             HHHHHHHhccCCcCCc
Q psy2399          90 SNRKKYLDGFYIKFDN  105 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~  105 (232)
                       .+.+++-++|++.+.
T Consensus       143 -~~~~~~lA~GlDp~k  157 (386)
T 3hzr_A          143 -DLMKYILAFGFNEDK  157 (386)
T ss_dssp             -HHHHHHHHTCCCGGG
T ss_pred             -HHHHHHHHcCCCCcc
Confidence             555677788888764

>2g36_A Tryptophanyl-tRNA synthetase; TM0492, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI, ligase; HET: TRP; 2.50A {Thermotoga maritima}

Probab=95.95  E-value=0.02  Score=50.53  Aligned_cols=73  Identities=12%  Similarity=0.144  Sum_probs=44.7

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      .+.+...  |||.|||||..+.+.   -.+.+...|     +++.++. .|.|+.-..      ..+|+++ .+......
T Consensus        14 ~v~~G~~--PTG~lHLGn~~g~l~---~~~~lQ~~G-----~~~~~~I-aD~ha~t~~------~~dp~~~-~~~~~~~~   75 (340)
T 2g36_A           14 RILSGMR--PTGKLHIGHLVGALE---NWVKLQEEG-----NECFYFV-ADWHALTTH------YDDVSKL-KEYTRDLV   75 (340)
T ss_dssp             EEEEEEC--CCSSCBHHHHHTHHH---HHHHHHHTT-----CEEEEEE-CHHHHHHHH------TTCCTTH-HHHHHHHH
T ss_pred             eEEEeeC--CCCcccHHhHHHHHH---HHHHHHHCC-----CCEEEEE-ecceeecCC------CCCHHHH-HHHHHHHH
Confidence            3444444  568999999998653   223344578     8888776 445544321      2345543 33444555


Q ss_pred             HHHhccCCcCC
Q psy2399          94 KYLDGFYIKFD  104 (232)
Q Consensus        94 ~~l~~lgI~~d  104 (232)
                      +++.++|++++
T Consensus        76 ~~~lA~Gldp~   86 (340)
T 2g36_A           76 RGFLACGIDPE   86 (340)
T ss_dssp             HHHHHTTCCTT
T ss_pred             HHHHHhCCChh
Confidence            67778999887

>2dlc_X Tyrosyl-tRNA synthetase, cytoplasmic; tyrrs, ligase-tRNA complex; HET: 2MG OMG M2G PSU 6IA 5MC 5MU 1MA YMP; 2.40A {Saccharomyces cerevisiae}

Probab=95.94  E-value=0.0093  Score=53.67  Aligned_cols=78  Identities=17%  Similarity=0.151  Sum_probs=45.1

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHH----HH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEF----IN   86 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~----~~   86 (232)
                      ++++.|.++. -|||.|||||+++.+.   +.++++ .|     +++.+..+ |.|+.-..     .. .+.+.    +.
T Consensus        37 ~~p~~vy~G~-~PTG~LHlG~~~~al~---~~~~~q-~g-----~~~ii~I~-D~ha~t~~-----~~-~~~e~~~~~~~   99 (394)
T 2dlc_X           37 KRHLKLYWGT-APTGRPHCGYFVPMTK---LADFLK-AG-----CEVTVLLA-DLHAFLDN-----MK-APLEVVNYRAK   99 (394)
T ss_dssp             CSCCEEEEEE-CCCSCCBGGGHHHHHH---HHHHHH-TT-----CEEEEEEC-HHHHHHTT-----TS-SCTTHHHHHHH
T ss_pred             CCCeEEEEEe-CCCCCccHHHHHHHHH---HHHHHH-cC-----CcEEEEEc-CCccccCC-----CC-CcHHHHHHHHH
Confidence            3554444443 5589999999877655   333444 67     77766653 33332210     00 12222    33


Q ss_pred             HHHHHHHHHHhccCCcCCc
Q psy2399          87 NISSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI~~d~  105 (232)
                      .+...+.+.|.++|++++.
T Consensus       100 ~~~~~i~~~l~a~Gldp~k  118 (394)
T 2dlc_X          100 YYELTIKAILRSINVPIEK  118 (394)
T ss_dssp             HHHHHHHHHHHHTTCCCTT
T ss_pred             HHHHHHHHHHHHcCCChhH
Confidence            4556677788999999886

>2zp1_A Tyrosyl-tRNA synthetase; tRNA synthetases class I, ligase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, nucleotide-binding; HET: IYR; 1.70A {Methanocaldococcus jannaschii} PDB: 1zh6_A* 1j1u_A* 1u7d_A 2q1g_A* 2pxh_A* 1zh0_A* 2q1i_A* 2ag6_A* 3qe4_A* 3d6u_A* 3d6v_A* 1u7x_A 3n2y_A* 2hgz_A*

Probab=95.87  E-value=0.017  Score=50.33  Aligned_cols=80  Identities=16%  Similarity=0.194  Sum_probs=47.1

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      +++.|.++. -|+|.||||| ...+  -.+.++ ...|     +++.+..| |.|+.-.    .  ..++++ +.++...
T Consensus        27 ~~~~vy~G~-~PTg~lHlGh-l~~l--~~~~~l-Q~~g-----~~~~~~i~-D~~a~~~----~--~~~~e~-i~~~~~~   88 (314)
T 2zp1_A           27 DEKSAYIGF-EPSGKIHLGH-YLQI--KKMIDL-QNAG-----FDIIILLA-DLAAYLN----Q--KGELDE-IRKIGDY   88 (314)
T ss_dssp             SSEEEEEEE-CCCSSCBHHH-HHHH--HHHHHH-HHTT-----EEEEEEEC-HHHHHHT----T--CCCHHH-HHHHHHH
T ss_pred             CCCEEEEcc-CCCCCcchhh-HHHH--HHHHHH-HHCC-----CCEEEEEe-cceEecC----C--CCCHHH-HHHHHHH
Confidence            445554443 5679999999 4332  233344 4468     88877664 3333221    1  124444 4555588


Q ss_pred             HHHHHhccCCcCCccccCC
Q psy2399          92 RKKYLDGFYIKFDNWYSTD  110 (232)
Q Consensus        92 ~~~~l~~lgI~~d~~~~t~  110 (232)
                      +.+++.++|++ ..|+.-+
T Consensus        89 ~~~~~~a~G~d-~~~~~qs  106 (314)
T 2zp1_A           89 NKKVFEAMGLK-AKYVYGS  106 (314)
T ss_dssp             HHHHHHHTTCC-CEEEEGG
T ss_pred             HHHHHHhcCCC-eEEEECC
Confidence            88999999998 5565444

>3tzl_A Tryptophanyl-tRNA synthetase; structural genomics, center for structural genomics of infec diseases, csgid, alpha-beta structure; HET: ADP TRP; 2.15A {Campylobacter jejuni subsp} SCOP: c.26.1.0 PDB: 3m5w_A*

Probab=95.87  E-value=0.0081  Score=52.64  Aligned_cols=66  Identities=20%  Similarity=0.252  Sum_probs=42.3

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|+|.|||||..+.+..  +.++++  |     +++.+..+ |.|+.-.       ..+++++ .++...+..++.++|+
T Consensus        11 ~PTg~lHlG~~lg~l~~--~~~lQ~--g-----~~~~~~ia-D~ha~~~-------~~~~~~l-~~~~~~~~~~~lA~Gl   72 (322)
T 3tzl_A           11 QPSGDLHIGNYFGAIKQ--MVDAQE--K-----SQMFMFIA-NYHAMTS-------SQDGEKL-KQNSLKAAAAFLSLGI   72 (322)
T ss_dssp             CCSSCCBHHHHHHTHHH--HHHTTT--T-----SCCEEEEC-HHHHTTT-------CCCHHHH-HHHHHHHHHHHHHTTC
T ss_pred             CCCccccHHHHHHHHHH--HHHHhc--C-----CCEEEEEe-cCeeecC-------CCCHHHH-HHHHHHHHHHHHHcCC
Confidence            57799999999875543  444444  8     88877665 5554321       1245554 4445566677778999


Q ss_pred             cCCc
Q psy2399         102 KFDN  105 (232)
Q Consensus       102 ~~d~  105 (232)
                      +++.
T Consensus        73 dp~k   76 (322)
T 3tzl_A           73 DPQK   76 (322)
T ss_dssp             CTTT
T ss_pred             Cccc
Confidence            8763

>3prh_A Tryptophanyl-tRNA synthetase; TRPRS, protein biosynthesis, translation, class I tRNA synth rossman fold, high motif, KMSKS motif; 2.80A {Bacillus subtilis}

Probab=95.77  E-value=0.011  Score=53.03  Aligned_cols=88  Identities=14%  Similarity=0.224  Sum_probs=51.3

Q ss_pred             CcEE----EEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHH
Q psy2399          12 RRIF----VTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINN   87 (232)
Q Consensus        12 ~~~~----v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~   87 (232)
                      ++++    |.++. -|+|.|||||..+.+..  +.+++  .|     +++.+.. .|.|..-.       ..+++++.+.
T Consensus        30 ~p~~m~~ri~sG~-~PTG~lHLGhyvGal~~--~~~LQ--~~-----~~~~~~I-aD~hAlt~-------~~~~~~lr~~   91 (388)
T 3prh_A           30 DPFTMKQTIFSGI-QPSGSVTLGNYIGAMKQ--FVELQ--HD-----YNSYFCI-VDQHAITV-------PQDRLELRKN   91 (388)
T ss_dssp             -----CCEEEEEE-CCCSCCBHHHHHHTHHH--HHHTT--TT-----SEEEEEE-CHHHHTTS-------CCCHHHHHHH
T ss_pred             CCcccCCeEEEee-CCCCcchHHHHHHHHHH--HHHHH--cc-----CcEEEEE-ecceeeec-------CCCHHHHHHH
Confidence            5666    66665 78899999998876542  12222  37     8887665 35555331       3466665444


Q ss_pred             HHHHHHHHHhccCCcCCc--cccCC-ChhHHHHH
Q psy2399          88 ISSNRKKYLDGFYIKFDN--WYSTD-SIENIDLV  118 (232)
Q Consensus        88 ~~~~~~~~l~~lgI~~d~--~~~t~-~~~~~~~v  118 (232)
                      . .....++.++|++++.  ++.-| -++|.+..
T Consensus        92 ~-~~~aa~~lA~GlDp~kt~if~qS~v~~~~el~  124 (388)
T 3prh_A           92 I-RNLAALYLAVGLDPEKATLFIQSEVPAHAQAG  124 (388)
T ss_dssp             H-HHHHHHHHHTTCCTTTEEEEEGGGSTHHHHHH
T ss_pred             H-HHHHHHHHHhCCChhHeEEEecccccchHHHH
Confidence            4 4666778889999875  33333 34554443

>2cya_A Tyrosyl-tRNA synthetase; tyrrs, aminoacylation, structural genomics, NPPSFA, national on protein structural and functional analyses; 2.20A {Aeropyrum pernix}

Probab=95.76  E-value=0.021  Score=50.87  Aligned_cols=77  Identities=13%  Similarity=0.058  Sum_probs=45.7

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNR   92 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~   92 (232)
                      +..|.++. -|+|.||||| ...  .-.+.+++ ..|     +++.+..| |.|+.-.    .+.|.+++++. ++...+
T Consensus        35 ~~~iy~G~-~PTg~lHlG~-l~~--l~~~~~lQ-~~G-----~~~~~~ia-D~~a~~~----~ps~~~~e~i~-~~~~~~   98 (364)
T 2cya_A           35 RIKGYIGY-EPSGVAHIGW-LVW--MYKVKDLV-EAG-----VDFSVLEA-TWHAYIN----DKLGGDMDLIR-AAARIV   98 (364)
T ss_dssp             CCEEEEEE-CCCSSCBTHH-HHH--HHHHHHHH-HTT-----CEEEEEEC-HHHHHHT----TGGGGCHHHHH-HHHHHH
T ss_pred             CCEEEecc-CCCCCccHhH-HHH--HHHHHHHH-HCC-----CCEEEEEe-CcchhhC----CCCCCCHHHHH-HHHHHH
Confidence            34444443 5679999999 432  23334443 458     88877765 4444321    11234555544 444677


Q ss_pred             HHHHhccCCcCCc
Q psy2399          93 KKYLDGFYIKFDN  105 (232)
Q Consensus        93 ~~~l~~lgI~~d~  105 (232)
                      .+++.++|++++.
T Consensus        99 ~~~~la~G~dp~k  111 (364)
T 2cya_A           99 RRVMEAAGVPVER  111 (364)
T ss_dssp             HHHHHHTTCCGGG
T ss_pred             HHHHHHhCCCccc
Confidence            7889999998875

>1i6k_A TRPRS, tryptophanyl-tRNA synthetase; class I tRNA synthetase, AARS, induced FIT, ligase; HET: TYM; 1.72A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 1i6l_A* 1i6m_A* 1m83_A* 1mau_A* 1maw_A* 1mb2_A* 2ov4_A* 3fhj_A* 3fi0_A* 1d2r_A 3u1v_A

Probab=95.73  E-value=0.011  Score=51.87  Aligned_cols=65  Identities=17%  Similarity=0.253  Sum_probs=41.6

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|||.|||||..+.+..-+  +++  .|     +++.+..| |.|+.-.       ..+++++ .++...+.+++.++|+
T Consensus         9 ~PTG~lHlGn~vg~l~~~~--~lQ--~g-----~~~~~~Ia-D~ha~~~-------~~~~e~i-~~~~~~~~~~~la~Gl   70 (328)
T 1i6k_A            9 QPSGVITIGNYIGALRQFV--ELQ--HE-----YNCYFCIV-DQHAITV-------WQDPHEL-RQNIRRLAALYLAVGI   70 (328)
T ss_dssp             CCCSCCBHHHHHHTHHHHH--HHT--TT-----SEEEEEEC-HHHHTTS-------CCCHHHH-HHHHHHHHHHHHHTTC
T ss_pred             CCCCcccHHHHHHHHHHHH--HHH--cC-----CcEEEEEe-CceeecC-------CCCHHHH-HHHHHHHHHHHHHhCC
Confidence            4669999999987763222  332  28     88866654 4444321       1456544 4455577788899999


Q ss_pred             cCC
Q psy2399         102 KFD  104 (232)
Q Consensus       102 ~~d  104 (232)
                      +++
T Consensus        71 dp~   73 (328)
T 1i6k_A           71 DPT   73 (328)
T ss_dssp             CTT
T ss_pred             Chh
Confidence            987

>1n3l_A Tyrosyl-tRNA synthetase; rossmann fold AS catalytic domain, unique anticodon recognit domain, dimer, ligase; 1.18A {Homo sapiens} SCOP: c.26.1.1 PDB: 1q11_A*

Probab=95.58  E-value=0.023  Score=50.64  Aligned_cols=74  Identities=16%  Similarity=0.132  Sum_probs=42.7

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHH---HHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEF---INNISSN   91 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~---~~~~~~~   91 (232)
                      .|.++. -|||.|||||+.+.+.   +.++++ .|     +++.+..| |.|+.-..      -.++.++   ...+.+.
T Consensus        37 ~vy~G~-~PTG~lHlG~~~~~l~---~~~~~q-~g-----~~~i~~I~-D~ha~t~~------~~~~~~l~~~~~~~~~~   99 (372)
T 1n3l_A           37 KIYWGT-ATTGKPHVAYFVPMSK---IADFLK-AG-----CEVTILFA-DLHAYLDN------MKAPWELLELRVSYYEN   99 (372)
T ss_dssp             EEEEEE-CCSSCCBGGGHHHHHH---HHHHHH-TT-----CEEEEEEC-HHHHHHTT------TTSCHHHHHHHHHHHHH
T ss_pred             EEEeCc-CCCCcccHHHHHHHHH---HHHHHH-CC-----CCEEEEEc-CCceeeCC------CCCHHHHHHHHHHHHHH
Confidence            444443 3779999999877655   444444 68     78776654 22322210      0134443   3444444


Q ss_pred             -HHHHHhccCCcCCc
Q psy2399          92 -RKKYLDGFYIKFDN  105 (232)
Q Consensus        92 -~~~~l~~lgI~~d~  105 (232)
                       +...|.++|++++.
T Consensus       100 ~i~~~lla~Gldp~k  114 (372)
T 1n3l_A          100 VIKAMLESIGVPLEK  114 (372)
T ss_dssp             HHHHHHHHHTCCCTT
T ss_pred             HHHHHHHHcCCChhh
Confidence             66667899998874

>3tze_A Tryptophanyl-tRNA synthetase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, amino acylation; HET: TRP; 2.60A {Encephalitozoon cuniculi}

Probab=95.41  E-value=0.055  Score=48.84  Aligned_cols=79  Identities=13%  Similarity=0.116  Sum_probs=48.2

Q ss_pred             CCCcEEEEcCCCCCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      +++++.|.++. -|+| .|||||..+.   ..+.++++.-|     ..+.+..| |.|....      ...+++++. ++
T Consensus        98 ~~~p~~vy~G~-~PTg~~lHLGh~v~~---~~~~~lQ~~~g-----~~~~i~Ia-D~~a~l~------~~~~~e~i~-~~  160 (406)
T 3tze_A           98 NNRPFYLYTGR-GPSSKTMHIGHTIPF---LLCKYMQDAFK-----IRLVIQIT-DDEKFLW------KSMRLEDAM-AY  160 (406)
T ss_dssp             TTCCEEEEEEE-CCCSSCCBGGGHHHH---HHHHHHHHHHT-----CCEEEEEC-HHHHHHH------SSCCHHHHH-HH
T ss_pred             cCCCeEEEEee-CCCCCcccHHHHHHH---HHHHHHHHhcC-----CcEEEEee-ChHHHcC------CCCCHHHHH-HH
Confidence            35677777765 7888 7999996654   33333444447     67766543 4442111      135666554 44


Q ss_pred             HHHHHHHHhccCCcCCc
Q psy2399          89 SSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~  105 (232)
                      ...+.+++-++|++.+.
T Consensus       161 ~~~~~~~~lA~GlDp~k  177 (406)
T 3tze_A          161 GRENIKDIVTLGFDPKL  177 (406)
T ss_dssp             HHHHHHHHHTTTCCGGG
T ss_pred             HHHHHHHHHHcCCCccc
Confidence            45666777789998764

>3hv0_A Tryptophanyl-tRNA synthetase; tRNA-ligase, ATP-binding, aminoacyl-tRNA synthetase, ligase, nucleotide-binding; HET: TRP; 2.42A {Cryptosporidium parvum iowa II} SCOP: c.26.1.0

Probab=95.35  E-value=0.047  Score=49.07  Aligned_cols=78  Identities=14%  Similarity=0.110  Sum_probs=47.1

Q ss_pred             CCcEEEEcCCCCCC-CcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH-cCCCHHHHHHHH
Q psy2399          11 VRRIFVTTALPYAN-GELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK-AGMTPKEFINNI   88 (232)
Q Consensus        11 ~~~~~v~~~~P~~n-G~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~-~g~~~~e~~~~~   88 (232)
                      ++++.|.++. -|+ |.|||||..+.+   .+.++++.-|     ..|.+..| |.|      +... ...+++++ .++
T Consensus        72 g~~~~vy~G~-~PTa~~lHlGh~v~~~---~~~~lQ~~~~-----~~v~i~I~-D~~------~~~~r~~~~~e~i-~~~  134 (393)
T 3hv0_A           72 GELFYLYTGR-GPSSESLHVGHLVPFL---FTKYLQDTFK-----VPLVIQLT-DDE------KFIFKSNLTLEET-HNY  134 (393)
T ss_dssp             TCCCEEEEEE-CCSSSSCBSTTHHHHH---HHHHHHHHHC-----CCEEEEEC-HHH------HHHHCTTCCHHHH-HHH
T ss_pred             CCCeEEEeCC-CCCCCCccHHHHHHHH---HHHHHHHhcC-----CCeEeecc-ChH------HHhhccCCCHHHH-HHH
Confidence            4456666665 677 689999965544   4444555557     67666543 221      2122 25666555 444


Q ss_pred             HHHHHHHHhccCCcCCc
Q psy2399          89 SSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~  105 (232)
                      ...+.+++.++|++.+.
T Consensus       135 ~~~~~~~~lA~GlDp~k  151 (393)
T 3hv0_A          135 AYENMKDIIACGFDPEL  151 (393)
T ss_dssp             HHHHHHHHHTTCCCTTT
T ss_pred             HHHHHHHHHHcCCCCcc
Confidence            44666778889998764

>2ip1_A Tryptophanyl-tRNA synthetase; rossmann fold, structural genomics, PSI-2, protein structure initiative; HET: PG4; 1.80A {Saccharomyces cerevisiae} PDB: 3kt0_A* 3kt3_A* 3kt6_A* 3kt8_A*

Probab=95.31  E-value=0.039  Score=50.20  Aligned_cols=79  Identities=15%  Similarity=0.187  Sum_probs=48.4

Q ss_pred             CCcEEEEcCCCCCC-CcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYAN-GELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        11 ~~~~~v~~~~P~~n-G~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      ++++.|.++. -|+ |.|||||..+.+.   +.+++...|     .++.++.| |.++.--     ...++++.+ .++.
T Consensus       100 g~~~~vy~G~-dPTag~LHLGh~v~~~~---l~~lQ~~~g-----~~~i~lI~-D~ta~l~-----~~~~t~e~i-~~~~  163 (432)
T 2ip1_A          100 GKPFFLYTGR-GPSSDSMHLGHMIPFVF---TKWLQEVFD-----VPLVIELT-DDEKFLF-----KHKLTINDV-KNFA  163 (432)
T ss_dssp             TCCCEEEEEE-CCCSSCCBGGGHHHHHH---HHHHHHHHT-----CCEEEEEC-HHHHHHH-----CTTCCHHHH-HHHH
T ss_pred             CCCeEEEEee-cCCCCCccHHHHHHHHH---HHHHHHHcC-----CeEEEEEe-cccceeC-----CCCCCHHHH-HHHH
Confidence            3456666665 677 8999999886542   334444478     88887776 4333220     112565554 4444


Q ss_pred             HHHHHHHhccCCcCCc
Q psy2399          90 SNRKKYLDGFYIKFDN  105 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~  105 (232)
                      ..+.+++.++|++.+.
T Consensus       164 ~~~~~~~lA~GlDp~k  179 (432)
T 2ip1_A          164 RENAKDIIAVGFDPKN  179 (432)
T ss_dssp             HHHHHHHHTTTCCGGG
T ss_pred             HHHHHHHHHhCCCCCc
Confidence            4556677788998763

>2j5b_A Tyrosyl-tRNA synthetase; ligase, protein biosynthesis, ATP-binding; HET: TYE; 2.20A {Acanthamoeba polyphaga mimivirus}

Probab=95.23  E-value=0.047  Score=48.22  Aligned_cols=79  Identities=15%  Similarity=0.091  Sum_probs=45.9

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      ++..|.++. -|+|.|||||..  +..-.+.+++ ..|     +++.+..| |.|+.-.    .+.|.++++ +.++...
T Consensus        39 ~~~~vy~G~-~PTg~lHlGhyl--~~l~~~~~lQ-~~G-----~~~~~~i~-D~~a~~~----~~~~~~~e~-i~~~~~~  103 (348)
T 2j5b_A           39 RIFTAYNGF-EPSGRIHIAQAL--ITVMNTNNMI-ECG-----GQMIIYIA-DWFAKMN----LKMNGDINK-IRELGRY  103 (348)
T ss_dssp             CCEEEEEEE-CCCSSCBHHHHH--HHHHHHHHHH-HTT-----EEEEEEEC-HHHHHHT----TGGGGCHHH-HHHHHHH
T ss_pred             CCCEEEecc-CCCCCCchhHHH--HHHHHHHHHH-HcC-----CcEEEEec-cchhhhC----CCCCCCHHH-HHHHHHH
Confidence            344554444 566999999932  2223344444 458     88877664 3343221    122345544 4555567


Q ss_pred             HHHHHhccCCcCCc
Q psy2399          92 RKKYLDGFYIKFDN  105 (232)
Q Consensus        92 ~~~~l~~lgI~~d~  105 (232)
                      +.+++.++|++.+.
T Consensus       104 ~~~~~la~Gldp~k  117 (348)
T 2j5b_A          104 FIEVFKACGINLDG  117 (348)
T ss_dssp             HHHHHHHTTCCGGG
T ss_pred             HHHHHHHhcCCccc
Confidence            77788899998764

>1r6t_A Tryptophanyl-tRNA synthetase; class IC tRNA synthetase, rossmann fold catalytical domain, recognition domain, bound Trp-AMP, ligase; HET: TYM; 2.10A {Homo sapiens} SCOP: a.16.1.3 c.26.1.1 PDB: 2azx_A* 2quh_A* 2qui_A* 2quj_A* 2quk_A

Probab=95.13  E-value=0.042  Score=50.60  Aligned_cols=78  Identities=12%  Similarity=0.134  Sum_probs=48.5

Q ss_pred             CCcEEEEcCCCCCC-CcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYAN-GELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        11 ~~~~~v~~~~P~~n-G~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      ++++.|.++. -|+ |.|||||..+.+.   +.+++...|     .++.++.|- .++.--    +  .++++++. ++.
T Consensus       153 ~~~~~vy~G~-dPTag~LHLGh~v~~~~---~~~lQ~~~g-----~~~iilI~D-~~a~ig----d--~lt~e~i~-~n~  215 (477)
T 1r6t_A          153 KKPFYLYTGR-GPSSEAMHVGHLIPFIF---TKWLQDVFN-----VPLVIQMTD-DEKYLW----K--DLTLDQAY-GDA  215 (477)
T ss_dssp             TCCEEEEEEE-CCCTTCCBGGGHHHHHH---HHHHHHHHT-----CCEEEEECH-HHHHHH----S--SCCHHHHH-HHH
T ss_pred             CCCcEEEEcc-cCCCCCccHHHHHHHHH---HHHHHHHhC-----CcEEEEEec-ceeeec----C--CCCHHHHH-HHH
Confidence            4567777765 677 8999999887652   333444478     887776653 232221    1  46666544 444


Q ss_pred             HHHHHHHhccCCcCCc
Q psy2399          90 SNRKKYLDGFYIKFDN  105 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~  105 (232)
                      ..+..++.++|++++.
T Consensus       216 ~~~~~~~lA~GlDp~k  231 (477)
T 1r6t_A          216 VENAKDIIACGFDINK  231 (477)
T ss_dssp             HHHHHHHHTTCCCTTS
T ss_pred             HHHHHHHHHhCCCCCc
Confidence            4456667788988763

>3foc_A Tryptophanyl-tRNA synthetase; structural genomics, giardiasi aminoacyl-tRNA synthetase, ligase; 2.09A {Giardia lamblia atcc 50803}

Probab=95.10  E-value=0.078  Score=48.46  Aligned_cols=80  Identities=18%  Similarity=0.184  Sum_probs=48.2

Q ss_pred             CCCcEEEEcCCCCCC-CcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYAN-GELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus        10 ~~~~~~v~~~~P~~n-G~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      +++++.|.++. -|| |.|||||..+.+   .+.+++..-|     ..+.+..| |.+ .    ...+...+++++. ++
T Consensus        88 ~g~p~~vytG~-dPTagsLHLGH~v~~~---~l~~lQ~~~g-----~~v~I~Ig-D~~-a----~~~r~~lt~E~I~-~n  151 (451)
T 3foc_A           88 KGHPIYIYTGR-GPSSGALHLGHLLPFI---FTKYLQDAFK-----CYVVIQIT-DDE-K----FLRNRSLSYAEVD-SY  151 (451)
T ss_dssp             TTCCEEEEEEE-CCCSSCCBHHHHHHHH---HHHHHHHHHT-----CEEEEEEC-HHH-H----HHHCTTCCHHHHH-HH
T ss_pred             cCCCeEEEecC-CCCCCCccHHHHHHHH---HHHHHHHccC-----ceEEEEee-CcH-H----hhcccCCCHHHHH-HH
Confidence            34677777776 788 899999966543   3344445447     77777543 221 1    1122245666554 44


Q ss_pred             HHHHHHHHhccCCcCCc
Q psy2399          89 SSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~  105 (232)
                      ...+.+++-++|++.+.
T Consensus       152 ~~~~~~~~lA~GlDpek  168 (451)
T 3foc_A          152 TRENIKDIIACGFDPDK  168 (451)
T ss_dssp             HHHHHHHHHTTTCCGGG
T ss_pred             HHHHHHHHHHcCCCCCc
Confidence            44666777888987653

>1yi8_B Tryptophanyl-tRNA synthetase; ligase; HET: TRP; 2.10A {Deinococcus radiodurans} PDB: 1yia_B* 1yid_B* 2a4m_A*

Probab=95.09  E-value=0.064  Score=47.43  Aligned_cols=73  Identities=16%  Similarity=0.113  Sum_probs=43.4

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHc-CCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQ-QDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSN   91 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~-G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~   91 (232)
                      +..|.++. -|+|.|||||..+.+.     .|.+++ .     +++.+.. .|.|+.-..      ..+++++. ++...
T Consensus        22 ~~~vysG~-~PTG~lHLGn~~g~l~-----~~~~lQ~~-----~~~~~~I-aD~ha~~~~------~~~~e~i~-~~~~~   82 (351)
T 1yi8_B           22 RPRVLTGD-RPTGALHLGHLAGSLQ-----NRVRLQDE-----AELFVLL-ADVQALTDH------FDRPEQVR-ENVLA   82 (351)
T ss_dssp             CSEEEEEE-CCSSCCBHHHHHHTHH-----HHHHHTSS-----SEEEEEE-CHHHHHHHH------TTCHHHHH-HHHHH
T ss_pred             CcEEEEee-CCCCCccHHHHHHHHH-----HHHHHHHh-----CCeEEEE-ecchhhcCC------CCCHHHHH-HHHHH
Confidence            33444433 5679999999987642     333333 3     4665444 455554422      35666554 44445


Q ss_pred             HHHHHhccCCcCC
Q psy2399          92 RKKYLDGFYIKFD  104 (232)
Q Consensus        92 ~~~~l~~lgI~~d  104 (232)
                      +.+++.++|++++
T Consensus        83 ~~~~~la~Gldp~   95 (351)
T 1yi8_B           83 VALDYLAAGLDPQ   95 (351)
T ss_dssp             HHHHHHHHTCCTT
T ss_pred             HHHHHHHhCCChh
Confidence            6677888999887

>2yy5_A Tryptophanyl-tRNA synthetase; aminoaccyl tRNA synthetase, structural genomics, NPPSFA; HET: WSA; 2.55A {Mycoplasma pneumoniae}

Probab=95.00  E-value=0.021  Score=50.51  Aligned_cols=77  Identities=18%  Similarity=0.286  Sum_probs=45.4

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|+|.|||||..+.+..-  .+++.  |     +++.+..+ |.|+.-.       ..+|+++.+ +...+.+++.++|+
T Consensus        12 ~PTG~lHLGn~vg~l~~~--~~lQ~--~-----~~~~~~Ia-D~ha~~~-------~~d~~~i~~-~~~~~~~~~lA~Gl   73 (348)
T 2yy5_A           12 QASGKQHLGNYLGVMQSL--IELQE--Q-----CQLFVFVA-DLHSITV-------DFQPQALKQ-NNFDLVRTLLAVGL   73 (348)
T ss_dssp             CCCTTCBHHHHHHTGGGH--HHHHH--H-----SEEEEEEC-HHHHTTS-------CCCHHHHHH-HHHHHHHHHHHTTC
T ss_pred             CCCCcccHHHHHHHHHHH--HHHHh--C-----CcEEEEEc-ChhhccC-------CCCHHHHHH-HHHHHHHHHHHhCC
Confidence            466999999998766322  23333  7     77765543 3343321       146665544 45566677888999


Q ss_pred             cCCc--cccCC-ChhHHH
Q psy2399         102 KFDN--WYSTD-SIENID  116 (232)
Q Consensus       102 ~~d~--~~~t~-~~~~~~  116 (232)
                      +++.  ++.-| -+.|.+
T Consensus        74 dp~k~~if~qS~~~~~~e   91 (348)
T 2yy5_A           74 DPQKACLFLQSDLLEHSM   91 (348)
T ss_dssp             CTTTEEEEEGGGCHHHHH
T ss_pred             ChhHeEEEECCcccchhH
Confidence            9873  33333 344443

>3vgj_A Tyrosyl-tRNA synthetase, putative; tyrrs, ligase; HET: YAP; 2.21A {Plasmodium falciparum}

Probab=94.91  E-value=0.059  Score=48.10  Aligned_cols=77  Identities=14%  Similarity=0.151  Sum_probs=44.3

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      ..|.++. -|+|.|||||.  .+..-.+.++ ...|     +++.+..| |.|+.-.    .+.|.+++++ .++...+.
T Consensus        57 ~~iy~G~-~PTg~lHlG~g--vl~~~~~~~l-Q~~G-----~~~~~lIa-D~ha~i~----d~~~~~~~~i-~~~~~~~~  121 (373)
T 3vgj_A           57 LICYDGF-EPSGRMHIAQG--LLKSIIVNKL-TSNG-----CTFIFWIA-DWFAHLN----NKMSGDLKKI-KKVGSYFI  121 (373)
T ss_dssp             CEEEEEE-CCCSSCBHHHH--HHHHHHHHHH-HTTT-----CEEEEEEC-HHHHHHT----TGGGGCHHHH-HHHHHHHH
T ss_pred             ceEEeCC-CCCCCceehhh--HHHHHHHHHH-HHCC-----CcEEEEEe-cceeEec----CCCCCCHHHH-HHHHHHHH
Confidence            3444443 56689999992  2222224444 4468     88887775 5454321    1233445443 44445566


Q ss_pred             HHHhccCCcCCc
Q psy2399          94 KYLDGFYIKFDN  105 (232)
Q Consensus        94 ~~l~~lgI~~d~  105 (232)
                      +.+.++|++++.
T Consensus       122 ~~~~a~G~dp~k  133 (373)
T 3vgj_A          122 EVWKSCGMNMEN  133 (373)
T ss_dssp             HHHHHTTCCSTT
T ss_pred             HHHHHcCCChhh
Confidence            788889998764

>3i05_A Tryptophanyl-tRNA synthetase; APO tRNA-ligase, ATP-binding, aminoacyl-tRNA synthetase, LIG nucleotide-binding, protein biosynthesis; 2.80A {Trypanosoma brucei} SCOP: c.26.1.0

Probab=94.85  E-value=0.054  Score=48.70  Aligned_cols=79  Identities=10%  Similarity=0.107  Sum_probs=48.6

Q ss_pred             CCCcEEEEcCCCCCCC-cCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYANG-ELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG-~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      +++++.|.++. -|+| .|||||..+.   ..+.++++.-|     ..+.++.|-+.+       +.....+++++. ++
T Consensus        75 ~~~~~~vy~G~-~PTg~~lHLGh~v~~---~~~~~lQ~~~~-----~~v~i~I~D~~~-------~l~~~~~~e~i~-~~  137 (395)
T 3i05_A           75 SGQPFYLYTGR-GPSSESMHMGHLIPF---MFTKWLQDSFR-----VPLVIQMTDDEK-------FYFRNIPMEQVE-AM  137 (395)
T ss_dssp             TTCCEEEEEEE-CCCSSCCBGGGSHHH---HHHHHHHHHHT-----CCEEEEECHHHH-------HHHSCCCHHHHH-HH
T ss_pred             cCCCeEEEEee-cCCCccchHHHHHHH---HHHHHHHHhcC-----CcEEEEEcchHH-------HhcCCCCHHHHH-HH
Confidence            34567777765 7889 6999997554   34444555557     777776443321       111236666654 44


Q ss_pred             HHHHHHHHhccCCcCCc
Q psy2399          89 SSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~  105 (232)
                      ...+.+++.++|++.+.
T Consensus       138 ~~~~~~~~lA~GlDp~k  154 (395)
T 3i05_A          138 TTENIKDIIAMGFDPEL  154 (395)
T ss_dssp             HHHHHHHHHTTTCCTTS
T ss_pred             HHHHHHHHHHcCCCCCc
Confidence            45666777889997764

>1r6u_A Tryptophanyl-tRNA synthetase; class IC tRNA synthetase, rossmann fold catalytic domain, AN recognition domain, bound Trp-AMP, ligase; HET: TYM; 2.00A {Homo sapiens} SCOP: c.26.1.1 PDB: 1ulh_A 2dr2_A* 2ake_A* 1o5t_A

Probab=94.80  E-value=0.081  Score=48.19  Aligned_cols=79  Identities=11%  Similarity=0.131  Sum_probs=49.1

Q ss_pred             CCCcEEEEcCCCCCC-CcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHH
Q psy2399          10 DVRRIFVTTALPYAN-GELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNI   88 (232)
Q Consensus        10 ~~~~~~v~~~~P~~n-G~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~   88 (232)
                      .++++.|.++. -|| |.|||||..+.+.   +.+++...|     .++.++.|- .++.--.      .++++++. ++
T Consensus       105 ~~~~~~vy~G~-dPTag~LHLGh~v~~~~---~~~lQ~~~G-----~~~iilIgD-~ta~igd------~lt~e~i~-~n  167 (437)
T 1r6u_A          105 NKKPFYLYTGR-GPSSEAMHVGHLIPFIF---TKWLQDVFN-----VPLVIQMTD-DEKYLWK------DLTLDQAY-GD  167 (437)
T ss_dssp             TTCCEEEEEEE-CCCSSCCBHHHHHHHHH---HHHHHHHHT-----CCEEEEECH-HHHHHHS------SCCHHHHH-HH
T ss_pred             cCCCcEEEEcc-cCCCCCccHHHHHHHHH---HHHHHHHhC-----CcEEEEEec-ceeeecC------CCCHHHHH-HH
Confidence            34567777765 677 8999999887652   334444478     887776653 3332211      46666644 44


Q ss_pred             HHHHHHHHhccCCcCCc
Q psy2399          89 SSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~  105 (232)
                      ...+..++.++|++.+.
T Consensus       168 ~~~~~~~~lA~GlDp~k  184 (437)
T 1r6u_A          168 AVENAKDIIACGFDINK  184 (437)
T ss_dssp             HHHHHHHHHTTTCCGGG
T ss_pred             HHHHHHHHHHhCCCccc
Confidence            44456677788987663

>3p0j_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, tyrrs, pseudod translation, ATP-binding, nucleotide-binding, ligase; HET: TYE; 2.89A {Leishmania major} PDB: 3p0i_A* 3p0h_A*

Probab=94.77  E-value=0.062  Score=51.71  Aligned_cols=78  Identities=15%  Similarity=0.097  Sum_probs=46.6

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHH-HHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQAD-IWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~D-vl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      ++..|.++. -|||.|||||   .++.- .+.++ ...|     +++.+..| |-|+.-.    .+.|.++++ +.++..
T Consensus        39 ~~~~vy~G~-~PTg~lHLG~---~v~~~~~~~~l-Q~~G-----~~~~~lIa-D~ha~~~----d~~~~~~e~-i~~~~~  102 (690)
T 3p0j_A           39 PLIRCYDGF-EPSGRMHIAQ---GIFKAVNVNKC-TAAG-----CEFVFWVA-DWFALMN----DKVGGELEK-IRIVGR  102 (690)
T ss_dssp             TTEEEEEEE-CCCSCCBHHH---HHHHHHHHHHH-HHTT-----EEEEEEEC-CGGGGGG----CTTTTHHHH-HHHHHH
T ss_pred             CCceEEeee-cCCCcchhHh---hHHHHHHHHHH-HHCC-----CcEEEEEe-eeEEEec----CCCcchHHH-HHHHHH
Confidence            455565554 6779999999   22222 23444 4568     89887766 5555321    112333444 344446


Q ss_pred             HHHHHHhccCCcCCc
Q psy2399          91 NRKKYLDGFYIKFDN  105 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~  105 (232)
                      .+.+++.++|++++.
T Consensus       103 ~~~~~~lA~GlDp~k  117 (690)
T 3p0j_A          103 YLIEVWKAAGMDMDK  117 (690)
T ss_dssp             HHHHHHHHTTCCGGG
T ss_pred             HHHHHHHHcCCChHH
Confidence            667788899998764

>3sz3_A Tryptophanyl-tRNA synthetase; structural genomics, center for structural genomics of infec diseases, csgid, rossmann fold; HET: TRP; 1.50A {Vibrio cholerae o1 biovar el tor}

Probab=94.66  E-value=0.038  Score=48.76  Aligned_cols=79  Identities=15%  Similarity=0.278  Sum_probs=47.1

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|+|.|||||..+.+..  +.+++.  +     +++.+..+ |.|..-.       ..+++++ .++...+..++.++|+
T Consensus        14 ~PTG~lHLGhy~g~l~~--~~~lQ~--~-----~~~~~~ia-D~ha~~~-------~~~~~~~-~~~~~~~~~~~lA~Gl   75 (341)
T 3sz3_A           14 QPSGELSIGNYLGALRQ--WQQMQD--D-----YDCQYCVV-DLHAITV-------RQDPQAL-HEATLDALAICLAVGV   75 (341)
T ss_dssp             CSSSCCBHHHHHHTGGG--HHHHHH--H-----SEEEEEEC-HHHHTTS-------CCCHHHH-HHHHHHHHHHHHHTTC
T ss_pred             CCCCcccHHHHHHHHHH--HHHHHh--c-----CeEEEEEe-cceeEcC-------CCCHHHH-HHHHHHHHHHHHHcCC
Confidence            56799999999876632  233433  5     67766543 5554331       2466554 4445567778889999


Q ss_pred             cCCc--cccCC-ChhHHHHH
Q psy2399         102 KFDN--WYSTD-SIENIDLV  118 (232)
Q Consensus       102 ~~d~--~~~t~-~~~~~~~v  118 (232)
                      +++.  ++.-| -++|.+..
T Consensus        76 Dp~k~~i~~qS~v~~~~el~   95 (341)
T 3sz3_A           76 DPKKSTLFVQSHVPEHAQLG   95 (341)
T ss_dssp             CTTTSEEEEGGGCTHHHHHH
T ss_pred             ChhhcEEEeccchhhhHHHH
Confidence            8874  33333 34454433

>2cyc_A Tyrosyl-tRNA synthetase; tyrosine, tyrrs, aminoacylation, structural genomics; HET: TYR; 2.20A {Pyrococcus horikoshii}

Probab=94.37  E-value=0.056  Score=48.27  Aligned_cols=79  Identities=14%  Similarity=0.037  Sum_probs=43.6

Q ss_pred             cEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHH----H
Q psy2399          13 RIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINN----I   88 (232)
Q Consensus        13 ~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~----~   88 (232)
                      ++.|.++. -|||.|||||....+  -.+.+++ ..|     +++.+..| |.|+.-    ..+.|.+++++...    +
T Consensus        33 ~~~vy~G~-~PTg~lHlG~yl~~l--~~~~~lQ-~~G-----~~~~~~ia-D~ha~~----~~~~g~~~e~i~~~~~~~~   98 (375)
T 2cyc_A           33 PLQHYIGF-EISGYIHLGTGLMAG--AKIADFQ-KAG-----IKTRVFLA-DWHSWI----NDKLGGDLEVIQEVALKYF   98 (375)
T ss_dssp             CCBEEEEE-CCCSCCBHHHHHHHH--HHHHHHH-HTT-----CBCEEEEC-HHHHHH----TTGGGGCHHHHHHHHHHTH
T ss_pred             CcEEEeCC-CCCCCcCchHHHHHH--HHHHHHH-HCC-----CcEEEEec-CcEEEc----CCCCCCCHHHHHHHHHHHH
Confidence            33444443 567999999944322  2333444 468     88777654 333322    12234455554433    3


Q ss_pred             HHHHHHHHhccCCcCCc
Q psy2399          89 SSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        89 ~~~~~~~l~~lgI~~d~  105 (232)
                      ...+.+++.++|++++.
T Consensus        99 ~~~~~~~~la~G~dp~k  115 (375)
T 2cyc_A           99 KVGMEKSIEVMGGDPKK  115 (375)
T ss_dssp             HHHHHHHHHHTTCCGGG
T ss_pred             HHHHHHHHHHhCCCccc
Confidence            33444888899998763

>3n9i_A Tryptophanyl-tRNA synthetase; tryptophan-tRNA ligase, csgid, structural genomics, niaid, center for structural genomics infectious diseases; 1.95A {Yersinia pestis} SCOP: c.26.1.1

Probab=93.82  E-value=0.058  Score=47.65  Aligned_cols=65  Identities=17%  Similarity=0.225  Sum_probs=40.8

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHH-cCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCM-QQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFY  100 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~-~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lg  100 (232)
                      -|+|.|||||..+.+.     .|.++ .+     +++.+..+ |.|..-.       ..+|+++ .++......++.++|
T Consensus        23 ~PTG~lHLGh~vg~l~-----~~~~lQ~~-----~~~~~~ia-D~hA~t~-------~~~~~~~-~~~~~~~~~~~lA~G   83 (346)
T 3n9i_A           23 QPSGELTIGNYMGALR-----QWVQMQDD-----YDCIYCIV-DLHAITA-------RQDPALL-RKRTLDTLALYLACG   83 (346)
T ss_dssp             CSCSCCBHHHHHHTHH-----HHHTTTTT-----SEEEEEEC-HHHHTTS-------CCCHHHH-HHHHHHHHHHHHHHT
T ss_pred             CCCCcccHHHHHHHHH-----HHHHHHhh-----CcEEEEEe-cceeecC-------CCCHHHH-HHHHHHHHHHHHHcC
Confidence            5679999999887652     22222 25     77766553 5554331       2456554 444456677788899


Q ss_pred             CcCCc
Q psy2399         101 IKFDN  105 (232)
Q Consensus       101 I~~d~  105 (232)
                      ++++.
T Consensus        84 lDp~k   88 (346)
T 3n9i_A           84 IDPKK   88 (346)
T ss_dssp             CCTTT
T ss_pred             CCccc
Confidence            98874

>2el7_A Tryptophanyl-tRNA synthetase; aminoacyl-tRNA synthetase, translation, structural GEN NPPSFA; 2.50A {Thermus thermophilus}

Probab=93.67  E-value=0.13  Score=45.28  Aligned_cols=69  Identities=19%  Similarity=0.256  Sum_probs=38.3

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|||.|||||..+.+.  -+.++++.-+     +++.+..| |.|+.-..    + +-+++++ .++...+..++.++|+
T Consensus         9 ~PTg~lHlGh~~g~l~--~~~~lQ~~G~-----~~~~~~Ia-D~~a~~~~----~-~~~~~~i-~~~~~~~~~~~la~Gl   74 (337)
T 2el7_A            9 QPSGEIHIGNYLGAIK--QWVAIGEKLG-----RDAFFCIV-DYHALTNP----L-AYDPSTL-AQRTFEAALVNIAAGL   74 (337)
T ss_dssp             CSCSCCBHHHHHTHHH--HHHHHHHHHG-----GGEEEEEC-GGGGGGST----T-TSCHHHH-HHHHHHHHHHHHHHTC
T ss_pred             CCCCcccHHHHHHHHH--HHHHHHhcCC-----CCEEEEEe-CceeecCC----C-CCCHHHH-HHHHHHHHHHHHHhCC
Confidence            4668999999987752  2334554432     35544332 33432210    0 2345444 4444555667778999


Q ss_pred             cCC
Q psy2399         102 KFD  104 (232)
Q Consensus       102 ~~d  104 (232)
                      +++
T Consensus        75 dp~   77 (337)
T 2el7_A           75 DPE   77 (337)
T ss_dssp             CTT
T ss_pred             Chh
Confidence            876

>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*

Probab=90.28  E-value=0.14  Score=46.41  Aligned_cols=79  Identities=16%  Similarity=0.215  Sum_probs=40.3

Q ss_pred             cEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChh--hHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          13 RIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAH--GAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        13 ~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~--G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      +..|.++. -|||+ |||||...   .-.+.+++ ..|     +++.++.|-.+.  |.|--...++.-++++++. ++.
T Consensus        32 ~~~iy~G~-dPTg~sLHlGh~v~---l~~~~~lQ-~~G-----~~~~~lIgd~ta~igdp~gk~~~R~~l~~e~i~-~n~  100 (420)
T 1jil_A           32 QVTLYCGA-DPTADSLHIGHLLP---FLTLRRFQ-EHG-----HRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVD-KNI  100 (420)
T ss_dssp             CCEEEEEE-CCSSSSCBHHHHHH---HHHHHHHH-HTT-----CEEEEEECTTGGGTCCCTTCSSCCCCCCHHHHH-HHH
T ss_pred             CCEEEEee-CCCCCCccHHHHHH---HHHHHHHH-HCC-----CcEEEEEcCceeEecCCCccccccccCCHHHHH-HHH
Confidence            34454444 67798 99999663   33344444 568     888877653321  2220000011113555443 444


Q ss_pred             HHHHHHHhccCCcC
Q psy2399          90 SNRKKYLDGFYIKF  103 (232)
Q Consensus        90 ~~~~~~l~~lgI~~  103 (232)
                      ..+++++.++ +++
T Consensus       101 ~~~~~~~~~~-ld~  113 (420)
T 1jil_A          101 EGISKQMHNI-FEF  113 (420)
T ss_dssp             HHHHHHHHHH-SCC
T ss_pred             HHHHHHHHHH-hCC
Confidence            5555655555 544

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=90.00  E-value=0.64  Score=34.36  Aligned_cols=65  Identities=6%  Similarity=-0.046  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHhccCC-cCC---ccccCCChhHHHHHHHHHHHHHhhcC-CEE------ecccceeeccCCCcc
Q psy2399          83 EFINNISSNRKKYLDGFYI-KFD---NWYSTDSIENIDLVQKIYDTLYNKAK-LII------NKKINQFFDPIKNIF  148 (232)
Q Consensus        83 e~~~~~~~~~~~~l~~lgI-~~d---~~~~t~~~~~~~~v~~~~~~L~~~kG-~iy------~~~~~~~~~~~~~~~  148 (232)
                      .++..+.+.+.+..+.=|. ...   ..+...+-.+.+..+..|..+. +.- .+.      +.....|+|..|+..
T Consensus         7 si~~~i~~~~~~~A~~~g~~~V~~V~l~IG~ls~v~~e~l~f~f~~~~-~gt~~~e~a~L~i~~~p~~~~C~~CG~~   82 (119)
T 2kdx_A            7 SVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFR-EESLVCKDAILDIVDEKVELECKDCSHV   82 (119)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCCCCEEEEEEETTSCCCHHHHHHHHHHHG-GGCTTTSSCCEEEEEECCEEECSSSSCE
T ss_pred             HHHHHHHHHHHHHHHHcCCCeEEEEEEEeehhccccHHHHHHHHHHHH-hCChhhcCcEEEEEeccceEEcCCCCCE
Confidence            4566666777776666565 222   2334444467788888888886 443 222      334456665555543

>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A*

Probab=89.65  E-value=0.74  Score=41.76  Aligned_cols=43  Identities=26%  Similarity=0.298  Sum_probs=26.9

Q ss_pred             CCcEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCC
Q psy2399          11 VRRIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICAD   63 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~   63 (232)
                      ++++.|.++. -|||+ |||||..   .--.+.+++ ..|     +++.++.|-
T Consensus        35 ~~~~~vy~G~-dPTg~sLHlGh~v---~l~~l~~lQ-~~G-----~~~i~lIgD   78 (432)
T 1h3f_A           35 GRPLTVKLGA-DPTRPDLHLGHAV---VLRKMRQFQ-ELG-----HKVVLIIGD   78 (432)
T ss_dssp             CSCCEEEEEE-CTTCCSCBHHHHH---HHHHHHHHH-HTT-----CEEEEEECC
T ss_pred             CCCcEEEEcc-cCCCCCCchhhHH---HHHHHHHHH-HCC-----CCEEEEEcc
Confidence            3445555544 67785 9999976   234444554 468     888776653

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=89.40  E-value=0.65  Score=35.43  Aligned_cols=65  Identities=12%  Similarity=-0.005  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHhccCC-cCC---ccccCCChhHHHHHHHHHHHHHhhcCCEEe-------cccceeeccCCCccc
Q psy2399          83 EFINNISSNRKKYLDGFYI-KFD---NWYSTDSIENIDLVQKIYDTLYNKAKLIIN-------KKINQFFDPIKNIFL  149 (232)
Q Consensus        83 e~~~~~~~~~~~~l~~lgI-~~d---~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~-------~~~~~~~~~~~~~~l  149 (232)
                      .++..+.+.+.+..+.-|. ...   ..+...+..+.+..+..|..+. + |-+.+       .....|+|..|+...
T Consensus         5 sia~~iv~~v~~~A~~~g~~~V~~V~l~IG~ls~v~~e~l~faf~~~~-~-gt~~e~A~L~i~~~p~~~~C~~CG~~~   80 (139)
T 3a43_A            5 ALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLF-A-GTIAEGAEIEFVEEEAVFKCRNCNYEW   80 (139)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSEEEEEEEEEETTCCCCHHHHHHHHHHHH-T-TSTTTTCEEEEEEECCEEEETTTCCEE
T ss_pred             HHHHHHHHHHHHHHHHcCCCeehhHHhhHHHHhhhhHHHHHHHHHHHH-c-CCcccCCEEEEEecCCcEECCCCCCEE
Confidence            4566667777777766665 222   2334444467778888888876 4 33322       345667766666543

>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubre like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A

Probab=88.88  E-value=0.45  Score=38.25  Aligned_cols=35  Identities=0%  Similarity=-0.051  Sum_probs=22.4

Q ss_pred             ChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCC
Q psy2399         111 SIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKN  146 (232)
Q Consensus       111 ~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~  146 (232)
                      ..+|......++.+|. ....+.+.....|-|+.|+
T Consensus       128 E~ehe~~~~~~l~~l~-~~~~~~~~~~~~~~C~~CG  162 (191)
T 1lko_A          128 EEFHEKRFLDFARNIK-EGRVFLREQATKWRCRNCG  162 (191)
T ss_dssp             HHHHHHHHHHHHHHHH-HTCSSEEEEEEEEEETTTC
T ss_pred             HHHHHHHHHHHHHhhh-cccccccCCCceEEECCCC
Confidence            4468888999999987 5444444444566654444

>2pid_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, protein-substrate complex, ATP-BI ligase, mitochondrion, nucleotide-binding, protein biosynth; HET: YSA; 2.20A {Homo sapiens} PDB: 3zxi_A*

Probab=88.65  E-value=0.3  Score=43.21  Aligned_cols=40  Identities=15%  Similarity=0.267  Sum_probs=25.2

Q ss_pred             cEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecC
Q psy2399          13 RIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICA   62 (232)
Q Consensus        13 ~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g   62 (232)
                      +..|.++. -|+|+ |||||+.. +  -.+.+++ ..|     +++.++.|
T Consensus        46 ~~~vy~G~-~PTg~sLHLGhl~~-l--~~~~~lQ-~~G-----~~~~~lIa   86 (356)
T 2pid_A           46 PQTIYCGF-DPTADSLHVGHLLA-L--LGLFHLQ-RAG-----HNVIALVG   86 (356)
T ss_dssp             CCEEEEEE-CCSSSSCBHHHHHH-H--HHHHHHH-HTT-----CEEEEEEC
T ss_pred             CCEEEEee-cCCCCcccHHHHHH-H--HHHHHHH-HCC-----CcEEEEEc
Confidence            35555544 67796 99999442 2  2355554 468     88877664

>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A

Probab=88.51  E-value=0.29  Score=44.26  Aligned_cols=41  Identities=22%  Similarity=0.341  Sum_probs=26.0

Q ss_pred             cEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCC
Q psy2399          13 RIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICAD   63 (232)
Q Consensus        13 ~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~   63 (232)
                      +..|.++. -|||+ |||||...   .-.+.+++ ..|     +++.++.|-
T Consensus        30 ~~~iy~G~-dPTg~sLHlGh~v~---l~~l~~lQ-~~G-----~~~i~lIgd   71 (419)
T 2ts1_A           30 RVTLYCGF-DPTADSLHIGHLAT---ILTMRRFQ-QAG-----HRPIALVGG   71 (419)
T ss_dssp             CCEEEEEE-CCSSSSCBGGGHHH---HHHHHHHH-HTT-----CEEEEEECT
T ss_pred             CCEEEEee-CCCCCCccHHHHHH---HHHHHHHH-HCC-----CcEEEEEcC
Confidence            34444443 67799 99999663   33444444 568     888877653

>2yxn_A Tyrosyl-tRNA synthetase; tRNA synthetases class I, structural genomics, NPPSFA, natio project on protein structural and functional analyses; HET: AZY; 1.80A {Escherichia coli str} PDB: 1wq3_A* 1wq4_A* 1x8x_A* 1vbn_A* 1vbm_A*

Probab=87.91  E-value=0.42  Score=41.62  Aligned_cols=40  Identities=18%  Similarity=0.282  Sum_probs=25.3

Q ss_pred             cEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecC
Q psy2399          13 RIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICA   62 (232)
Q Consensus        13 ~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g   62 (232)
                      +..|.++. -|+|+ |||||...   .-.+.++ ...|     +++.++.|
T Consensus        33 ~~~vy~G~-~PTg~slHlGh~l~---l~~~~~l-Q~~g-----~~~~~~i~   73 (322)
T 2yxn_A           33 PIALVCGF-DPTADSLHLGHLVP---LLCLKRF-QQAG-----HKPVALVG   73 (322)
T ss_dssp             CCEEEEEE-CCSSSSCBHHHHHH---HHHHHHH-HHTT-----CEEEEEEC
T ss_pred             CCEEEEee-cCCCCcccHHHHHH---HHHHHHH-HHcC-----CcEEEEEc
Confidence            44454444 67799 99999662   3334444 4558     88877665

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=87.27  E-value=0.12  Score=35.97  Aligned_cols=37  Identities=16%  Similarity=0.298  Sum_probs=16.6

Q ss_pred             ccCCCcccccceeccCCCCCCccccCCCcCccCCCCC
Q psy2399         142 DPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIY  178 (232)
Q Consensus       142 ~~~~~~~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~  178 (232)
                      ||.++..|.-.--...|+.|++.-...-+|+.||..+
T Consensus         5 CP~C~~~l~~~~~~~~C~~C~~~~~~~afCPeCgq~L   41 (81)
T 2jrp_A            5 CPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPL   41 (81)
T ss_dssp             CSSSCSCCEECSSEEECTTTCCEEEEEEECSSSCSCC
T ss_pred             CCCCCCccccCCCceECccccccCCCcccCcchhhHH
Confidence            4555554433222334555554433334455555544

>1y42_X Tyrosyl-tRNA synthetase, mitochondrial; CYT-18, tRNA ligase, group I intron; HET: TYR; 1.95A {Neurospora crassa} PDB: 2rkj_A

Probab=86.91  E-value=0.6  Score=41.82  Aligned_cols=40  Identities=15%  Similarity=0.277  Sum_probs=25.4

Q ss_pred             cEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecC
Q psy2399          13 RIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICA   62 (232)
Q Consensus        13 ~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g   62 (232)
                      +..|.++. -|||+ |||||...   .-.+.+++ ..|     +++.++.|
T Consensus        64 ~~~vy~G~-dPTg~sLHlGhlv~---l~~l~~lQ-~~G-----~~~~~lIg  104 (392)
T 1y42_X           64 RIGAYVGI-DPTAPSLHVGHLLP---LMPLFWMY-LEG-----YKAFTLIG  104 (392)
T ss_dssp             CCEEEEEE-CCCSSSCBGGGHHH---HHHHHHHH-HHT-----CEEEEEEC
T ss_pred             CCEEEEee-cCCCCCccHHHHHH---HHHHHHHH-HcC-----CcEEEEEc
Confidence            34444443 67799 99999763   23355554 458     88877654

>3p0j_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, tyrrs, pseudod translation, ATP-binding, nucleotide-binding, ligase; HET: TYE; 2.89A {Leishmania major} PDB: 3p0i_A* 3p0h_A*

Probab=86.60  E-value=1.9  Score=41.41  Aligned_cols=75  Identities=12%  Similarity=0.033  Sum_probs=47.6

Q ss_pred             CCCcCCchHHHhHHHHHHHHHHHHHc-CCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          23 ANGELHIGHIMEYIQADIWVRFQCMQ-QDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        23 ~nG~lHiGH~~~~v~~Dvl~R~lr~~-G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      ++|.+||||+-...-  ++..|++.. |     .+|.++.+-++.=     .-++.|.+++ -+.++.....+++.++|.
T Consensus       390 s~g~lHLGh~v~~~k--~l~~~~~~~~g-----~~v~ilIaD~~A~-----i~d~~g~~~e-~i~~~~~y~~~~~~alG~  456 (690)
T 3p0j_A          390 ALLKVPLDVAEGMIK--VTKDFIAAHPE-----GTVTLVLPDWSAV-----ASDEITGVEK-DISAALQVNCALLKAYGL  456 (690)
T ss_dssp             CCSSCBHHHHHHHHH--HHHHHHHHCSS-----CEEEEEECTTHHH-----HTTCTTCCHH-HHHHHHHHHHHHHHHHTC
T ss_pred             CCCCcccchHHHHHH--HHHHHHHHcCC-----CeEEEEEecchhh-----hCCCCCCCHH-HHHHHHHHHHHHHHhcCC
Confidence            789999999987543  345666664 6     7888887655311     1123455544 445556777888999998


Q ss_pred             cC-CccccCC
Q psy2399         102 KF-DNWYSTD  110 (232)
Q Consensus       102 ~~-d~~~~t~  110 (232)
                      +. -.|++.|
T Consensus       457 d~k~~fv~~S  466 (690)
T 3p0j_A          457 PSSVKIVTEN  466 (690)
T ss_dssp             CTTSEEEEHH
T ss_pred             CcCeEEEECC
Confidence            63 2344444

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=85.81  E-value=0.83  Score=36.05  Aligned_cols=21  Identities=14%  Similarity=-0.029  Sum_probs=14.1

Q ss_pred             ChhHHHHHHHHHHHHHhhcCCEE
Q psy2399         111 SIENIDLVQKIYDTLYNKAKLII  133 (232)
Q Consensus       111 ~~~~~~~v~~~~~~L~~~kG~iy  133 (232)
                      ...|.+....++..|.  +|..+
T Consensus       113 E~~H~~~~~~~l~~l~--~~~~~  133 (170)
T 3pwf_A          113 EKIHAELYRKAKEKAE--KGEDI  133 (170)
T ss_dssp             HHHHHHHHHHHHHHHT--TTCCC
T ss_pred             HHHHHHHHHHHHHHHh--cCCcC
Confidence            4468888888888775  44443

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=85.77  E-value=0.47  Score=41.61  Aligned_cols=37  Identities=22%  Similarity=0.392  Sum_probs=22.9

Q ss_pred             CcccccceeccCCCCCCccc-------cCC-CcCccCCCCCCCcc
Q psy2399         146 NIFLPDRYIKGECPICNAKD-------QYG-DFCECCSSIYTPTK  182 (232)
Q Consensus       146 ~~~l~~~~v~g~cp~c~~~~-------~~g-~~Ce~Cg~~~~~~~  182 (232)
                      +.|-++-.+...||.|+...       ..| -.|.+||.++.+..
T Consensus        12 ~~~~~~~~~~~~Cp~Cg~~~~~iv~D~~~G~~vC~~CG~Vl~e~~   56 (345)
T 3k7a_M           12 GRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKL   56 (345)
T ss_dssp             -----CCCCCCCCSTTCCSCCCCCCCSSSCSCCCSSSCCCCCCCC
T ss_pred             cccCccccCCCcCcCCCCCCCceEEECCCCCEecCCCCeEccccc
Confidence            33566666677899998851       123 46999999987543

>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}

Probab=85.09  E-value=0.73  Score=41.80  Aligned_cols=40  Identities=20%  Similarity=0.287  Sum_probs=25.1

Q ss_pred             cEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecC
Q psy2399          13 RIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICA   62 (232)
Q Consensus        13 ~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g   62 (232)
                      +..|.++. -|||+ |||||+..   .-.+.+++ ..|     +++.++.|
T Consensus        32 ~~~iy~G~-dPTg~sLHLGhlv~---l~~l~~lQ-~~G-----~~~i~lIg   72 (432)
T 2jan_A           32 PMTVYAGF-DPTAPSLHAGHLVP---LLTLRRFQ-RAG-----HRPIVLAG   72 (432)
T ss_dssp             CCEEEEEE-CCSSSSCBGGGHHH---HHHHHHHH-HTT-----CEEEEEEC
T ss_pred             CCEEEEee-CCCCCCcCHHHHHH---HHHHHHHH-HCC-----CcEEEEEc
Confidence            44444443 67795 99999442   23455554 468     88887764

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=84.94  E-value=0.35  Score=37.70  Aligned_cols=32  Identities=13%  Similarity=0.180  Sum_probs=21.4

Q ss_pred             CCCcCccCCCCCCCccccCCcccCCCCccEEEE
Q psy2399         167 YGDFCECCSSIYTPTKLINPYSILSGTKPIIKS  199 (232)
Q Consensus       167 ~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~  199 (232)
                      +...|.+||+.+... -....|+.||+++...+
T Consensus       131 ~~y~C~~Cg~~~~~~-~~~~~Cp~CG~~~~~~~  162 (165)
T 2lcq_A          131 WRYVCIGCGRKFSTL-PPGGVCPDCGSKVKLIP  162 (165)
T ss_dssp             CCEEESSSCCEESSC-CGGGBCTTTCCBEEECC
T ss_pred             EEEECCCCCCcccCC-CCCCcCCCCCCcceeCC
Confidence            445699999888643 11238999999865443

>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A

Probab=84.18  E-value=0.67  Score=37.62  Aligned_cols=31  Identities=10%  Similarity=0.078  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWV   42 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~   42 (232)
                      ..+|....-|++.-|. -+-++...+.+...+
T Consensus        13 ~~~~~~~~~~~~~~g~-T~~nL~~a~~gE~~a   43 (202)
T 1yuz_A           13 ATNFNMVADSKTAVGS-TLENLKAAIAGETGA   43 (202)
T ss_dssp             CSCCCCCSSCCCCCCC-HHHHHHHHHHHHHHH
T ss_pred             CccceecCCCcccchH-HHHHHHHHHHHHHHH
Confidence            3455555555565555 445555555544444

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=83.64  E-value=0.31  Score=34.92  Aligned_cols=23  Identities=13%  Similarity=0.070  Sum_probs=8.1

Q ss_pred             hcCCEEecccceeeccCCCcccc
Q psy2399         128 KAKLIINKKINQFFDPIKNIFLP  150 (232)
Q Consensus       128 ~kG~iy~~~~~~~~~~~~~~~l~  150 (232)
                      ..|++-++......||.|+..|.
T Consensus        21 ~~~~~~~~~~M~~~CP~Cq~eL~   43 (101)
T 2jne_A           21 SSGLVPRGSHMELHCPQCQHVLD   43 (101)
T ss_dssp             ----------CCCBCSSSCSBEE
T ss_pred             ccccccCcccccccCccCCCcce
Confidence            45555555544466777766654

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=82.54  E-value=0.66  Score=29.98  Aligned_cols=25  Identities=24%  Similarity=0.530  Sum_probs=16.2

Q ss_pred             CCCCCCcc----c-cCC-CcCccCCCCCCCc
Q psy2399         157 ECPICNAK----D-QYG-DFCECCSSIYTPT  181 (232)
Q Consensus       157 ~cp~c~~~----~-~~g-~~Ce~Cg~~~~~~  181 (232)
                      .||.|+..    + ..| -.|..||.++...
T Consensus        13 ~Cp~C~~~~lv~D~~~ge~vC~~CGlVl~e~   43 (58)
T 1dl6_A           13 TCPNHPDAILVEDYRAGDMICPECGLVVGDR   43 (58)
T ss_dssp             SBTTBSSSCCEECSSSCCEECTTTCCEECCS
T ss_pred             cCcCCCCCceeEeCCCCeEEeCCCCCEEecc
Confidence            69988762    1 223 4588888877654

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=81.90  E-value=1.3  Score=27.34  Aligned_cols=30  Identities=23%  Similarity=0.278  Sum_probs=23.5

Q ss_pred             cCccCCCCCCCcccc---CCcccCCCCccEEEE
Q psy2399         170 FCECCSSIYTPTKLI---NPYSILSGTKPIIKS  199 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~---~~~~~~~g~~~~~~~  199 (232)
                      -|-.||+.++.+||.   .-+|+.||-.+..+-
T Consensus         5 ~C~rCg~~fs~~el~~lP~IrCpyCGyrii~Kv   37 (48)
T 4ayb_P            5 RCGKCWKTFTDEQLKVLPGVRCPYCGYKIIFMV   37 (48)
T ss_dssp             CCCCTTTTCCCCCSCCCSSSCCTTTCCSCEECC
T ss_pred             EeeccCCCccHHHHhhCCCcccCccCcEEEEEe
Confidence            388899999988883   458999998877543

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=81.84  E-value=0.39  Score=33.33  Aligned_cols=17  Identities=29%  Similarity=0.696  Sum_probs=8.3

Q ss_pred             CCCCCCccccCCCcCccCCC
Q psy2399         157 ECPICNAKDQYGDFCECCSS  176 (232)
Q Consensus       157 ~cp~c~~~~~~g~~Ce~Cg~  176 (232)
                      .||.|+.+.+   .|-.||.
T Consensus        33 fCPeCgq~Le---~lkACGA   49 (81)
T 2jrp_A           33 LCPDCRQPLQ---VLKACGA   49 (81)
T ss_dssp             ECSSSCSCCC---EEEETTE
T ss_pred             cCcchhhHHH---HHHhcCC
Confidence            5555555442   2445554

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=81.76  E-value=0.7  Score=28.62  Aligned_cols=27  Identities=26%  Similarity=0.744  Sum_probs=17.4

Q ss_pred             CCCCCCc-c---c-cCC-CcCccCCCCCCCccc
Q psy2399         157 ECPICNA-K---D-QYG-DFCECCSSIYTPTKL  183 (232)
Q Consensus       157 ~cp~c~~-~---~-~~g-~~Ce~Cg~~~~~~~l  183 (232)
                      .||.|+. .   + ..| -.|..||..+....+
T Consensus         7 ~CP~C~~~~l~~d~~~gelvC~~CG~v~~e~~i   39 (50)
T 1pft_A            7 VCPACESAELIYDPERGEIVCAKCGYVIEENII   39 (50)
T ss_dssp             SCTTTSCCCEEEETTTTEEEESSSCCBCCCCCC
T ss_pred             eCcCCCCcceEEcCCCCeEECcccCCccccccc
Confidence            5888877 2   1 112 468899988876554

>3v2d_5 50S ribosomal protein L32; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_4 2hgj_4 2hgu_4 2j03_5 2jl6_5 2jl8_5 2v47_5 2v49_5 2wdi_5 2wdj_5 2wdl_5 2wdn_5 2wh2_5 2wh4_5 2wrj_5 2wrl_5 2wro_5 2wrr_5 2x9s_5 2x9u_5 ...

Probab=81.00  E-value=0.69  Score=30.20  Aligned_cols=21  Identities=29%  Similarity=0.632  Sum_probs=16.2

Q ss_pred             cCCCCCCccccCCCcCccCCC
Q psy2399         156 GECPICNAKDQYGDFCECCSS  176 (232)
Q Consensus       156 g~cp~c~~~~~~g~~Ce~Cg~  176 (232)
                      -.||.||+....--.|..||.
T Consensus        31 ~~c~~cGe~~~~H~vc~~CG~   51 (60)
T 3v2d_5           31 VPCPECKAMKPPHTVCPECGY   51 (60)
T ss_dssp             EECTTTCCEECTTSCCTTTCE
T ss_pred             eECCCCCCeecceEEcCCCCc
Confidence            358888888777777888884

>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...

Probab=80.81  E-value=1  Score=29.37  Aligned_cols=21  Identities=33%  Similarity=0.836  Sum_probs=17.2

Q ss_pred             CCCCCCccccCCCcCccCCCC
Q psy2399         157 ECPICNAKDQYGDFCECCSSI  177 (232)
Q Consensus       157 ~cp~c~~~~~~g~~Ce~Cg~~  177 (232)
                      .||.||+....--.|..||.+
T Consensus        32 ~c~~cG~~~~pH~vc~~CG~Y   52 (60)
T 2zjr_Z           32 ECPQCHGKKLSHHICPNCGYY   52 (60)
T ss_dssp             ECTTTCCEECTTBCCTTTCBS
T ss_pred             ECCCCCCEeCCceEcCCCCcC
Confidence            689999888777889999954

---

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	232
d1pfva2	350	c.26.1.1 (A:4-140,A:176-388) Methionyl-tRNA synthe	1e-29
d1rqga2	361	c.26.1.1 (A:1-138,A:174-396) Methionyl-tRNA synthe	5e-22
d2d5ba2	348	c.26.1.1 (A:1-348) Methionyl-tRNA synthetase (MetR	8e-22
d1h3na3	494	c.26.1.1 (A:1-225,A:418-686) Leucyl-tRNA synthetas	4e-21
d1ilea3	452	c.26.1.1 (A:1-197,A:387-641) Isoleucyl-tRNA synthe	8e-15
d1pfva3	35	g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (Me	1e-14
d1rqga3	35	g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (Me	2e-13
d1ivsa4	425	c.26.1.1 (A:1-189,A:343-578) Valyl-tRNA synthetase	6e-13
d1ffya3	450	c.26.1.1 (A:1-200,A:395-644) Isoleucyl-tRNA synthe	2e-11
d1irxa2	317	c.26.1.1 (A:3-319) Class I lysyl-tRNA synthetase {	2e-06

>d1pfva2 c.26.1.1 (A:4-140,A:176-388) Methionyl-tRNA synthetase (MetRS) {Escherichia coli [TaxId: 562]} Length = 350

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Escherichia coli [TaxId: 562]

 Score =  111 bits (277), Expect = 1e-29
 Identities = 69/157 (43%), Positives = 101/157 (64%), Gaps = 7/157 (4%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           ++I VT ALPYANG +H+GH++E+IQAD+WVR+Q M+        V FICADDAHG  IM
Sbjct: 2   KKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRMRGHE-----VNFICADDAHGTPIM 56

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
           + A++ G+TP++ I  +S   +    GF I +DN++ST S EN  L + IY  L  +   
Sbjct: 57  LKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRLK-ENGF 115

Query: 132 IINKKINQFFDPIKNIFLPDRY-IKGECPICNAKDQY 167
           I N+ I+Q +DP K +FLPDR+ + G  P+    + +
Sbjct: 116 IKNRTISQLYDPEKGMFLPDRFVVSGATPVMRDSEHF 152

>d1rqga2 c.26.1.1 (A:1-138,A:174-396) Methionyl-tRNA synthetase (MetRS) {Pyrococcus abyssi [TaxId: 29292]} Length = 361

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Pyrococcus abyssi [TaxId: 29292]

 Score = 90.8 bits (224), Expect = 5e-22
 Identities = 54/220 (24%), Positives = 88/220 (40%), Gaps = 11/220 (5%)

Query: 13  RIFVTTALPYANGELHIGHIM-EYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           R  VT+ALPYANG +H GH+   Y+ ADI+VR+  ++ ++     V FIC  D HG  I 
Sbjct: 3   RYMVTSALPYANGPIHAGHLAGAYLPADIFVRYLRLKGED-----VVFICGTDEHGTPIS 57

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
             A K G +P+E ++      K       I FD +  T+   +  L Q+ +   Y     
Sbjct: 58  FRALKEGRSPREIVDEFHEQIKITFQRAKISFDFFGRTELPIHYKLSQEFFLKAYENGH- 116

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILS 191
           ++ K   Q +     +FLPDR+     PI      +        +      L        
Sbjct: 117 LVKKVTKQAYCEHDKMFLPDRFAICGRPISFRDSAHYYIKMQDFAER----LKRWIEKQP 172

Query: 192 GTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQPEIF 231
               +      +  +  ++R I     W I     + ++ 
Sbjct: 173 WKPNVKNMVLSWIEEGLEERAITRDLNWGIPVPLDEEDMK 212

>d2d5ba2 c.26.1.1 (A:1-348) Methionyl-tRNA synthetase (MetRS) {Thermus thermophilus [TaxId: 274]} Length = 348

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Thermus thermophilus [TaxId: 274]

 Score = 89.7 bits (221), Expect = 8e-22
 Identities = 35/171 (20%), Positives = 66/171 (38%), Gaps = 6/171 (3%)

Query: 12  RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIM 71
           +  +VTT + Y N E H+GH    + AD   R+  +          +F+   D HG  + 
Sbjct: 3   KVFYVTTPIYYVNAEPHLGHAYTTVVADFLARWHRLDGYR-----TFFLTGTDEHGETVY 57

Query: 72  IAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL 131
            AA+ AG  PK F++ +S   K+  D   I +D++  T    +  +VQ +   +Y +A  
Sbjct: 58  RAAQAAGEDPKAFVDRVSGRFKRAWDLLGIAYDDFIRTTEERHKKVVQLVLKKVY-EAGD 116

Query: 132 IINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTK 182
           I   +    +      F  ++ +       + +                 +
Sbjct: 117 IYYGEYEGLYCVSCERFYTEKELVEGLCPIHGRPVERRKEGNYFFRMEKYR 167

>d1h3na3 c.26.1.1 (A:1-225,A:418-686) Leucyl-tRNA synthetase (LeuRS) {Thermus thermophilus [TaxId: 274]} Length = 494

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Leucyl-tRNA synthetase (LeuRS)
species: Thermus thermophilus [TaxId: 274]

 Score = 88.9 bits (219), Expect = 4e-21
 Identities = 36/149 (24%), Positives = 60/149 (40%), Gaps = 7/149 (4%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
           +V    PY +G+LH+GH+  Y   D+  RF+ MQ        V      DA G     AA
Sbjct: 36  YVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQGYE-----VLHPMGWDAFGLPAENAA 90

Query: 75  EKAGMTPKEFINNISSNRKKYLD--GFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLI 132
            K G+ PK++        K+ L   G    +D   +T   E     Q I+  ++ K    
Sbjct: 91  LKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAY 150

Query: 133 INKKINQFFDPIKNIFLPDRYIKGECPIC 161
             K +  +    + +   ++ ++G C   
Sbjct: 151 RAKGLVNWCPKCQTVLANEQVVEGRCWRH 179

>d1ilea3 c.26.1.1 (A:1-197,A:387-641) Isoleucyl-tRNA synthetase (IleRS) {Thermus thermophilus [TaxId: 274]} Length = 452

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Isoleucyl-tRNA synthetase (IleRS)
species: Thermus thermophilus [TaxId: 274]

 Score = 70.7 bits (172), Expect = 8e-15
 Identities = 33/211 (15%), Positives = 60/211 (28%), Gaps = 16/211 (7%)

Query: 2   KKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFIC 61
           +K     K   R  V    P ANG  H+GH       D++ R++ M+             
Sbjct: 28  QKSVENRKGGPRYTVYEGPPTANGLPHVGHAQARSYKDLFPRYKTMRGYY-----APRRA 82

Query: 62  ADDAHGAAIMIAAE-KAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQK 120
             D HG  + +  E K G+  K  I      R               S  + E       
Sbjct: 83  GWDTHGLPVELEVEKKLGLKSKREIEAYGIERFNQA--------CRESVFTYEKEWEAFT 134

Query: 121 IYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSSIYTP 180
                +   +         + + I      + + +G     +    Y             
Sbjct: 135 ERIAYWVDLEDAYATLEPTYIESIWWSLK-NLFDRGLLYRDHKVVPY-CPRCGTPLSSHE 192

Query: 181 TKLINPYSILSGTKPIIKSSKHFFFKLSDKR 211
             L  P+     T  +  +++ +F K +  +
Sbjct: 193 VALGYPHCWRCSTPLMYYATESWFIKNTLFK 223

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]} Length = 35

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Escherichia coli [TaxId: 562]

 Score = 63.5 bits (155), Expect = 1e-14
 Identities = 20/35 (57%), Positives = 25/35 (71%)

Query: 154 IKGECPICNAKDQYGDFCECCSSIYTPTKLINPYS 188
           +KG CP C + DQYGD CE C + Y+PT+LI P S
Sbjct: 1   VKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKS 35

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]} Length = 35

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

 Score = 60.4 bits (147), Expect = 2e-13
 Identities = 18/33 (54%), Positives = 20/33 (60%)

Query: 154 IKGECPICNAKDQYGDFCECCSSIYTPTKLINP 186
           + G CP C A+DQ GD CE C    TP  LINP
Sbjct: 1   VIGTCPYCGAEDQKGDQCEVCGRPLTPEILINP 33

>d1ivsa4 c.26.1.1 (A:1-189,A:343-578) Valyl-tRNA synthetase (ValRS) {Thermus thermophilus [TaxId: 274]} Length = 425

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Valyl-tRNA synthetase (ValRS)
species: Thermus thermophilus [TaxId: 274]

 Score = 64.9 bits (157), Expect = 6e-13
 Identities = 26/229 (11%), Positives = 63/229 (27%), Gaps = 30/229 (13%)

Query: 15  FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA 74
            +    P   G LH+GH ++    D  +R++ M+          ++   D  G A  +  
Sbjct: 37  VIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRGFE-----AVWLPGTDHAGIATQVVV 91

Query: 75  EKAGMTPKEFINNISSNRKKYLD------------------GFYIKFDNWYSTDSIENID 116
           E+  +   +  +++   +                       G    +     T   +   
Sbjct: 92  ERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSR 151

Query: 117 LVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECCSS 176
            V+  +   Y++       ++   + P     L D         C+      ++      
Sbjct: 152 AVRYAFSRYYHEGLAYRAPRL-VNWCPRCETTLSDLE----VETCSRCGTPIEYAIFPQW 206

Query: 177 IYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKR 225
                 L            I    + +     D   ++ ++ W I  + 
Sbjct: 207 WLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMD--WLENVKDWNISRQL 253

>d1ffya3 c.26.1.1 (A:1-200,A:395-644) Isoleucyl-tRNA synthetase (IleRS) {Staphylococcus aureus [TaxId: 1280]} Length = 450

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Isoleucyl-tRNA synthetase (IleRS)
species: Staphylococcus aureus [TaxId: 1280]

 Score = 60.4 bits (145), Expect = 2e-11
 Identities = 44/236 (18%), Positives = 77/236 (32%), Gaps = 22/236 (9%)

Query: 2   KKHDSEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFIC 61
            K   + K      +    PYANG LH+GH +  I  D  VR++ MQ          ++ 
Sbjct: 38  HKALEKNKGNETFILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQGFY-----APYVP 92

Query: 62  ADDAHGAAIMIAAEKAG-----MTPKEFINNISSNRKKYLDGFYIKF---------DNWY 107
             D HG  I  A  K G     M+  EF         + ++     F         ++ Y
Sbjct: 93  GWDTHGLPIEQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFNDPY 152

Query: 108 STDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQY 167
            T   E      +I+  + +K  +   KK   ++ P     L +  I+        K   
Sbjct: 153 ITLKPEYEAAQIRIFGEMADKGLIYKGKKP-VYWSPSSESSLAEAEIEYPHDWRTKKPVI 211

Query: 168 GDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKR--CIDFLRKWAI 221
                   +  +  +     +I +    +       +  + D+    I   R W +
Sbjct: 212 FRATPQWFASISKVRQDILDAIENTNFKVNWGKTRIYNMVRDRGEWVISRQRVWGV 267

>d1irxa2 c.26.1.1 (A:3-319) Class I lysyl-tRNA synthetase {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 317

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Class I lysyl-tRNA synthetase
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

 Score = 45.5 bits (106), Expect = 2e-06
 Identities = 17/169 (10%), Positives = 42/169 (24%), Gaps = 6/169 (3%)

Query: 7   EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAH 66
             +  +  +V  +    +G +H+G+  E   A I       +        V  I   D +
Sbjct: 12  RERGEKEKYVVESGITPSGYVHVGNFRELFTAYIVGHALRDKGYE-----VRHIHMWDDY 66

Query: 67  GAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYIKFDNWYSTDS-IENIDLVQKIYDTL 125
                +               IS     +              +  +E + +   +    
Sbjct: 67  DRFRKVPRNVPQEWKDYLGMPISEVPDPWGCHESYAEHFMRKFEEEVEKLGIEVDLLYAS 126

Query: 126 YNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDFCECC 174
               +   +++I   F+    I       +         + +      C
Sbjct: 127 ELYKRGEYSEEIRLAFEKRDKIMEILNKYREIAKQPPLPENWWPAMVYC 175

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	232
d1pfva2	350	Methionyl-tRNA synthetase (MetRS) {Escherichia col	100.0
d1h3na3	494	Leucyl-tRNA synthetase (LeuRS) {Thermus thermophil	100.0
d1ilea3	452	Isoleucyl-tRNA synthetase (IleRS) {Thermus thermop	100.0
d1ffya3	450	Isoleucyl-tRNA synthetase (IleRS) {Staphylococcus	100.0
d1ivsa4	425	Valyl-tRNA synthetase (ValRS) {Thermus thermophilu	100.0
d2d5ba2	348	Methionyl-tRNA synthetase (MetRS) {Thermus thermop	100.0
d1rqga2	361	Methionyl-tRNA synthetase (MetRS) {Pyrococcus abys	100.0
d1li5a2	315	Cysteinyl-tRNA synthetase (CysRS) {Escherichia col	99.89
d1f7ua2	348	Arginyl-tRNA synthetase (ArgRS) {Baker's yeast (Sa	99.62
d1iq0a2	370	Arginyl-tRNA synthetase (ArgRS) {Thermus thermophi	99.53
d1irxa2	317	Class I lysyl-tRNA synthetase {Archaeon Pyrococcus	99.52
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	99.49
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	99.41
d1j09a2	305	Glutamyl-tRNA synthetase (GluRS) {Thermus thermoph	99.24
d1nzja_	286	Glutamyl-Q tRNA-Asp synthetase YadB {Escherichia c	99.13
d1gtra2	331	Glutaminyl-tRNA synthetase (GlnRS) {Escherichia co	99.11
d1j1ua_	306	Tyrosyl-tRNA synthetase (TyrRS) {Archaeon Methanoc	96.56
d1r6ta2	386	Tryptophanyl-tRNA synthetase (TrpRS) {Human (Homo	96.21
d1n3la_	339	Tyrosyl-tRNA synthetase (TyrRS) {Human (Homo sapie	95.44
d1i6la_	326	Tryptophanyl-tRNA synthetase (TrpRS) {Bacillus ste	94.71
d1h3fa1	343	Tyrosyl-tRNA synthetase (TyrRS) {Thermus thermophi	94.05
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	92.9
d2ts1a_	319	Tyrosyl-tRNA synthetase (TyrRS) {Bacillus stearoth	91.1
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	90.68
d3bula2	156	Methionine synthase, C-terminal domain {Escherichi	89.73
d1jila_	323	Tyrosyl-tRNA synthetase (TyrRS) {Staphylococcus au	86.74
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	85.79
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	85.69
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	84.17
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	82.87
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	82.56
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	81.83

>d1pfva2 c.26.1.1 (A:4-140,A:176-388) Methionyl-tRNA synthetase (MetRS) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.7e-39  Score=286.60  Aligned_cols=174  Identities=46%  Similarity=0.883  Sum_probs=163.1

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      .|+|+|++|||||||+|||||+|++|++|+++||+|++|     ++|.+++|+|+||++|+.+|+++|++++++++++..
T Consensus         1 ~~~~~i~~~~P~~nG~lHiGHar~~v~~D~l~R~lr~~G-----~~V~~v~~~dd~g~ki~~~a~~~g~~~~~~~~~~~~   75 (350)
T d1pfva2           1 AKKILVTCALPYANGSIHLGHMLEHIQADVWVRYQRMRG-----HEVNFICADDAHGTPIMLKAQQLGITPEQMIGEMSQ   75 (350)
T ss_dssp             CCEEEEEECCCBTTSCCBHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEEBCCSHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCeEEEeCCCCCCCCCccccccHHHHHHHHHHHHHHhcC-----CceEecCccCCccHHHHHHHHHcCCCHHHHHHhHHH
Confidence            378999999999999999999999999999999999999     999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCc
Q psy2399          91 NRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDF  170 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~  170 (232)
                      .+.++++.|+|+++.++.|.++.|.+.+++++.+|. ++|++|++...++||+.++++|+|+++                
T Consensus        76 ~~~~~~~~l~i~~~~~~~t~~~~~~~~~~~~~~~l~-~~g~~~~~~~~~~~d~~~~~~l~d~~~----------------  138 (350)
T d1pfva2          76 EHQTDFAGFNISYDNYHSTHSEENRQLSELIYSRLK-ENGFIKNRTISQLYDPEKGMFLPDRFV----------------  138 (350)
T ss_dssp             HHHHHHHHTTCCCSEEEESSSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEECCGGGT----------------
T ss_pred             HHHHHHHHcCCCcccCCCcCCcccchHHHHHHHHHh-hccceeeccceEEEeCCCCeEcCCcee----------------
Confidence            999999999999999999999999999999999999 999999999999999999999887644                


Q ss_pred             CccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCC
Q psy2399         171 CECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQP  228 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p  228 (232)
                                         .||.+++.+++++|||+|  ++|++.|.++ ++...++|
T Consensus       139 -------------------~~g~~~~~~~~~~~f~~l--~~~~~~l~~~-~~~~~~~~  174 (350)
T d1pfva2         139 -------------------VSGATPVMRDSEHFFFDL--PSFSEMLQAW-TRSGALQE  174 (350)
T ss_dssp             -------------------TTCCCCEEEEEEEEEECG--GGGHHHHHHH-HTTSCSCH
T ss_pred             -------------------ccCCCccceecchheeeh--HHHHHHHHHH-hhcCCCch
Confidence                               367788999999999999  9999999999 65544444

>d1h3na3 c.26.1.1 (A:1-225,A:418-686) Leucyl-tRNA synthetase (LeuRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Leucyl-tRNA synthetase (LeuRS)
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=6.2e-39  Score=294.43  Aligned_cols=177  Identities=23%  Similarity=0.253  Sum_probs=162.3

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      .++++++|+|++|||||||.||||||++++++|+++||+||+|     ++|.+++|+|+||+||+.+|++.+..|.++++
T Consensus        28 ~~~~~~~~~i~~~pP~~nG~lHiGH~~~~~~~D~~~R~~rm~G-----~~v~~~~G~D~~G~~~e~~~~k~~~~~~~~~~  102 (494)
T d1h3na3          28 LPGGRGKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQG-----YEVLHPMGWDAFGLPAENAALKFGVHPKDWTY  102 (494)
T ss_dssp             SCCTTCEEEEEECCCCSSSCCBHHHHHHHHHHHHHHHHHHHTT-----CEEECCCCBCCSSHHHHHHHHHTTCCHHHHHH
T ss_pred             cccCCCCeEEEeCCCCCCCchhhhHHHHHHHHHHHHHHHHccC-----CcccCcCCcCcchHHHHHHHHHhCCChHHHHH
Confidence            3566788999999999999999999999999999999999999     99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhccCC--cCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCcc
Q psy2399          87 NISSNRKKYLDGFYI--KFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAK  164 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI--~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~  164 (232)
                      ++...+++++++||+  +|+++++|+++.|.+.++++|.+|+ ++|+||++.+.++||+.|+++|+|.+|..        
T Consensus       103 ~~~~~~~~~~~~~g~~~d~~~~~~T~d~~~~~~~~~~f~~l~-~~g~iy~~~~~~~~~~~~~t~l~~~ev~~--------  173 (494)
T d1h3na3         103 ANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMW-EKGLAYRAKGLVNWCPKCQTVLANEQVVE--------  173 (494)
T ss_dssp             HHHHHHHHHHHHTTCCCCGGGCCBTTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEEECGGGEET--------
T ss_pred             HHHHHhHHHHHhcCcccCCCCceecCCccccchHHHHHHHhh-hCCcEEeeeEEEEeecCccceecchhccc--------
Confidence            999999999999998  5557899999999999999999999 99999999999999999999999999842        


Q ss_pred             ccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhh
Q psy2399         165 DQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKW  219 (232)
Q Consensus       165 ~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~  219 (232)
                         +                 ..+..++..++.+.+++|||++  +.+++.+..+
T Consensus       174 ---~-----------------~~~~~~~~~v~~~~~~~~~~~~--~~~~~~~~~~  206 (494)
T d1h3na3         174 ---G-----------------RCWRHEDTPVEKRELEQWYLRI--TAYAERLLKD  206 (494)
T ss_dssp             ---T-----------------EESSCTTSBCEEEEEEEEEECG--GGGHHHHHHT
T ss_pred             ---C-----------------ccccccCceEEeeccCchhhhh--hccccccccc
Confidence               0                 0122345678889999999999  9999999998

>d1ilea3 c.26.1.1 (A:1-197,A:387-641) Isoleucyl-tRNA synthetase (IleRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Isoleucyl-tRNA synthetase (IleRS)
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=1.8e-38  Score=288.68  Aligned_cols=180  Identities=18%  Similarity=0.163  Sum_probs=161.7

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCC------
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMT------   80 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~------   80 (232)
                      +++++++|+|++|||||||+|||||++++|++||++||+|++|     ++|.+++|+|+||++|+.+|++.+..      
T Consensus        33 ~~~~~~~f~i~~~pPy~nG~lHiGH~~~~v~~Dv~~Ry~r~~G-----~~V~~v~G~D~hG~~i~~~a~~~~~~~~~~~~  107 (452)
T d1ilea3          33 NRKGGPRYTVYEGPPTANGLPHVGHAQARSYKDLFPRYKTMRG-----YYAPRRAGWDTHGLPVELEVEKKLGLKSKREI  107 (452)
T ss_dssp             HTTTSCBCCBCCCCCCTTSCCCTTHHHHHHHHHHHHHHHHHTT-----CBCCCEEEECCCHHHHHHHHHHHTTCCSHHHH
T ss_pred             ccCCCCCEEEecCCCCCCCcchhhhHHHHHHHHHHHHHHHcCC-----CceeccCCcCCCCHHHHHHHHHhhccccccch
Confidence            3566788999999999999999999999999999999999999     99999999999999999999887642      


Q ss_pred             -----------HHHHHHHHHHHHHHHHhccCCcC--CccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCc
Q psy2399          81 -----------PKEFINNISSNRKKYLDGFYIKF--DNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNI  147 (232)
Q Consensus        81 -----------~~e~~~~~~~~~~~~l~~lgI~~--d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~  147 (232)
                                 +.+++.++.+.+.++++.||+..  +.+++|+++.|.+.++++|.+|+ ++|++|.+...++||+.+++
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~d~~~~~~T~~~~~~~~~~~~f~~l~-~~G~iy~~~~~~~~~~~~~~  186 (452)
T d1ilea3         108 EAYGIERFNQACRESVFTYEKEWEAFTERIAYWVDLEDAYATLEPTYIESIWWSLKNLF-DRGLLYRDHKVVPYCPRCGT  186 (452)
T ss_dssp             HHHCHHHHHHHHHHHTTTTHHHHTTHHHHTTCCCEEEEEEETTSHHHHHHHHHHHHHHH-HTTCEEEECCEEEEETTTTE
T ss_pred             hHHHHHHHHHHHhhHHhhhhhhHHHHHhhhccccccchhhhcCChHHHHHHHHHHHHHH-hcCCcccccccchhhccccc
Confidence                       23455566678888889999854  46789999999999999999999 99999999999999999999


Q ss_pred             ccccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhh
Q psy2399         148 FLPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAI  221 (232)
Q Consensus       148 ~l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~  221 (232)
                      +++++++++.||.|                           ..||.+++.+.+.+||+++  +.+++.+.+++.
T Consensus       187 ~~~~~~~~~~~p~c---------------------------~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~  231 (452)
T d1ilea3         187 PLSSHEVALGYPHC---------------------------WRCSTPLMYYATESWFIKN--TLFKDELIRNNQ  231 (452)
T ss_dssp             ECCHHHHHHTEEBC---------------------------SSSCCBCEEEECCEEEECG--GGGHHHHHHHHH
T ss_pred             ccccccccccCCCc---------------------------cCcCCceEEeeccchhhhh--ccchhhhhhhhc
Confidence            99999999988865                           3478899999999999999  999999999943

>d1ffya3 c.26.1.1 (A:1-200,A:395-644) Isoleucyl-tRNA synthetase (IleRS) {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Isoleucyl-tRNA synthetase (IleRS)
species: Staphylococcus aureus [TaxId: 1280]

Probab=100.00  E-value=3.7e-37  Score=281.97  Aligned_cols=183  Identities=23%  Similarity=0.329  Sum_probs=161.4

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHH-----
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPK-----   82 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~-----   82 (232)
                      ++.+++|+|++|||||||.|||||+++++++|+++||+||+|     ++|.+++|+|+||+||+.+|++.+.++.     
T Consensus        44 ~~~~~~f~~~~~pPy~nG~lHiGH~~~~~~~Dv~~Ry~rm~G-----~~V~~~~G~D~~G~pie~~~~~~~~~~~~~~~~  118 (450)
T d1ffya3          44 NKGNETFILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQG-----FYAPYVPGWDTHGLPIEQALTKKGVDRKKMSTA  118 (450)
T ss_dssp             TTTSCBCCEECCCCBSSSCCCHHHHHHHHHHHHHHHHHHTTT-----CBCCCCCEEBCCSHHHHHHHHHHTCCSTTTCHH
T ss_pred             cCCCCcEEEecCCCCCCCchhhhHHHHHHHHHHHHHHHHhcC-----CccccccccccCCcHHHHHHHhhCCccccccHH
Confidence            456678999999999999999999999999999999999999     9999999999999999999999876543     


Q ss_pred             -------HHHHHHHHHHHHHHhccCCc--CCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccce
Q psy2399          83 -------EFINNISSNRKKYLDGFYIK--FDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRY  153 (232)
Q Consensus        83 -------e~~~~~~~~~~~~l~~lgI~--~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~  153 (232)
                             +++..+.+.+++++++||++  ++..+.|+++.|.+.++++|.+|+ ++|+||++..+++|||.|++++++.+
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~lg~~~D~~~~~~T~~~~~~~~v~~~f~~l~-~~G~iy~~~~~v~~~p~~~~~~~~~e  197 (450)
T d1ffya3         119 EFREKCKEFALEQIELQKKDFRRLGVRGDFNDPYITLKPEYEAAQIRIFGEMA-DKGLIYKGKKPVYWSPSSESSLAEAE  197 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTTCCSCTTSCEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEETTTTEECCGGG
T ss_pred             HHhhhcchhhhhhhhhHHHHHHHHhhhcccccccccccHHHHHHHHHHHHHHH-HcCCeeccccccccccccCccccccc
Confidence                   34678889999999999995  557789999999999999999999 99999999999999888888887777


Q ss_pred             eccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCC
Q psy2399         154 IKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQP  228 (232)
Q Consensus       154 v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p  228 (232)
                      ++                             .|.|..|+.+++.+..++||+++  +.+++.+.+. .....+.|
T Consensus       198 ~~-----------------------------~~~~~r~~~~~~~~~~~qwf~~~--~~~~~~~~~~-~~~~~~~~  240 (450)
T d1ffya3         198 IE-----------------------------YPHDWRTKKPVIFRATPQWFASI--SKVRQDILDA-IENTNFKV  240 (450)
T ss_dssp             EE-----------------------------EEEETTTCCBCEEEEEEEEEECH--HHHHHHHHHH-HHTSEESS
T ss_pred             cc-----------------------------ccccccccCCceeeccccceecc--ccccccchhh-cccccccc
Confidence            65                             35566788899999999999999  9999999988 44433333

>d1ivsa4 c.26.1.1 (A:1-189,A:343-578) Valyl-tRNA synthetase (ValRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Valyl-tRNA synthetase (ValRS)
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=6.1e-36  Score=270.05  Aligned_cols=185  Identities=17%  Similarity=0.166  Sum_probs=159.4

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHc----CCCH-
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKA----GMTP-   81 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~----g~~~-   81 (232)
                      .+.++++|+|++|||||||+|||||++++|++||++||+|++|     ++|.+++|+|+||++|+.+|++.    |..+ 
T Consensus        29 ~~~~~~~f~i~~~pPy~NG~lHlGH~~~yv~~Dv~~Ry~r~~G-----~~V~~v~g~D~hG~~i~~~aek~~~~~~~~~~  103 (425)
T d1ivsa4          29 PKSGKPPFVIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRG-----FEAVWLPGTDHAGIATQVVVERLLLKEGKTRH  103 (425)
T ss_dssp             TTCCSCEEEEECCCCBSSSCCCHHHHHHHHHHHHHHHHHHTTT-----SEEEEECEEBCCTHHHHHHHHHHHHTTTCCGG
T ss_pred             CCCCCCcEEEEcCCCCCCCCchhhHHHHHHHHHHHHHHHHhCC-----CceeecCcccCCcchHHHHHHHhhcccCCChH
Confidence            4566788999999999999999999999999999999999999     99999999999999999999984    3322 


Q ss_pred             -----------HHHHHHHHHHHHHHHhccCCcCC--ccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcc
Q psy2399          82 -----------KEFINNISSNRKKYLDGFYIKFD--NWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIF  148 (232)
Q Consensus        82 -----------~e~~~~~~~~~~~~l~~lgI~~d--~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~  148 (232)
                                 ..++..+.+.++++|++||+..|  .+++|+++.|.+.++++|.+|. ++|++|++.+.++||+.|+++
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~d~~~~~~t~~~~~~~~~~~~~~~l~-~~G~iy~~~~~~~~c~~~~~~  182 (425)
T d1ivsa4         104 DLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYY-HEGLAYRAPRLVNWCPRCETT  182 (425)
T ss_dssp             GSTTTHHHHHHHHHHHHHHHHHHHHHHHTTCCCCGGGCEETTSHHHHHHHHHHHHHHH-TTSSEEEECCEEEEETTTTEE
T ss_pred             HhcHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcchhhcccchhhhhhhHHHHhhhh-ccCcccccceeeccccccccc
Confidence                       23466778999999999999655  5678999999999999999999 999999999999999999999


Q ss_pred             cccceeccCCCCCCccccCCCcCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhc-CCCCC
Q psy2399         149 LPDRYIKGECPICNAKDQYGDFCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIH-DKRLQ  227 (232)
Q Consensus       149 l~~~~v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~-~~~~~  227 (232)
                      |++.++.+.                               ..||..++.+.+++||+++  +++.+.+..+... ...+.
T Consensus       183 l~~~~~~~~-------------------------------~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  229 (425)
T d1ivsa4         183 LSDLEVETC-------------------------------SRCGTPIEYAIFPQWWLRM--RPLAEEVLKGLRRGDIAFV  229 (425)
T ss_dssp             CCGGGEEEE-------------------------------TTTCSBCEEEECCEEEECH--HHHHHHHHHHHHHTCCEES
T ss_pred             ccccccccc-------------------------------cccCcccccccccchhhcc--chhhccchhhhhcCCccee
Confidence            999888752                               2356778888999999999  9999999998332 33566


Q ss_pred             CCC
Q psy2399         228 PEI  230 (232)
Q Consensus       228 p~~  230 (232)
                      |+.
T Consensus       230 pe~  232 (425)
T d1ivsa4         230 PER  232 (425)
T ss_dssp             SST
T ss_pred             ccc
Confidence            654

>d2d5ba2 c.26.1.1 (A:1-348) Methionyl-tRNA synthetase (MetRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=9e-35  Score=254.69  Aligned_cols=173  Identities=25%  Similarity=0.506  Sum_probs=162.4

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISS   90 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~   90 (232)
                      +++|+||+|+|||||+|||||+|++|++|+++|++|++|     ++|.+++|+|++|++|+.+|+++|+++++++..+..
T Consensus         2 ~~~~~~~~~~PypnG~lHiGH~r~~v~~D~l~R~lr~~G-----~~V~~v~g~D~~g~~i~~~a~~~g~~~~~~~~~~~~   76 (348)
T d2d5ba2           2 EKVFYVTTPIYYVNAEPHLGHAYTTVVADFLARWHRLDG-----YRTFFLTGTDEHGETVYRAAQAAGEDPKAFVDRVSG   76 (348)
T ss_dssp             CCEEEEECCCEETTSCCCHHHHHHHHHHHHHHHHHHHTT-----CEEEEEEEEECCSHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCEEEecCCCCCCCCcccccCHHHHHHHHHHHHHHhcC-----CCeEecCcCCCCCHHHHHHHHHcCCCHHHhhhhHHH
Confidence            467999999999999999999999999999999999999     999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCCc
Q psy2399          91 NRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGDF  170 (232)
Q Consensus        91 ~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~~  170 (232)
                      .+++.++.+||.++.++++....+...++.++.++. ++|++|++...++|                             
T Consensus        77 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~~~~~~~-----------------------------  126 (348)
T d2d5ba2          77 RFKRAWDLLGIAYDDFIRTTEERHKKVVQLVLKKVY-EAGDIYYGEYEGLY-----------------------------  126 (348)
T ss_dssp             HHHHHHHHTTCCCSEEEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEE-----------------------------
T ss_pred             HHHHHHHhcCccccceeecccchhhHHHHHHHHHHH-hhCccccccccccc-----------------------------
Confidence            999999999999999999998899999999999999 99999999998888                             


Q ss_pred             CccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhh
Q psy2399         171 CECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWA  220 (232)
Q Consensus       171 Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~  220 (232)
                      |+.|++.+.+..++++.+..+|...+.....++++++  +.+.+.+.++.
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~  174 (348)
T d2d5ba2         127 CVSCERFYTEKELVEGLCPIHGRPVERRKEGNYFFRM--EKYRPWLQEYI  174 (348)
T ss_dssp             ETTTTEECCTTTSBTTBCTTTCSBCEEEEEEEEEECG--GGGHHHHHHHH
T ss_pred             cccccceeccccccccccccCCCceEEecccccccch--HhhhhhHHHhh
Confidence            5666666667777788888899999999999999999  99999999883

>d1rqga2 c.26.1.1 (A:1-138,A:174-396) Methionyl-tRNA synthetase (MetRS) {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Pyrococcus abyssi [TaxId: 29292]

Probab=100.00  E-value=3.7e-34  Score=251.93  Aligned_cols=174  Identities=30%  Similarity=0.559  Sum_probs=158.5

Q ss_pred             CCcEEEEcCCCCCCCcCCchHHH-hHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHH
Q psy2399          11 VRRIFVTTALPYANGELHIGHIM-EYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNIS   89 (232)
Q Consensus        11 ~~~~~v~~~~P~~nG~lHiGH~~-~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~   89 (232)
                      +.+|+|++|||||||+|||||++ ++|.+|+++||+|++|     ++|.+++|+|+||++|+.+|++.|++|+++++.+.
T Consensus         1 ~~~~~v~~~~P~p~G~lHiGH~~~~~i~~Dil~R~~r~~G-----~~V~~v~g~D~~g~~i~~~A~~~g~~~~~~~~~~~   75 (361)
T d1rqga2           1 MVRYMVTSALPYANGPIHAGHLAGAYLPADIFVRYLRLKG-----EDVVFICGTDEHGTPISFRALKEGRSPREIVDEFH   75 (361)
T ss_dssp             CCEEEEEECCCBTTSCCBHHHHHHHTHHHHHHHHHHHHTT-----CEEEEEEEEBCCSHHHHHHHHHHTCCHHHHHHHHH
T ss_pred             CceEEEecCCCCCCCCcccccccccHHHHHHHHHHHHhcC-----CceEecCccCcccHHHHHHHHHcCCCHHHHHHHHH
Confidence            36899999999999999999988 5899999999999999     99999999999999999999999999999999999


Q ss_pred             HHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeeccCCCcccccceeccCCCCCCccccCCC
Q psy2399          90 SNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPIKNIFLPDRYIKGECPICNAKDQYGD  169 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~~~~~g~  169 (232)
                      ..+.+++..+++.++.+.+|.+..+...++.++..+. ++|.+|++...++||+.+++++                    
T Consensus        76 ~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~--------------------  134 (361)
T d1rqga2          76 EQIKITFQRAKISFDFFGRTELPIHYKLSQEFFLKAY-ENGHLVKKVTKQAYCEHDKMFL--------------------  134 (361)
T ss_dssp             HHHHHHHHHHTCCCSEEEETTSHHHHHHHHHHHHHHH-HTTCEEEEEEEEEEBTTTTBCC--------------------
T ss_pred             Hhhcccccccccccccccccccchhhhhhhhhhhhcc-ccCceeeeeeeeecccccceec--------------------
Confidence            9999999999999999999999999999999999999 9999999999999966655542                    


Q ss_pred             cCccCCCCCCCccccCCcccCCCCccEEEEccceeEecCChhhHHHHHhhhhcCCCCCC
Q psy2399         170 FCECCSSIYTPTKLINPYSILSGTKPIIKSSKHFFFKLSDKRCIDFLRKWAIHDKRLQP  228 (232)
Q Consensus       170 ~Ce~Cg~~~~~~~l~~~~~~~~g~~~~~~~~~~~f~~L~~~~~~~~l~~~~~~~~~~~p  228 (232)
                                     .+.|..||.+++.+..++|||++  +.++++|.++ .+...+.|
T Consensus       135 ---------------~~~~~~~g~~~~~~~~~~~f~~~--~~~~~~l~~~-~~~~~~~~  175 (361)
T d1rqga2         135 ---------------PDRFAICGRPISFRDSAHYYIKM--QDFAERLKRW-IEKQPWKP  175 (361)
T ss_dssp             ---------------CGGGTTTCCBCEEEEEEEEEECG--GGTHHHHHHH-HHSSCCCH
T ss_pred             ---------------ccccccCCCcccccccceEEEec--chhhhhhhhc-cccccccc
Confidence                           34567788999999999999999  9999999998 55443433

>d1li5a2 c.26.1.1 (A:1-315) Cysteinyl-tRNA synthetase (CysRS) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Cysteinyl-tRNA synthetase (CysRS)
species: Escherichia coli [TaxId: 562]

Probab=99.89  E-value=3e-23  Score=180.26  Aligned_cols=127  Identities=12%  Similarity=0.113  Sum_probs=112.7

Q ss_pred             cCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           7 EFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         7 ~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      .++++-++|||  .|||||++||||+|++|++|+++|++|+.|     ++|.+++|+|+||.+|...|++.|++++++++
T Consensus        18 ~~~~~~~~yv~--Gptv~g~~HIGH~R~av~gD~laR~lr~~G-----~~V~~~~~~dd~G~~i~~~a~~~~~~~~e~~~   90 (315)
T d1li5a2          18 IHAGEVGMYVC--GITVYDLCHIGHGRTFVAFDVVARYLRFLG-----YKLKYVRNITDIDDKIIKRANENGESFVAMVD   90 (315)
T ss_dssp             SSTTEEEEEEC--CCBSSSCCBHHHHHHHHHHHHHHHHHHHHT-----CEEEEEECBBCCSHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCeEEEEec--CCcCCCCcccchhHHHHHHHHHHHHHHHcC-----CcEEEEecccchhHHHHHHHhhhhhccccccc
Confidence            34555667775  469999999999999999999999999999     99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCCEEecccceeec
Q psy2399          87 NISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKLIINKKINQFFD  142 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~  142 (232)
                      ++...+.++++.++|..+.+.++.. ++...+...+.+|. ++|.+|......+|+
T Consensus        91 ~~~~~~~~~~~~~~i~~~~~~~~~~-~~~~e~~~~~~~l~-~~~~~~~~~~~~~~~  144 (315)
T d1li5a2          91 RMIAEMHKDFDALNILRPDMEPRAT-HHIAEIIELTEQLI-AKGHAYVADNGDVMF  144 (315)
T ss_dssp             HHHHHHHHHHHHTTCCCCSBCCBGG-GCHHHHHHHHHHHH-HTTSEEECTTSCEEE
T ss_pred             cchhhhhhhHHhcCCCCCcEEEecc-hhhhhhhhHHHHhh-ccCceeccccceEEe
Confidence            9999999999999997776665554 67788888899999 999999887766554

>d1f7ua2 c.26.1.1 (A:136-483) Arginyl-tRNA synthetase (ArgRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Arginyl-tRNA synthetase (ArgRS)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.62  E-value=1.2e-15  Score=134.09  Aligned_cols=130  Identities=15%  Similarity=0.132  Sum_probs=105.2

Q ss_pred             CCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH---cCC-----
Q psy2399           8 FKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK---AGM-----   79 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~---~g~-----   79 (232)
                      ...+++++|-...|+|+|||||||+|+.+++|+|+|.++..|     ++|.....++|.|.+|...+..   .+.     
T Consensus         4 ~~~~kki~vE~~SaNpt~plHvGH~R~aiiGd~larlL~~~G-----~~V~re~yvnD~G~Qi~~l~~~~~~~~~~~~~~   78 (348)
T d1f7ua2           4 LVENKKVIIEFSSPNIAKPFHAGHLRSTIIGGFLANLYEKLG-----WEVIRMNYLGDWGKQFGLLAVGFERYGNEEALV   78 (348)
T ss_dssp             CSSCCEEEEECCCCBTTSCCBGGGHHHHHHHHHHHHHHHHTT-----CEEEEEEEEBCCSHHHHHHHHHHHHHCCHHHHH
T ss_pred             CCCCCEEEEEecCCCCCCCcchhhhhhHHHHHHHHHHHHHCC-----CeEEEEEEECCchHHHHHHHHHHHHhccccccc
Confidence            455688999999999999999999999999999999999999     9999999999999887655432   000     


Q ss_pred             ---------------------------------------------CH------HHHHHHHHHHHHHHHhccCCcCCcccc
Q psy2399          80 ---------------------------------------------TP------KEFINNISSNRKKYLDGFYIKFDNWYS  108 (232)
Q Consensus        80 ---------------------------------------------~~------~e~~~~~~~~~~~~l~~lgI~~d~~~~  108 (232)
                                                                   ++      +.+++...+.+++++++|||.+|.|..
T Consensus        79 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~~~~~~~~~~~~l~~~~~~~~~l~i~fD~~~~  158 (348)
T d1f7ua2          79 KDPIHHLFDVYVRINKDIEEEGDSIPLEQSTNGKAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYARLNIKYDVYSG  158 (348)
T ss_dssp             HCHHHHHHHHHHHHHHHHHHSTTSSCHHHHSSHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSEEEE
T ss_pred             cccchhHHHHHHHHHhhhcccchhhhhhhhhHhHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence                                                         00      012344457899999999999999988


Q ss_pred             CCChhHHHHHHHHHHHHHhhcCCEEecccceeeccC
Q psy2399         109 TDSIENIDLVQKIYDTLYNKAKLIINKKINQFFDPI  144 (232)
Q Consensus       109 t~~~~~~~~v~~~~~~L~~~kG~iy~~~~~~~~~~~  144 (232)
                      .++ .+......++..|. ++|++|..++..|++..
T Consensus       159 Es~-~~~~~~~~v~~~L~-~~~~~~~~~ga~~~~~~  192 (348)
T d1f7ua2         159 ESQ-VSKESMLKAIDLFK-EKGLTHEDKGAVLIDLT  192 (348)
T ss_dssp             GGG-CCHHHHHHHHHHHH-HTTCEEEETTEEEEEGG
T ss_pred             ccc-ccccchHHHHHHHH-hhccccccCCcccccch
Confidence            876 34455667899999 99999999999999653

>d1iq0a2 c.26.1.1 (A:97-466) Arginyl-tRNA synthetase (ArgRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Arginyl-tRNA synthetase (ArgRS)
species: Thermus thermophilus [TaxId: 274]

Probab=99.53  E-value=1.2e-14  Score=128.56  Aligned_cols=129  Identities=19%  Similarity=0.204  Sum_probs=102.0

Q ss_pred             CCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHH---cC------C
Q psy2399           9 KDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEK---AG------M   79 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~---~g------~   79 (232)
                      +.+++++|-...|+|+|+|||||+|+.+++|+|+|.++..|     ++|.-...+.|.|.++...+..   .+      .
T Consensus         4 ~~~~~i~vEf~SpN~~kplHvGHlRs~iiGd~laril~~~G-----~~V~r~nyigD~G~Qi~~l~~~~~~~~~~~~~~~   78 (370)
T d1iq0a2           4 RRPGVVLVEHTSVNPNKELHVGHLRNIALGDAIARILAYAG-----REVLVLNYIDDTGRQAAETLFALRHYGLTWDGKE   78 (370)
T ss_dssp             CEEEEEEEECCCCCTTSCCBHHHHHHHHHHHHHHHHHHHTT-----EEEEEEEEECTTSHHHHHHHHHHHHTTCCCCSSS
T ss_pred             CCCCeEEEEecCCCCCCCcchhhhhhHHHHHHHHHHHHHcC-----CEEEEEEeECCchHHHHHHHHHHHHhcccccccc
Confidence            34578999999999999999999999999999999999999     9999888899999887644422   11      1


Q ss_pred             CH------------------------------------HHHHHHHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHH
Q psy2399          80 TP------------------------------------KEFINNISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYD  123 (232)
Q Consensus        80 ~~------------------------------------~e~~~~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~  123 (232)
                      .+                                    .+..+++...++++|.+|||.+|.+...++-.....+..++.
T Consensus        79 ~~~~~~~~~y~~~~~~~~~~~~~~~~~e~~~~le~~~~~~~~~~~l~~~~~~l~~l~v~fD~~~~Es~l~~~~~~~~~i~  158 (370)
T d1iq0a2          79 KYDHFAGRAYVRLHQDPEYERLQPAIEEVLHALERGELREEVNRILLAQMATMHALNARYDLLVWESDIVRAGLLQKALA  158 (370)
T ss_dssp             CHHHHHHHHHHHHHHCTTTGGGHHHHHHHHHHHHTTTTHHHHHHHHHHHHHHHHHTTCCCSEEEEHHHHHHTTHHHHHHH
T ss_pred             chhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhccceeeceeeeecccccccchhhhHh
Confidence            11                                    111334456677889999999999998886556678899999


Q ss_pred             HHHhhcCCEEecc-----cceeecc
Q psy2399         124 TLYNKAKLIINKK-----INQFFDP  143 (232)
Q Consensus       124 ~L~~~kG~iy~~~-----~~~~~~~  143 (232)
                      .|. ++|.+|+..     ...|.+.
T Consensus       159 ~l~-~~~~~~~~~~~~~~ga~~~d~  182 (370)
T d1iq0a2         159 LLE-QSPHVFRPREGKYAGALVMDA  182 (370)
T ss_dssp             HHT-TSTTEECCSSSTTTTCEEEEC
T ss_pred             hhh-hccceeeccccccceEEEecC
Confidence            999 999999875     3555543

>d1irxa2 c.26.1.1 (A:3-319) Class I lysyl-tRNA synthetase {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Class I lysyl-tRNA synthetase
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=99.52  E-value=9.9e-16  Score=128.78  Aligned_cols=63  Identities=17%  Similarity=0.066  Sum_probs=54.2

Q ss_pred             ccCCCCCcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHH
Q psy2399           6 SEFKDVRRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAA   74 (232)
Q Consensus         6 ~~~~~~~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a   74 (232)
                      .+.+.+++++|. ++|||||+|||||+|++|++|+++|++|+.|     ++|.++.++|++|.++...+
T Consensus        12 ~~~~~k~~~v~~-~~~~PnG~lHIGHlr~~i~gD~laR~lr~~G-----~~V~~~~~~dd~g~~~~~~~   74 (317)
T d1irxa2          12 RERGEKEKYVVE-SGITPSGYVHVGNFRELFTAYIVGHALRDKG-----YEVRHIHMWDDYDRFRKVPR   74 (317)
T ss_dssp             HHSCCCSEEEEE-EEECCSSCCCHHHHHHHHHHHHHHHHHHTTT-----CEEEEEEEECTTSBCCCCCS
T ss_pred             HhcCCCCeEEEE-CCCCCCCCccccccHHHHHHHHHHHHHHHcC-----CCEEEEEEeccCcchhhhHH
Confidence            344555666666 5789999999999999999999999999999     99999999999998765544

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=99.49  E-value=6.7e-15  Score=85.50  Aligned_cols=35  Identities=51%  Similarity=1.001  Sum_probs=34.1

Q ss_pred             eccCCCCCCccccCCCcCccCCCCCCCccccCCcc
Q psy2399         154 IKGECPICNAKDQYGDFCECCSSIYTPTKLINPYS  188 (232)
Q Consensus       154 v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~  188 (232)
                      |+|+||.|++++++||+||.||+.+++.+|+||+|
T Consensus         1 V~G~CP~C~~~~a~GDqCe~CG~~~~p~eLinP~C   35 (35)
T d1rqga3           1 VIGTCPYCGAEDQKGDQCEVCGRPLTPEILINPRC   35 (35)
T ss_dssp             CCSBCSSSCCSCCCTTTCSSSCCCCCTTSSBSCBC
T ss_pred             CeEECCCCCCCcccCcchhhcCCccCHHHhcCCCC
Confidence            78999999999999999999999999999999998

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Escherichia coli [TaxId: 562]

Probab=99.41  E-value=1.4e-14  Score=84.01  Aligned_cols=35  Identities=57%  Similarity=1.243  Sum_probs=33.6

Q ss_pred             eccCCCCCCccccCCCcCccCCCCCCCccccCCcc
Q psy2399         154 IKGECPICNAKDQYGDFCECCSSIYTPTKLINPYS  188 (232)
Q Consensus       154 v~g~cp~c~~~~~~g~~Ce~Cg~~~~~~~l~~~~~  188 (232)
                      |+|+||.|++++++||+||.||+.++|.+|+||++
T Consensus         1 V~G~CP~C~~~~a~GDqCe~CG~~~~p~eLinP~S   35 (35)
T d1pfva3           1 VKGTCPKCKSPDQYGDNCEVCGATYSPTELIEPKS   35 (35)
T ss_dssp             EEEECTTTCCSSEETTBCTTTCCBCCGGGSEEEEE
T ss_pred             CeeECCCCCCcccccccHHHcCCcCCHHHhcCCCC
Confidence            78999999999999999999999999999999985

>d1j09a2 c.26.1.1 (A:1-305) Glutamyl-tRNA synthetase (GluRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Glutamyl-tRNA synthetase (GluRS)
species: Thermus thermophilus [TaxId: 274]

Probab=99.24  E-value=2.6e-12  Score=110.57  Aligned_cols=95  Identities=19%  Similarity=0.231  Sum_probs=74.9

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      +||--+|.|||.|||||++++++.+.+||  ...|        .++.-+||.+             +......+.+.|.+
T Consensus         2 vvtRfaPsPtG~lHiG~~rtal~n~~~Ak--~~~G--------~~iLRidDtD-------------~~R~~~~~~~~I~~   58 (305)
T d1j09a2           2 VVTRIAPSPTGDPHVGTAYIALFNYAWAR--RNGG--------RFIVRIEDTD-------------RARYVPGAEERILA   58 (305)
T ss_dssp             CEEEECCCCSSSCBHHHHHHHHHHHHHHH--HTTC--------EEEECBCCCC-------------TTSCCTTHHHHHHH
T ss_pred             eEEecCCCCCCcccHHHHHHHHHHHHHHH--HcCC--------EEEEEeCcCC-------------CccCchHHHHHHHH
Confidence            68889999999999999999999999998  3344        3444456543             33334567888999


Q ss_pred             HHhccCCcCCccc---------cCCChhHHHHHHHHHHHHHhhcCCEEec
Q psy2399          95 YLDGFYIKFDNWY---------STDSIENIDLVQKIYDTLYNKAKLIINK  135 (232)
Q Consensus        95 ~l~~lgI~~d~~~---------~t~~~~~~~~v~~~~~~L~~~kG~iy~~  135 (232)
                      +|++|||+||...         +.|  ++.+...+++.+|. ++|++|.-
T Consensus        59 dL~wLgi~wD~~p~~~~~~~~~~qS--~r~~~y~~~~~~Li-~~g~aY~C  105 (305)
T d1j09a2          59 ALKWLGLSYDEGPDVGGPHGPYRQS--ERLPLYQKYAEELL-KRGWAYRA  105 (305)
T ss_dssp             HHHHTTCCCSBBTTTBCTTCCCBGG--GCHHHHHHHHHHHH-HHTSEEEE
T ss_pred             HHHHHhcCcccCCcCCCCCcceeee--cchhHHHHHHHHHH-HcCCeeec
Confidence            9999999998632         333  68888999999999 99999964

>d1nzja_ c.26.1.1 (A:) Glutamyl-Q tRNA-Asp synthetase YadB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Glutamyl-Q tRNA-Asp synthetase YadB
species: Escherichia coli [TaxId: 562]

Probab=99.13  E-value=1.7e-11  Score=104.42  Aligned_cols=94  Identities=16%  Similarity=0.248  Sum_probs=73.4

Q ss_pred             EEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy2399          15 FVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKK   94 (232)
Q Consensus        15 ~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~   94 (232)
                      |||--+|.|||.|||||++++++.-.+||-  ..|     .   |+.=+||.             +++.....+.+.|.+
T Consensus         3 ~~tRFAPsPtG~lHiG~~rtal~n~~~Ak~--~~G-----~---~iLRieDt-------------D~~R~~~~~~~~I~~   59 (286)
T d1nzja_           3 YIGRFAPSPSGELHFGSLIAALGSYLQARA--RQG-----R---WLVRIEDI-------------DPPREVPGAAETILR   59 (286)
T ss_dssp             CEEEECCCTTSCCCHHHHHHHHHHHHHHHH--TTC-----E---EEEEECCS-------------CGGGSCTTHHHHHHH
T ss_pred             ceEeeCcCCCCcccHHHHHHHHHHHHHHHH--hCC-----E---EEEEeCCC-------------CCCcCCHHHHHHHHH
Confidence            688889999999999999999999999983  344     3   33333442             244445578899999


Q ss_pred             HHhccCCcCCc-cccCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          95 YLDGFYIKFDN-WYSTDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        95 ~l~~lgI~~d~-~~~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      +|++||+.||. .++.|  ++.+...+++.+|. ++|++|.
T Consensus        60 dL~wlgl~~d~~~~~QS--~r~~~Y~~~~~~L~-~~g~aY~   97 (286)
T d1nzja_          60 QLEHYGLHWDGDVLWQS--QRHDAYREALAWLH-EQGLSYY   97 (286)
T ss_dssp             HHHHTTCCCSSCCEEGG--GCHHHHHHHHHHHH-HTTCEEE
T ss_pred             HHHHhhhccccccchhH--HHHHHHHHHHHHHH-HcCCccc
Confidence            99999999996 43444  56778889999999 9999985

>d1gtra2 c.26.1.1 (A:8-338) Glutaminyl-tRNA synthetase (GlnRS) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Glutaminyl-tRNA synthetase (GlnRS)
species: Escherichia coli [TaxId: 562]

Probab=99.11  E-value=6.2e-11  Score=103.01  Aligned_cols=95  Identities=16%  Similarity=0.053  Sum_probs=75.5

Q ss_pred             EEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy2399          14 IFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRK   93 (232)
Q Consensus        14 ~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~   93 (232)
                      -|+|--.|.|||.|||||+|+++++-.+||-  ..|     .-++-+   ||             .++......+.+.|.
T Consensus        19 ~v~tRFAPSPTG~LHiG~~rtal~n~l~Ak~--~~G-----~fiLRI---ED-------------tD~~R~~~~~~~~I~   75 (331)
T d1gtra2          19 TVHTRFPPEPNGYLHIGHAKSICLNFGIAQD--YKG-----QCNLRF---DD-------------TNPVKEDIEYVESIK   75 (331)
T ss_dssp             SCEEEECCCSSSCCBHHHHHHHHHHHHHHHH--TTC-----EEEEEE---CC-------------CCGGGCCHHHHHHHH
T ss_pred             eEEEEeCCCCCCcccHHHHHHHHHHHHHHHH--hCC-----EEEEEe---Cc-------------CCCCcccchHHHHHH
Confidence            4777778999999999999999999999984  445     344444   33             345566778889999


Q ss_pred             HHHhccCCcCCccc-cCCChhHHHHHHHHHHHHHhhcCCEEe
Q psy2399          94 KYLDGFYIKFDNWY-STDSIENIDLVQKIYDTLYNKAKLIIN  134 (232)
Q Consensus        94 ~~l~~lgI~~d~~~-~t~~~~~~~~v~~~~~~L~~~kG~iy~  134 (232)
                      ++|++|||.||.-+ +.|  ++.+..++.+.+|. ++|++|.
T Consensus        76 ~dL~WLGl~wD~~~~~QS--~r~~~Y~~~~~~L~-~~G~aY~  114 (331)
T d1gtra2          76 NDVEWLGFHWSGNVRYSS--DYFDQLHAYAIELI-NKGLAYV  114 (331)
T ss_dssp             HHHHHTTCCCSSSCEEGG--GGHHHHHHHHHHHH-HTTSEEE
T ss_pred             HHHHHHhccccccceecc--hHHHHHHHHHHhhh-hcCCccc
Confidence            99999999998543 444  57788899999999 9999984

>d1j1ua_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.56  E-value=0.0051  Score=51.27  Aligned_cols=71  Identities=21%  Similarity=0.316  Sum_probs=44.3

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccCC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFYI  101 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lgI  101 (232)
                      -|||.|||||..   ....+.++++ .|     +++.+..| |.|..-       ..-+..+...++.......+.++|+
T Consensus        36 ~PTG~lHlGh~v---~~~~~~~lq~-~g-----~~~~~~Ia-D~~a~~-------~~~~~~~~~~~~~~~~~~~~~a~G~   98 (306)
T d1j1ua_          36 EPSGKIHLGHYL---QIKKMIDLQN-AG-----FDIIILLA-DLHAYL-------NQKGELDEIRKIGDYNKKVFEAMGL   98 (306)
T ss_dssp             CCCSSCBHHHHH---HHHHHHHHHH-TT-----EEEEEEEC-HHHHHH-------TTCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCcchHHHHH---HHHHHHHHHH-CC-----CcEEEEec-cHHHHh-------hhccchhhhhhhhhHHHHHHHhhhc
Confidence            567999999976   3334555555 49     89888765 333321       1112334455666777788889999


Q ss_pred             cCCccccC
Q psy2399         102 KFDNWYST  109 (232)
Q Consensus       102 ~~d~~~~t  109 (232)
                      +.+.+...
T Consensus        99 ~~~~~~~~  106 (306)
T d1j1ua_          99 KAKYVYGS  106 (306)
T ss_dssp             CCEEEEGG
T ss_pred             cccccccc
Confidence            87654433

>d1r6ta2 c.26.1.1 (A:82-467) Tryptophanyl-tRNA synthetase (TrpRS) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tryptophanyl-tRNA synthetase (TrpRS)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.21  E-value=0.0052  Score=53.04  Aligned_cols=79  Identities=11%  Similarity=0.176  Sum_probs=51.0

Q ss_pred             CCCCcEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHH-HcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           9 KDVRRIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQC-MQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         9 ~~~~~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr-~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      +++++++|.++. -|+|. +||||..+.+.    .||+. ..|     .+|.+.. .|.|-.      -...+++++...
T Consensus        70 ~~gkp~~vytG~-~PSg~~lHlGh~v~~~~----~~~~q~~~~-----~~v~i~i-aD~~a~------~~~~~~~~e~~~  132 (386)
T d1r6ta2          70 ENKKPFYLYTGR-GPSSEAMHVGHLIPFIF----TKWLQDVFN-----VPLVIQM-TDDEKY------LWKDLTLDQAYG  132 (386)
T ss_dssp             HTTCCEEEEEEE-CCCTTCCBGGGHHHHHH----HHHHHHHHT-----CCEEEEE-CHHHHH------HHSSCCHHHHHH
T ss_pred             HcCCCeEEEecc-CCCCchhHHHHHHHHHH----HHHHHHhcc-----cceEEEe-cchHhh------hcccCCHHHHHH
Confidence            456788888876 78896 89999987653    35554 456     6766553 444321      113566766544


Q ss_pred             HHHHHHHHHHhccCCcCCc
Q psy2399          87 NISSNRKKYLDGFYIKFDN  105 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI~~d~  105 (232)
                       +.....+++-++|++++.
T Consensus       133 -~~~e~~~~~lA~GlDp~k  150 (386)
T d1r6ta2         133 -DAVENAKDIIACGFDINK  150 (386)
T ss_dssp             -HHHHHHHHHHTTCCCTTS
T ss_pred             -HHHHHHHHHHHhCCCccc
Confidence             445566677789998874

>d1n3la_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.44  E-value=0.018  Score=48.40  Aligned_cols=79  Identities=13%  Similarity=0.120  Sum_probs=45.6

Q ss_pred             CcEEEEcCCCCCCCcCCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCC-C-HHHHHHHHH
Q psy2399          12 RRIFVTTALPYANGELHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGM-T-PKEFINNIS   89 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~-~-~~e~~~~~~   89 (232)
                      +++.|.++. -|||++||||+.+.+.   +.+++ ..|     +++.+..|- .|+.-.    ...+- . .+...+.+.
T Consensus        31 ~~~~vy~G~-~PTg~lHlG~~l~~~~---l~~~q-~~g-----~~~~~~IaD-~~a~~~----~~~~~~~~~~~~~~~~~   95 (339)
T d1n3la_          31 RELKIYWGT-ATTGKPHVAYFVPMSK---IADFL-KAG-----CEVTILFAD-LHAYLD----NMKAPWELLELRVSYYE   95 (339)
T ss_dssp             SCCEEEEEE-CCSSCCBGGGHHHHHH---HHHHH-HTT-----CEEEEEECH-HHHHHT----TTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEee-CCCCccHHHHHHHHHH---HHHHH-HCC-----CcEEEEecc-hhhhcc----CCCCchHHHHHHHHHHH
Confidence            344555544 5779999999887553   44444 468     888877642 332110    00000 0 122344555


Q ss_pred             HHHHHHHhccCCcCCc
Q psy2399          90 SNRKKYLDGFYIKFDN  105 (232)
Q Consensus        90 ~~~~~~l~~lgI~~d~  105 (232)
                      +.+...+.++|++++.
T Consensus        96 ~~~~~~~~a~g~d~~k  111 (339)
T d1n3la_          96 NVIKAMLESIGVPLEK  111 (339)
T ss_dssp             HHHHHHHHHHTCCCTT
T ss_pred             HHHHHHHHhhccChHH
Confidence            6677888899998764

>d1i6la_ c.26.1.1 (A:) Tryptophanyl-tRNA synthetase (TrpRS) {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tryptophanyl-tRNA synthetase (TrpRS)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.71  E-value=0.036  Score=46.19  Aligned_cols=65  Identities=17%  Similarity=0.211  Sum_probs=40.9

Q ss_pred             CCCCcCCchHHHhHHHHHHHHHHHHH-cCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccC
Q psy2399          22 YANGELHIGHIMEYIQADIWVRFQCM-QQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFINNISSNRKKYLDGFY  100 (232)
Q Consensus        22 ~~nG~lHiGH~~~~v~~Dvl~R~lr~-~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~lg  100 (232)
                      -|+|.+||||..+.+     ..|..+ .|     +++.+.. .|.|..-       ...+++++.+ ....+..++-++|
T Consensus         9 ~PSG~~HlG~~~g~i-----~~~~~lq~~-----~~~~i~i-AD~halt-------~~~~~~~l~~-~~~~~~~~~lA~G   69 (326)
T d1i6la_           9 QPSGVITIGNYIGAL-----RQFVELQHE-----YNCYFCI-VDQHAIT-------VWQDPHELRQ-NIRRLAALYLAVG   69 (326)
T ss_dssp             CCCSCCBHHHHHHTH-----HHHHHHTTT-----SEEEEEE-CHHHHTT-------SCCCHHHHHH-HHHHHHHHHHHTT
T ss_pred             CCCCccHHHHHHHHH-----HHHHHHhCC-----CCEEEEe-ehHHhhc-------cCCCHHHHHH-HHHHHHHHhhhhh
Confidence            467999999976543     333333 36     7876543 4666521       2335665544 4456667888999


Q ss_pred             CcCCc
Q psy2399         101 IKFDN  105 (232)
Q Consensus       101 I~~d~  105 (232)
                      ++++.
T Consensus        70 ~dp~k   74 (326)
T d1i6la_          70 IDPTQ   74 (326)
T ss_dssp             CCTTT
T ss_pred             ccccc
Confidence            98775

>d1h3fa1 c.26.1.1 (A:5-347) Tyrosyl-tRNA synthetase (TyrRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Thermus thermophilus [TaxId: 274]

Probab=94.05  E-value=0.055  Score=45.38  Aligned_cols=43  Identities=21%  Similarity=0.227  Sum_probs=29.8

Q ss_pred             CCCcEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecC
Q psy2399          10 DVRRIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICA   62 (232)
Q Consensus        10 ~~~~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g   62 (232)
                      +++++.|.++. -|||+ |||||+.+++.    .+++...|     +++.++.|
T Consensus        30 ~g~~~~vY~G~-~PTg~sLHlGh~v~~~~----~~~lq~~g-----~~~~~~ia   73 (343)
T d1h3fa1          30 EGRPLTVKLGA-DPTRPDLHLGHAVVLRK----MRQFQELG-----HKVVLIIG   73 (343)
T ss_dssp             TCSCCEEEEEE-CTTCCSCBHHHHHHHHH----HHHHHHTT-----CEEEEEEC
T ss_pred             cCCCCEEEEee-cCCCCcccHHHHHHHHH----HHHHHHCC-----CceEEEEe
Confidence            34666666665 78895 99999876432    45556679     88887654

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.90  E-value=0.024  Score=35.44  Aligned_cols=30  Identities=17%  Similarity=0.306  Sum_probs=20.4

Q ss_pred             ceeccCCCCCCccc-----cCC-CcCccCCCCCCCc
Q psy2399         152 RYIKGECPICNAKD-----QYG-DFCECCSSIYTPT  181 (232)
Q Consensus       152 ~~v~g~cp~c~~~~-----~~g-~~Ce~Cg~~~~~~  181 (232)
                      .-++..||.|++..     ..| ..|..||.++...
T Consensus         8 ~~~~~~Cp~Cgs~~ii~D~~~Ge~vC~~CG~Vlee~   43 (58)
T d1dl6a_           8 ALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDR   43 (58)
T ss_dssp             CCSCCSBTTBSSSCCEECSSSCCEECTTTCCEECCS
T ss_pred             cccccCCCCCCCCCEEEECCCCcEecccCCCEeccc
Confidence            44567899999875     234 3488888876543

>d2ts1a_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Bacillus stearothermophilus, nca 1503 [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Bacillus stearothermophilus, nca 1503 [TaxId: 1422]

Probab=91.10  E-value=0.058  Score=45.06  Aligned_cols=44  Identities=16%  Similarity=0.253  Sum_probs=30.2

Q ss_pred             CcEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCCh
Q psy2399          12 RRIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDA   65 (232)
Q Consensus        12 ~~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~   65 (232)
                      +++.+..+. -||++ |||||+.++.    .-|++...|     +.|..+.|-..
T Consensus        29 ~~~~~Y~G~-DPTa~sLHlGhlv~l~----~l~~~q~~G-----h~~i~LiG~~T   73 (319)
T d2ts1a_          29 ERVTLYCGF-DPTADSLHIGHLATIL----TMRRFQQAG-----HRPIALVGGAT   73 (319)
T ss_dssp             SCCEEEEEE-CCSSSSCBGGGHHHHH----HHHHHHHTT-----CEEEEEECTTG
T ss_pred             CCceEEEee-cCCCCcchHHHHHHHH----HHHHHHHcC-----CceeEEeeehh
Confidence            344444443 34555 9999999874    456778889     89888877654

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.68  E-value=0.044  Score=33.13  Aligned_cols=27  Identities=22%  Similarity=0.696  Sum_probs=17.5

Q ss_pred             ccCCCCCCccc-----cCC-CcCccCCCCCCCc
Q psy2399         155 KGECPICNAKD-----QYG-DFCECCSSIYTPT  181 (232)
Q Consensus       155 ~g~cp~c~~~~-----~~g-~~Ce~Cg~~~~~~  181 (232)
                      +..||.|++..     ..| ..|.+||.+....
T Consensus         5 ~~~Cp~Cgs~~iv~D~~~Ge~vC~~CG~Viee~   37 (50)
T d1pfta_           5 QKVCPACESAELIYDPERGEIVCAKCGYVIEEN   37 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCBCCCC
T ss_pred             cccCcCCCCCcEEEECCCCeEecccCCcEeccc
Confidence            34688888752     344 4488888876543

>d3bula2 c.23.6.1 (A:741-896) Methionine synthase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methionine synthase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.73  E-value=0.88  Score=33.46  Aligned_cols=83  Identities=11%  Similarity=0.136  Sum_probs=56.1

Q ss_pred             CCCCCcEEEEcCCCCCCCcCC-chHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCCChhhHHHHHHHHHcCCCHHHHHH
Q psy2399           8 FKDVRRIFVTTALPYANGELH-IGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICADDAHGAAIMIAAEKAGMTPKEFIN   86 (232)
Q Consensus         8 ~~~~~~~~v~~~~P~~nG~lH-iGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~D~~G~~i~~~a~~~g~~~~e~~~   86 (232)
                      .+++.++++.+    |-|+.| ||       ..+++.+++..|     ++|.++- .              +.+++++++
T Consensus         3 ~~~~gkivi~t----v~gD~HdiG-------~~iv~~~l~~~G-----~~Vi~LG-~--------------~~p~e~~~~   51 (156)
T d3bula2           3 CKTNGKMVIAT----VKGDVHDIG-------KNIVGVVLQCNN-----YEIVDLG-V--------------MVPAEKILR   51 (156)
T ss_dssp             CCCSCEEEEEE----BTTCCCCHH-------HHHHHHHHHTTT-----CEEEECC-S--------------SBCHHHHHH
T ss_pred             CCcCCEEEEEe----eCCChhhHH-------HHHHHHHHHHCC-----CEEEECC-C--------------CCCHHHHHH
Confidence            45566788876    449999 44       567888899999     9999873 2              356777766


Q ss_pred             HHHHHHHHHHhccCCcCCccccCCChhHHHHHHHHHHHHHhhcCC
Q psy2399          87 NISSNRKKYLDGFYIKFDNWYSTDSIENIDLVQKIYDTLYNKAKL  131 (232)
Q Consensus        87 ~~~~~~~~~l~~lgI~~d~~~~t~~~~~~~~v~~~~~~L~~~kG~  131 (232)
                      ...+   ..-+.++++      .+...+...+..+.+.|. +.|.
T Consensus        52 ~~~~---~~~d~i~lS------~l~~~~~~~~~~~~~~l~-~~g~   86 (156)
T d3bula2          52 TAKE---VNADLIGLS------GLITPSLDEMVNVAKEME-RQGF   86 (156)
T ss_dssp             HHHH---HTCSEEEEE------CCSTHHHHHHHHHHHHHH-HTTC
T ss_pred             HHHh---hCCCEEEEe------cccccchHHHHHHHHHHH-hccc
Confidence            5543   223344443      333467788888888888 8775

>d1jila_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Staphylococcus aureus [TaxId: 1280]

Probab=86.74  E-value=0.26  Score=40.94  Aligned_cols=41  Identities=15%  Similarity=0.302  Sum_probs=28.1

Q ss_pred             cEEEEcCCCCCCCc-CCchHHHhHHHHHHHHHHHHHcCCCCCCceeEEecCC
Q psy2399          13 RIFVTTALPYANGE-LHIGHIMEYIQADIWVRFQCMQQDNGKSRQVYFICAD   63 (232)
Q Consensus        13 ~~~v~~~~P~~nG~-lHiGH~~~~v~~Dvl~R~lr~~G~~~~~~~v~~~~g~   63 (232)
                      ++.+..+. =||++ |||||+.+..    .-|++...|     +.+.++.|-
T Consensus        31 ~~~~Y~G~-DPTa~sLHlGhlv~l~----~l~~~q~~G-----h~~i~LiG~   72 (323)
T d1jila_          31 QVTLYCGA-DPTADSLHIGHLLPFL----TLRRFQEHG-----HRPIVLIGG   72 (323)
T ss_dssp             CCEEEEEE-CCSSSSCBHHHHHHHH----HHHHHHHTT-----CEEEEEECT
T ss_pred             CcEEEEcc-cCCCccccHHHHHHHH----HHHHHHHhC-----CceEEeehh
Confidence            33444433 46677 9999998764    357778889     888877654

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=85.79  E-value=0.12  Score=28.65  Aligned_cols=27  Identities=15%  Similarity=0.196  Sum_probs=18.4

Q ss_pred             CccCCCCCCCc---cccCCcccCCCCccEE
Q psy2399         171 CECCSSIYTPT---KLINPYSILSGTKPII  197 (232)
Q Consensus       171 Ce~Cg~~~~~~---~l~~~~~~~~g~~~~~  197 (232)
                      |.+||++|...   ..++++|-.||.++..
T Consensus         5 C~~CG~~Yh~~~~pPk~~g~CD~cG~~L~q   34 (35)
T d1zina2           5 CRNCGATYHLIFHPPAKPGVCDKCGGELYQ   34 (35)
T ss_dssp             ETTTCCEEETTTBCCSSTTBCTTTCCBEEC
T ss_pred             CcCcCchhccccCCCCCCCcCCCCCCCccc
Confidence            77788766422   3367899899987653

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=85.69  E-value=0.071  Score=30.08  Aligned_cols=28  Identities=11%  Similarity=0.087  Sum_probs=18.8

Q ss_pred             CccCCCCCCCc---cccCCcccCCCCccEEE
Q psy2399         171 CECCSSIYTPT---KLINPYSILSGTKPIIK  198 (232)
Q Consensus       171 Ce~Cg~~~~~~---~l~~~~~~~~g~~~~~~  198 (232)
                      |..||++|...   -.++++|-.||.++..|
T Consensus         5 c~~cG~~Yh~~~~pPk~~g~CD~cg~~L~qR   35 (37)
T d2ak3a2           5 HPGSGRVYNIEFNPPKTMGIDDLTGEPLVQR   35 (37)
T ss_dssp             ETTTTEEEETTTBCCSSTTBCTTTCCBCBCC
T ss_pred             eCCcCChhhhccCCccccCCccCCCCcCEec
Confidence            77777666422   33678888898876644

>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Thermus thermophilus [TaxId: 274]

Probab=84.17  E-value=0.43  Score=29.54  Aligned_cols=22  Identities=27%  Similarity=0.593  Sum_probs=17.7

Q ss_pred             cCCCCCCccccCCCcCccCCCC
Q psy2399         156 GECPICNAKDQYGDFCECCSSI  177 (232)
Q Consensus       156 g~cp~c~~~~~~g~~Ce~Cg~~  177 (232)
                      ..||.||+..-.--.|.+||.+
T Consensus        30 ~~C~~CG~~~~pHrvC~~CG~Y   51 (59)
T d2j0151          30 VPCPECKAMKPPHTVCPECGYY   51 (59)
T ss_dssp             BCCSSSSSCBCTTCBCTTTCCS
T ss_pred             eECCCCCCcccceeECCCCCeE
Confidence            3699999888777889999954

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=82.87  E-value=0.13  Score=28.54  Aligned_cols=26  Identities=8%  Similarity=0.094  Sum_probs=17.4

Q ss_pred             CccCCCCCCCc---cccCCcccCCCCccE
Q psy2399         171 CECCSSIYTPT---KLINPYSILSGTKPI  196 (232)
Q Consensus       171 Ce~Cg~~~~~~---~l~~~~~~~~g~~~~  196 (232)
                      |..||++|...   ..++++|-.||.++.
T Consensus         5 c~~cG~~Yh~~~~PPk~~g~CD~cg~~L~   33 (35)
T d1e4va2           5 HAPSGRVYHVKFNPPKVEGKDDVTGEELT   33 (35)
T ss_dssp             ETTTTEEEETTTBCCSSTTBCTTTCCBCB
T ss_pred             CcCcCChhhhccCccccCCcccCCCCEee
Confidence            67777666422   236788888888765

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=82.56  E-value=0.22  Score=27.59  Aligned_cols=27  Identities=15%  Similarity=0.283  Sum_probs=18.3

Q ss_pred             CccCCCCCCCc---cccCCcccCCCCccEE
Q psy2399         171 CECCSSIYTPT---KLINPYSILSGTKPII  197 (232)
Q Consensus       171 Ce~Cg~~~~~~---~l~~~~~~~~g~~~~~  197 (232)
                      |.+||+.|...   ..++++|-.||.++..
T Consensus         5 C~~CG~~Yh~~~~pPk~~g~CD~cg~~L~q   34 (35)
T d1s3ga2           5 CKVCGTSYHLLFNPPQVEGKCDKDGGELYQ   34 (35)
T ss_dssp             ETTTCCEEETTTBCCSBTTBCTTTCCBEEC
T ss_pred             CcCcCchhccccCCCCCCCccCCCCCCcee
Confidence            77778766322   3467889889887653

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.83  E-value=0.2  Score=28.30  Aligned_cols=28  Identities=7%  Similarity=0.044  Sum_probs=19.0

Q ss_pred             CccCCCCCCCc---cccCCcccCCCCccEEE
Q psy2399         171 CECCSSIYTPT---KLINPYSILSGTKPIIK  198 (232)
Q Consensus       171 Ce~Cg~~~~~~---~l~~~~~~~~g~~~~~~  198 (232)
                      |..||++|...   ..++++|-.||.+++.|
T Consensus         5 C~~cG~~Yh~~~~ppk~~g~CD~cg~~L~qR   35 (38)
T d1akya2           5 HPASGRSYHKIFNPPKEDMKDDVTGEALVQR   35 (38)
T ss_dssp             CTTTCCEEETTTBCCSSTTBCTTTCCBCBCC
T ss_pred             CcCccchhhhhccCcCcCCccCCCCCEeeec
Confidence            77788766421   33678898899876654