Psyllid ID: psy7420

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------6
Protein Sequence
MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERMKTGY
Secondary Structure (PSIPRED)
ccccccccEEEEEEcccHHHHccccccccccEEEEEcccccccccccHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEcccccEEEEEcccccHHHHcEcccccccEEEcHHHHHHcccccccHHHHHHHcccc
Coil and Loop (DISEMBL)
mqlysipdiriffsedsgflnqfrteDVNQKIVFKFLLRElllprsyrpeIEERMKTGY
Flexible Loop (DISEMBL)
mqlysipdiriFFSEDSGFLNQFRTEDVNQKIVFKFllrelllprsyrpeieermktgy
Low Complexity Region (SEG)
MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERMKTGY
Disordered region (IsUnstruct)
***YSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPR**************
Disordered Region (DISOPRED)
MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEER*****
Disordered Region (DISEMBL)
MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEI********
Disordered Region (DISPRO)
MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERMKTGY
Positional Conservation
no confident homologs detected

---

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	59	2.2.26 [Sep-21-2011]
Q6AYQ3	472	Phenylalanine--tRNA ligas	yes	N/A	0.593	0.074	0.6	7e-06
Q99M01	451	Phenylalanine--tRNA ligas	yes	N/A	0.627	0.082	0.567	3e-05
O95363	451	Phenylalanine--tRNA ligas	yes	N/A	0.627	0.082	0.540	0.0001

>sp|Q6AYQ3|SYFM_RAT Phenylalanine--tRNA ligase, mitochondrial OS=Rattus norvegicus GN=Fars2 PE=2 SV=1

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 21/35 (60%), Positives = 26/35 (74%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M LY IPDIR+F+SED  FL QFR  D+NQ + F+
Sbjct: 321 MVLYDIPDIRLFWSEDERFLKQFRLSDINQSVKFQ 355

Catalyzes direct attachment of p-Tyr (Tyr) to tRNAPhe. Permits also, with a lower efficiency, the attachment of m-Tyr to tRNAPhe, thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins.
Rattus norvegicus (taxid: 10116)
EC: 6EC: .EC: 1EC: .EC: 1EC: .EC: 2EC: 0

>sp|Q99M01|SYFM_MOUSE Phenylalanine--tRNA ligase, mitochondrial OS=Mus musculus GN=Fars2 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/37 (56%), Positives = 26/37 (70%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFL 37
           M LY IPDIR+F+SED  FL QF   D+NQ + F+ L
Sbjct: 321 MVLYDIPDIRLFWSEDERFLKQFLLSDINQSVKFQPL 357

Catalyzes direct attachment of p-Tyr (Tyr) to tRNAPhe. Permits also, with a lower efficiency, the attachment of m-Tyr to tRNAPhe, thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|O95363|SYFM_HUMAN Phenylalanine--tRNA ligase, mitochondrial OS=Homo sapiens GN=FARS2 PE=1 SV=1

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/37 (54%), Positives = 26/37 (70%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFL 37
           M LY IPDIR+F+ ED  FL QF   ++NQK+ F+ L
Sbjct: 321 MILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPL 357

Catalyzes direct attachment of p-Tyr (Tyr) to tRNAPhe. Permits also, with a lower efficiency, the attachment of m-Tyr to tRNAPhe, thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

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	59
225708744	422	Probable phenylalanyl-tRNA synthetase, m	0.593	0.082	0.685	2e-06
444731414	405	Phenylalanyl-tRNA synthetase, mitochondr	0.593	0.086	0.628	8e-06
156550087	438	PREDICTED: probable phenylalanyl-tRNA sy	0.593	0.079	0.685	8e-06
426251406	440	PREDICTED: LOW QUALITY PROTEIN: phenylal	0.627	0.084	0.621	1e-05
66506607	421	PREDICTED: probable phenylalanyl-tRNA sy	0.593	0.083	0.685	1e-05
380011861	439	PREDICTED: probable phenylalanine--tRNA	0.593	0.079	0.685	3e-05
332375771	368	unknown [Dendroctonus ponderosae]	0.593	0.095	0.6	3e-05
348566181	451	PREDICTED: phenylalanyl-tRNA synthetase,	0.627	0.082	0.621	3e-05
351703467	406	Phenylalanyl-tRNA synthetase, mitochondr	0.627	0.091	0.621	4e-05
358253386	502	phenylalanyl-tRNA synthetase alpha chain	0.593	0.069	0.571	4e-05

>gi|225708744|gb|ACO10218.1| Probable phenylalanyl-tRNA synthetase, mitochondrial precursor [Caligus rogercresseyi]

 Score = 56.6 bits (135), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 32/35 (91%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M+LY IPDIR+F+S+DSGFL+QF T+DVN+ IV+K
Sbjct: 292 MKLYQIPDIRLFWSKDSGFLDQFVTDDVNKDIVYK 326

Source: Caligus rogercresseyi

Species: Caligus rogercresseyi

Genus: Caligus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|444731414|gb|ELW71768.1| Phenylalanyl-tRNA synthetase, mitochondrial [Tupaia chinensis]

 Score = 54.7 bits (130), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 22/35 (62%), Positives = 27/35 (77%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M LY IPDIR+F+SED  FL QFR  D+NQK+ F+
Sbjct: 364 MILYDIPDIRLFWSEDERFLKQFRVSDINQKVTFQ 398

Source: Tupaia chinensis

Species: Tupaia chinensis

Genus: Tupaia

Family: Tupaiidae

Order: Scandentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|156550087|ref|XP_001605577.1| PREDICTED: probable phenylalanyl-tRNA synthetase, mitochondrial-like [Nasonia vitripennis]

 Score = 54.3 bits (129), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 24/35 (68%), Positives = 29/35 (82%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M LYSIPDIR+F+S D GFLNQF T+DVN+ I +K
Sbjct: 308 MCLYSIPDIRLFWSTDPGFLNQFITDDVNKAITYK 342

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|426251406|ref|XP_004019414.1| PREDICTED: LOW QUALITY PROTEIN: phenylalanine--tRNA ligase, mitochondrial [Ovis aries]

 Score = 54.3 bits (129), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/37 (62%), Positives = 29/37 (78%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFL 37
           M LY IPDIR+F+SED  FL QFR +D+NQK+ F+ L
Sbjct: 310 MILYDIPDIRLFWSEDERFLKQFRVQDINQKVTFQPL 346

Source: Ovis aries

Species: Ovis aries

Genus: Ovis

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|66506607|ref|XP_396590.2| PREDICTED: probable phenylalanyl-tRNA synthetase, mitochondrial [Apis mellifera]

 Score = 53.9 bits (128), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 28/35 (80%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M LY IPDIR+F+S+DSGFLNQF+ ED N  I FK
Sbjct: 290 MCLYDIPDIRLFWSKDSGFLNQFKVEDPNMTIKFK 324

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380011861|ref|XP_003690012.1| PREDICTED: probable phenylalanine--tRNA ligase, mitochondrial-like [Apis florea]

 Score = 52.8 bits (125), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 28/35 (80%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M LY IPDIR+F+S+DSGFLNQF+ ED N  I FK
Sbjct: 307 MCLYDIPDIRLFWSKDSGFLNQFKVEDPNTIIKFK 341

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332375771|gb|AEE63026.1| unknown [Dendroctonus ponderosae]

 Score = 52.4 bits (124), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 29/35 (82%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M LY IPDIR+F+S+DSGFL QF+T ++N+ I +K
Sbjct: 297 MCLYKIPDIRLFWSKDSGFLCQFKTHNINEAITYK 331

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|348566181|ref|XP_003468881.1| PREDICTED: phenylalanyl-tRNA synthetase, mitochondrial-like [Cavia porcellus]

 Score = 52.4 bits (124), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/37 (62%), Positives = 28/37 (75%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFL 37
           M LY IPDIR+F+SED  FL QFR  D+NQK+ F+ L
Sbjct: 321 MILYDIPDIRLFWSEDDRFLKQFRLSDINQKVKFQPL 357

Source: Cavia porcellus

Species: Cavia porcellus

Genus: Cavia

Family: Caviidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|351703467|gb|EHB06386.1| Phenylalanyl-tRNA synthetase, mitochondrial [Heterocephalus glaber]

 Score = 52.4 bits (124), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/37 (62%), Positives = 28/37 (75%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFL 37
           M LY IPDIR+F+SED  FL QFR  D+NQK+ F+ L
Sbjct: 321 MILYDIPDIRLFWSEDERFLKQFRLSDINQKVSFQPL 357

Source: Heterocephalus glaber

Species: Heterocephalus glaber

Genus: Heterocephalus

Family: Bathyergidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|358253386|dbj|GAA52951.1| phenylalanyl-tRNA synthetase alpha chain [Clonorchis sinensis]

 Score = 52.4 bits (124), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 31/35 (88%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           MQLY+IPDIR+F++ED+GFL+QF T+D+  ++ +K
Sbjct: 349 MQLYNIPDIRLFWTEDTGFLHQFETDDIFAQLTYK 383

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

---

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	59
UNIPROTKB|E2RK98	452	FARS2 "Uncharacterized protein	0.593	0.077	0.628	1.2e-06
UNIPROTKB|Q08D87	446	FARS2 "Uncharacterized protein	0.593	0.078	0.6	2e-06
RGD|1309416	472	Fars2 "phenylalanyl-tRNA synth	0.593	0.074	0.6	4.6e-06
MGI|MGI:1917205	451	Fars2 "phenylalanine-tRNA synt	0.593	0.077	0.571	2.4e-05
ZFIN|ZDB-GENE-070928-38	465	fars2 "phenylalanyl-tRNA synth	0.593	0.075	0.542	6.8e-05
UNIPROTKB|O95363	451	FARS2 "Phenylalanine--tRNA lig	0.593	0.077	0.542	0.00011
FB|FBgn0020766	453	Aats-phe "Phenylalanyl-tRNA sy	0.593	0.077	0.514	0.00061

UNIPROTKB|E2RK98 FARS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 120 (47.3 bits), Expect = 1.2e-06, P = 1.2e-06
 Identities = 22/35 (62%), Positives = 27/35 (77%)

Query:     1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
             M LY IPDIR+F+SED  FL QFR  D+NQK+ F+
Sbjct:   322 MILYDIPDIRLFWSEDERFLKQFRVSDINQKVKFQ 356

GO:0008033 "tRNA processing" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

UNIPROTKB|Q08D87 FARS2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 118 (46.6 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 21/35 (60%), Positives = 27/35 (77%)

Query:     1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
             M LY IPDIR+F+S+D  FL QFR  D+NQK+ F+
Sbjct:   316 MILYDIPDIRLFWSQDERFLKQFRVPDINQKVTFQ 350

GO:0008033 "tRNA processing" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

RGD|1309416 Fars2 "phenylalanyl-tRNA synthetase 2, mitochondrial" [Rattus norvegicus (taxid:10116)]

 Score = 115 (45.5 bits), Expect = 4.6e-06, P = 4.6e-06
 Identities = 21/35 (60%), Positives = 26/35 (74%)

Query:     1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
             M LY IPDIR+F+SED  FL QFR  D+NQ + F+
Sbjct:   321 MVLYDIPDIRLFWSEDERFLKQFRLSDINQSVKFQ 355

GO:0000049 "tRNA binding" evidence=IEA;ISO;ISS

GO:0000287 "magnesium ion binding" evidence=IEA

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

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=ISO;ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISO

GO:0005759 "mitochondrial matrix" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=ISO;ISS

GO:0008033 "tRNA processing" evidence=ISO;ISS

GO:0043039 "tRNA aminoacylation" evidence=IEA

MGI|MGI:1917205 Fars2 "phenylalanine-tRNA synthetase 2 (mitochondrial)" [Mus musculus (taxid:10090)]

 Score = 108 (43.1 bits), Expect = 2.4e-05, P = 2.4e-05
 Identities = 20/35 (57%), Positives = 25/35 (71%)

Query:     1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
             M LY IPDIR+F+SED  FL QF   D+NQ + F+
Sbjct:   321 MVLYDIPDIRLFWSEDERFLKQFLLSDINQSVKFQ 355

GO:0000049 "tRNA binding" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

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

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006412 "translation" evidence=IEA

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

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=ISO

GO:0008033 "tRNA processing" evidence=ISO

GO:0016874 "ligase activity" evidence=IEA

GO:0043039 "tRNA aminoacylation" evidence=IEA

ZFIN|ZDB-GENE-070928-38 fars2 "phenylalanyl-tRNA synthetase 2, mitochondrial" [Danio rerio (taxid:7955)]

 Score = 104 (41.7 bits), Expect = 6.8e-05, P = 6.8e-05
 Identities = 19/35 (54%), Positives = 25/35 (71%)

Query:     1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
             M L+ IPDIR+F+SED  FL QFR  D+ Q + F+
Sbjct:   335 MVLFGIPDIRLFWSEDERFLKQFRLSDIYQPVTFQ 369

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

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

GO:0043039 "tRNA aminoacylation" evidence=IEA

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

GO:0008033 "tRNA processing" evidence=IEA

UNIPROTKB|O95363 FARS2 "Phenylalanine--tRNA ligase, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 102 (41.0 bits), Expect = 0.00011, P = 0.00011
 Identities = 19/35 (54%), Positives = 25/35 (71%)

Query:     1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
             M LY IPDIR+F+ ED  FL QF   ++NQK+ F+
Sbjct:   321 MILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQ 355

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IDA

GO:0000049 "tRNA binding" evidence=IDA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IDA

GO:0008033 "tRNA processing" evidence=IDA

GO:0005759 "mitochondrial matrix" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

FB|FBgn0020766 Aats-phe "Phenylalanyl-tRNA synthetase" [Drosophila melanogaster (taxid:7227)]

 Score = 95 (38.5 bits), Expect = 0.00061, P = 0.00061
 Identities = 18/35 (51%), Positives = 26/35 (74%)

Query:     1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
             M L+ IPDIR+F+S DSGFL+QF  +D++    +K
Sbjct:   319 MVLFDIPDIRLFWSNDSGFLSQFSEKDLHNLPKYK 353


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.327   0.145   0.414    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       59        59   0.00091  102 3  11 22  0.45    27
                                                     29  0.49    27


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  386 (41 KB)
  Total size of DFA:  65 KB (2060 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  7.52u 0.08s 7.60t   Elapsed:  00:00:03
  Total cpu time:  7.52u 0.08s 7.60t   Elapsed:  00:00:03
  Start:  Thu Aug 15 12:21:12 2013   End:  Thu Aug 15 12:21:15 2013

GO:0005739 "mitochondrion" evidence=ISS

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=ISS

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=ISS;NAS

GO:0000049 "tRNA binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

---

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)
O95363	SYFM_HUMAN	6, ., 1, ., 1, ., 2, 0	0.5405	0.6271	0.0820	yes	N/A
Q6AYQ3	SYFM_RAT	6, ., 1, ., 1, ., 2, 0	0.6	0.5932	0.0741	yes	N/A
Q99M01	SYFM_MOUSE	6, ., 1, ., 1, ., 2, 0	0.5675	0.6271	0.0820	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	59
TIGR00469	460	TIGR00469, pheS_mito, phenylalanyl-tRNA synthetase	1e-05
PLN02788	402	PLN02788, PLN02788, phenylalanine-tRNA synthetase	4e-05
PRK00488	339	PRK00488, pheS, phenylalanyl-tRNA synthetase subun	0.002

>gnl|CDD|129561 TIGR00469, pheS_mito, phenylalanyl-tRNA synthetase, mitochondrial

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 18/35 (51%), Positives = 23/35 (65%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M L+ IPDIR+F+S D GFL QF   D++    FK
Sbjct: 327 MLLFDIPDIRLFWSNDEGFLRQFSEGDLHLIPKFK 361

Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This model models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species [Protein synthesis, tRNA aminoacylation]. Length = 460

>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase

 Score = 38.2 bits (89), Expect = 4e-05
 Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 2/35 (5%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M L+ IPDIR+F+S+D  F +QF+   +  K  FK
Sbjct: 276 MVLFDIPDIRLFWSDDERFTSQFKEGQLGVK--FK 308

Length = 402

>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha; Validated

 Score = 33.5 bits (78), Expect = 0.002
 Identities = 12/23 (52%), Positives = 14/23 (60%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQF 23
           M  Y I DIR+F+  D  FL QF
Sbjct: 317 MLKYGIDDIRLFYENDLRFLKQF 339

Length = 339

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	59
KOG2783|consensus	436		99.87
PLN02788	402	phenylalanine-tRNA synthetase	99.78
TIGR00469	460	pheS_mito phenylalanyl-tRNA synthetase, mitochondr	99.75
PF01409	247	tRNA-synt_2d: tRNA synthetases class II core domai	98.86
PRK00488	339	pheS phenylalanyl-tRNA synthetase subunit alpha; V	98.81
TIGR00468	294	pheS phenylalanyl-tRNA synthetase, alpha subunit.	98.69
COG0016	335	PheS Phenylalanyl-tRNA synthetase alpha subunit [T	98.57
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	97.34
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	96.39
PF03147	94	FDX-ACB: Ferredoxin-fold anticodon binding domain;	96.1
CHL00192	704	syfB phenylalanyl-tRNA synthetase beta chain; Prov	94.34
PRK00629	791	pheT phenylalanyl-tRNA synthetase subunit beta; Re	94.26
COG0072	650	PheT Phenylalanyl-tRNA synthetase beta subunit [Tr	93.6
TIGR00472	798	pheT_bact phenylalanyl-tRNA synthetase, beta subun	93.27
PRK06253	529	O-phosphoseryl-tRNA synthetase; Reviewed	87.79
TIGR00470	533	sepS O-phosphoseryl-tRNA(Cys) synthetase. This fam	85.8

>KOG2783|consensus

Probab=99.87  E-value=1e-23  Score=160.31  Aligned_cols=51  Identities=31%  Similarity=0.455  Sum_probs=48.1

Q ss_pred             CccCCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHh
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEE   53 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~   53 (59)
                      |++|+|||||+||+.|.|||+||..+.+..  +|||+|||||||+||||||.+
T Consensus       308 Mll~~IpDiRlfWs~DeRFlkqF~~g~I~~--~FKp~SkYP~c~~DiSFWl~~  358 (436)
T KOG2783|consen  308 MLLFDIPDIRLFWSFDERFLKQFSPGKIEP--KFKPYSKYPPCYKDISFWLPQ  358 (436)
T ss_pred             HHHhcCcchheeeccchHHHHhcCcccccc--cccccccCCCcccceeEeecc
Confidence            899999999999999999999999999843  899999999999999999965

>PLN02788 phenylalanine-tRNA synthetase

Probab=99.78  E-value=2.5e-20  Score=139.79  Aligned_cols=53  Identities=30%  Similarity=0.506  Sum_probs=47.2

Q ss_pred             CccCCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhhh
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      |++|||||||+||++|+|||+||......  .+|+|+|+||+|+|||||+|++.+
T Consensus       276 ml~~~I~DIRlf~~~D~rfl~Qf~~~~~~--~~fkp~SkfP~v~RDiSf~v~~~v  328 (402)
T PLN02788        276 MVLFDIPDIRLFWSDDERFTSQFKEGQLG--VKFKPYSKYPPCYKDISFWISDEF  328 (402)
T ss_pred             HhhcCCchhhhhhcccHHHHHhccccccc--cccCcCCCCCCcceeEEEEECCCC
Confidence            78999999999999999999999976531  279999999999999999997654

>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase, mitochondrial

Probab=99.75  E-value=1.1e-19  Score=138.74  Aligned_cols=55  Identities=35%  Similarity=0.493  Sum_probs=49.4

Q ss_pred             CccCCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhhh
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      |++|||+|||+||++|+|||+||..+...+..+|+|+|+||+|.|||||+|++.+
T Consensus       327 Ml~~gi~DiR~~~~~d~rfl~qf~~~~~~~~~~fkpiSKfP~v~RDISfvV~~~v  381 (460)
T TIGR00469       327 MLLFDIPDIRLFWSNDEGFLRQFSEGDLHLIPKFKPISHHPGCFNDLAFWLPEDI  381 (460)
T ss_pred             HHHcCccHHHHHhcccHHHHHhhcccccccccccCcCCCCCCccccEEEEecCCC
Confidence            8999999999999999999999987744444789999999999999999997654

Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This alignment models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species.

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

Probab=98.86  E-value=3.5e-10  Score=79.59  Aligned_cols=23  Identities=57%  Similarity=1.005  Sum_probs=21.5

Q ss_pred             CccCCCCcccccccCChhhhhcc
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQF   23 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF   23 (59)
                      |++|||+|||+||++|+|||+||
T Consensus       225 m~~~gi~diR~~~~~d~~fl~qf  247 (247)
T PF01409_consen  225 MLKYGIPDIRLLYSNDLRFLRQF  247 (247)
T ss_dssp             HHHHT-SSGGHHHTTTHHHHGGG
T ss_pred             HHHcCCchHHHHhcCcHhHHhcC
Confidence            89999999999999999999998

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

>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated

Probab=98.81  E-value=6.3e-10  Score=82.57  Aligned_cols=23  Identities=52%  Similarity=0.936  Sum_probs=22.6

Q ss_pred             CccCCCCcccccccCChhhhhcc
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQF   23 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF   23 (59)
                      |++|||+|||+||+||+|||+||
T Consensus       317 Ml~ygi~DiR~~~~~D~rfl~qF  339 (339)
T PRK00488        317 MLKYGIDDIRLFYENDLRFLKQF  339 (339)
T ss_pred             HHHhCCcHHHHHHhcCHhHHhcC
Confidence            89999999999999999999998

>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit

Probab=98.69  E-value=2.7e-09  Score=76.02  Aligned_cols=24  Identities=46%  Similarity=0.767  Sum_probs=23.3

Q ss_pred             CccCCCCcccccccCChhhhhccC
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFR   24 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~   24 (59)
                      |++|||+|||.|++||+|||+||+
T Consensus       270 m~~~~i~dir~~~~~d~~~l~~~~  293 (294)
T TIGR00468       270 MLKYGIDDIRDLYENDLRFLRQFK  293 (294)
T ss_pred             HHHhCCcHHHHHHcCChHHHhhcC
Confidence            899999999999999999999995

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

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

Probab=98.57  E-value=6.8e-09  Score=77.24  Aligned_cols=22  Identities=50%  Similarity=0.815  Sum_probs=21.4

Q ss_pred             CccCCCCcccccccCChhhhhc
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQ   22 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~Q   22 (59)
                      ||+|||+|||.||++|+|||+|
T Consensus       314 MLkygI~DIR~l~~~D~rfl~q  335 (335)
T COG0016         314 MLKYGIPDIRDLYENDLRFLRQ  335 (335)
T ss_pred             HHHhCCcHHHHHHhccchhhcC
Confidence            8999999999999999999987

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=97.34  E-value=3.9e-05  Score=57.97  Aligned_cols=23  Identities=30%  Similarity=0.445  Sum_probs=21.7

Q ss_pred             CccCCCCcccccccCChhhhhcc
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQF   23 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF   23 (59)
                      |++|||+|||.||++|++||++-
T Consensus       466 m~~~~~~dir~l~~~d~~~~~~~  488 (489)
T PRK04172        466 MLRLGLDDIRDLYSSDIEWLRER  488 (489)
T ss_pred             HHHhCCcHHHHHHhcChHHHhcC
Confidence            89999999999999999999874

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=96.39  E-value=0.00072  Score=52.88  Aligned_cols=25  Identities=36%  Similarity=0.590  Sum_probs=21.9

Q ss_pred             CccCCCCccccccc--CChhhhhccCC
Q psy7420           1 MQLYSIPDIRIFFS--EDSGFLNQFRT   25 (59)
Q Consensus         1 MlkygIpDIRlfws--~D~RFL~QF~~   25 (59)
                      |++|||+|||.|++  .|+.||+.-..
T Consensus       461 Ml~ygi~DIR~l~~~k~Dl~~lr~~p~  487 (492)
T PLN02853        461 MILYGIDNIRDLFGHKVDLGLIKRNPI  487 (492)
T ss_pred             HHHhCCcHHHHHhCCCCCHHHHhhCcc
Confidence            89999999999999  78999886543

>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs

Probab=96.10  E-value=0.00059  Score=41.22  Aligned_cols=18  Identities=11%  Similarity=-0.003  Sum_probs=13.0

Q ss_pred             ccCCCCCccchHhhHhhh
Q psy7420          38 LRELLLPRSYRPEIEERM   55 (59)
Q Consensus        38 SkyPp~~rd~s~~i~~~~   55 (59)
                      |+||++.||+||+|.+.+
T Consensus         1 S~fP~~~RDiS~~v~~~~   18 (94)
T PF03147_consen    1 SKFPSVERDISFVVPEDV   18 (94)
T ss_dssp             -SS--EEEEEEEEEETTS
T ss_pred             CcCCCccccEEEEECCCC
Confidence            799999999999997644

Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....

>CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional

Probab=94.34  E-value=0.013  Score=46.54  Aligned_cols=51  Identities=10%  Similarity=0.046  Sum_probs=34.1

Q ss_pred             cCCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhhh
Q psy7420           3 LYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus         3 kygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      .|+|+.==.++|=|+.-|.+.....  ...+|+|+|+||++.||+||.|++.+
T Consensus       577 ~~~l~~~v~~~Ei~l~~l~~~~~~~--~~~~~~~~skfP~v~RDia~vv~~~i  627 (704)
T CHL00192        577 KLNLNTEIYLFEINLDILQYSIQQN--NLISYQPYSSYPKIIRDLSFIIKKSI  627 (704)
T ss_pred             HcCCCCCeEEEEEEHHHhhhhhccc--cccccCCCCCCCCccceEEEEECCCC
Confidence            3555532256677777665544211  01369999999999999999987654

>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed

Probab=94.26  E-value=0.015  Score=46.58  Aligned_cols=48  Identities=15%  Similarity=0.137  Sum_probs=31.9

Q ss_pred             CCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhhh
Q psy7420           4 YSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus         4 ygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      |+|+.==.+.|=|+.-|.+....    ..+|+|+|+||++.||+|+.+++.+
T Consensus       667 ~~l~~~v~~~Ei~l~~l~~~~~~----~~~~~~~skfP~v~RDls~vv~~~v  714 (791)
T PRK00629        667 LDLPGRTYVFELDLDALLEAARK----LPKYKPISKFPAVRRDLALVVDEDV  714 (791)
T ss_pred             cCCCCCEEEEEEEHHHhhhhhcc----cCCCCCCCCCCCccccEEEEECCCC
Confidence            44443124456676666543211    2379999999999999999987654

>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]

Probab=93.60  E-value=0.025  Score=44.73  Aligned_cols=24  Identities=17%  Similarity=0.153  Sum_probs=21.2

Q ss_pred             ccceeecccCCCCCccchHhhHhh
Q psy7420          31 KIVFKFLLRELLLPRSYRPEIEER   54 (59)
Q Consensus        31 ~~~Fkp~SkyPp~~rd~s~~i~~~   54 (59)
                      ...|+|+|+||++.||++|.|++.
T Consensus       551 ~~~~~~~s~~pa~~RDia~~v~~~  574 (650)
T COG0072         551 KPAYKPISKFPAVRRDIALVVDED  574 (650)
T ss_pred             ccccCCCCCCCcccceeEEEecCC
Confidence            378899999999999999999654

>TIGR00472 pheT_bact phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial

Probab=93.27  E-value=0.028  Score=44.95  Aligned_cols=48  Identities=8%  Similarity=0.020  Sum_probs=31.8

Q ss_pred             CCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhhh
Q psy7420           4 YSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus         4 ygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      |+|+.==.++|=|+.-|.+.....    .+|+|+|+||++.||+|+.+++.+
T Consensus       675 ~~l~~~v~~~Ei~l~~l~~~~~~~----~~~~~~sk~P~~~RDls~~v~~~v  722 (798)
T TIGR00472       675 YDLKEPTFVAELDLDRLLESLKKV----PKYRPISKFPAVTRDISFLVPKDV  722 (798)
T ss_pred             cCCCCCeEEEEEEHHHHhhhhccc----CCcCCCCCCCCcceeEEEEECCCC
Confidence            444421145566666554433211    379999999999999999997654

Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end, however.

>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed

Probab=87.79  E-value=0.23  Score=39.63  Aligned_cols=49  Identities=18%  Similarity=0.097  Sum_probs=33.5

Q ss_pred             cCCCCcccccccCChhhhhccCCC--CCCCccceeecccCCCCCccchHhhH
Q psy7420           3 LYSIPDIRIFFSEDSGFLNQFRTE--DVNQKIVFKFLLRELLLPRSYRPEIE   52 (59)
Q Consensus         3 kygIpDIRlfws~D~RFL~QF~~~--~~~~~~~Fkp~SkyPp~~rd~s~~i~   52 (59)
                      .|||+.-=..++=|+.-|.+....  .+- ...|+++|+||++.||+|+-|.
T Consensus       311 ~fDI~~pV~aFELDLErL~~i~~~~~dir-~~~Y~~~SkFPav~RDLA~Vi~  361 (529)
T PRK06253        311 EYGIDVPVMNLGLGVERLAMILYGAEDVR-EMVYPQFYEWELSDREIARMIK  361 (529)
T ss_pred             HcCCCCceEEEEEeHHHHHhhhcCccccc-ccCcCCCCCCCCccceEEEEEe
Confidence            466664335677788777654432  110 1269999999999999999883

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

Probab=85.80  E-value=0.24  Score=39.72  Aligned_cols=27  Identities=26%  Similarity=0.550  Sum_probs=21.8

Q ss_pred             CccCCCCcccc-----ccc----CChhhhhccCCCC
Q psy7420           1 MQLYSIPDIRI-----FFS----EDSGFLNQFRTED   27 (59)
Q Consensus         1 MlkygIpDIRl-----fws----~D~RFL~QF~~~~   27 (59)
                      |++|||+|||.     ++.    +|..+++..+-..
T Consensus       329 Mi~ygi~DIR~l~~pql~~~~~~sd~~~~~~~~~~~  364 (533)
T TIGR00470       329 MILYGYEDVRAMVYPQIYGEYRLSDRDIAGMIRVDK  364 (533)
T ss_pred             HHHhCCcHHHhhcccccccccccchHHHHhhCcccc
Confidence            89999999999     665    7888888766443

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	59
3cmq_A	415	Crystal Structure Of Human Mitochondrial Phenylalan		1e-05

>pdb|3CMQ|A Chain A, Crystal Structure Of Human Mitochondrial Phenylalanine Trna Synthetase Length = 415

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/37 (54%), Positives = 26/37 (70%)
Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFL 37
           M LY IPDIR+F+ ED  FL QF   ++NQK+ F+ L
Sbjct: 285 MILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPL 321

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	59
3cmq_A	415	Phenylalanyl-tRNA synthetase, mitochondrial; class	6e-09
3pco_A	327	Phenylalanyl-tRNA synthetase, alpha subunit; amino	3e-05
1b7y_A	350	Phers, protein (phenylalanyl-tRNA synthetase); enz	4e-05
2rhq_A	294	Phenylalanyl-tRNA synthetase alpha chain; heterote	4e-05

>3cmq_A Phenylalanyl-tRNA synthetase, mitochondrial; classii aarss fold, RRM domain, RNA recogntion, aminoacyl-tRNA synthetase, ATP-binding, ligase; HET: FA5; 2.20A {Homo sapiens} PDB: 3hfv_A* 3teg_A* 3tup_A Length = 415

 Score = 48.7 bits (116), Expect = 6e-09
 Identities = 19/35 (54%), Positives = 25/35 (71%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M LY IPDIR+F+ ED  FL QF   ++NQK+ F+
Sbjct: 285 MILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQ 319

>3pco_A Phenylalanyl-tRNA synthetase, alpha subunit; aminoacylation, tRNA-binding, DNA-binding domain, four-helix aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP; 3.02A {Escherichia coli} Length = 327

 Score = 37.9 bits (89), Expect = 3e-05
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFR 24
           M  Y + D+R FF  D  FL QF+
Sbjct: 304 MLRYGVTDLRSFFENDLRFLKQFK 327

>1b7y_A Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta homodimer, ligase; HET: FYA; 2.50A {Thermus thermophilus} SCOP: d.104.1.1 PDB: 1b70_A* 1eiy_A 1jjc_A* 1pys_A 2iy5_A* 3hfz_A* 3teh_A* 2aly_A* 2akw_A* 2amc_A* Length = 350

 Score = 38.0 bits (89), Expect = 4e-05
 Identities = 13/26 (50%), Positives = 14/26 (53%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTE 26
           M  Y IPDIR FF     FL QF+  
Sbjct: 324 MLRYGIPDIRYFFGGRLKFLEQFKGV 349

>2rhq_A Phenylalanyl-tRNA synthetase alpha chain; heterotetramer, phenylalanine, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus haemolyticus} PDB: 2rhs_A* Length = 294

 Score = 37.6 bits (88), Expect = 4e-05
 Identities = 12/27 (44%), Positives = 16/27 (59%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTED 27
           M  Y I DIR F++ D  FL QF+  +
Sbjct: 264 MLKYGIEDIRYFYTNDVRFLEQFKAVE 290

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	59
3cmq_A	415	Phenylalanyl-tRNA synthetase, mitochondrial; class	99.78
1b7y_A	350	Phers, protein (phenylalanyl-tRNA synthetase); enz	99.03
2rhq_A	294	Phenylalanyl-tRNA synthetase alpha chain; heterote	99.01
3pco_A	327	Phenylalanyl-tRNA synthetase, alpha subunit; amino	98.99
2du3_A	534	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	98.47
3l4g_A	508	Phenylalanyl-tRNA synthetase alpha chain; aminoacy	96.91
3pco_B	795	Phenylalanyl-tRNA synthetase, beta chain; aminoacy	95.03
2rhq_B	795	Phenylalanyl-tRNA synthetase beta chain; heterotet	94.79
1b7y_B	785	Phers, protein (phenylalanyl-tRNA synthetase); enz	93.9
2du7_A	549	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	93.58
2odr_D	685	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.69
2odr_C	701	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.67
2odr_B	648	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.57
2odr_A	665	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	92.46
3qtc_A	290	Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthet	81.05

>3cmq_A Phenylalanyl-tRNA synthetase, mitochondrial; classii aarss fold, RRM domain, RNA recogntion, aminoacyl-tRNA synthetase, ATP-binding, ligase; HET: FA5; 2.20A {Homo sapiens} PDB: 3hfv_A* 3teg_A* 3tup_A

Probab=99.78  E-value=1.7e-20  Score=137.73  Aligned_cols=54  Identities=37%  Similarity=0.578  Sum_probs=48.3

Q ss_pred             CccCCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhh
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEER   54 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~   54 (59)
                      |++|||||||+||++|+|||+||+.....+..+|+|+|+||++.||+||+|++.
T Consensus       285 ~~~~~i~DiR~~~~~d~rfl~qf~~~~~~~~~~~~~~skfP~v~RDla~~v~~~  338 (415)
T 3cmq_A          285 MILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKYPAVINDISFWLPSE  338 (415)
T ss_dssp             HHHSCCCCGGGGGCCCHHHHGGGCCSSTTSCCCCCCCCCCCCEEEEEEEECCTT
T ss_pred             hhhcCcchhhhhhcccHHHHHhcccccccccccccCcCCCCCcceeEEEEEcCC
Confidence            679999999999999999999998775533469999999999999999999664

>1b7y_A Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta homodimer, ligase; HET: FYA; 2.50A {Thermus thermophilus} SCOP: d.104.1.1 PDB: 1b70_A* 1eiy_A 1jjc_A* 1pys_A 2iy5_A* 3hfz_A* 3teh_A* 2aly_A* 2akw_A* 2amc_A*

Probab=99.03  E-value=3.7e-11  Score=86.94  Aligned_cols=25  Identities=52%  Similarity=0.883  Sum_probs=23.8

Q ss_pred             CccCCCCcccccccCChhhhhccCC
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFRT   25 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~~   25 (59)
                      |++|||+|||+||++|+|||+||+.
T Consensus       324 ml~~gi~DiR~~~~~d~rfl~qf~~  348 (350)
T 1b7y_A          324 MLRYGIPDIRYFFGGRLKFLEQFKG  348 (350)
T ss_dssp             HHHTTCCCGGGTTSCCHHHHGGGTT
T ss_pred             HHHcCCChHHHHhcCCHHHHHhhhc
Confidence            8999999999999999999999964

>2rhq_A Phenylalanyl-tRNA synthetase alpha chain; heterotetramer, phenylalanine, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus haemolyticus} PDB: 2rhs_A*

Probab=99.01  E-value=3.3e-11  Score=84.01  Aligned_cols=26  Identities=46%  Similarity=0.836  Sum_probs=24.1

Q ss_pred             CccCCCCcccccccCChhhhhccCCC
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFRTE   26 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~~~   26 (59)
                      |++|||+|||+||++|+|||+||+..
T Consensus       264 m~~~~i~diR~~~~~d~rfl~qf~~~  289 (294)
T 2rhq_A          264 MLKYGIEDIRYFYTNDVRFLEQFKAV  289 (294)
T ss_dssp             HHHHTCCCTTHHHHCCHHHHTTCCSC
T ss_pred             HHHcCCCHHHHHhcCCHHHHHHhCcc
Confidence            78999999999999999999999743

>3pco_A Phenylalanyl-tRNA synthetase, alpha subunit; aminoacylation, tRNA-binding, DNA-binding domain, four-helix aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP; 3.02A {Escherichia coli}

Probab=98.99  E-value=5e-11  Score=85.98  Aligned_cols=24  Identities=46%  Similarity=0.877  Sum_probs=23.1

Q ss_pred             CccCCCCcccccccCChhhhhccC
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFR   24 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~   24 (59)
                      |++|||+|||+||+||+|||+||+
T Consensus       304 ml~~~i~diR~~~~~d~rfl~qf~  327 (327)
T 3pco_A          304 MLRYGVTDLRSFFENDLRFLKQFK  327 (327)
T ss_dssp             HHHHTCSCGGGGTTCCHHHHHTTC
T ss_pred             HHHcCCcHHHHHHhcChhHHhccC
Confidence            799999999999999999999995

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

Probab=98.47  E-value=5.2e-09  Score=80.03  Aligned_cols=38  Identities=16%  Similarity=-0.004  Sum_probs=33.9

Q ss_pred             CccCCCCcccccccCCh--hhhhccCCCCCCCccceeecccCCCC
Q psy7420           1 MQLYSIPDIRIFFSEDS--GFLNQFRTEDVNQKIVFKFLLRELLL   43 (59)
Q Consensus         1 MlkygIpDIRlfws~D~--RFL~QF~~~~~~~~~~Fkp~SkyPp~   43 (59)
                      |++|||+|||+||++|+  |||+||.  ++   ..++|+|++|.+
T Consensus       335 Ml~~gi~DIR~~~~~d~~~rfl~qf~--~i---~~~~~~~~~P~~  374 (534)
T 2du3_A          335 MILYGYDDVRKMVYPQIHGEIKLSDL--DI---AREIKVKEVPQT  374 (534)
T ss_dssp             HHHTTCSCHHHHHCTTTTTCCCCCHH--HH---HHHCEESSCCSS
T ss_pred             HhhcCCchhhhhhcccccHhHHhhhh--hh---hcCccHhhCCCc
Confidence            78999999999999999  9999994  34   688999999954

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

Probab=96.91  E-value=0.00031  Score=53.50  Aligned_cols=28  Identities=18%  Similarity=0.218  Sum_probs=24.6

Q ss_pred             CccCCCCcccccccC--ChhhhhccCCCCC
Q psy7420           1 MQLYSIPDIRIFFSE--DSGFLNQFRTEDV   28 (59)
Q Consensus         1 MlkygIpDIRlfws~--D~RFL~QF~~~~~   28 (59)
                      |++|||+|||.|+++  |+.|++.-..+-+
T Consensus       466 ml~~gi~diR~l~~~~~dl~~~~~~~~~~~  495 (508)
T 3l4g_A          466 MIKYGINNIRELVGHKVNLQMVYDSPLCRL  495 (508)
T ss_dssp             TTTTTCSCGGGTSSTTCCHHHHHHCCCTTS
T ss_pred             HHHcCCcHHHHHhcCCcCHHHHhhCcchhh
Confidence            899999999999998  9999998766554

>3pco_B Phenylalanyl-tRNA synthetase, beta chain; aminoacylation, tRNA-binding, DNA-binding domain, four-helix aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP; 3.02A {Escherichia coli}

Probab=95.03  E-value=0.0035  Score=49.34  Aligned_cols=25  Identities=12%  Similarity=-0.083  Sum_probs=21.9

Q ss_pred             ccceeecccCCCCCccchHhhHhhh
Q psy7420          31 KIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus        31 ~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      ..+|+|+|+||++.||+||.+++..
T Consensus       694 ~~~~~~~skfP~v~RDlA~vv~~~v  718 (795)
T 3pco_B          694 VPQAREISRFPANRRDIAVVVAENV  718 (795)
T ss_dssp             CCCCCCCCCSCCEEEEEEEEEETTS
T ss_pred             CCCcCCCCCCCCcceeEEEEeCCCC
Confidence            3789999999999999999997653

>2rhq_B Phenylalanyl-tRNA synthetase beta chain; heterotetramer, phenylalanine, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus haemolyticus} PDB: 2rhs_B*

Probab=94.79  E-value=0.005  Score=48.24  Aligned_cols=48  Identities=10%  Similarity=0.065  Sum_probs=34.8

Q ss_pred             cCCCCcccccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhhh
Q psy7420           3 LYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus         3 kygIpDIRlfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      .|||+.= ..|+=|+.-|.+-...    ..+|+|+|+||++.||+++.+++..
T Consensus       674 ~~~l~~~-~afEL~le~L~~~~~~----~~~~~~~skfP~v~RDlA~vv~~~v  721 (795)
T 2rhq_B          674 DNDLKRT-YVFELNYDAMMQVAVG----YINYEQIPKFPGVTRDIALEVNHDV  721 (795)
T ss_dssp             HTTCCSE-EEEEEEHHHHTTCCCC----SCCCCCCCSSCCEEEEEECBEETTS
T ss_pred             HcCCCCc-EEEEEEHHHHhhhccc----CCccCCCCCCCCcceeEEEEECCCC
Confidence            4677644 7788777655432221    1589999999999999999997643

>1b7y_B Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta homodimer, ligase; HET: FYA; 2.50A {Thermus thermophilus} SCOP: a.6.1.1 a.6.1.1 b.40.4.4 b.153.1.1 d.58.13.1 d.104.1.1 PDB: 1b70_B* 1eiy_B 1jjc_B* 1pys_B 2akw_B* 2aly_B* 2amc_B* 3hfz_B* 3teh_B* 2iy5_B*

Probab=93.90  E-value=0.006  Score=47.96  Aligned_cols=43  Identities=14%  Similarity=0.074  Sum_probs=31.4

Q ss_pred             cCCCCccc-ccccCChhhhhccCCCCCCCccceeecccCCCCCccchHhhHhhh
Q psy7420           3 LYSIPDIR-IFFSEDSGFLNQFRTEDVNQKIVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus         3 kygIpDIR-lfws~D~RFL~QF~~~~~~~~~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      .|||+  + ..|+=|+. |. -.     . .+|+|+|+||++.||++|.+++..
T Consensus       662 ~~~l~--~v~afEl~Ld-L~-~~-----~-~~~~~~skfP~v~RDlA~vv~~~v  705 (785)
T 1b7y_B          662 ELELP--PVHLFELRLP-LP-DK-----P-LAFQDPSRHPAAFRDLAVVVPAPT  705 (785)
T ss_dssp             HTTCC--CCEEEEEEES-CC-CC-----C-CCCCCCCCSCCEEEEECCCEESSS
T ss_pred             HCCCC--cEEEEEEEee-hh-hC-----c-ccccCCCCCCCcceeEEEEeCCCC
Confidence            36665  4 56666766 54 11     1 589999999999999999986543

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

Probab=93.58  E-value=0.0059  Score=47.10  Aligned_cols=19  Identities=16%  Similarity=0.095  Sum_probs=16.1

Q ss_pred             eeecccCCCCCccchHhhH
Q psy7420          34 FKFLLRELLLPRSYRPEIE   52 (59)
Q Consensus        34 Fkp~SkyPp~~rd~s~~i~   52 (59)
                      |+++|+||++-||+++-|+
T Consensus       352 ~~dlsrFPav~RDlAlvVd  370 (549)
T 2du7_A          352 YPQFYEYRLSDRDIAGMIR  370 (549)
T ss_dssp             SSSSSCCCCCHHHHHTTCC
T ss_pred             cCCcccCCcccccEEEEEc
Confidence            4567899999999999887

>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.69  E-value=0.011  Score=46.97  Aligned_cols=19  Identities=11%  Similarity=0.169  Sum_probs=16.1

Q ss_pred             eeecccCCCCCccchHhhH
Q psy7420          34 FKFLLRELLLPRSYRPEIE   52 (59)
Q Consensus        34 Fkp~SkyPp~~rd~s~~i~   52 (59)
                      |+++|+||++-||+++-|+
T Consensus       359 ~~dISRFPaV~RDIAlVVd  377 (685)
T 2odr_D          359 YPQFYEHKLNDRNVASMVK  377 (685)
T ss_dssp             CGGGSCCCCCHHHHHHHEE
T ss_pred             cCCcCCCCcccccEEEEEC
Confidence            4567899999999999886

>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.67  E-value=0.012  Score=46.94  Aligned_cols=19  Identities=11%  Similarity=0.169  Sum_probs=16.2

Q ss_pred             eeecccCCCCCccchHhhH
Q psy7420          34 FKFLLRELLLPRSYRPEIE   52 (59)
Q Consensus        34 Fkp~SkyPp~~rd~s~~i~   52 (59)
                      |+++|+||++-||+++-|+
T Consensus       359 ~~dISRFPaV~RDIAlVVd  377 (701)
T 2odr_C          359 YPQFYEHKLNDRNVASMVK  377 (701)
T ss_dssp             CGGGSCCCCCHHHHHHHBC
T ss_pred             cCCcCCCCccccCEEEEEC
Confidence            4667899999999999886

>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.57  E-value=0.01  Score=46.80  Aligned_cols=19  Identities=11%  Similarity=0.169  Sum_probs=15.8

Q ss_pred             eeecccCCCCCccchHhhH
Q psy7420          34 FKFLLRELLLPRSYRPEIE   52 (59)
Q Consensus        34 Fkp~SkyPp~~rd~s~~i~   52 (59)
                      |+++|+||++-||+++-|+
T Consensus       359 ~~diSRFPaV~RDIAlVVd  377 (648)
T 2odr_B          359 YPQFYEHKLNDRNVASMVK  377 (648)
T ss_dssp             CGGGSCCCCCHHHHHTTEE
T ss_pred             cCCcCCCCcccccEEEEEC
Confidence            4567889999999998885

>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=92.46  E-value=0.011  Score=46.82  Aligned_cols=19  Identities=11%  Similarity=0.169  Sum_probs=15.8

Q ss_pred             eeecccCCCCCccchHhhH
Q psy7420          34 FKFLLRELLLPRSYRPEIE   52 (59)
Q Consensus        34 Fkp~SkyPp~~rd~s~~i~   52 (59)
                      |+++|+||++-||+++-|+
T Consensus       359 ~~diSRFPaV~RDIAlVVd  377 (665)
T 2odr_A          359 YPQFYEHKLNDRNVASMVK  377 (665)
T ss_dssp             CGGGSCCCCCHHHHHTTEE
T ss_pred             cCCcCCCCcccccEEEEEC
Confidence            4567889999999998885

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

Probab=81.05  E-value=0.24  Score=33.69  Aligned_cols=14  Identities=7%  Similarity=-0.107  Sum_probs=12.0

Q ss_pred             CccCCCCccccccc
Q psy7420           1 MQLYSIPDIRIFFS   14 (59)
Q Consensus         1 MlkygIpDIRlfws   14 (59)
                      |++|||+|||.|..
T Consensus       265 ~~~~~~~dir~~~~  278 (290)
T 3qtc_A          265 KVKHDFKNIKRAAR  278 (290)
T ss_dssp             HHHHTCSSGGGGSS
T ss_pred             HHHcCCcHHHHHhc
Confidence            57899999999873

---

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	59
d1jjca_	266	d.104.1.1 (A:) Phenyl-tRNA synthetase (PheRS) alph	2e-06

>d1jjca_ d.104.1.1 (A:) Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS {Thermus thermophilus [TaxId: 274]} Length = 266

class: Alpha and beta proteins (a+b)
fold: Class II aaRS and biotin synthetases
superfamily: Class II aaRS and biotin synthetases
family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
domain: Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS
species: Thermus thermophilus [TaxId: 274]

 Score = 40.4 bits (94), Expect = 2e-06
 Identities = 13/24 (54%), Positives = 14/24 (58%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFR 24
           M  Y IPDIR FF     FL QF+
Sbjct: 240 MLRYGIPDIRYFFGGRLKFLEQFK 263

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	59
d1jjca_	266	Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS	99.11
d1jjcb4	104	Phenylalanyl-tRNA synthetase {Thermus thermophilus	97.77

>d1jjca_ d.104.1.1 (A:) Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Class II aaRS and biotin synthetases
superfamily: Class II aaRS and biotin synthetases
family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
domain: Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS
species: Thermus thermophilus [TaxId: 274]

Probab=99.11  E-value=3.4e-12  Score=88.97  Aligned_cols=25  Identities=52%  Similarity=0.883  Sum_probs=24.1

Q ss_pred             CccCCCCcccccccCChhhhhccCC
Q psy7420           1 MQLYSIPDIRIFFSEDSGFLNQFRT   25 (59)
Q Consensus         1 MlkygIpDIRlfws~D~RFL~QF~~   25 (59)
                      |++|||+|||+||++|+|||+||++
T Consensus       240 Ml~~gI~DIR~f~~~D~rfl~QFk~  264 (266)
T d1jjca_         240 MLRYGIPDIRYFFGGRLKFLEQFKG  264 (266)
T ss_dssp             HHHHTCSCGGGTTTCCHHHHGGGGG
T ss_pred             HHHcCCChHHHHhcCCHHHHHHhhc
Confidence            8999999999999999999999985

>d1jjcb4 d.58.13.1 (B:682-785) Phenylalanyl-tRNA synthetase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Anticodon-binding domain of PheRS
family: Anticodon-binding domain of PheRS
domain: Phenylalanyl-tRNA synthetase
species: Thermus thermophilus [TaxId: 274]

Probab=97.77  E-value=6.3e-07  Score=53.46  Aligned_cols=24  Identities=13%  Similarity=0.018  Sum_probs=21.1

Q ss_pred             cceeecccCCCCCccchHhhHhhh
Q psy7420          32 IVFKFLLRELLLPRSYRPEIEERM   55 (59)
Q Consensus        32 ~~Fkp~SkyPp~~rd~s~~i~~~~   55 (59)
                      .+|+|+|+||++.||+||+|++..
T Consensus         1 i~y~~~S~fP~v~RDiS~~v~~~~   24 (104)
T d1jjcb4           1 LAFQDPSRHPAAFRDLAVVVPAPT   24 (104)
T ss_dssp             CCCCCCCCSCCEEEEECCEEESSS
T ss_pred             CeeccCCCCCCcceeEEEEECCCC
Confidence            379999999999999999996643