RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014218
(428 letters)
>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
Length = 402
Score = 794 bits (2052), Expect = 0.0
Identities = 313/402 (77%), Positives = 352/402 (87%), Gaps = 5/402 (1%)
Query: 32 PFSSTSTSTSPLPL--KKKWRPPAASALELGGVKMAKDDIVR-DDPTNNVPDTIFTKLGM 88
PFSS++ T +++R PA SA+E+GGV +A+D++VR DDPTNNVPD IF+K+GM
Sbjct: 1 PFSSSALVTPATAKSSSRRYRAPAVSAVEIGGVAIARDEVVREDDPTNNVPDHIFSKIGM 60
Query: 89 QLHKRNQHPIGILKNAIYEYFDSNYPNKFNKFDDLCPIVSVKQNFDDVLVPADHVSRSYN 148
QLH+R HP+GILKNAIY+YFD NY NKF KFDDL PIVS KQNFDDVLVP DHVSRSYN
Sbjct: 61 QLHRRPDHPLGILKNAIYDYFDENYSNKFKKFDDLSPIVSTKQNFDDVLVPPDHVSRSYN 120
Query: 149 DTYYVDSQTVLRCHTSAHQAELLKE-HNHFLVTGDVYRRDSIDSTHYPVFHQMEGVSIFY 207
DTYYVD+QTVLRCHTSAHQAELL+ H HFLVTGDVYRRDSID+THYPVFHQMEGV +F
Sbjct: 121 DTYYVDAQTVLRCHTSAHQAELLRAGHTHFLVTGDVYRRDSIDATHYPVFHQMEGVRVFS 180
Query: 208 PDEWGAAGLDATEYAAKDLKRCLEGLARHLFGAVEMRWVDTYFPFTNPSYELEIFFKENW 267
P+EW A+GLD T+ AA+DLK+ LEGLARHLFG VEMRWVD YFPFTNPS+ELEIFFK W
Sbjct: 181 PEEWEASGLDGTDLAAEDLKKTLEGLARHLFGDVEMRWVDAYFPFTNPSFELEIFFKGEW 240
Query: 268 LEVLGCGVTEQEILKRSGKLNNVAWAFGLGLERLAMVLFDIPDIRLFWSSDERFTSQFSQ 327
LEVLGCGVTEQEILK +G+ +NVAWAFGLGLERLAMVLFDIPDIRLFWS DERFTSQF +
Sbjct: 241 LEVLGCGVTEQEILKNNGRSDNVAWAFGLGLERLAMVLFDIPDIRLFWSDDERFTSQFKE 300
Query: 328 GQLGIKFKPFSKYPPCYKDMSFWINESFTENNLCEVVRGVAGDLVEEVRLIDNFTN-KKG 386
GQLG+KFKP+SKYPPCYKD+SFWI++ FTENNLCEVVRG+AGDLVEEV+LIDNFTN KKG
Sbjct: 301 GQLGVKFKPYSKYPPCYKDISFWISDEFTENNLCEVVRGIAGDLVEEVKLIDNFTNPKKG 360
Query: 387 MTSHCYRIAYRSMERSLTDEDINELQWNVREQVQSKLNVVLR 428
TSHCYRI YRSMERSLTDE+IN LQ VRE+VQ KL V LR
Sbjct: 361 KTSHCYRIVYRSMERSLTDEEINALQDKVREEVQKKLGVELR 402
>gnl|CDD|129561 TIGR00469, pheS_mito, phenylalanyl-tRNA synthetase, mitochondrial.
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
Score = 374 bits (960), Expect = e-126
Identities = 169/460 (36%), Positives = 245/460 (53%), Gaps = 96/460 (20%)
Query: 51 PPAASALELGGVKMAKDDIVRDDPTNNVPDTIFTKLGMQLHKRNQHPIGILKNAIYEYFD 110
P LE+ G+K A D T NV D I H + HP+GI+++ I + F+
Sbjct: 2 PLKPPHLEINGIKYATDG-----QTTNVTDKIIKLTDANKHLKEDHPLGIIRDLIEKKFN 56
Query: 111 SNYPNK-----FNKFDDLCPIVSVKQNFDDVLVPADHVSRSYNDTYYVDSQTVLRCHTSA 165
N+ F FD+ P+V+ +NFD++ PADH R +D YY++ Q +LR HTSA
Sbjct: 57 GADNNQRGNPLFKIFDNFKPVVTTMENFDNLGFPADHPGRQKSDCYYINEQHLLRAHTSA 116
Query: 166 HQAELLKE--------HNHFLVTGDVYRRDSIDSTHYPVFHQMEGVSIF----------- 206
H+ E + + FL++ DVYRRD ID THYPVFHQ +G +I
Sbjct: 117 HELECFQGGLDDSDNIKSGFLISADVYRRDEIDKTHYPVFHQADGAAIRKRTKADLFEKE 176
Query: 207 ----------------------------YPDEWGAAGLDATEYAAK--------DLKRCL 230
EYA+ +LK +
Sbjct: 177 PGYIEKFEEDIRGTEADLNKENVKIILDDDSIPLKENNPKQEYASDLAVDLCEHELKHSI 236
Query: 231 EGLARHLFG----------------AVEMRWVDTYFPFTNPSYELEIFFKENWLEVLGCG 274
EG+ + LFG +++RW+D YFPFT PS+E+EI+FK+ WLE+ GCG
Sbjct: 237 EGITKDLFGKKISSMIKNKANNTPKELKVRWIDAYFPFTAPSWEIEIWFKDEWLELCGCG 296
Query: 275 VTEQEILKRSG--KLNNVAWAFGLGLERLAMVLFDIPDIRLFWSSDERFTSQFSQGQLGI 332
+ +IL R+G + WAFGLGL+R+AM+LFDIPDIRLFWS+DE F QFS+G L +
Sbjct: 297 IIRHDILLRAGVHPSETIGWAFGLGLDRIAMLLFDIPDIRLFWSNDEGFLRQFSEGDLHL 356
Query: 333 --KFKPFSKYPPCYKDMSFWINE------SFTENNLCEVVRGVAGDLVEEVRLIDNFTN- 383
KFKP S +P C+ D++FW+ E F EN+ +++R +AGDLVE+++L+D F +
Sbjct: 357 IPKFKPISHHPGCFNDLAFWLPEDIEDDAGFHENDFMDIIRNIAGDLVEQIKLVDKFKHP 416
Query: 384 KKGMTSHCYRIAYRSMERSLTDEDINELQWNVREQVQSKL 423
K G S C+RI Y+ M+R+LT+ ++NE+ + + S L
Sbjct: 417 KTGKKSMCFRINYQHMDRNLTNAEVNEIH----DMIASAL 452
>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
alpha chain catalytic core domain. PheRS belongs to
class II aminoacyl-tRNA synthetases (aaRS) based upon
its structure and the presence of three characteristic
sequence motifs. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. While class II aaRSs generally
aminoacylate the 3'-OH ribose of the appropriate tRNA,
PheRS is an exception in that it attaches the amino acid
at the 2'-OH group, like class I aaRSs. PheRS is an
alpha-2/ beta-2 tetramer.
Length = 218
Score = 274 bits (704), Expect = 3e-91
Identities = 88/234 (37%), Positives = 128/234 (54%), Gaps = 25/234 (10%)
Query: 96 HPIGILKNAIYEYFDSNYPNKFNKFDDLCPIVSVKQNFDDVLVPADHVSRSYNDTYYVDS 155
HP+ + I + F S F + + + + NFD + +P DH +R DT+Y++
Sbjct: 1 HPLNKVIEEIEDIFVSM---GFTEVEGP-EVETDFYNFDALNIPQDHPARDMQDTFYIND 56
Query: 156 Q--TVLRCHTSAHQAELLKEHNH---FLVTGDVYRRDSIDSTHYPVFHQMEGVSIFYPDE 210
+LR HTSA QA L + G VYR D ID+TH P FHQ+EG+ +
Sbjct: 57 PARLLLRTHTSAVQARALAKLKPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGL- 115
Query: 211 WGAAGLDATEYAAKDLKRCLEGLARHLFG-AVEMRWVDTYFPFTNPSYELEIFFKE--NW 267
DLK LE A+ LFG ++R+ +YFPFT PS+E++++ W
Sbjct: 116 -----------TFADLKGTLEEFAKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGCLGW 164
Query: 268 LEVLGCGVTEQEILKRSG-KLNNVAWAFGLGLERLAMVLFDIPDIRLFWSSDER 320
LE+LGCG+ E+L+ +G +AFG+GLERLAM+ + IPDIRLF+S+D R
Sbjct: 165 LEILGCGMVRPEVLENAGIDEEYSGFAFGIGLERLAMLKYGIPDIRLFYSNDLR 218
>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 207 bits (528), Expect = 2e-63
Identities = 82/211 (38%), Positives = 118/211 (55%), Gaps = 24/211 (11%)
Query: 126 IVSVKQNFDDVLVPADHVSRSYNDTYYVD---SQTVLRCHTSAHQAELLKEHNH----FL 178
I + NFD + +P DH +R DT+Y+ + +LR HTS QA L E+
Sbjct: 137 IETDFYNFDALNIPQDHPARDMQDTFYLKDDREKLLLRTHTSPVQARTLAENAKIPIKIF 196
Query: 179 VTGDVYRRDSIDSTHYPVFHQMEGVSIFYPDEWGAAGLDATEYAAKDLKRCLEGLARHLF 238
G VYR D++D+TH P FHQ+EG+ + D+ + + DLK LE A+ F
Sbjct: 197 SPGRVYRNDTVDATHSPEFHQIEGLVV---DK------NIS---FADLKGTLEEFAKKFF 244
Query: 239 GA-VEMRWVDTYFPFTNPSYELEIFFKEN--WLEVLGCGVTEQEILKRSGKLNNV--AWA 293
G V++R+ +YFPFT PS E++++ WLE+LGCG+ +L+ G +A
Sbjct: 245 GEDVKVRFRPSYFPFTEPSAEVDVYCPGCGGWLEILGCGMVHPNVLEAVGIDPEEYSGFA 304
Query: 294 FGLGLERLAMVLFDIPDIRLFWSSDERFTSQ 324
FGLGLERLAM+ + IPDIR + +D RF Q
Sbjct: 305 FGLGLERLAMLKYGIPDIRDLYENDLRFLRQ 335
>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Validated.
Length = 339
Score = 181 bits (463), Expect = 1e-53
Identities = 78/212 (36%), Positives = 116/212 (54%), Gaps = 30/212 (14%)
Query: 132 NFDDVLVPADHVSRSYNDTYYVDSQTVLRCHTSAHQAELLKEHN---HFLVTGDVYRRDS 188
NF+ + +P DH +R DT+Y+D +LR HTS Q +++ + G VYR DS
Sbjct: 140 NFEALNIPKDHPARDMQDTFYIDDGLLLRTHTSPVQIRTMEKQKPPIRIIAPGRVYRNDS 199
Query: 189 IDSTHYPVFHQMEGVSIFYPDEWGAAGLDATEYAAKDLKRCLEGLARHLFGA-VEMRWVD 247
D+TH P+FHQ+EG+ + D+ + + DLK LE + FG V++R+
Sbjct: 200 DDATHSPMFHQVEGLVV---DK------NIS---FADLKGTLEDFLKAFFGEDVKIRFRP 247
Query: 248 TYFPFTNPSYELEIFF------------KENWLEVLGCGVTEQEILKRSGKLNNV--AWA 293
+YFPFT PS E+++ WLE+LGCG+ +L+ G +A
Sbjct: 248 SYFPFTEPSAEVDVSCFKCGGKGCRVCKGTGWLEILGCGMVHPNVLRNVGIDPEEYSGFA 307
Query: 294 FGLGLERLAMVLFDIPDIRLFWSSDERFTSQF 325
FG+G+ERLAM+ + I DIRLF+ +D RF QF
Sbjct: 308 FGMGIERLAMLKYGIDDIRLFYENDLRFLKQF 339
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 173 bits (441), Expect = 1e-51
Identities = 79/215 (36%), Positives = 116/215 (53%), Gaps = 27/215 (12%)
Query: 126 IVSVKQNFDDVLVPADHVSRSYNDTYYV-------DSQTVLRCHTSAHQAELLKEHNH-- 176
+ S NFD + +P DH +R DT+Y+ D + +LR HT+ QA L + N
Sbjct: 43 VESDFYNFDALNIPQDHPARDMQDTFYLKKPLKEEDRRLLLRTHTTPVQARTLAKKNKPP 102
Query: 177 --FLVTGDVYRRDSIDSTHYPVFHQMEGVSIFYPDEWGAAGLDATEYAAKDLKRCLEGLA 234
G V+RRD +D+TH P FHQ+EG+ + DE + DLK LE
Sbjct: 103 IKIFSIGRVFRRDQVDATHLPEFHQVEGLVV---DE---------NVSFADLKGVLEEFL 150
Query: 235 RHLFGA-VEMRWVDTYFPFTNPSYELEIFFKEN--WLEVLGCGVTEQEILKRSGKLNNV- 290
R FG V++R+ +YFPFT PS E++++ + W+E+ G G+ +L+ G
Sbjct: 151 RKFFGFEVKVRFRPSYFPFTEPSAEVDVYCCKLGGWIEIGGAGMVHPNVLEAVGIDEEYP 210
Query: 291 AWAFGLGLERLAMVLFDIPDIRLFWSSDERFTSQF 325
+AFGLG+ERLAM+ + I DIR + +D RF QF
Sbjct: 211 GFAFGLGVERLAMLKYGIDDIRDLYENDLRFLRQF 245
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. 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 [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 172 bits (438), Expect = 1e-50
Identities = 74/201 (36%), Positives = 112/201 (55%), Gaps = 19/201 (9%)
Query: 132 NFDDVLVPADHVSRSYNDTYYVDSQTVLRCHTSAHQAELLKEHNH----FLVTGDVYRRD 187
NFD + +P DH +R DT+Y+ + +LR HT+A Q ++E G V+R D
Sbjct: 104 NFDALNIPQDHPARDMQDTFYIKDRLLLRTHTTAVQLRTMEEQEKPPIRIFSPGRVFRND 163
Query: 188 SIDSTHYPVFHQMEGVSIFYPDEWGAAGLDATEYAAKDLKRCLEGLARHLFGAVEMRWVD 247
++D+TH P FHQ+EG+ I + +LK LE + +FG E+R+
Sbjct: 164 TVDATHLPEFHQVEGLVIDK------------NISFTNLKGFLEEFLKKMFGETEIRFRP 211
Query: 248 TYFPFTNPSYELEI--FFKENWLEVLGCGVTEQEILKRSG-KLNNVAWAFGLGLERLAMV 304
+YFPFT PS E+++ + WLEVLG G+ E+L+ G +A+G+G+ERLAM+
Sbjct: 212 SYFPFTEPSAEIDVYCPEGKGWLEVLGAGMFRPEVLEPMGIDPTYPGFAWGIGIERLAML 271
Query: 305 LFDIPDIRLFWSSDERFTSQF 325
+ I DIR + +D RF QF
Sbjct: 272 KYGITDIRDLYENDLRFLRQF 292
>gnl|CDD|214893 smart00896, FDX-ACB, Ferredoxin-fold anticodon binding domain.
This is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold, consisting of an alpha+beta sandwich
with anti-parallel beta-sheets (beta-alpha-beta x2).
Length = 93
Score = 117 bits (296), Expect = 3e-32
Identities = 31/93 (33%), Positives = 53/93 (56%), Gaps = 2/93 (2%)
Query: 338 SKYPPCYKDMSFWINESFTENNLCEVVRGVAGDLVEEVRLIDNFTNK--KGMTSHCYRIA 395
SK+P +D++F ++E L + +R GDL+E+VRL D + +G S YR+
Sbjct: 1 SKFPAVRRDLAFVVDEDVPAAELLDAIREAGGDLLEDVRLFDVYEGGIPEGKKSLAYRLT 60
Query: 396 YRSMERSLTDEDINELQWNVREQVQSKLNVVLR 428
Y+S +R+LTDE++N + + ++ K LR
Sbjct: 61 YQSPDRTLTDEEVNAIHDKIVAALEKKFGAELR 93
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 120 bits (303), Expect = 8e-30
Identities = 70/233 (30%), Positives = 106/233 (45%), Gaps = 62/233 (26%)
Query: 132 NFDDVLVPADHVSRSYNDTYYVDS------------------------------------ 155
NFD + P DH +R DT+Y+
Sbjct: 265 NFDALFQPQDHPAREMQDTFYLKYPGIGDLPEELVERVKEVHEHGGDTGSRGWGYKWDED 324
Query: 156 ---QTVLRCHTSAHQAELLKEHNH-----FLVTGDVYRRDSIDSTHYPVFHQMEGVSIFY 207
+ VLR HT+A A L F + G V+R D+ID+TH P F+Q+EG+ +
Sbjct: 325 IAKRLVLRTHTTALSARYLASRPEPPQKYFSI-GRVFRPDTIDATHLPEFYQLEGIVM-- 381
Query: 208 PDEWGAAGLDATEYAAKDLKRCLEGLARHLFGAVEMRWVDTYFPFTNPSYELEIFF-KEN 266
+ + +DL L+ + L G E+++ YFPFT PS E+E++
Sbjct: 382 ----------GEDVSFRDLLGILKEFYKRL-GFEEVKFRPAYFPFTEPSVEVEVYHEGLG 430
Query: 267 WLEVLGCGVTEQEILKRSG-KLNNVAWAFGLGLERLAMVLFDIPDIRLFWSSD 318
W+E+ G G+ E+L+ G + +AW GLG+ERLAM+ + DIR +SSD
Sbjct: 431 WVELGGAGIFRPEVLEPLGIDVPVLAW--GLGIERLAMLRLGLDDIRDLYSSD 481
>gnl|CDD|202554 pfam03147, FDX-ACB, Ferredoxin-fold anticodon binding domain. This
is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold.
Length = 94
Score = 101 bits (254), Expect = 2e-26
Identities = 30/94 (31%), Positives = 56/94 (59%), Gaps = 3/94 (3%)
Query: 338 SKYPPCYKDMSFWINESFTENNLCEVVRGVAGDLVEEVRLIDNFTNKK---GMTSHCYRI 394
SK+P +D++F ++E ++ +V+R G+L+E+V L D + KK G S +R+
Sbjct: 1 SKFPAVRRDLAFVVDEDVPAADILDVIRKAGGELLEDVELFDVYRGKKIPEGKKSLAFRL 60
Query: 395 AYRSMERSLTDEDINELQWNVREQVQSKLNVVLR 428
++S ER+LTDE++N + + + ++ K LR
Sbjct: 61 TFQSPERTLTDEEVNAIHEKIVKALEKKFGAELR 94
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 98.9 bits (247), Expect = 3e-22
Identities = 28/99 (28%), Positives = 52/99 (52%), Gaps = 2/99 (2%)
Query: 332 IKFKPFSKYPPCYKDMSFWINESFTENNLCEVVRGVAGDLVEEVRLIDNFT--NKKGMTS 389
+KP SK+P +D++ ++E ++ + ++ G L+E V L D + +G S
Sbjct: 552 PAYKPISKFPAVRRDIALVVDEDVPAGDIVKAIKKAGGKLLESVNLFDVYQKGLGEGKKS 611
Query: 390 HCYRIAYRSMERSLTDEDINELQWNVREQVQSKLNVVLR 428
R+ ++ ER+LTDE++N L + E ++ K LR
Sbjct: 612 LAIRLTFQDPERTLTDEEVNALVNKIVEALKEKFGAELR 650
>gnl|CDD|234804 PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 791
Score = 87.1 bits (217), Expect = 3e-18
Identities = 28/100 (28%), Positives = 52/100 (52%), Gaps = 3/100 (3%)
Query: 332 IKFKPFSKYPPCYKDMSFWINESFTENNLCEVVRGVAGDLVEEVRLIDNFTNKK---GMT 388
K+KP SK+P +D++ ++E ++ + ++ G L+E V L D + K G
Sbjct: 691 PKYKPISKFPAVRRDLALVVDEDVPAADILKAIKKAGGKLLESVELFDVYEGKGIGEGKK 750
Query: 389 SHCYRIAYRSMERSLTDEDINELQWNVREQVQSKLNVVLR 428
S +R+ ++ +R+LTDE+IN + ++ K LR
Sbjct: 751 SLAFRLTFQDPDRTLTDEEINAAMDKIVAALEEKFGAELR 790
>gnl|CDD|232990 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit,
non-spirochete bacterial. 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, so This
model was built in fragment mode [Protein synthesis,
tRNA aminoacylation].
Length = 797
Score = 82.0 bits (203), Expect = 1e-16
Identities = 33/100 (33%), Positives = 56/100 (56%), Gaps = 3/100 (3%)
Query: 332 IKFKPFSKYPPCYKDMSFWINESFTENNLCEVVRGVAGDLVEEVRLIDNFTNK---KGMT 388
K++P SK+P +D+SF + + N + ++++ +L+EEV L D + K +G
Sbjct: 698 PKYRPISKFPAVTRDISFLVPKDVPANEIIKLIKKSGLELLEEVELFDVYQGKNIGEGKK 757
Query: 389 SHCYRIAYRSMERSLTDEDINELQWNVREQVQSKLNVVLR 428
S R+ R ER+LTDE+IN++ V ++ KL LR
Sbjct: 758 SLALRLVLRDKERTLTDEEINKIVEKVLNALKEKLGAELR 797
>gnl|CDD|214391 CHL00192, syfB, phenylalanyl-tRNA synthetase beta chain;
Provisional.
Length = 704
Score = 67.4 bits (165), Expect = 5e-12
Identities = 31/100 (31%), Positives = 61/100 (61%), Gaps = 3/100 (3%)
Query: 332 IKFKPFSKYPPCYKDMSFWINESFTENNLCEVVRGVAGDLVEEVRLIDNFTNK---KGMT 388
I ++P+S YP +D+SF I +S + + + E++ +L+E + L D + K G T
Sbjct: 604 ISYQPYSSYPKIIRDLSFIIKKSISISKIKELIYQNGDNLLESITLFDYYKGKSIPNGHT 663
Query: 389 SHCYRIAYRSMERSLTDEDINELQWNVREQVQSKLNVVLR 428
S R+ ++S ++LT+E+I+ +Q N+++ ++ KLN +R
Sbjct: 664 SLGLRLTFQSENKTLTNEEIDRIQQNLQKVLEKKLNAEIR 703
>gnl|CDD|240361 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain;
Provisional.
Length = 494
Score = 61.1 bits (149), Expect = 4e-10
Identities = 54/190 (28%), Positives = 83/190 (43%), Gaps = 57/190 (30%)
Query: 155 SQTVLRCHTSAHQAELLKE-HNHFLVTGD-----------VYRRDSIDSTHYPVFHQMEG 202
+ +LR HT+A A +L + + TG V+R +++D+TH FHQ+EG
Sbjct: 326 RKNILRTHTTAVSARMLYKLAQEYKKTGPFKPKKYFSIDRVFRNETLDATHLAEFHQVEG 385
Query: 203 VSIFYPDEWGAAGLDATEYAAKDLKRCLEGLARHLFGAVE----------MRWVDTYFPF 252
I D ++L L L G + +R+ + P+
Sbjct: 386 FVI-----------D------RNL-----TLG-DLIGTIREFFRRIGITKLRFKPAFNPY 422
Query: 253 TNPSYELEIF-FKE---NWLEVLGCGVTEQEILKRSGKLNNV---AWAFGLGLERLAMVL 305
T PS +EIF + W+EV G+ E+L+ G +V AW GL LER M+
Sbjct: 423 TEPS--MEIFGYHPGLKKWVEVGNSGIFRPEMLRPMGFPEDVTVIAW--GLSLERPTMIK 478
Query: 306 FDIPDIR-LF 314
+ I +IR LF
Sbjct: 479 YGIKNIRDLF 488
>gnl|CDD|215458 PLN02853, PLN02853, Probable phenylalanyl-tRNA synthetase alpha
chain.
Length = 492
Score = 59.7 bits (145), Expect = 1e-09
Identities = 57/176 (32%), Positives = 82/176 (46%), Gaps = 40/176 (22%)
Query: 158 VLRCHTSAHQAELLKEHNHFLVTGD-----------VYRRDSIDSTHYPVFHQMEGVSIF 206
+LR HT+A + +L + L V+R +++D TH FHQ+EG+
Sbjct: 319 LLRTHTTAVSSRML----YKLAQKGFKPKRYFSIDRVFRNEAVDRTHLAEFHQVEGLVCD 374
Query: 207 YPDEWGAAGLDATEYAAKDLKRCLEGLARHLFGAVEMRWVDTYFPFTNPSYELEIF-FKE 265
GL DL LE L G ++R+ Y P+T PS +EIF + E
Sbjct: 375 R-------GL-----TLGDLIGVLEDFFSRL-GMTKLRFKPAYNPYTEPS--MEIFSYHE 419
Query: 266 ---NWLEVLGCGVTEQEILKRSG---KLNNVAWAFGLGLERLAMVLFDIPDIR-LF 314
W+EV G+ E+L G +N +AW GL LER M+L+ I +IR LF
Sbjct: 420 GLKKWVEVGNSGMFRPEMLLPMGLPEDVNVIAW--GLSLERPTMILYGIDNIRDLF 473
>gnl|CDD|238391 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl
synthetase-like catalytic core domain. Class II amino
acyl-tRNA synthetases (aaRS) share a common fold and
generally attach an amino acid to the 3' OH of ribose of
the appropriate tRNA. PheRS is an exception in that it
attaches the amino acid at the 2'-OH group, like class I
aaRSs. These enzymes are usually homodimers. This domain
is primarily responsible for ATP-dependent formation of
the enzyme bound aminoacyl-adenylate. The substrate
specificity of this reaction is further determined by
additional domains. Intererestingly, this domain is also
found is asparagine synthase A (AsnA), in the accessory
subunit of mitochondrial polymerase gamma and in the
bacterial ATP phosphoribosyltransferase regulatory
subunit HisZ.
Length = 211
Score = 44.8 bits (106), Expect = 2e-05
Identities = 36/172 (20%), Positives = 52/172 (30%), Gaps = 30/172 (17%)
Query: 152 YVDSQTVLRCHTSAHQAELLKEH-----NHFLVTGDVYR--RDSIDSTHYPVFHQMEGVS 204
+ LR L H G +R F Q+EG
Sbjct: 48 ENEEDLYLRPTLEPGLVRLFVSHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEV 107
Query: 205 IFYPDEWGAAGLDATEYAAKDLKRCLEGLARHLFGAVEMRWV-DTYFPFTN----PSYEL 259
E ++L E L R L +++ +V T F+ P +E+
Sbjct: 108 FGEDGE--------EASEFEELIELTEELLRALGIKLDIVFVEKTPGEFSPGGAGPGFEI 159
Query: 260 EIFFKEN-WLEVLGCGVTEQEI-----LKRSGKLNNV----AWAFGLGLERL 301
E+ E LE+ G + E L + FGLGLERL
Sbjct: 160 EVDHPEGRGLEIGSGGYRQDEQARAADLYFLDEALEYRYPPTIGFGLGLERL 211
>gnl|CDD|224935 COG2024, COG2024, Phenylalanyl-tRNA synthetase alpha subunit
(archaeal type) [Translation, ribosomal structure and
biogenesis].
Length = 536
Score = 36.3 bits (84), Expect = 0.029
Identities = 46/215 (21%), Positives = 74/215 (34%), Gaps = 36/215 (16%)
Query: 121 DDLCPIVSVKQNFDDVLVPA--DHVSRSYNDTYYVDSQTVLRCH-------TSAHQAELL 171
DDL ++ DD + V + D S LR H T + +
Sbjct: 145 DDLVHEIAEALEVDDGTGLRVLEEVFPEFKDLKPESSTLTLRSHMTSGWFITLSEILKRE 204
Query: 172 KEHNHFLVTGDVYRRDSI-DSTHYPVFHQMEGVSIFYPDEWGAAGLDATEYAAKDLKRCL 230
+RR+ D++H +H V + DE + D K
Sbjct: 205 DPPLKLFSIDRCFRREQREDASHLMTYHSASCVVV---DE---------DVTVDDGKAVA 252
Query: 231 EGLARHL-FGAVEMRWVDTYFPFTNPSYELEIF------------FKENWLEVLGCGVTE 277
EGL R F R + + P + E++ + + W+E+ G+
Sbjct: 253 EGLLRQFGFEKFRFRPDEKKSKYYVPGTQTEVYAYHPKLVGSIEKYSDGWIEIATFGLYS 312
Query: 278 QEILKRSGKLNNVAWAFGLGLERLAMVLFDIPDIR 312
L G ++ GLG+ERLAM+L D+R
Sbjct: 313 PIALAEYG-IDYPVMNLGLGVERLAMILHGADDVR 346
>gnl|CDD|235754 PRK06253, PRK06253, O-phosphoseryl-tRNA synthetase; Reviewed.
Length = 529
Score = 35.3 bits (82), Expect = 0.054
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 295 GLGLERLAMVLFDIPDIR 312
GLG+ERLAM+L+ D+R
Sbjct: 322 GLGVERLAMILYGAEDVR 339
>gnl|CDD|129562 TIGR00470, sepS, O-phosphoserine--tRNA ligase. 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 [Amino acid
biosynthesis, Serine family, Protein synthesis, tRNA
aminoacylation].
Length = 533
Score = 33.7 bits (77), Expect = 0.22
Identities = 48/208 (23%), Positives = 75/208 (36%), Gaps = 30/208 (14%)
Query: 121 DDLCPIVSVKQNFDDV--LVPADHVSRSYNDTYYVDSQTVLRCH-------TSAHQAELL 171
DDL ++ N + L + V + D + LR H T + +
Sbjct: 145 DDLVFEIAKALNVSNEMGLKVLETVFPEFKDLKPESTTLTLRSHMTSGWFITLSSIIDKR 204
Query: 172 KEHNHFLVTGDVYRRDSI-DSTHYPVFHQMEGVSIFYPDEWGAAGLDATEYAAKDLKRCL 230
K +RR+ D +H +H V + DE E + D K
Sbjct: 205 KLPLKLFSIDRCFRREQREDRSHLMTYHSASCVVV---DE---------EVSVDDGKAVA 252
Query: 231 EGLARHL-FGAVEMRWVDTYFPFTNPSYELEIF-----FKENWLEVLGCGVTEQEILKRS 284
EGL F R + + P + E++ E W+EV GV L +
Sbjct: 253 EGLLAQFGFTKFRFRPDEKKSKYYIPETQTEVYAYHPKLGE-WIEVATFGVYSPIALAKY 311
Query: 285 GKLNNVAWAFGLGLERLAMVLFDIPDIR 312
++ GLG+ERLAM+L+ D+R
Sbjct: 312 N-IDVPVMNLGLGVERLAMILYGYEDVR 338
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 33.2 bits (77), Expect = 0.24
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 294 FGLGLERLAMVLFDIPDIR---LF 314
FGLGLERL M L + +IR LF
Sbjct: 405 FGLGLERLTMKLLGLENIREAVLF 428
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 32.2 bits (74), Expect = 0.60
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 294 FGLGLERLAMVLFDIPDIR 312
FGLGLERL M + + +IR
Sbjct: 403 FGLGLERLVMYILGLDNIR 421
>gnl|CDD|238399 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II
core domain. Assignment to class II aminoacyl-tRNA
synthetases (aaRS) based upon its structure and the
presence of three characteristic sequence motifs in the
core domain. This family includes AsnRS as well as a
subgroup of AspRS. AsnRS and AspRS are homodimers,
which attach either asparagine or aspartate to the 3'OH
group of ribose of the appropriate tRNA. While archaea
lack asnRS, they possess a non-discriminating aspRS,
which can mischarge Asp-tRNA with Asn. Subsequently, a
tRNA-dependent aspartate amidotransferase converts the
bound aspartate to asparagine. The catalytic core domain
is primarily responsible for the ATP-dependent formation
of the enzyme bound aminoacyl-adenylate.
Length = 322
Score = 31.4 bits (72), Expect = 0.85
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 294 FGLGLERLAMVLFDIPDIR 312
FGLGLERL M L + +IR
Sbjct: 294 FGLGLERLVMWLLGLDNIR 312
>gnl|CDD|237194 PRK12765, PRK12765, flagellar capping protein; Provisional.
Length = 595
Score = 31.0 bits (70), Expect = 1.2
Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 15/89 (16%)
Query: 73 DPTNNVPDTIFTKLGMQLHKRNQHPIGILKNAIYEYFDSNYPNKFNKFDDLCPIV----- 127
D + P G++ + I +NA + Y N DDL V
Sbjct: 225 DTSTIDPGKDKKGYGIKDASLH---IQTAQNAEFTYNGIKITRSSNTIDDLGVGVTLTLN 281
Query: 128 -------SVKQNFDDVLVPADHVSRSYND 149
++Q+ + V + + +YN+
Sbjct: 282 KTGSINFDIQQDTEGVTKAVEDLVDAYNN 310
>gnl|CDD|219956 pfam08658, Rad54_N, Rad54 N terminal. This is the N terminal of
the DNA repair protein Rad54.
Length = 191
Score = 30.4 bits (69), Expect = 1.4
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 21 TNSLKRFA--FRVPFSSTSTSTSPLPLKKK 48
T+SL R F+VP S+T T S P +K+
Sbjct: 8 TDSLDRLTKPFKVPGSATPTRESDRPARKR 37
>gnl|CDD|181036 PRK07568, PRK07568, aspartate aminotransferase; Provisional.
Length = 397
Score = 30.6 bits (70), Expect = 1.7
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 168 AELLKEHNHFLVTGDVYRRDSIDSTHYPVFHQMEGVS 204
AE+ K+H+ FL++ +VYR D Y +EG+
Sbjct: 188 AEIAKKHDLFLISDEVYREFVYDGLKYTSALSLEGLE 224
>gnl|CDD|238398 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core
domain. Class II LysRS is a dimer which attaches a
lysine to the 3' OH group of ribose of the appropriate
tRNA. Its assignment to class II aaRS is based upon its
structure and the presence of three characteristic
sequence motifs in the core domain. It is found in
eukaryotes as well as some prokaryotes and archaea.
However, LysRS belongs to class I aaRS's in some
prokaryotes and archaea. The catalytic core domain is
primarily responsible for the ATP-dependent formation of
the enzyme bound aminoacyl-adenylate.
Length = 329
Score = 30.2 bits (69), Expect = 2.0
Identities = 23/78 (29%), Positives = 31/78 (39%), Gaps = 16/78 (20%)
Query: 181 GDVYRRDSIDSTHYPVFHQMEGVSIFY---PDEWGAAGLDATEYAAKDLKRCLEGLARHL 237
G +R + ID TH P F +E FY D L TE DL GL + +
Sbjct: 83 GRNFRNEGIDLTHNPEFTMIE----FYEAYADYNDMMDL--TE----DL---FSGLVKKI 129
Query: 238 FGAVEMRWVDTYFPFTNP 255
G ++ + FT P
Sbjct: 130 NGKTKIEYGGKELDFTPP 147
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 29.9 bits (68), Expect = 2.4
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 294 FGLGLERLAMVLFDIPDIR 312
GLGL+RL M+L + IR
Sbjct: 317 IGLGLDRLVMLLTGLESIR 335
>gnl|CDD|173847 cd01158, SCAD_SBCAD, Short chain acyl-CoA dehydrogenases and
eukaryotic short/branched chain acyl-CoA dehydrogenases.
Short chain acyl-CoA dehydrogenase (SCAD). SCAD is a
mitochondrial beta-oxidation enzyme. It catalyzes the
alpha,beta dehydrogenation of the corresponding
trans-enoyl-CoA by FAD, which becomes reduced. The
reduced form of SCAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. This subgroup also contains the eukaryotic
short/branched chain acyl-CoA dehydrogenase(SBCAD), the
bacterial butyryl-CoA dehydorgenase(BCAD) and
2-methylbutyryl-CoA dehydrogenase, which is involved in
isoleucine catabolism. These enzymes are homotetramers.
Length = 373
Score = 29.5 bits (67), Expect = 3.5
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 205 IFYPDEWGAAGLDATEYAAKDLKRCLEGLARH 236
I P+E+G AGLD YA +E LA+
Sbjct: 47 IPIPEEYGGAGLDFLAYA-----IAIEELAKV 73
>gnl|CDD|193573 cd09849, M20_Acy1L2_like_2, M20 Peptidase Aminoacylase 1-like
protein 2, amidohydrolase family. Peptidase M20 family,
Aminoacylase 1-like protein 2 (ACY1L2;
amidohydrolase)-like subfamily. This group contains many
uncharacterized proteins predicted as amidohydrolases,
including gene products of abgA and abgB that catalyze
the cleavage of p-aminobenzoyl-glutamate, a folate
catabolite in Escherichia coli , to p-aminobenzoate and
glutamate. p-Aminobenzoyl-glutamate utilization is
catalyzed by the abg region gene product, AbgT.
Aminoacylase 1 (ACY1) proteins are a class of zinc
binding homodimeric enzymes involved in hydrolysis of
N-acetylated proteins. N-terminal acetylation of
proteins is a widespread and highly conserved process
that is involved in the protection and stability of
proteins. Several types of aminoacylases can be
distinguished on the basis of substrate specificity.
ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino
acids (except L-aspartate), especially
N-acetyl-methionine and acetyl-glutamate into L-amino
acids and an acyl group. However, ACY1 can also catalyze
the reverse reaction, the synthesis of acetylated amino
acids. ACY1 may also play a role in xenobiotic
bioactivation as well as the inter-organ processing of
amino acid-conjugated xenobiotic derivatives
(S-substituted-N-acetyl-L-cysteine).
Length = 388
Score = 28.7 bits (65), Expect = 6.0
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 213 AAGLDATEYAAKDLKRCLEGLARHLFGAVEMRWVDTYFPFTNPSYELEIFFKENWLEVLG 272
AA +DA + A K + R L+ A L G VE++ Y P Y L +EN ++ G
Sbjct: 264 AATIDAIKDANKKVDRALKAGAYALGGKVEIKTQPGYLPLLQDRY-LNNLVRENADDLGG 322
Query: 273 CGVTEQ 278
G Q
Sbjct: 323 IGRIIQ 328
>gnl|CDD|169215 PRK08091, PRK08091, ribulose-phosphate 3-epimerase; Validated.
Length = 228
Score = 28.3 bits (63), Expect = 6.4
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 18/69 (26%)
Query: 300 RLAMVLFDIPDIRLFWSSDERFTSQFSQGQLGIKFKPFSKYPPCYKDMSFWINESFTENN 359
+L ++ FDI +D +F+ F+ G + IK P C+KD+ + + F
Sbjct: 38 QLRLLHFDI--------ADGQFSPFFTVGAIAIKQFP----THCFKDVHLMVRDQF---- 81
Query: 360 LCEVVRGVA 368
EV +
Sbjct: 82 --EVAKACV 88
>gnl|CDD|177383 PHA02548, 24, capsid vertex protein; Provisional.
Length = 412
Score = 28.2 bits (63), Expect = 8.5
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 13/56 (23%)
Query: 91 HKRNQHPI--GILKNAIYEYFDSNYPNKFNKFDDLCPIVSVKQNFDDVLVPADHVS 144
K P+ G L+N + Y D+N P FD + IV K + ++ +HV
Sbjct: 286 EKDEDDPLAYGYLRNGLPVYADTNSP-----FDYV--IVGCKHDIGEM----EHVG 330
>gnl|CDD|235654 PRK05957, PRK05957, aspartate aminotransferase; Provisional.
Length = 389
Score = 28.1 bits (63), Expect = 8.9
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 386 GMTSHCY-RIAYRSMERSLTDEDINELQWNVREQVQS 421
GM + CY RIAY +++++ E I L ++ VQ
Sbjct: 353 GMKNGCYLRIAYGALQKATAKEGIERLVQGLKTIVQQ 389
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.136 0.420
Gapped
Lambda K H
0.267 0.0879 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,160,170
Number of extensions: 2163945
Number of successful extensions: 1742
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1690
Number of HSP's successfully gapped: 50
Length of query: 428
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 328
Effective length of database: 6,502,202
Effective search space: 2132722256
Effective search space used: 2132722256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (26.6 bits)