RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17941
(679 letters)
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 882 bits (2281), Expect = 0.0
Identities = 353/681 (51%), Positives = 446/681 (65%), Gaps = 18/681 (2%)
Query: 9 ELAPLRAAVKEQGDIVRALKAEGAPELDVKKAVAELKLRKKVLDERELKLAPFVSSFD-- 66
LA +AAV QG+ VRALKA A + ++ A+ +LK K E +L V +
Sbjct: 8 ALAEKQAAVTAQGNAVRALKASKADKAEIDAAIEKLKALKLEKSALEKELQAAVGAGGDG 67
Query: 67 -------RAKMEDLLKRRFFYDQSFSIYGGISGQYDFGPMGCALKTNMLSAWRQFFVLEE 119
R + + L+RR FY SF IYGG++G YD+GP GCA+K+N+L+ WRQ FVLEE
Sbjct: 68 AASKEAFRQAVVNTLERRLFYIPSFKIYGGVAGLYDYGPPGCAVKSNVLAFWRQHFVLEE 127
Query: 120 QMLEVDCSILTLEPVLKASGHVDRFADLMVKDLKTGECFRLDHLIKAHL-EKLAAEPKTP 178
MLEV+C +T E VLKASGHVD+F DLMVKD KTG CFR DHL+K EKL +
Sbjct: 128 NMLEVECPCVTPEVVLKASGHVDKFTDLMVKDEKTGTCFRADHLLKDFCEEKLEKDLTIS 187
Query: 179 QSVKEECADIVIKLDGMSKNEMDDVLKKYNIKSPLTKNDLSEPMEFNLMFATQIGPSGLI 238
E D++ LD +S E+ +K+Y IK+P TKN LS+P FNLMF T IGPSGL
Sbjct: 188 AEKAAELKDVLAVLDDLSAEELGAKIKEYGIKAPDTKNPLSDPYPFNLMFQTSIGPSGLS 247
Query: 239 KGYLRPETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIE 298
GY+RPETAQGIFVNF+ L +N G+LPFAAAQIG AFRNEISPR GL+RVREFT+AEIE
Sbjct: 248 VGYMRPETAQGIFVNFRDLYYYNGGKLPFAAAQIGQAFRNEISPRQGLLRVREFTLAEIE 307
Query: 299 HFCDPTDKSHAKFSDVETTQMMVLYSACNQMDGKPAERITIGEAVRSNLVANETLGYFMA 358
HF DP DKSH KFS+V + +L+ Q+ G+ A+ + +GEAV +V NETLGYF+
Sbjct: 308 HFVDPEDKSHPKFSEVADLE-FLLFPREEQLGGQKAKPMRLGEAVSKGIVNNETLGYFIG 366
Query: 359 RIQKFMISVGIDPEKLRFRQHMGNEMAHYACDCWDAECLTSYGWVECVGCADRSAYDLTQ 418
R F+ +GID E+LRFRQH+ NEMAHYA DCWDAE SYGW+ECVG ADRSAYDL
Sbjct: 367 RTYLFLTKLGIDKERLRFRQHLANEMAHYAADCWDAEIECSYGWIECVGIADRSAYDLKA 426
Query: 419 HFKATGVRLSAEKHLPEPQTREIVEPVLNKGIIGKEFKKDAKTICDALAALDLNSVSAVE 478
H + V L A + EP+ E++ V NK +G FK D K + +AL A++ ++
Sbjct: 427 HSDKSKVPLVAHEKFAEPREVEVLVIVPNKKELGLAFKGDQKVVVEALEAMNEKEAMEMK 486
Query: 479 ESLNTNGKYELLVDD--KEFVLTKDMISIKKSTKTFHVEEIIPSVIEPSFGIGRIMYALF 536
L + G+ E V KE + K+M+SI K K H PSVIEPSFGIGRI+Y LF
Sbjct: 487 AKLESKGEAEFYVCTLGKEVEIKKNMVSISKEKKKEHQRVFTPSVIEPSFGIGRIIYCLF 546
Query: 537 EHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDD 596
EH+F R GDEQ PPLVAP+K ++ PL N + K++S EL+ GIS K+D
Sbjct: 547 EHSFYTRPGDEQLNVFRFPPLVAPIKCTVFPLVQNQQLNAVAKVISKELTAAGISHKIDI 606
Query: 597 SGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIKDLS 656
+G SIGKRYARTDE+ +PF +T+D D SVT+RERDS QVRV V EVASV+KDL+
Sbjct: 607 TGTSIGKRYARTDELGVPFAVTVDSDG-----SVTIRERDSKDQVRVPVEEVASVVKDLT 661
Query: 657 LAKITWEDVQSKYPKFEAQEG 677
++TWEDV +KYP +
Sbjct: 662 DGRMTWEDVTAKYPAHSSAAD 682
>gnl|CDD|223500 COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 558
Score = 701 bits (1812), Expect = 0.0
Identities = 269/602 (44%), Positives = 366/602 (60%), Gaps = 48/602 (7%)
Query: 64 SFDRAKMEDLLKRRFFYDQSFSIYGGISGQYDFGPMGCALKTNMLSAWRQFFVLE-EQML 122
+FD K+ +L KRR F S IYGG++G YD+GP+G LK N+ AWR+ FV E E ++
Sbjct: 3 AFDMEKIVELAKRRGFVFPSSEIYGGLAGFYDYGPLGVELKNNIKEAWRKSFVTEREDVV 62
Query: 123 EVDCSILTLEPVLKASGHVDRFADLMVKDLKTGECFRLDHLIKAHLEKLAAEPKTPQSVK 182
E+D I+ E V KASGHVD+F+D +V+ K GE +R DHLI+ +L K
Sbjct: 63 EIDTPIILPEEVWKASGHVDKFSDPLVECKKCGERYRADHLIEEYLGKDGH--------- 113
Query: 183 EECADIVIKLDGMSKNEMDDVLKKYNIKSPLTKNDLSEPMEFNLMFATQIGPSGLIKGYL 242
MS E+ +++++Y+I+ P +L+E EFNLMF T IGP GYL
Sbjct: 114 ----------GNMSPEELTEIIREYDIRCPECGGELNEVREFNLMFKTTIGPVEDSLGYL 163
Query: 243 RPETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIEHFCD 302
RPETAQGIFVNFK LLEF +LPF AQIG +FRNEISPR+GL R REF AEIE F D
Sbjct: 164 RPETAQGIFVNFKNLLEFARNKLPFGIAQIGKSFRNEISPRNGLFRTREFEQAEIEFFVD 223
Query: 303 PTDKSHAKFSDVETTQMMVLYSACNQMDGKPAERITIGEAVRSNLVANETLGYFMARIQK 362
P +K H KF++V+ + L Q +G T EAV +V NETL YF+AR +
Sbjct: 224 PEEKEHPKFNEVKDE-KLPLLPREAQEEG------TEEEAVEEGIVENETLAYFIARTKF 276
Query: 363 FMISVGIDPEKLRFRQHMGNEMAHYACDCWDAECLTS-YGWVECVGCADRSAYDLTQHFK 421
F+ +GIDPEKLRFRQH+ E+AHY+ D WDAE GW+E VG ADR+ YDL++H K
Sbjct: 277 FLEDLGIDPEKLRFRQHLPEELAHYSKDTWDAEYKFPFGGWIELVGIADRTDYDLSRHSK 336
Query: 422 ATGVRLSAEKHLPEPQTREIVEPVLNKGIIGKEFKKDAKTICDALAALDLNSVSAVEESL 481
+G L+ + EP+ E ++ +G EFKKDAK + +AL+ L+
Sbjct: 337 FSGEDLTVFREYDEPKEVERWHSKVDLKFLGPEFKKDAKKVAEALSELE----------- 385
Query: 482 NTNGKYELLVDDKEFVLTKDMISIKKSTKTFHVEEIIPSVIEPSFGIGRIMYALFEHNFK 541
EL + + ++KD++ I++ K E+ IP VIEPSFGI RI YAL EH +
Sbjct: 386 ------ELEKELNGYEVSKDLVIIEEVEKV-TGEKYIPHVIEPSFGIDRIFYALLEHAYT 438
Query: 542 MRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSI 601
+ +E+R L LPP +AP+K ++LPL E K + +L + G + DDS GSI
Sbjct: 439 EEEVEEKRIVLRLPPDLAPIKVAVLPLVKKDELVEIAKEIFEKLRELGFNVDYDDS-GSI 497
Query: 602 GKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIKDLSLAKIT 661
G+RY R DEI PF +T+DF+TL++ ++VT+RERDSM QVRVK+ E+A +++L
Sbjct: 498 GRRYRRQDEIGTPFCVTVDFETLED-NTVTIRERDSMEQVRVKIEELADYLRELIKGGFE 556
Query: 662 WE 663
W
Sbjct: 557 WA 558
>gnl|CDD|232951 TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, dimeric type.
This model describes a glycyl-tRNA synthetase distinct
from the two alpha and two beta chains of the tetrameric
E. coli glycyl-tRNA synthetase. This enzyme is a
homodimeric class II tRNA synthetase and is recognized
by pfam model tRNA-synt_2b, which recognizes His, Ser,
Pro, and this set of glycyl-tRNA synthetases [Protein
synthesis, tRNA aminoacylation].
Length = 551
Score = 660 bits (1704), Expect = 0.0
Identities = 292/593 (49%), Positives = 374/593 (63%), Gaps = 45/593 (7%)
Query: 65 FDRAKMEDLLKRRFFYDQSFSIYGGISGQYDFGPMGCALKTNMLSAWRQFFVLEEQMLEV 124
+ + LLKRR F QSF IYGG++G +D+GP+G LK N+ +AWR+FF+ E++LE+
Sbjct: 1 VNMEVIMSLLKRRGFVFQSFEIYGGLAGFWDYGPLGAVLKNNIKNAWRKFFIKNERVLEI 60
Query: 125 DCSILTLEPVLKASGHVDRFADLMVKDLKTGECFRLDHLIKAHLEKLAAEPKTPQSVKEE 184
D I+T E VLKASGHVD F D MV E FR DHLI+ L K
Sbjct: 61 DTPIITPEEVLKASGHVDNFTDWMVDCKSCKERFRADHLIEEKLGK-------------- 106
Query: 185 CADIVIKLDGMSKNEMDDVLKKYNIKSPLTKND-LSEPMEFNLMFATQIGPSGLIKGYLR 243
+L G S E+++V++KY+I P + L+E FNLMF T+IG G KGYLR
Sbjct: 107 ------RLWGFSGPELNEVMEKYDINCPNCGGENLTEVRSFNLMFQTEIGVVGKRKGYLR 160
Query: 244 PETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIEHFCDP 303
PETAQGIF+NFKRLL+F +LPF AQIG +FRNEISPR+GL RVREF AEIE F P
Sbjct: 161 PETAQGIFINFKRLLQFFRRKLPFGVAQIGKSFRNEISPRNGLFRVREFEQAEIEFFVHP 220
Query: 304 TDKSHAKFSDVETTQMMVLYSACNQMDGKPAERITIGEAVRSNLVANETLGYFMARIQKF 363
DKSH KF +V+ + +L + + IGEAV S ++ NETLGYF+AR+++F
Sbjct: 221 LDKSHPKFEEVKQDILPLL--------PRQMQESGIGEAVESGMIENETLGYFIARVKQF 272
Query: 364 MISVGIDPEKLRFRQHMGNEMAHYACDCWDAECLTSYGWVECVGCADRSAYDLTQHFKAT 423
++ +GI+P+KLRFRQH NEMAHYA DCWD E LT YGW+ECVG ADR YDLTQH K +
Sbjct: 273 LLEIGINPDKLRFRQHDKNEMAHYAKDCWDFEFLTPYGWIECVGIADRGDYDLTQHSKFS 332
Query: 424 GVRLSAEKHLPEPQTREIVEPVLNKGIIGKEFKKDAKTICDALAALDLNSVSAVEESLNT 483
G LS L EP+ E NK G +F+KDAK I L+ DL
Sbjct: 333 GKSLSVFDKLDEPREVTKWEIEPNKKKFGPKFRKDAKKIESNLSEDDLEER--------- 383
Query: 484 NGKYELLVDDKEFVLTKDMISIKKSTKTFHVEEIIPSVIEPSFGIGRIMYALFEHNFKMR 543
E +D E L KD++ I+ T+ H E+ IP VIEPSFGI RI+YAL EH+++
Sbjct: 384 ----EEELDKNEVELDKDLVEIEMVTEVVHGEKYIPHVIEPSFGIDRIIYALLEHSYQEE 439
Query: 544 DGD-EQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSIG 602
D E+R L LPP +AP+K ++LPL + E + K + L + GI K DDS G+IG
Sbjct: 440 VLDGEEREVLRLPPHLAPIKVAVLPLVNKEELKEIAKEIFQALRKTGIRIKYDDS-GTIG 498
Query: 603 KRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIKDL 655
KRY R DEI PF +TIDF+TL++ +VT+RERDSM QVRVK+ E+ S IK L
Sbjct: 499 KRYRRADEIGTPFCVTIDFETLED-ETVTIRERDSMKQVRVKIKELPSYIKKL 550
>gnl|CDD|235240 PRK04173, PRK04173, glycyl-tRNA synthetase; Provisional.
Length = 456
Score = 374 bits (963), Expect = e-123
Identities = 130/366 (35%), Positives = 184/366 (50%), Gaps = 70/366 (19%)
Query: 69 KMEDLLKRRFFYDQSFSIYGGISGQYDFGPMGCALKTNMLSAWRQFFVLEEQ-MLEVDCS 127
K+ L KRR F S IYGG++G +D+GP+G LK N+ AW + FV E + ++ +D
Sbjct: 6 KIVSLAKRRGFVFPSSEIYGGLAGFWDYGPLGVELKNNIKRAWWKSFVQEREDVVGIDSP 65
Query: 128 ILTLEPVLKASGHVDRFADLMVKDLKTGECFRLDHLIKAHLEKLAAEPKTPQSVKEECAD 187
I+ V +ASGHVD F+D +V+ K + +R DHLI+
Sbjct: 66 IIMPPEVWEASGHVDNFSDPLVECKKCKKRYRADHLIEELGIDAEGL------------- 112
Query: 188 IVIKLDGMSKNEMDDVLKKYNIKSPLTKN-DLSEPMEFNLMFATQIGP--SGLIKGYLRP 244
S E+ +++++ +IK P + +E +FNLMF T IGP GYLRP
Sbjct: 113 --------SNEELKELIRENDIKCPECGGENWTEVRQFNLMFKTFIGPVEDSKSLGYLRP 164
Query: 245 ETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIEHFCDPT 304
ETAQGIFVNFK +L +LPF AQIG +FRNEI+PR+ + R REF E+E F P
Sbjct: 165 ETAQGIFVNFKNVLRTARKKLPFGIAQIGKSFRNEITPRNFIFRTREFEQMELEFFVKPG 224
Query: 305 DKSHAKFSDVETTQMMVLYSACNQMDGKPAERITIGEAVRSNLVANETLGYFMARIQKFM 364
NE Y++ + ++
Sbjct: 225 TD-------------------------------------------NEWFAYWIELRKNWL 241
Query: 365 ISVGIDPEKLRFRQHMGNEMAHYACDCWDAECLTSYG--WVECVGCADRSAYDLTQHFKA 422
+ +GIDPE LRFR+H+ E+AHY+ WD E +G W E G A+R+ YDL++H K
Sbjct: 242 LDLGIDPENLRFREHLPEELAHYSKATWDIEYKFPFGRFWGELEGIANRTDYDLSRHSKH 301
Query: 423 TGVRLS 428
+G LS
Sbjct: 302 SGEDLS 307
Score = 176 bits (448), Expect = 2e-48
Identities = 64/144 (44%), Positives = 93/144 (64%), Gaps = 7/144 (4%)
Query: 515 EEIIPSVIEPSFGIGRIMYALFEHNFKMRD--GDEQRTYLALPPLVAPLKASILPLSSNP 572
E+ IP VIEPS G+ R++ A E + + G ++RT L LPP +AP+K ++LPL
Sbjct: 316 EKYIPYVIEPSAGLDRLLLAFLEDAYTEEELGGGDKRTVLRLPPALAPVKVAVLPLVKKE 375
Query: 573 EFQPFIKMLSSELSQNGISFKVD-DSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVT 631
+ + + +EL ++ F VD D GSIGKRY R DEI PF IT+DFDTL E ++VT
Sbjct: 376 KLSEKAREIYAELRKD---FNVDYDDSGSIGKRYRRQDEIGTPFCITVDFDTL-EDNTVT 431
Query: 632 LRERDSMTQVRVKVNEVASVIKDL 655
+R+RD+M QVRVK++E+ + +
Sbjct: 432 IRDRDTMEQVRVKIDELKDYLAEK 455
>gnl|CDD|238397 cd00774, GlyRS-like_core, Glycyl-tRNA synthetase (GlyRS)-like class
II core catalytic domain. GlyRS functions as a homodimer
in eukaryotes, archaea and some bacteria and as a
heterotetramer in the remainder of prokaryotes. It is
responsible for the attachment of glycine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP binding and hydrolysis.
This alignment contains only sequences from the GlyRS
form which homodimerizes. The heterotetramer glyQ is in
a different family of class II aaRS. Class II assignment
is based upon its structure and the presence of three
characteristic sequence motifs. This domain is also
found at the N-terminus of the accessory subunit of
mitochondrial polymerase gamma (Pol gamma b). Pol gamma
b stimulates processive DNA synthesis and is functional
as a homodimer, which can associate with the catalytic
subunit Pol gamma alpha to form a heterotrimer. Despite
significant both structural and sequence similarity with
GlyRS, Pol gamma b lacks conservation of several class
II functional residues.
Length = 254
Score = 292 bits (749), Expect = 2e-94
Identities = 107/194 (55%), Positives = 116/194 (59%), Gaps = 6/194 (3%)
Query: 226 LMFATQIGP--SGLIKGYLRPETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPR 283
LMF T IGP SG GYLRPETAQGIFVNFK LLEFN +LPF AQIG +FRNEISPR
Sbjct: 65 LMFKTSIGPVESGGNLGYLRPETAQGIFVNFKNLLEFNRRKLPFGVAQIGKSFRNEISPR 124
Query: 284 SGLIRVREFTMAEIEHFCDPTDKSHAKFSDVETTQMMVLYSACNQMDGKPAERITIGEAV 343
+GL RVREFT AEIE F DP +KSH F Q + Q R+T E
Sbjct: 125 NGLFRVREFTQAEIEFFVDP-EKSHPWFDYWA-DQRLKWLPKFAQ--SPENLRLTDHEKE 180
Query: 344 RSNLVANETLGYFMARIQKFMISVGIDPEKLRFRQHMGNEMAHYACDCWDAECLTSYGWV 403
ANETL YF A F+ GI RF QH NE AHYA DCWDAE L GW+
Sbjct: 181 ELAHYANETLDYFYAFPHGFLELEGIANRGDRFLQHHPNESAHYASDCWDAEKLYVPGWI 240
Query: 404 ECVGCADRSAYDLT 417
E G ADR+ YDL
Sbjct: 241 EVSGGADRTDYDLL 254
Score = 108 bits (273), Expect = 1e-26
Identities = 38/75 (50%), Positives = 51/75 (68%), Gaps = 2/75 (2%)
Query: 70 MEDLLKRRFFYDQSFSIYGGISGQYDFGPMGCALKTNMLSAWRQFFVLEE-QMLEVDCSI 128
+ +L KRR F S IYGG++G YD+GP+G LK N+ SAWR+ FVLEE MLE+D I
Sbjct: 1 LVELAKRRGFVFPSSEIYGGVAGFYDYGPLGVELKNNIKSAWRKSFVLEEEDMLEIDSPI 60
Query: 129 LTLEPVLK-ASGHVD 142
+T E + K + G V+
Sbjct: 61 ITPELMFKTSIGPVE 75
>gnl|CDD|237851 PRK14894, PRK14894, glycyl-tRNA synthetase; Provisional.
Length = 539
Score = 208 bits (531), Expect = 2e-59
Identities = 191/629 (30%), Positives = 275/629 (43%), Gaps = 144/629 (22%)
Query: 73 LLKRRFFYDQSFSIYGGISGQYDFGPMGCALKTNMLSAWRQFFVLEEQMLE-VDCSILTL 131
L KRR F S IYGG+ G YD+GP+G LK N+++ W + V E +E +D +IL
Sbjct: 12 LAKRRGFIFPSSEIYGGLQGVYDYGPLGVELKNNIIADWWRTNVYERDDMEGLDAAILMN 71
Query: 132 EPVLKASGHVDRFADLMVKDLKTGECFRLDHLIKAHLEKLAAEPKTPQSVKEECADIVIK 191
V K SGH + F D +V +R DH+ Q V C
Sbjct: 72 RLVWKYSGHEETFNDPLVDCRDCKMRWRADHI---------------QGVCPNCG----- 111
Query: 192 LDGMSKNEMDDVLKKYNIKSPLTKNDLSEPMEFNLMFATQIGPSGLIK--GYLRPETAQG 249
DL+EP FN+MF TQIGP YLRPETAQG
Sbjct: 112 -----------------------SRDLTEPRPFNMMFRTQIGPVADSDSFAYLRPETAQG 148
Query: 250 IFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIEHFCDP--TDKS 307
IFVNF +L ++ +LPF AQ+G AFRNEI+PR+ L RVREF EIE+F P ++
Sbjct: 149 IFVNFANVLATSARKLPFGIAQVGKAFRNEINPRNFLFRVREFEQMEIEYFVMPGTDEEW 208
Query: 308 HAKFSDVETTQMMVLYSACNQMDGKPAERITIGEAVRSNLVANETLGYFMARIQKFMISV 367
H ++ + + L E +G +RI + +
Sbjct: 209 HQRW-------------------------------LEARLAWWEQIGIPRSRITIYDVPP 237
Query: 368 GIDPEKLRFRQHMGNEMAHYACDCWDAECLTSY---GWVECVGCADRSAYDLTQHFK-AT 423
+E+AHY+ +D + Y G E G A+R+ YDL H K
Sbjct: 238 --------------DELAHYSKRTFD--LMYDYPNIGVQEIEGIANRTDYDLGSHSKDQE 281
Query: 424 GVRLSAEKHLPEPQT-----------REIVEPVLNKGI-IGKEF-----KKDAKTICDAL 466
+ L+A + E T R +V V+ +G+ + A+ + A+
Sbjct: 282 QLNLTARVNPNEDSTARLTYFDQASGRHVVPYVIEPSAGVGRCMLAVMCEGYAEELTKAI 341
Query: 467 AALDLNSVS-AVEESLNTNGKYELLVDDKEFVLTKDMISIKKSTKTFHVEEIIPSV--IE 523
L +V A+E L + G+ E L + +D I + + E +P V +
Sbjct: 342 PGEKLAAVGDALEAFLKSVGRSEKLAGE-----ARDAILARGEALLQALPERLPEVEQLL 396
Query: 524 PSFGIGRIMYALFEHNFKMRDGDEQ-------RTYLALPPLVAPLKASILPLSSNPE-FQ 575
G +I E K+R G Q RT L L P +AP+K ++ PL N E
Sbjct: 397 AMPGADQI-----ELGKKLR-GQAQPLIDEHYRTVLRLKPRLAPIKVAVFPLKRNHEGLV 450
Query: 576 PFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPH------S 629
K + +L G V D G+IGK Y R DEI PF IT+DFDT+ + +
Sbjct: 451 ATAKAVRRQLQVGGRMRTVYDDTGAIGKLYRRQDEIGTPFCITVDFDTIGQGKDPALAGT 510
Query: 630 VTLRERDSMTQVRVKVNEVASVIKDLSLA 658
VT+R+RD+M Q RV ++E+ + ++D A
Sbjct: 511 VTVRDRDTMAQERVPISELEAYLRDRVSA 539
>gnl|CDD|238435 cd00858, GlyRS_anticodon, GlyRS Glycyl-anticodon binding domain.
GlyRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 121
Score = 190 bits (485), Expect = 1e-57
Identities = 66/122 (54%), Positives = 86/122 (70%), Gaps = 2/122 (1%)
Query: 535 LFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKV 594
L EH+F++R+GDE R L LPP +AP+K ++LPL E K +S EL + G S K
Sbjct: 1 LLEHSFRVREGDEGRIVLRLPPALAPIKVAVLPLVKRDELVEIAKEISEELRELGFSVKY 60
Query: 595 DDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIKD 654
DDS GSIG+RYAR DEI PF +T+DFDTL E +VT+RERDSM QVRVK+ E+ S +++
Sbjct: 61 DDS-GSIGRRYARQDEIGTPFCVTVDFDTL-EDGTVTIRERDSMRQVRVKIEELPSYLRE 118
Query: 655 LS 656
L
Sbjct: 119 LI 120
>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G,
H, P, S and T). Other tRNA synthetase sub-families are
too dissimilar to be included. This domain is the core
catalytic domain of tRNA synthetases and includes
glycyl, histidyl, prolyl, seryl and threonyl tRNA
synthetases.
Length = 171
Score = 104 bits (261), Expect = 7e-26
Identities = 36/155 (23%), Positives = 47/155 (30%), Gaps = 47/155 (30%)
Query: 241 YLRPETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIEHF 300
YLRP GI FK + LP QIG FR E PR GL RVREFT + E F
Sbjct: 58 YLRPTAEVGITRLFKNEILSYR-ELPLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIF 116
Query: 301 CDPTDKSHAKFSDVETTQMMVLYSACNQMDGKPAERITIGEAVRSNLVANETLGYFMARI 360
P + E L +
Sbjct: 117 GTPEQ-------------------------------------------SEEELEELLKLA 133
Query: 361 QKFMISVGIDPEKLRFRQHMGNEMAHYACDCWDAE 395
++ + +G+ R ++ A D E
Sbjct: 134 EEILQDLGLP---YRVVLATTGDLGGSASKEGDLE 165
Score = 40.7 bits (96), Expect = 7e-04
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 103 LKTNMLSAWRQFFVLEEQMLEVDCSILTLEPVLKASGHVDRFAD-LMVKDLKTGE 156
L+ + + R+ EVD IL + + + SGH D + + M K G
Sbjct: 1 LRNALENFIRELLK-RYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGG 54
>gnl|CDD|202547 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain
is found in histidyl, glycyl, threonyl and prolyl tRNA
synthetases it is probably the anticodon binding domain.
Length = 93
Score = 93.8 bits (234), Expect = 3e-23
Identities = 28/94 (29%), Positives = 53/94 (56%), Gaps = 1/94 (1%)
Query: 562 KASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDF 621
+ ++PL E + + + L+ EL + GI ++DD S+GK++ D I IPF + +
Sbjct: 1 QVVVIPLGEKDELEDYAQKLAEELREAGIRVELDDRNESLGKKFRDADLIGIPFRLVVGE 60
Query: 622 DTLKEPHSVTLRERDSMTQVRVKVNEVASVIKDL 655
L+ +VT+R+RD+ + V + E+ +K+L
Sbjct: 61 KELEN-GTVTVRDRDTGEKETVSLEELVEKLKEL 93
>gnl|CDD|238472 cd00935, GlyRS_RNA, GlyRS_RNA binding domain. This short
RNA-binding domain is found at the N-terminus of GlyRS
in several higher eukaryote aminoacyl-tRNA synthetases
(aaRSs). This domain consists of a helix-turn-helix
structure , which is similar to other RNA-binding
proteins. It is involved in both protein-RNA
interactions by binding tRNA and protein-protein
interactions, which are important for the formation of
aaRSs into multienzyme complexes.
Length = 51
Score = 83.7 bits (207), Expect = 4e-20
Identities = 38/51 (74%), Positives = 46/51 (90%)
Query: 10 LAPLRAAVKEQGDIVRALKAEGAPELDVKKAVAELKLRKKVLDERELKLAP 60
LAPLRAAVKEQGD+VR LK EGAP++D+KKAVAELK RKK+L+++EL L P
Sbjct: 1 LAPLRAAVKEQGDLVRKLKEEGAPDVDIKKAVAELKARKKLLEDKELALQP 51
>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA
synthetase class II core domain. This domain is the core
catalytic domain of tRNA synthetases of the subgroup
containing glycyl, histidyl, prolyl, seryl and threonyl
tRNA synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. These enzymes belong to class II
aminoacyl-tRNA synthetases (aaRS) based upon their
structure and the presence of three characteristic
sequence motifs in the core domain. This domain is also
found at the C-terminus of eukaryotic GCN2 protein
kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ and
the accessory subunit of mitochondrial polymerase gamma
(Pol gamma b) . Most class II tRNA synthetases are
dimers, with this subgroup consisting of mostly
homodimers. These enzymes attach a specific amino acid
to the 3' OH group of ribose of the appropriate tRNA.
Length = 235
Score = 63.2 bits (154), Expect = 4e-11
Identities = 28/65 (43%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 241 YLRPETAQGIFVNF-KRLLEFNSGR-LPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIE 298
LRP + I+ F +L S R LP QIG FR+E S R GL+RVREF E
Sbjct: 64 VLRPAACEPIYQIFSGEIL---SYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYV 120
Query: 299 HFCDP 303
F +P
Sbjct: 121 VFGEP 125
Score = 29.7 bits (67), Expect = 4.8
Identities = 10/49 (20%), Positives = 15/49 (30%), Gaps = 1/49 (2%)
Query: 100 GCALKTNMLSAWRQFFVLEEQMLEVDCSILTLEPVLKASGHVDRFADLM 148
G AL + E E+ L + GH+D + M
Sbjct: 1 GTALWRALERFLDDRMA-EYGYQEILFPFLAPTVLFFKGGHLDGYRKEM 48
>gnl|CDD|238379 cd00738, HGTP_anticodon, HGTP anticodon binding domain, as found at
the C-terminus of histidyl, glycyl, threonyl and prolyl
tRNA synthetases, which are classified as a group of
class II aminoacyl-tRNA synthetases (aaRS). In aaRSs,
the anticodon binding domain is responsible for
specificity in tRNA-binding, so that the activated amino
acid is transferred to a ribose 3' OH group of the
appropriate tRNA only. This domain is also found in the
accessory subunit of mitochondrial polymerase gamma (Pol
gamma b).
Length = 94
Score = 57.8 bits (140), Expect = 1e-10
Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 2/90 (2%)
Query: 560 PLKASILPLS-SNPEFQPFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGIT 618
P+ +I+PL+ E + + + L + L NGI DD IGK++ D +PF +
Sbjct: 1 PIDVAIVPLTDPRVEAREYAQKLLNALLANGIRVLYDDRERKIGKKFREADLRGVPFAVV 60
Query: 619 IDFDTLKEPHSVTLRERDSMTQVRVKVNEV 648
+ D L E VT++ RD+ + V+E+
Sbjct: 61 VGEDEL-ENGKVTVKSRDTGESETLHVDEL 89
>gnl|CDD|238605 cd01200, WHEPGMRS_RNA, EPRS-like_RNA binding domain. This short
RNA-binding domain is found in several higher eukaryote
aminoacyl-tRNA synthetases (aaRSs). It is found in
three copies in the mammalian bifunctional EPRS in a
region that separates the N-terminal GluRS from the
C-terminal ProRS. In the Drosophila EPRS, this domain
is repeated six times. It is found at the N-terminus of
TrpRS, HisRS and GlyR and at the C-terminus of MetRS.
This domain consists of a helix- turn- helix structure,
which is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 42
Score = 54.5 bits (132), Expect = 6e-10
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 14 RAAVKEQGDIVRALKAEGAPELDVKKAVAELKLRKKVLDERE 55
+ EQGD+VR LKAE AP+ ++ AV +L K E
Sbjct: 1 YEKIAEQGDLVRKLKAEKAPKEEIDAAVKKLLALKAQYKEAT 42
>gnl|CDD|215929 pfam00458, WHEP-TRS, WHEP-TRS domain.
Length = 56
Score = 55.0 bits (133), Expect = 6e-10
Identities = 19/43 (44%), Positives = 25/43 (58%)
Query: 13 LRAAVKEQGDIVRALKAEGAPELDVKKAVAELKLRKKVLDERE 55
L + QGD+VR LKA+ AP+ DV AV +L KK E+
Sbjct: 1 LYEKIAAQGDLVRKLKAKKAPKEDVDAAVKKLLALKKQYKEKT 43
>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 = 56.7 bits (137), Expect = 4e-09
Identities = 28/63 (44%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 241 YLRPETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAEIEHF 300
YLRP G+ F + +LP A+IG AFRNE R GL RVREFT E E F
Sbjct: 54 YLRPTLEPGLVRLFVSHIR----KLPLRLAEIGPAFRNEGGRR-GLRRVREFTQLEGEVF 108
Query: 301 CDP 303
+
Sbjct: 109 GED 111
Score = 30.2 bits (68), Expect = 3.2
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 103 LKTNMLSAWRQFFVLEEQMLEVDCSILTLEPVLKASGH 140
+++ + R+F E EV+ I+ EP+L+ +GH
Sbjct: 1 IRSKIEQKLRRFMA-ELGFQEVETPIVEREPLLEKAGH 37
>gnl|CDD|214960 smart00991, WHEP-TRS, A conserved domain of 46 amino acids,
called WHEP-TRS has been shown.to exist in a number of
higher eukaryote aminoacyl-transfer RNA synthetases.
This domain is present one to six times in the several
enzymes. There are three copies in mammalian
multifunctional aminoacyl-tRNA synthetase in a region
that separates the N-terminal glutamyl-tRNA synthetase
domain from the C-terminal prolyl-tRNA synthetase
domain, and six copies in the intercatalytic region of
the Drosophila enzyme. The domain is found at the
N-terminal extremity of the mammalian tryptophanyl-
tRNA synthetase and histidyl-tRNA synthetase, and the
mammalian, insect, nematode and plant glycyl- tRNA
synthetases. This domain could contain a central
alpha-helical region and may play a role in the
association of tRNA-synthetases into multienzyme
complexes.
Length = 56
Score = 50.4 bits (121), Expect = 2e-08
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 14 RAAVKEQGDIVRALKAEGAPELDVKKAVAELKLRKKVLDE-RELKLAPFVSSFDRA 68
AV QG++VR LKAE A + ++ AVA+L K L E P D
Sbjct: 1 EEAVAAQGELVRKLKAEKASKDEIDAAVAKLLALKAQLKEATGQDYKPGAPPGDTP 56
>gnl|CDD|235190 PRK03991, PRK03991, threonyl-tRNA synthetase; Validated.
Length = 613
Score = 48.3 bits (116), Expect = 1e-05
Identities = 33/131 (25%), Positives = 62/131 (47%), Gaps = 6/131 (4%)
Query: 524 PSFGIGRIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSS 583
P+ I R++YAL E K + + LP ++P + ++P+S + + ++
Sbjct: 466 PTGSIERVIYALLEKAAKEEEEGKVP---MLPTWLSPTQVRVIPVSE--RHLDYAEEVAD 520
Query: 584 ELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRV 643
+L GI VDD S+GK+ + IP+ + I D E +T+ R+ +V +
Sbjct: 521 KLEAAGIRVDVDDRDESLGKKIRDAGKEWIPYVVVIG-DKEMESGKLTVTIREESEKVEM 579
Query: 644 KVNEVASVIKD 654
+ E+ IK+
Sbjct: 580 TLEELIERIKE 590
>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase. This model represents
the threonyl-tRNA synthetase found in most organisms.
This protein is a class II tRNA synthetase, and is
recognized by the pfam model tRNA-synt_2b. Note that B.
subtilis has closely related isozymes thrS and thrZ. The
N-terminal regions are quite dissimilar between archaeal
and eubacterial forms, while some eukaryotic forms are
missing sequence there altogether. [Protein synthesis,
tRNA aminoacylation].
Length = 563
Score = 48.1 bits (115), Expect = 1e-05
Identities = 31/143 (21%), Positives = 59/143 (41%), Gaps = 20/143 (13%)
Query: 515 EEIIPSVIE--PSFGIGRIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNP 572
EE P +I I R + L E P +AP++ ++P++
Sbjct: 434 EEKRPVMIHRAILGSIERFIAILLEK-----------YAGNFPLWLAPVQVVVIPVNE-- 480
Query: 573 EFQPFIKMLSSELSQNGISFKVDDSGGSIGK--RYARTDEIAIPFGITIDFDTLKEPHSV 630
+ K ++ +L + GI VDD +GK R A+ + IP+ + + D E +V
Sbjct: 481 RHLDYAKKVAQKLKKAGIRVDVDDRNERLGKKIREAQKQK--IPYMLVVG-DKEMESLAV 537
Query: 631 TLRERDSMTQVRVKVNEVASVIK 653
+R R ++ ++E ++
Sbjct: 538 NVRTRKGQKLEKMSLDEFLEKLR 560
Score = 34.6 bits (80), Expect = 0.17
Identities = 24/63 (38%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 241 YLRPETAQGIFVNFKRLLEFNSGR-LPFAAAQIGNAFRNEISPR-SGLIRVREFTMAEIE 298
L+P G F+ FK S R LP A++G + R E S GL+RVR FT +
Sbjct: 258 MLKPMNCPGHFLIFKS--SLRSYRDLPLRIAELGYSHRYEQSGELHGLMRVRGFTQDDAH 315
Query: 299 HFC 301
FC
Sbjct: 316 IFC 318
>gnl|CDD|238402 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II
core catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain. This
subfamily contains the core domain of ProRS from
prokaryotes and from the mitochondria of eukaryotes.
Length = 255
Score = 46.8 bits (112), Expect = 1e-05
Identities = 17/30 (56%), Positives = 19/30 (63%)
Query: 265 LPFAAAQIGNAFRNEISPRSGLIRVREFTM 294
LP QI FR+EI PR GL+R REF M
Sbjct: 112 LPLNLYQIQTKFRDEIRPRFGLMRGREFLM 141
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 47.7 bits (113), Expect = 2e-05
Identities = 37/104 (35%), Positives = 54/104 (51%), Gaps = 8/104 (7%)
Query: 4 PKVEAELAPLRAAVKEQGDIVRALKAEGAPELDVKKAVAELKLRKKVLD--ERELKLAPF 61
P EA++ R VKE+G++V LKA A + ++ AVAELK+ K+ L E KL P
Sbjct: 231 PPTEADVEAARLIVKERGEVVAQLKAAKASKEEITAAVAELKIAKESLAHIEERSKLKPG 290
Query: 62 VSSFDRAKMEDLLKRRFFYDQSFSIYGGISGQYDFGPMGCALKT 105
+ D K++ + FF Q+F +SGQ CAL +
Sbjct: 291 LPKKD-GKID--YSKDFFGRQAFLT---VSGQLQVETYACALSS 328
>gnl|CDD|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 47.5 bits (114), Expect = 2e-05
Identities = 25/103 (24%), Positives = 50/103 (48%), Gaps = 5/103 (4%)
Query: 553 ALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIA 612
A P +AP++ I+P+ + + ++ +L GI +VD S + K+ R +
Sbjct: 469 AFPFWLAPVQVVIIPV--ADAHNEYAEEVAKKLRAAGIRVEVDTSNERLNKK-IRNAQKQ 525
Query: 613 -IPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIKD 654
IP+ + + D E +V++R RD + ++E +IK+
Sbjct: 526 KIPY-MLVVGDKEVEAGTVSVRTRDGEQLNGMPLDEFIELIKE 567
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 46.5 bits (111), Expect = 4e-05
Identities = 33/128 (25%), Positives = 58/128 (45%), Gaps = 18/128 (14%)
Query: 530 RIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNG 589
R + L EH + ALP +AP++ ++P++ E + K ++ +L + G
Sbjct: 468 RFIGILLEH-YAG----------ALPTWLAPVQVRVIPVAD--EHLDYAKEVAEKLRKAG 514
Query: 590 ISFKVDDSGGSIGK--RYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNE 647
I +DD +GK R A T + IP+ I + D E +V +R R Q + + E
Sbjct: 515 IRVDIDDRNEKLGKKIREAGTQK--IPYVIVVG-DKEVETGTVVVRRRGGKQQKSMTLEE 571
Query: 648 VASVIKDL 655
+ +K
Sbjct: 572 LVEELKKE 579
>gnl|CDD|236405 PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional.
Length = 565
Score = 45.8 bits (110), Expect = 6e-05
Identities = 15/24 (62%), Positives = 17/24 (70%)
Query: 271 QIGNAFRNEISPRSGLIRVREFTM 294
QI FR+EI PR GL+R REF M
Sbjct: 134 QIQTKFRDEIRPRFGLMRGREFIM 157
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 44.9 bits (107), Expect = 1e-04
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 242 LRPETAQGIFVNFKRLLEFNSGR-LPFAAAQIGNAFRNEISPRSGLIRVREFTMAE 296
LRP T++ + + R S + LP QI + FR+E PR GL+R REF M +
Sbjct: 106 LRP-TSEEVITDMFRK-WIRSYKDLPLKLYQIQSKFRDEKRPRFGLLRGREFLMKD 159
>gnl|CDD|236327 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional.
Length = 477
Score = 44.7 bits (107), Expect = 1e-04
Identities = 41/150 (27%), Positives = 75/150 (50%), Gaps = 20/150 (13%)
Query: 525 SFGIG-RIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQP----FIK 579
S+G+ R++ AL M GD++ L LPP +AP++ I+P+ E + + K
Sbjct: 258 SWGVSTRLIGALI-----MTHGDDKG--LVLPPKIAPIQVVIVPIFKKEEKKEEVLEYAK 310
Query: 580 MLSSELSQNGISFKVDD-SGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSM 638
L+ EL + GI K+DD S + G ++ + +P I I L+ ++V L RD++
Sbjct: 311 ELAEELKKAGIRVKLDDRSDKTPGWKFNEWELKGVPLRIEIGPRDLEN-NTVVLVRRDTL 369
Query: 639 TQVRVKVNEVASVIKDLSLAKITWEDVQSK 668
+ V ++E+ + +L E++Q
Sbjct: 370 EKETVPLDELVEKVPEL------LEEIQEN 393
>gnl|CDD|238437 cd00860, ThrRS_anticodon, ThrRS Threonyl-anticodon binding domain.
ThrRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 91
Score = 39.4 bits (93), Expect = 4e-04
Identities = 23/95 (24%), Positives = 47/95 (49%), Gaps = 5/95 (5%)
Query: 560 PLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIA-IPFGIT 618
P++ ++P+ E + K ++ +LS GI +VD +GK+ R ++ IP+ +
Sbjct: 1 PVQVVVIPV--TDEHLDYAKEVAKKLSDAGIRVEVDLRNEKLGKK-IREAQLQKIPYILV 57
Query: 619 IDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIK 653
+ D E +V++R RD + ++E +K
Sbjct: 58 VG-DKEVETGTVSVRTRDGGDLGSMSLDEFIEKLK 91
>gnl|CDD|232961 TIGR00408, proS_fam_I, prolyl-tRNA synthetase, family I.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent families. This family includes the archaeal
enzyme, the Pro-specific domain of a human
multifunctional tRNA ligase, and the enzyme from the
spirochete Borrelia burgdorferi. The other family
includes enzymes from Escherichia coli, Bacillus
subtilis, Synechocystis PCC6803, and one of the two
prolyL-tRNA synthetases of Saccharomyces cerevisiae
[Protein synthesis, tRNA aminoacylation].
Length = 472
Score = 43.2 bits (102), Expect = 4e-04
Identities = 36/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 525 SFGIG-RIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPL----SSNPEFQPFIK 579
S+GI R++ AL DE+ L LPP VAP++ I+P+ N + +
Sbjct: 253 SYGISTRVIGALI-----AIHSDEKG--LVLPPRVAPIQVVIIPIIFKKKENEKVMEAAR 305
Query: 580 MLSSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMT 639
+ S L + G +DD G+++ + + IP I + + E + + RD+
Sbjct: 306 EVRSRLKKAGFRVHIDDRDNRPGRKFYQWEIKGIPLRIEVGPND-IEKNIAVISRRDTGE 364
Query: 640 QVRVKVNEVASVIKDL------SLAKITWEDVQSK 668
+ +V ++++ + +L +L WE + K
Sbjct: 365 KYQVSLDQLEERVVELLNNIQENLRNRAWERFEQK 399
Score = 37.4 bits (87), Expect = 0.027
Identities = 24/87 (27%), Positives = 31/87 (35%), Gaps = 9/87 (10%)
Query: 230 TQIGPSGL-IKGYLRPETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIR 288
T G S L LRP T++ + + LP Q N FR E +R
Sbjct: 89 THGGLSKLDEPLALRP-TSETAMYPMFKKWVKSYTDLPLKINQWVNVFRYETKHTRPFLR 147
Query: 289 VREFTMAEIEHFCDPTDKSHAKFSDVE 315
REFT E +HA + E
Sbjct: 148 TREFTWQE-------AHTAHATAEEAE 167
>gnl|CDD|237059 PRK12325, PRK12325, prolyl-tRNA synthetase; Provisional.
Length = 439
Score = 42.2 bits (100), Expect = 7e-04
Identities = 34/132 (25%), Positives = 59/132 (44%), Gaps = 11/132 (8%)
Query: 525 SFGIG--RIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPL-SSNPEFQPFIKML 581
S+GIG R++ A+ E + D++ + P VAP K I+ L + + L
Sbjct: 315 SYGIGVSRLVAAIIEASH-----DDKG--IIWPESVAPFKVGIINLKQGDEACDAACEKL 367
Query: 582 SSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQV 641
+ LS GI DD+ G ++A D I +P+ I + L E V L++R + +
Sbjct: 368 YAALSAAGIDVLYDDTDERPGAKFATMDLIGLPWQIIVGPKGLAE-GKVELKDRKTGERE 426
Query: 642 RVKVNEVASVIK 653
+ V + +
Sbjct: 427 ELSVEAAINRLT 438
Score = 36.4 bits (85), Expect = 0.043
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 265 LPFAAAQIGNAFRNEISPRSGLIRVREFTM 294
LP I FR+EI PR G++R REF M
Sbjct: 128 LPLNLYHIQWKFRDEIRPRFGVMRGREFLM 157
>gnl|CDD|238473 cd00936, WEPRS_RNA, WEPRS_RNA binding domain. This short
RNA-binding domain is found in several higher eukaryote
aminoacyl-tRNA synthetases (aaRSs). It is found in
multiple copies in eukaryotic bifunctional
glutamyl-prolyl-tRNA synthetases (EPRS) in a region
that separates the N-terminal glutamyl-tRNA synthetase
(GluRS) from the C-terminal prolyl-tRNA synthetase
(ProRS). It is also found at the N-terminus of
vertebrate tryptophanyl-tRNA synthetases (TrpRS). This
domain consists of a helix-turn-helix structure, which
is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 50
Score = 36.8 bits (86), Expect = 0.001
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 17 VKEQGDIVRALKAEGAPELDVKKAVAEL 44
+ QGD+VR LKA+ AP+ ++ AV +L
Sbjct: 5 IAAQGDLVRELKAKKAPKEEIDAAVKKL 32
>gnl|CDD|232962 TIGR00409, proS_fam_II, prolyl-tRNA synthetase, family II.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent groups. This group includes enzymes from
Escherichia coli, Bacillus subtilis, Aquifex aeolicus,
the spirochete Treponema pallidum, Synechocystis
PCC6803, and one of the two prolyL-tRNA synthetases of
Saccharomyces cerevisiae. The other group includes the
Pro-specific domain of a human multifunctional tRNA
ligase and the prolyl-tRNA synthetases from the Archaea,
the Mycoplasmas, and the spirochete Borrelia burgdorferi
[Protein synthesis, tRNA aminoacylation].
Length = 568
Score = 40.2 bits (94), Expect = 0.003
Identities = 17/31 (54%), Positives = 20/31 (64%)
Query: 264 RLPFAAAQIGNAFRNEISPRSGLIRVREFTM 294
+LP QI FR+EI PR GL+R REF M
Sbjct: 127 QLPLNLYQIQTKFRDEIRPRFGLMRGREFIM 157
Score = 35.2 bits (81), Expect = 0.11
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 555 PPLVAPLKASILPLSSNPEFQ-PFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIAI 613
P +AP I+ ++ E Q + L SEL G+ +DD G ++A ++ I I
Sbjct: 468 PKAIAPYDVVIVVMNMKDEEQQQLAEELYSELLAQGVDVLLDDRNERAGVKFADSELIGI 527
Query: 614 PFGITIDFDTLKE 626
P + + L
Sbjct: 528 PLRVVVGKKNLDN 540
>gnl|CDD|239106 cd02426, Pol_gamma_b_Cterm, C-terminal domain of mitochondrial DNA
polymerase gamma B subunit, which is required for
processivity. Polymerase gamma replicates and repairs
mitochondrial DNA. The c-terminal domain of its B
subunit is strikingly similar to the anticodon-binding
domain of glycyl tRNA synthetase.
Length = 128
Score = 37.0 bits (86), Expect = 0.006
Identities = 28/99 (28%), Positives = 44/99 (44%), Gaps = 5/99 (5%)
Query: 543 RDGDEQRTYLALPPLVAPLKASILPLSSNP-EFQPFIKMLSSELSQNGISFKVDDS---G 598
R QR L L P +AP K +I + E + + L +EL + G+S
Sbjct: 10 RKKGRQRQVLKLHPCLAPYKVAIDCGKGDTAELRDLCQGLKNELREAGLSVWPGYLETQH 69
Query: 599 GSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDS 637
S+ + + DE+ + F + I TL E + LR RD+
Sbjct: 70 SSLEQLLDKYDEMGVLFTLLISEQTL-ENGLLQLRSRDT 107
>gnl|CDD|238395 cd00772, ProRS_core, Prolyl-tRNA synthetase (ProRS) class II core
catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 264
Score = 38.5 bits (89), Expect = 0.007
Identities = 18/32 (56%), Positives = 21/32 (65%)
Query: 265 LPFAAAQIGNAFRNEISPRSGLIRVREFTMAE 296
LP QIGN FR+EI PR G +R REF M +
Sbjct: 118 LPQHLNQIGNKFRDEIRPRFGFLRAREFIMKD 149
>gnl|CDD|184902 PRK14938, PRK14938, Ser-tRNA(Thr) hydrolase; Provisional.
Length = 387
Score = 39.1 bits (91), Expect = 0.007
Identities = 30/100 (30%), Positives = 48/100 (48%), Gaps = 3/100 (3%)
Query: 554 LPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIAI 613
LP + P++ ILP+ +F F ++ L + GI VDD S+G + R I
Sbjct: 268 LPDWLNPIQVRILPVKK--DFLDFSIQVAERLRKEGIRVNVDDLDDSLGNKIRRAGTEWI 325
Query: 614 PFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIK 653
PF I I +K ++T++ R + Q + V E+ IK
Sbjct: 326 PFVIIIGEREVKT-STLTVKIRANNEQKSMTVEELVKEIK 364
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 38.6 bits (91), Expect = 0.010
Identities = 26/131 (19%), Positives = 54/131 (41%), Gaps = 21/131 (16%)
Query: 525 SFGIGRIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSE 584
+ G+ R++ L E P+ ++PL + E L+ +
Sbjct: 301 AIGVERLLLLLEELG------------------EEPVDVYVVPLGEDAELAALK--LAEK 340
Query: 585 LSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVK 644
L GI ++D G + K++ D+ F + + D L +VT+++ + Q V
Sbjct: 341 LRAAGIRVELDYGGRKLKKQFKYADKSGARFVLILGEDELAN-GTVTVKDLRTGEQQTVP 399
Query: 645 VNEVASVIKDL 655
++E+ +K+L
Sbjct: 400 LDELVEALKEL 410
>gnl|CDD|184826 PRK14799, thrS, threonyl-tRNA synthetase; Provisional.
Length = 545
Score = 38.7 bits (90), Expect = 0.011
Identities = 26/120 (21%), Positives = 55/120 (45%), Gaps = 14/120 (11%)
Query: 528 IGRIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQ 587
I R + L EH FK + LP ++ ++ +LP++ E + + + +++ +
Sbjct: 417 IDRFVAILLEH-FKGK----------LPTWLSSVQVRVLPITD--EVNEYAEKVLNDMRK 463
Query: 588 NGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNE 647
I ++D +G ++ KR + +P+ I I +VT+R R ++ VK +
Sbjct: 464 RRIRAEIDYAGETLSKRIKNAYDQGVPY-ILIVGKKEASEGTVTVRARGNIEVRNVKFEK 522
>gnl|CDD|234752 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 38.1 bits (90), Expect = 0.013
Identities = 23/104 (22%), Positives = 49/104 (47%), Gaps = 7/104 (6%)
Query: 553 ALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSIGK--RYARTDE 610
A P +AP++ +LP++ + + K ++ +L GI +VD IG R A+ +
Sbjct: 532 AFPTWLAPVQVVVLPITD--KHADYAKEVAKKLKAAGIRVEVDLRNEKIGYKIREAQLQK 589
Query: 611 IAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIKD 654
+P+ + + D E +V++R R + ++E + +
Sbjct: 590 --VPYMLVVG-DKEVEAGTVSVRRRGGKDLGTMSLDEFIERLLE 630
Score = 30.0 bits (69), Expect = 4.7
Identities = 21/52 (40%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 260 FNSG----R-LPFAAAQIGNAFRNEIS-PRSGLIRVREFTM--AEIEHFCDP 303
+ G R LP A+ G R E S GL+RVR FT A I FC P
Sbjct: 341 YKQGLRSYRDLPLRLAEFGTVHRYEPSGALHGLMRVRGFTQDDAHI--FCTP 390
>gnl|CDD|238436 cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain.
HisRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 91
Score = 34.4 bits (80), Expect = 0.028
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 580 MLSSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMT 639
L+ +L GI ++D G + K++ D F + + D L VT+++ ++
Sbjct: 19 ELAEQLRDAGIKAEIDYGGRKLKKQFKYADRSGARFAVILGEDELAA-GVVTVKDLETGE 77
Query: 640 QVRVKVNEVASVIK 653
Q V ++E+ +K
Sbjct: 78 QETVALDELVEELK 91
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 37.1 bits (87), Expect = 0.028
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 16/109 (14%)
Query: 525 SFGIGRIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSE 584
+ GI R++ L E LPP + ++PL E + L+ +
Sbjct: 300 AIGIERLLLLLEELGL-------------LPPEESSPDVYVVPLGEEAELEALK--LAQK 344
Query: 585 LSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLR 633
L + GI +VD G + K+ D++ F + I D L +VTL+
Sbjct: 345 LRKAGIRVEVDLGGRKLKKQLKYADKLGARFAVIIGEDELAN-GTVTLK 392
>gnl|CDD|238475 cd00939, MetRS_RNA, MetRS_RNA binding domain. This short
RNA-binding domain is found at the C-terminus of MetRS
in several higher eukaryote aminoacyl-tRNA synthetases
(aaRSs). It is repeated in Drosophila MetRS. This
domain consists of a helix-turn-helix structure, which
is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 45
Score = 31.7 bits (72), Expect = 0.085
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 10/43 (23%)
Query: 13 LRAAVKEQGDIVRALKAEGA------PE----LDVKKAVAELK 45
L V EQG+ VR LKA A PE LD+KK +A +
Sbjct: 1 LEKEVAEQGNKVRKLKASKADKSVWQPEVNKLLDLKKQLALAE 43
>gnl|CDD|238474 cd00938, HisRS_RNA, HisRS_RNA binding domain. This short
RNA-binding domain is found at the N-terminus of HisRS
in several higher eukaryote aminoacyl-tRNA synthetases
(aaRSs). This domain consists of a helix- turn- helix
structure, which is similar to other RNA-binding
proteins. It is involved in both protein-RNA
interactions by binding tRNA and protein-protein
interactions, which are important for the formation of
aaRSs into multienzyme complexes.
Length = 45
Score = 31.3 bits (71), Expect = 0.11
Identities = 17/34 (50%), Positives = 23/34 (67%)
Query: 11 APLRAAVKEQGDIVRALKAEGAPELDVKKAVAEL 44
A L AVK QG++VR LKAE A + + + VA+L
Sbjct: 1 AKLEEAVKLQGELVRKLKAEKASKEQIAEEVAKL 34
>gnl|CDD|238438 cd00861, ProRS_anticodon_short, ProRS Prolyl-anticodon binding
domain, short version found predominantly in bacteria.
ProRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 94
Score = 32.2 bits (74), Expect = 0.17
Identities = 21/95 (22%), Positives = 43/95 (45%), Gaps = 2/95 (2%)
Query: 560 PLKASILPLSSN-PEFQPFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGIT 618
P I+P++ Q + L +EL G+ +DD G ++A D I IP+ I
Sbjct: 1 PFDVVIIPMNMKDEVQQELAEKLYAELQAAGVDVLLDDRNERPGVKFADADLIGIPYRIV 60
Query: 619 IDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIK 653
+ + E V ++ R + + + ++E+ ++
Sbjct: 61 VGKKSAAEGI-VEIKVRKTGEKEEISIDELLEFLQ 94
>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core
catalytic domain. ThrRS is a homodimer. It is
responsible for the attachment of threonine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 298
Score = 33.7 bits (78), Expect = 0.25
Identities = 19/42 (45%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 265 LPFAAAQIGNAFRNEISPR-SGLIRVREFTM--AEIEHFCDP 303
LP A+ G R E S GL RVR FT A I FC P
Sbjct: 110 LPLRLAEFGTVHRYEQSGALHGLTRVRGFTQDDAHI--FCTP 149
>gnl|CDD|102340 PRK06366, PRK06366, acetyl-CoA acetyltransferase; Provisional.
Length = 388
Score = 33.4 bits (76), Expect = 0.35
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 276 FRNEISPRSGLIR---VREFTMAEIEHFCDPTDK-------SHAKFSDVETTQMMVLYSA 325
FRNEI P + L R +R+ TM ++ DK + A+ SD + +M A
Sbjct: 199 FRNEIVPFNDLDRDEGIRKTTMEDLAKLPPAFDKNGILTAGNSAQLSDGGSALVMASEKA 258
Query: 326 CNQMDGKPAERIT 338
N+ KP RIT
Sbjct: 259 INEYGLKPIARIT 271
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 32.8 bits (75), Expect = 0.62
Identities = 22/124 (17%), Positives = 48/124 (38%), Gaps = 20/124 (16%)
Query: 525 SFGIGRIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSE 584
SFG+ I AL + T I+PL + +++
Sbjct: 319 SFGLDVIYTAL-----SQK-ETISST----------ADVFIIPLGTE---LQCLQIAQQL 359
Query: 585 LSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVK 644
S G+ +++ +G + K ++ IP+ + I + + +V LR ++V+V
Sbjct: 360 RSTTGLKVELELAGRKLKKALNYANKENIPYVLIIGEEEVST-GTVMLRNMKEGSEVKVP 418
Query: 645 VNEV 648
++ +
Sbjct: 419 LSSL 422
>gnl|CDD|217671 pfam03683, UPF0175, Uncharacterized protein family (UPF0175). This
family contains small proteins of unknown function.
Length = 76
Score = 29.9 bits (68), Expect = 0.67
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 191 KLDGMSKNEMDDVLKKYNIKSPLTKNDLSEPME 223
+L GMS+ E ++L + I + +L E +E
Sbjct: 42 ELAGMSRWEFLELLARRGIPRHYDEEELEEDLE 74
>gnl|CDD|238401 cd00778, ProRS_core_arch_euk, Prolyl-tRNA synthetase (ProRS) class
II core catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain. This
subfamily contains the core domain of ProRS from
archaea, the cytoplasm of eukaryotes and some bacteria.
Length = 261
Score = 32.2 bits (74), Expect = 0.69
Identities = 26/99 (26%), Positives = 33/99 (33%), Gaps = 11/99 (11%)
Query: 230 TQIGPSGL-IKGYLRPETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIR 288
T G L LRP T++ + LP Q N FR E +R
Sbjct: 83 THGGLEELEEPLALRP-TSETAIYPMFSKWIRSYRDLPLKINQWVNVFRWETKTTRPFLR 141
Query: 289 VREFTMAEIEHFCDPTDKSHAKFSDV--ETTQMMVLYSA 325
REF E H HA + E Q++ LY
Sbjct: 142 TREFLWQEG-HTA------HATEEEAEEEVLQILDLYKE 173
>gnl|CDD|224680 COG1766, fliF, Flagellar basal body M-ring protein [Cell motility
and secretion].
Length = 545
Score = 32.4 bits (74), Expect = 0.98
Identities = 24/106 (22%), Positives = 40/106 (37%), Gaps = 20/106 (18%)
Query: 569 SSNPEFQPFIKMLSSE--------LSQNGISFKVDDSGGSI----GKRYARTDEIA---I 613
S P+++ LS E L Q I +KV GG+I + Y ++A +
Sbjct: 45 SRQPKYRTLYSNLSEEDAGRIVQELDQMNIPYKVSSDGGTILVPEDQVYELRLKLAAEGL 104
Query: 614 PFGITIDFDTLKEPHSVTLRERDSMTQVRVKV---NEVASVIKDLS 656
P + ++ + L D M QV + E+A I +
Sbjct: 105 PKSGNVGYELFDDNSKFGL--TDFMQQVNYQRALEGELARTIVAID 148
>gnl|CDD|232984 TIGR00462, genX, EF-P lysine aminoacylase GenX. Many Gram-negative
bacteria have a protein closely homologous to the
C-terminal region of lysyl-tRNA synthetase (LysS).
Multiple sequence alignment of these proteins with the
homologous regions of collected LysS proteins shows that
these proteins form a distinct set rather than just
similar truncations of LysS. The protein is termed GenX
after its designation in E. coli. Interestingly, genX
often is located near a homolog of
lysine-2,3-aminomutase. Its function is unknown [Unknown
function, General].
Length = 290
Score = 31.8 bits (73), Expect = 1.0
Identities = 30/74 (40%), Positives = 34/74 (45%), Gaps = 19/74 (25%)
Query: 228 FATQ-IGPSGL-IKGYLR--PETAQGIFVNFKRLLEFNSGRLPFAAAQIGNAFRN-EISP 282
FAT+ +GP G YL+ PE A KRLL SG + F QI FRN E
Sbjct: 28 FATEFVGPDGQGRPLYLQTSPEYA------MKRLLAAGSGPI-F---QICKVFRNGERGR 77
Query: 283 RSGLIRVREFTMAE 296
R EFTM E
Sbjct: 78 R----HNPEFTMLE 87
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 31.8 bits (73), Expect = 1.1
Identities = 30/131 (22%), Positives = 59/131 (45%), Gaps = 16/131 (12%)
Query: 525 SFGIGRIMYALFEHNFKMRDGDEQRTYLALPPLVAPLKASILPLSSNPEFQPFIKMLSSE 584
+ G+ R++ AL E P+ + ++PL + +P L+ +
Sbjct: 313 AIGVERLILALEEEGK-------------EDPVETRVDVYVVPLG--EDAEPEALKLAQK 357
Query: 585 LSQNGISFKVDDSGGSIGKRYARTDEIAIPFGITIDFDTLKEPHSVTLRERDSMTQVRVK 644
L GIS +VD SG + K++ D++ F + + D L VT+++ + Q V
Sbjct: 358 LRAAGISVEVDYSGRKLKKQFKYADKLGARFAVILGEDELAN-GVVTVKDLATGEQEEVP 416
Query: 645 VNEVASVIKDL 655
++E+ +K+L
Sbjct: 417 LDELVEELKEL 427
>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed.
Length = 542
Score = 32.2 bits (74), Expect = 1.1
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 569 SSNPEFQPFIKMLSSE--------LSQNGISFKVDDSGGSI----GKRYARTDEIA---I 613
+S P+++ LS + L Q GI +KV D GG+I K ++A +
Sbjct: 45 ASRPDYRVLYSNLSDQDAGQIVAALDQAGIPYKVADDGGTILVPADKVDELRLKLASEGL 104
Query: 614 PFGITIDFDTL 624
P ++ ++
Sbjct: 105 PKSGSVGYELF 115
>gnl|CDD|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed.
Length = 639
Score = 32.0 bits (73), Expect = 1.2
Identities = 22/101 (21%), Positives = 46/101 (45%), Gaps = 2/101 (1%)
Query: 553 ALPPLVAPLKASILPLSSNPEFQPFIKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIA 612
A P +AP++ ++P+ SN + ++ +L+Q GI + D+ +G +
Sbjct: 534 AFPAWLAPVQVKVIPV-SNAVHVQYADEVADKLAQAGIRVERDERDEKLGYKIREAQMQK 592
Query: 613 IPFGITIDFDTLKEPHSVTLRERDSMTQVRVKVNEVASVIK 653
IP+ + I D E +V +R+ ++++ IK
Sbjct: 593 IPYVLVIG-DKEMENGAVNVRKYGEEKSEVIELDMFVESIK 632
>gnl|CDD|215450 PLN02837, PLN02837, threonine-tRNA ligase.
Length = 614
Score = 30.6 bits (69), Expect = 3.0
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 265 LPFAAAQIGNAFRNEIS-PRSGLIRVREFTMAEIEHFCDP 303
LP A++G +R E+S GL RVR FT + FC
Sbjct: 328 LPIRVAELGTVYRYELSGSLHGLFRVRGFTQDDAHIFCLE 367
>gnl|CDD|151678 pfam11236, DUF3037, Protein of unknown function (DUF3037). This
bacterial family of proteins has no known function.
Length = 118
Score = 28.7 bits (65), Expect = 4.4
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 254 FKRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIR 288
F+ + P AA I FR +PRS +I+
Sbjct: 60 FEAICAGGKAAGPIAALDIRERFRWLTAPRSTVIQ 94
>gnl|CDD|236774 PRK10839, PRK10839, 16S rRNA pseudouridylate synthase A;
Provisional.
Length = 232
Score = 29.7 bits (67), Expect = 4.6
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 413 AYDLTQHFKATGVRLSAEKHLPEPQTREIVEPVL 446
A D + F A GV+L EK L +P E++ P
Sbjct: 141 ADDTAEQF-AKGVQLHNEKDLTKPAVLEVITPTQ 173
>gnl|CDD|227193 COG4856, COG4856, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 403
Score = 29.7 bits (67), Expect = 4.8
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 486 KYELLVDDKEFVLTKDMISI---KKSTKTFHVE-EIIPSVIEPSFGIGRIM 532
+ E L D + + ++ KK TK F V EI S I+P + I +
Sbjct: 111 QVEGLPDGLTVSVNPEKATVTIEKKVTKKFPVSVEIDQSKIDPGYSIEKPE 161
>gnl|CDD|132318 TIGR03275, methan_mark_8, putative methanogenesis marker protein 8.
Members of this protein family, to date, are found in a
completed prokaryotic genome if and only if the species
is one of the archaeal methanogens. The exact function
is unknown, but likely is linked to methanogenesis or a
process closely connected to it.
Length = 259
Score = 28.9 bits (65), Expect = 7.0
Identities = 10/41 (24%), Positives = 20/41 (48%)
Query: 578 IKMLSSELSQNGISFKVDDSGGSIGKRYARTDEIAIPFGIT 618
I+ ++ E + I F++DD G R + + + FG +
Sbjct: 38 IEEITPEAIRKNIEFRIDDFGMFTKNRRLESSDRFVGFGAS 78
>gnl|CDD|236820 PRK11014, PRK11014, transcriptional repressor NsrR; Provisional.
Length = 141
Score = 28.1 bits (63), Expect = 7.7
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 331 GKPAERITIGEAVRS 345
GKPA I IG+ VR
Sbjct: 68 GKPASTIRIGDVVRE 82
>gnl|CDD|236474 PRK09350, PRK09350, poxB regulator PoxA; Provisional.
Length = 306
Score = 28.7 bits (65), Expect = 8.8
Identities = 18/42 (42%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 255 KRLLEFNSGRLPFAAAQIGNAFRNEISPRSGLIRVREFTMAE 296
KRLL SG QI +FRNE + R EFTM E
Sbjct: 71 KRLLAAGSG----PIFQICKSFRNEEAGRYHNP---EFTMLE 105
>gnl|CDD|184316 PRK13771, PRK13771, putative alcohol dehydrogenase; Provisional.
Length = 334
Score = 28.8 bits (65), Expect = 9.1
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 421 KATGVRLSAEKHLPEPQTREIVEPVLNKGIIGKEFKKDAKTICDALAALDLNSVSAVEE- 479
KA G ++ A +IV + I+G +F ++ K I A ++ +EE
Sbjct: 184 KALGAKVIAVTSSES--KAKIVSKYADYVIVGSKFSEEVKKIGGADIVIETVGTPTLEES 241
Query: 480 --SLNTNGK 486
SLN GK
Sbjct: 242 LRSLNMGGK 250
>gnl|CDD|219721 pfam08118, MDM31_MDM32, Yeast mitochondrial distribution and
morphology (MDM) proteins. Proteins in this family are
yeast mitochondrial inner membrane proteins MDM31 and
MDM32. These proteins are required for the maintenance
of mitochondrial morphology, and the stability of
mitochondrial DNA.
Length = 503
Score = 29.0 bits (65), Expect = 9.5
Identities = 24/103 (23%), Positives = 36/103 (34%), Gaps = 13/103 (12%)
Query: 60 PFVSSFDRAKMEDLLKRRFFYDQSFSIYGGISGQYD---------FGPMGCALKTNMLSA 110
PF S ++ L K FYD F +SG YD ++ S
Sbjct: 240 PFQVSIFNCELPQLRKHWLFYD--FLNANSMSGTYDNSMFTIHKKQRLDDFDESSSPSSP 297
Query: 111 WRQFFVLEEQMLEVDCSILTLEPVLK--ASGHVDRFADLMVKD 151
W++ + L +D LE SG VD D+++
Sbjct: 298 WKKVTRMRVDSLNIDHLNAGLEGPFGWITSGKVDMIGDVLLPQ 340
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
0.319 0.135 0.388
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,747,510
Number of extensions: 3486591
Number of successful extensions: 3188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3129
Number of HSP's successfully gapped: 95
Length of query: 679
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 576
Effective length of database: 6,369,140
Effective search space: 3668624640
Effective search space used: 3668624640
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 (21.7 bits)
S2: 62 (27.7 bits)