RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 009329
(537 letters)
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 777 bits (2007), Expect = 0.0
Identities = 334/519 (64%), Positives = 402/519 (77%), Gaps = 11/519 (2%)
Query: 3 ASKETGTVAAPKMDLTLKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAV 62
A G A+ +L L YN+M+++KELF P V GKVGMYVCGVTAYDLSH+GHAR V
Sbjct: 46 ALASNGAPASRGRELHL--YNTMSRKKELFKPKVEGKVGMYVCGVTAYDLSHIGHARVYV 103
Query: 63 SFDLLYRYLEHLKCEVTYVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQC 122
+FD+LYRYL+HL EV YVRNFTDVDDKII RAN+LGE+P+SLS RYC+E+L DMA L C
Sbjct: 104 TFDVLYRYLKHLGYEVRYVRNFTDVDDKIIARANELGEDPISLSRRYCEEFLSDMAYLHC 163
Query: 123 LPPTYQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRLENNRAG 182
LPP+ +PRVSDH+ QI DMI QI++N CAY V+GDV+F+V+K P YG+LSG++LE+NRAG
Sbjct: 164 LPPSVEPRVSDHIPQIIDMIKQILDNGCAYRVDGDVYFSVDKFPEYGKLSGRKLEDNRAG 223
Query: 183 ERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGG 242
ERVAVDSRK+NPADFALWKAAK GEP WDSPWGPGRPGWHIECSAMSA YL FDIHGG
Sbjct: 224 ERVAVDSRKKNPADFALWKAAKEGEPFWDSPWGPGRPGWHIECSAMSAAYLGHSFDIHGG 283
Query: 243 GIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHP 302
G+DL+FPHHENEIAQSCAAC DSN+SYW+HNG VT ++EKMSKSLGNFFTIRQ+ + YHP
Sbjct: 284 GMDLVFPHHENEIAQSCAACCDSNISYWIHNGFVTVDSEKMSKSLGNFFTIRQVIDLYHP 343
Query: 303 LALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAA 362
LALR FL+ HYRSP+NYS +QL+SAS+ +FYIYQTL DCE +L + + P
Sbjct: 344 LALRLFLLGTHYRSPINYSDVQLESASERIFYIYQTLHDCEESLQQHDSTFEKDSVPPDT 403
Query: 363 EDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLK-KKQPKQQQLSLIESL 421
+CINK DEF MSDDL+T + A + LK IN L+ K KKQ K+ +ESL
Sbjct: 404 LNCINKFHDEFVTSMSDDLHTP-VALAALSEPLKTINDLLHTRKGKKQEKR-----LESL 457
Query: 422 RKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDF 481
+E ++++VL +LGL+P +YSE LQQL++KAL+RA+LTEE VLQ IEER ARKNK++
Sbjct: 458 AALEKKIRDVLSVLGLMPT-SYSEALQQLREKALRRAKLTEEQVLQKIEERTVARKNKEY 516
Query: 482 SKSDQIRADLTRKGIALMDMGKETIWRPCV-LVEQEQEA 519
KSD IR DL GIALMD T WRP + L QEQ A
Sbjct: 517 EKSDAIRKDLAAVGIALMDSPDGTTWRPAIPLALQEQVA 555
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 689 bits (1780), Expect = 0.0
Identities = 232/492 (47%), Positives = 299/492 (60%), Gaps = 33/492 (6%)
Query: 18 TLKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCE 77
LKIYN++T+QKE F P+ PGKV MYVCG T YD +H+GHAR+ V FD+L RYL +L +
Sbjct: 2 MLKIYNTLTRQKEEFKPLEPGKVKMYVCGPTVYDYAHIGHARSFVVFDVLRRYLRYLGYK 61
Query: 78 VTYVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQ 137
VTYVRN TD+DDKII+RAN+ GE+ L+ RY + DM L LPP +PR ++H+ +
Sbjct: 62 VTYVRNITDIDDKIIKRANEEGESIKELTERYIAAFHEDMDALNVLPPDIEPRATEHIPE 121
Query: 138 IKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADF 197
I ++I ++I+ AY +GDV+F V K P+YG+LSG+ L+ +AG RV V KR+P DF
Sbjct: 122 IIELIERLIDKGHAYEADGDVYFDVRKFPDYGKLSGRNLDELQAGARVEVAEEKRDPLDF 181
Query: 198 ALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQ 257
ALWKAAK GEPSW+SPWG GRPGWHIECSAMS YL FDIHGGG DLIFPHHENEIAQ
Sbjct: 182 ALWKAAKPGEPSWESPWGKGRPGWHIECSAMSTKYLGETFDIHGGGADLIFPHHENEIAQ 241
Query: 258 SCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSP 317
S AA +YWMHNG VT N EKMSKSLGNFFTIR + ++Y P LR FL+SAHYRSP
Sbjct: 242 SEAATGKPFANYWMHNGFVTVNGEKMSKSLGNFFTIRDLLKKYDPEVLRFFLLSAHYRSP 301
Query: 318 LNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARM 377
LN+S L+ A A+ +Y L + + A + + ++ F M
Sbjct: 302 LNFSEEALEQAKKALERLYNALAETALGEDD-----------EALLAELEEFKERFIEAM 350
Query: 378 SDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGL 437
DD NT L + + IN +L K E+ + ++ + +LGL
Sbjct: 351 DDDFNTPEALA-VLFELAREINRALETKDK-----------EAAAALAALLRALADVLGL 398
Query: 438 LPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIA 497
+ EL + ++ LIEER ARK KDF+ +D IR +L GI
Sbjct: 399 EQ--------DEEALFEAAADELLDAEIEALIEERQEARKAKDFALADAIRDELAALGIV 450
Query: 498 LMDMGKE-TIWR 508
L D + T WR
Sbjct: 451 LED-TPDGTTWR 461
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 609 bits (1572), Expect = 0.0
Identities = 229/494 (46%), Positives = 291/494 (58%), Gaps = 35/494 (7%)
Query: 18 TLKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCE 77
LK+YN++T+QKE F PI PGKV MYVCG T YD +H+GHAR V FD+L RYL +L +
Sbjct: 1 MLKLYNTLTRQKEEFVPIDPGKVKMYVCGPTVYDYAHIGHARTYVVFDVLRRYLRYLGYK 60
Query: 78 VTYVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQ 137
VTYVRN TD+DDKII RA + G + ++ RY + DM L LPP +PR ++H+++
Sbjct: 61 VTYVRNITDIDDKIINRAREEGLSIREVAERYIAAFFEDMDALNVLPPDIEPRATEHIDE 120
Query: 138 IKDMITQIINNDCAYVVE-GDVFFAVEKSPNYGRLSG-QRLENNRAGERVAVDSRKRNPA 195
I + I ++I AYV + GDV+F V K +YG+LSG LE +AG RV VD KRNP
Sbjct: 121 IIEFIEKLIEKGYAYVADDGDVYFDVSKFKDYGKLSGRDSLEELQAGARVEVDEEKRNPL 180
Query: 196 DFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEI 255
DF LWKAAK GEPSWDSPWG GRPGWHIECSAMS YL FDIHGGG DLIFPHHENEI
Sbjct: 181 DFVLWKAAKPGEPSWDSPWGKGRPGWHIECSAMSTKYLGETFDIHGGGSDLIFPHHENEI 240
Query: 256 AQSCAACQDSN-VSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHY 314
AQS AA YWMHNG + + EKMSKSLGNF T+R + ++Y P LR FL+S+HY
Sbjct: 241 AQSEAATGVKPFAKYWMHNGFLNIDGEKMSKSLGNFITVRDLLKKYDPEVLRLFLLSSHY 300
Query: 315 RSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFH 374
RSPL++S L+ A A+ +Y L+ A + + F
Sbjct: 301 RSPLDFSEELLEEAKKALERLYNALRRLRDLA------------GDAELADLKEFEARFR 348
Query: 375 ARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRI 434
+ DD NT L + K IN L + K + LS + K +L I
Sbjct: 349 EALDDDFNTPKALA-VLFELAKEINRLLE--EGKSDAKAVLSAL----------KALLAI 395
Query: 435 LGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRK 494
LGL G + + Q E +E++ LIEER ARK K+++ +D+IR +L
Sbjct: 396 LGLKVLGLFPQSGAQE-------DESDDEEIEALIEERLEARKAKNWALADEIRDELLAL 448
Query: 495 GIALMDMGKETIWR 508
GI L D T WR
Sbjct: 449 GIILEDTPDGTTWR 462
>gnl|CDD|232974 TIGR00435, cysS, cysteinyl-tRNA synthetase. This model finds the
cysteinyl-tRNA synthetase from most but not from all
species. The enzyme from one archaeal species,
Archaeoglobus fulgidus, is found but the equivalent
enzymes from some other Archaea, including Methanococcus
jannaschii, are not found, although biochemical evidence
suggests that tRNA(Cys) in these species are charged
directly with Cys rather than through a misacylation and
correction pathway as for tRNA(Gln) [Protein synthesis,
tRNA aminoacylation].
Length = 464
Score = 522 bits (1347), Expect = 0.0
Identities = 231/491 (47%), Positives = 304/491 (61%), Gaps = 29/491 (5%)
Query: 19 LKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEV 78
LK+YN++T+QKE F P+V GKV MYVCG T YD H+GHAR A+ FD+L RYL +L +V
Sbjct: 1 LKLYNTLTRQKEEFEPLVQGKVKMYVCGPTVYDYCHIGHARTAIVFDVLRRYLRYLGYKV 60
Query: 79 TYVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQI 138
YV+N TD+DDKII+RA + GE+ +S R+ + Y DM L LPP +PR ++H+++I
Sbjct: 61 QYVQNITDIDDKIIKRARENGESVYEVSERFIEAYFEDMKALNVLPPDLEPRATEHIDEI 120
Query: 139 KDMITQIINNDCAYVVE-GDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADF 197
+ I Q+I AYV + GDV+F V K +YG+LS Q L+ AG RV VD KRN DF
Sbjct: 121 IEFIEQLIEKGYAYVSDNGDVYFDVSKFKDYGKLSKQDLDQLEAGARVDVDEAKRNKLDF 180
Query: 198 ALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQ 257
LWK++K GEP WDSPWG GRPGWHIECSAM+ YL + DIHGGG+DLIFPHHENEIAQ
Sbjct: 181 VLWKSSKEGEPKWDSPWGKGRPGWHIECSAMNDKYLGDQIDIHGGGVDLIFPHHENEIAQ 240
Query: 258 SCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSP 317
S AA YWMHNG + +NEKMSKSLGNFFT+R + + Y P LR+FL+S HYRSP
Sbjct: 241 SEAAFGKQLAKYWMHNGFLMIDNEKMSKSLGNFFTVRDVLKNYDPEILRYFLLSVHYRSP 300
Query: 318 LNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARM 377
L++S L++A +A+ +Y+ L+ + +L+ + + F M
Sbjct: 301 LDFSEELLEAAKNALERLYKALRVLDTSLAYSGNQSLNKFPDE------KEFEARFVEAM 354
Query: 378 SDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGL 437
DDLNT++ L F + K IN + K LIE L +E L +L
Sbjct: 355 DDDLNTANALAVLF-ELAKSINLTF------VSKADAALLIEHLIFLE----SRLGLLLG 403
Query: 438 LPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIA 497
LP S+ +Q + L E LIEER+ ARK KDF+K+D+IR +L +KGI
Sbjct: 404 LP----SKPVQAGSNDDLGEIE-------ALIEERSIARKEKDFAKADEIRDELAKKGIV 452
Query: 498 LMDMGKETIWR 508
L D + T WR
Sbjct: 453 LEDTPQGTTWR 463
>gnl|CDD|216482 pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic
domain. This family includes only cysteinyl tRNA
synthetases.
Length = 301
Score = 446 bits (1150), Expect = e-156
Identities = 171/291 (58%), Positives = 211/291 (72%), Gaps = 1/291 (0%)
Query: 32 FTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDDKI 91
F P+ GKV MYVCG T YD SH+GHAR+AV+FD+L RYL+ L +V +V+NFTD+DDKI
Sbjct: 2 FVPLHQGKVNMYVCGPTVYDDSHIGHARSAVAFDVLRRYLQALGYDVQFVQNFTDIDDKI 61
Query: 92 IRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCA 151
I+RA GE+ L+ R+ Y DM L LPP +PRV++H+++I + I ++I A
Sbjct: 62 IKRAQQQGESFRELAARFITAYTKDMDALNVLPPDLEPRVTEHIDEIIEFIERLIKKGYA 121
Query: 152 YVVE-GDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFALWKAAKAGEPSW 210
YV + GDV+F V P+YG+LSGQ LE AG R V KR+P DFALWKA+K GEPSW
Sbjct: 122 YVSDNGDVYFDVSSFPDYGKLSGQNLEQLEAGARGEVGEGKRDPLDFALWKASKEGEPSW 181
Query: 211 DSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYW 270
DSPWG GRPGWHIECSAM+ YL S+ DIHGGG+DL FPHHENEIAQS AA YW
Sbjct: 182 DSPWGKGRPGWHIECSAMARKYLGSQIDIHGGGVDLKFPHHENEIAQSEAAFDQQLAKYW 241
Query: 271 MHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 321
+HNGH+ EKMSKSLGNF TIR + +RY P LR+FL+S HYRSPL++S
Sbjct: 242 LHNGHLMIEGEKMSKSLGNFLTIRDVLKRYDPRILRYFLLSVHYRSPLDFS 292
>gnl|CDD|173001 PRK14535, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 699
Score = 383 bits (984), Expect = e-125
Identities = 216/505 (42%), Positives = 283/505 (56%), Gaps = 54/505 (10%)
Query: 21 IYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEVTY 80
IYN++T+QKE F PI P V MYVCG+T YD HLGHAR V FD++ R+L +TY
Sbjct: 230 IYNTLTRQKEPFAPIDPENVRMYVCGMTVYDYCHLGHARVMVVFDMIARWLRECGYPLTY 289
Query: 81 VRNFTDVDDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKD 140
VRN TD+DDKII RA + GE L+ R+ Q D L L P +P+ ++++ Q+
Sbjct: 290 VRNITDIDDKIIARAAENGETIGELTARFIQAMHEDADALGVLRPDIEPKATENIPQMIA 349
Query: 141 MITQIINNDCAY-VVEGDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFAL 199
MI +I N AY GDV++AV + YG+LSG+ L++ RAGERV VD KR+P DF L
Sbjct: 350 MIETLIQNGKAYPAANGDVYYAVREFAAYGQLSGKSLDDLRAGERVEVDGFKRDPLDFVL 409
Query: 200 WKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSC 259
WKAAKAGEP+W+SPWG GRPGWHIECSAMS + FDIHGGG DL FPHHENEIAQS
Sbjct: 410 WKAAKAGEPAWESPWGNGRPGWHIECSAMSENLFGDTFDIHGGGADLQFPHHENEIAQSV 469
Query: 260 AACQD----------------SNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPL 303
A S+V YW+HNG + + EKMSKSLGNFFTIR++ ++Y P
Sbjct: 470 GATGHTCGHHHAQTHHGQSIASHVKYWLHNGFIRVDGEKMSKSLGNFFTIREVLKQYDPE 529
Query: 304 ALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAE 363
+R F++ AHYRSPLNYS LD A A+ +Y TL++ A
Sbjct: 530 VVRFFILRAHYRSPLNYSDAHLDDAKGALTRLYTTLKNTPAA-------------EFMLS 576
Query: 364 DCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRK 423
+ +N F+A M+DD T + F+ A +N Q
Sbjct: 577 ENVNDYTRRFYAAMNDDFGTVEAVAVLFELA-----GEVNKTNDAQ-------------- 617
Query: 424 IENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSK 483
+ +K + I+GLL +E LQ L+ E++ LI R AR +K++++
Sbjct: 618 LAGCLKALGGIIGLLQRDP-TEFLQ----GGAASDGLSNEEIEDLIARRKQARADKNWAE 672
Query: 484 SDQIRADLTRKGIALMDMGKETIWR 508
SD+IR L I L D T WR
Sbjct: 673 SDRIRDLLNEHKIILEDNAGGTTWR 697
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 375 bits (966), Expect = e-123
Identities = 195/568 (34%), Positives = 276/568 (48%), Gaps = 67/568 (11%)
Query: 14 KMDLTLKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLE- 72
K LK+ NS+T K F P +V Y CG T YD SHLGHAR V+FD++ R LE
Sbjct: 35 KYLTGLKVNNSLTGGKVEFVPQNGRQVRWYTCGPTVYDSSHLGHARTYVTFDIIRRILED 94
Query: 73 HLKCEVTYVRNFTDVDDKIIRRANDLG-ENPLSLSNRYCQEYLVDMADLQCLPPTYQPRV 131
+ +V YV N TD+DDKII+RA + L L+ ++ +E+ DM L PP RV
Sbjct: 95 YFGYDVFYVMNITDIDDKIIKRAREEKLSIFLELARKWEKEFFEDMKALNVRPPDVITRV 154
Query: 132 SDHMEQIKDMITQIINNDCAYVVEGDVFFAVEK----SPNYGRL---SGQRLENNRAGER 184
S+++ +I D I +II+N AY G V+F VE Y +L S + GE
Sbjct: 155 SEYVPEIVDFIQKIIDNGFAYESNGSVYFDVEAFRKAGHVYPKLEPESVADEDRIAEGEG 214
Query: 185 V--AVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGG 242
V KR+P DFALWKA+K GEPSWDSPWG GRPGWHIECSAM+++ L DIH G
Sbjct: 215 ALGKVSGEKRSPNDFALWKASKPGEPSWDSPWGKGRPGWHIECSAMASNILGDPIDIHSG 274
Query: 243 GIDLIFPHHENEIAQSCAACQDSN--VSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERY 300
GIDL FPHH+NE+AQS A D + V+Y++H+GH+ KMSKSL NF TIRQ +Y
Sbjct: 275 GIDLKFPHHDNELAQS-EAYFDKHQWVNYFLHSGHLHIKGLKMSKSLKNFITIRQALSKY 333
Query: 301 HPLALR-HFLISAHYRSPLNYSVLQLDSA--SDAVFYIYQTLQDCEVALSPFQEHGKTAR 357
+R FL+ + P+NYS +D A D VF+ + + ++ L + +
Sbjct: 334 TARQIRLLFLLH-KWDKPMNYSDESMDEAIEKDKVFFNF--FANVKIKLRESEL-TSPQK 389
Query: 358 INPAAEDCINKLR---DEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQ 414
+ HA + D+ +T L A Q + N+ LN +QP
Sbjct: 390 WTQHDFELNELFEETKSAVHAALLDNFDTPEALQ-ALQKLISATNTYLN--SGEQPSAPL 446
Query: 415 LSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE--- 471
LR + V ++L I GL+ Q T E+ L+E
Sbjct: 447 ------LRSVAQYVTKILSIFGLVEGSDGLGSQGQNS---------TSENFKPLLEALLR 491
Query: 472 -----RAAARKNKD-----------FSKSDQIRAD-LTRKGIALMDM-GKETIWRPC--- 510
R AA+ D++R + L GI + D ++W+
Sbjct: 492 FRDEVRDAAKAEMKLISLDKKKKQLLQLCDKLRDEWLPNLGIRIEDKPDGPSVWKLDDKE 551
Query: 511 -VLVEQEQEAPPAEKEKKPAATGEEQKA 537
+ E+E++ E+++ +E+K
Sbjct: 552 ELQREKEEKEALKEQKRLRKLKKQEEKK 579
>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 490
Score = 339 bits (870), Expect = e-111
Identities = 178/527 (33%), Positives = 255/527 (48%), Gaps = 74/527 (14%)
Query: 17 LTLKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKC 76
+ L++YN++ +Q+E F PI G V +Y CG T Y+ +H+G+ R V D L R L L
Sbjct: 1 MALRLYNTLGRQQEEFQPIEHGHVRLYGCGPTVYNYAHIGNLRTYVFQDTLRRTLHFLGY 60
Query: 77 EVTYVRNFTDV----------DDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPT 126
VT+V N TDV +DK+++ A + G++ L ++ Y + D A L P+
Sbjct: 61 RVTHVMNITDVGHLTDDADSGEDKMVKSAQEHGKSVLEIAAHYTAAFFRDTARLNIERPS 120
Query: 127 YQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRLENNRAGERVA 186
++H++ + +I ++ Y G+V+F + P+YG L+ +E+ +AG R+
Sbjct: 121 IVCNATEHIQDMIALIKRLEARGHTYCAGGNVYFDIRTFPSYGSLASAAVEDLQAGARIE 180
Query: 187 VDSRKRNPADFALWKAAKAGEP---SWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGG 243
D+ KRNP DF LW E +WDSPWG G PGWHIECSAMS YL + DIH GG
Sbjct: 181 HDTNKRNPHDFVLWFTRSKFENHALTWDSPWGRGYPGWHIECSAMSMKYLGEQCDIHIGG 240
Query: 244 IDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQITER-YHP 302
+D I HH NEIAQ AA V YW+H+ + N KMSKS G F T+ + E+ + P
Sbjct: 241 VDHIRVHHTNEIAQCEAATGKPWVRYWLHHEFLLMNKGKMSKSAGQFLTLSSLQEKGFQP 300
Query: 303 LALRHFLISAHYRSPLNYS------------------VLQLDSASDAVFYIYQTLQDC-- 342
L R FL+ HYRS L +S +D+A + TL +C
Sbjct: 301 LDYRFFLLGGHYRSQLAFSWEALKTAKAARRSLVRRVARVVDAARATTGSVRGTLAECAA 360
Query: 343 -EVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSS 401
VA S +E + +F A + DD +T L S
Sbjct: 361 ERVAESR----------ASESELLL----TDFRAALEDDFSTPKAL------------SE 394
Query: 402 LNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELT 461
L L K L L + ++ + +LGL G E L + A +
Sbjct: 395 LQKLVKDTSVPPSLCL--------SVLQAMDTVLGL---GLIQEATASLSAQV--PAGPS 441
Query: 462 EEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWR 508
EE++ QLIE RA AR+ KDF +D+IR L +GI L D TIW+
Sbjct: 442 EEEIGQLIEARAHARQTKDFPLADEIRDKLKAEGIELEDTHLGTIWK 488
>gnl|CDD|132488 TIGR03447, mycothiol_MshC, cysteine--1-D-myo-inosityl
2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Members
of this protein family are MshC,
l-cysteine:1-D-myo-inosityl
2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an
enzyme that uses ATP to ligate a Cys residue to a
mycothiol precursor molecule, in the second to last step
in mycothiol biosynthesis. This enzyme shows
considerable homology to Cys--tRNA ligases, and many
instances are misannotated as such. Mycothiol is found
in Mycobacterium tuberculosis, Corynebacterium
glutamicum, Streptomyces coelicolor, and various other
members of the Actinobacteria. Mycothiol is an analog to
glutathione [Biosynthesis of cofactors, prosthetic
groups, and carriers, Glutathione and analogs].
Length = 411
Score = 275 bits (705), Expect = 2e-87
Identities = 135/379 (35%), Positives = 204/379 (53%), Gaps = 39/379 (10%)
Query: 19 LKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEV 78
L+++++ Q P + GMYVCG+T YD +HLGHA ++FDL+ R V
Sbjct: 18 LRLFDTADGQVRPVEP--GPEAGMYVCGITPYDATHLGHAATYLTFDLVNRVWRDAGHRV 75
Query: 79 TYVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQI 138
YV+N TDVDD + RA G + L + DM L+ LPP + ++++
Sbjct: 76 HYVQNVTDVDDPLFERAERDGVDWRELGTSQIDLFREDMEALRVLPPRDYIGAVESIDEV 135
Query: 139 KDMITQIINNDCAYVVEG----DVFFAVEKSPNYGRLSG------QRLENNRAG--ERVA 186
+M+ +++ + AY+VEG DV+F+++ + +G SG L R G +R
Sbjct: 136 VEMVEKLLASGAAYIVEGPEYPDVYFSIDATEQFGYESGYDRATMLELFAERGGDPDRPG 195
Query: 187 VDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDL 246
KR+P D LW+AA+ GEPSWDSP+G GRPGWHIECSA++ + L + FDI GGG DL
Sbjct: 196 ----KRDPLDALLWRAAREGEPSWDSPFGRGRPGWHIECSAIALNRLGAGFDIQGGGSDL 251
Query: 247 IFPHHENEIAQSCAACQDSNVS-YWMHNGHVTNNNEKMSKSLGNFFTIRQIT-ERYHPLA 304
IFPHHE A + AA ++ +++H G + + EKMSKSLGN + ++ P A
Sbjct: 252 IFPHHEFSAAHAEAATGVRRMARHYVHAGMIGLDGEKMSKSLGNLVFVSKLRAAGVDPAA 311
Query: 305 LRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAED 364
+R L++ HYR ++ +DAV L + E L+ ++ P A D
Sbjct: 312 IRLGLLAGHYRQDRDW--------TDAV------LAEAEARLARWRA-ALALPDAPDATD 356
Query: 365 CINKLRDEFHARMSDDLNT 383
I +LR +++DL+T
Sbjct: 357 LIARLRQH----LANDLDT 371
>gnl|CDD|183518 PRK12418, PRK12418, cysteinyl-tRNA synthetase; Provisional.
Length = 384
Score = 261 bits (670), Expect = 1e-82
Identities = 131/361 (36%), Positives = 192/361 (53%), Gaps = 30/361 (8%)
Query: 34 PIVPG-KVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDDKII 92
P+ PG MYVCG+T YD +HLGHA ++FDL+ R +V YV+N TDVDD ++
Sbjct: 3 PVAPGGTATMYVCGITPYDATHLGHAATYLAFDLVNRVWRDAGHDVHYVQNVTDVDDPLL 62
Query: 93 RRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAY 152
RA G + L+ R + DM L+ LPP + + ++ +++ +++ + AY
Sbjct: 63 ERAARDGVDWRDLAEREIALFREDMEALRVLPPRDYVGAVESIPEVVELVEKLLASGAAY 122
Query: 153 VVEG----DVFFAVEKSPNYGRLSGQRLENNRA--GERVAVDSR--KRNPADFALWKAAK 204
VV+ DV+F+V+ +P +G SG ER R KR+P D LW+AA+
Sbjct: 123 VVDDEEYPDVYFSVDATPQFGYESGYDRATMLELFAERGGDPDRPGKRDPLDALLWRAAR 182
Query: 205 AGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAAC-Q 263
GEPSW SP+GPGRPGWHIECSA++ + L S FDI GGG DLIFPHHE A + AA +
Sbjct: 183 PGEPSWPSPFGPGRPGWHIECSAIALNRLGSGFDIQGGGSDLIFPHHEFSAAHAEAATGE 242
Query: 264 DSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQIT-ERYHPLALRHFLISAHYRSPLNYSV 322
+++H G + + EKMSKS GN + ++ P A+R L++ HYR+ ++
Sbjct: 243 RRFARHYVHAGMIGLDGEKMSKSRGNLVFVSRLRAAGVDPAAIRLALLAGHYRADREWTD 302
Query: 323 LQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLN 382
L A L A + P A D + ++R ++DDL+
Sbjct: 303 AVLAEAEA-------RLARWRAAAA--------LPAGPDAADVVARVRA----ALADDLD 343
Query: 383 T 383
T
Sbjct: 344 T 344
>gnl|CDD|173000 PRK14534, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 481
Score = 216 bits (551), Expect = 5e-64
Identities = 149/512 (29%), Positives = 238/512 (46%), Gaps = 59/512 (11%)
Query: 17 LTLKIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKC 76
+ LK+YN+ T+ KV Y CG T Y+ +H+G+ R + DLL + L LK
Sbjct: 1 MLLKLYNTKTKDLSELKNFSDVKV--YACGPTVYNYAHIGNFRTYIFEDLLIKSLRLLKY 58
Query: 77 EVTYVRNFTDV----------DDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPT 126
V Y N TD+ +DK+++ A + G +S + + + D L + P
Sbjct: 59 NVNYAMNITDIGHLTGDFDDGEDKVVKAARERGLTVYEISRFFTEAFFDDCKKLNIVYPD 118
Query: 127 YQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRLENNR--AGER 184
S+++ + +++ + N Y V G+V+F +YG+++G L + + + R
Sbjct: 119 KVLVASEYIPIMIEVVKVLEENGFTYFVNGNVYFDTSCFKSYGQMAGINLNDFKDMSVSR 178
Query: 185 VAVDSRKRNPADFALW---KAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHG 241
V +D KRN +DF LW K E WDSPWG G P WH+EC+AM+ Y S DIH
Sbjct: 179 VEIDKSKRNKSDFVLWFTNSKFKDQEMKWDSPWGFGYPSWHLECAAMNLEYFKSTLDIHL 238
Query: 242 GGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQI-TERY 300
GG+D I HH NEIA + ++H + EKMSKS NF TI+ + + +
Sbjct: 239 GGVDHIGVHHINEIAIAECYLNKKWCDMFVHGEFLIMEYEKMSKSNNNFITIKDLEDQGF 298
Query: 301 HPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINP 360
PL R+F ++AHYR+ L ++ L + A + L +L F +N
Sbjct: 299 SPLDFRYFCLTAHYRTQLKFTFNNLKACKIARENMLNKLTYFYSSLDQFD-------LNL 351
Query: 361 AAEDCIN-------KLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQ 413
+D N + D F +++ DLN L L K
Sbjct: 352 LNKDLENIEFSLEKEYYDSFLEKIAFDLNIPQGLA----------------LLWDIIKDD 395
Query: 414 QLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERA 473
LS + LR + + EVL + G E+L+++++ + + ++++ LIEER
Sbjct: 396 NLSFLSKLR-LAFKFDEVLSL------GLREEILREIENHRI----VIDDNMKSLIEERR 444
Query: 474 AARKNKDFSKSDQIRADLTRKGIALMDMGKET 505
A+ KDF ++D+IR KG L+D + T
Sbjct: 445 LAKCEKDFKRADEIREYFASKGFVLIDTEEGT 476
>gnl|CDD|173899 cd00672, CysRS_core, catalytic core domain of cysteinyl tRNA
synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding.
Length = 213
Score = 195 bits (498), Expect = 2e-59
Identities = 64/101 (63%), Positives = 76/101 (75%)
Query: 221 WHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNN 280
WHIECSAM+ YL FDIHGGG+DLIFPHHENEIAQS AA YW+H GH+T +
Sbjct: 113 WHIECSAMAMKYLGETFDIHGGGVDLIFPHHENEIAQSEAATGKPFARYWLHTGHLTIDG 172
Query: 281 EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 321
EKMSKSLGNF T+R ++Y P LR L+S+HYRSPL++S
Sbjct: 173 EKMSKSLGNFITVRDALKKYDPEVLRLALLSSHYRSPLDFS 213
Score = 175 bits (447), Expect = 5e-52
Identities = 58/112 (51%), Positives = 78/112 (69%)
Query: 20 KIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEVT 79
++YN++T+QKE F P+ PG V MYVCG T YD +H+GHAR V FD+L RYLE L +V
Sbjct: 1 RLYNTLTRQKEEFVPLNPGLVTMYVCGPTVYDYAHIGHARTYVVFDVLRRYLEDLGYKVR 60
Query: 80 YVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRV 131
YV+N TD+DDKII+RA + G + +++ Y +E+ DM L LPP PRV
Sbjct: 61 YVQNITDIDDKIIKRAREEGLSWKEVADYYTKEFFEDMKALNVLPPDVVPRV 112
>gnl|CDD|153417 cd07963, Anticodon_Ia_Cys, Anticodon-binding domain of cysteinyl
tRNA synthetases. This domain is found in cysteinyl
tRNA synthetases (CysRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. CysRS catalyzes the
transfer of cysteine to the 3'-end of its tRNA.
Length = 156
Score = 90.7 bits (226), Expect = 2e-21
Identities = 50/188 (26%), Positives = 78/188 (41%), Gaps = 38/188 (20%)
Query: 324 QLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNT 383
L+ A A+ +Y L+ D + F A M DD NT
Sbjct: 3 NLEDARAALERLYTALRGVPPT--------------TVDIDWGEPFAERFIAAMDDDFNT 48
Query: 384 SHILTGAFQDALKF-INSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLL--PP 440
A A+ F + +N LKK+ ++ +L L+ + +LGLL P
Sbjct: 49 P----EAL--AVLFELAREINRLKKEDIEKAA-ALAALLKALGG-------VLGLLQQDP 94
Query: 441 GAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMD 500
A+ LQ L+ ++ LI +R ARK KD++++D+IR +L +GI L D
Sbjct: 95 EAF---LQG----GTGEGGLSVAEIEALIAQRNQARKAKDWAEADRIRDELAAQGIILED 147
Query: 501 MGKETIWR 508
+ T WR
Sbjct: 148 SPEGTTWR 155
>gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino
acyl-tRNA synthetase. Class I amino acyl-tRNA
synthetase (aaRS) catalytic core domain. These enzymes
are mostly monomers which aminoacylate the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 143
Score = 61.3 bits (149), Expect = 2e-11
Identities = 27/117 (23%), Positives = 42/117 (35%), Gaps = 13/117 (11%)
Query: 42 MYVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDDKIIRRANDLGEN 101
G+T H+GH R V+FD L + L +V + D I AN GEN
Sbjct: 1 TTFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDPANKKGEN 60
Query: 102 PLSLSNRYCQ------EYLVDMADLQCL----PPTYQPRVSDHM---EQIKDMITQI 145
+ R+ + EY+ A L SD + E +++ +
Sbjct: 61 AKAFVERWIERIKEDVEYMFLQAADFLLLYETECDIHLGGSDQLGHIELGLELLKKA 117
Score = 44.0 bits (104), Expect = 3e-05
Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 220 GWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQS-CAACQDSNVSYWMHNGHVT- 277
+ +A ++ DIH GG D + H E + A + + G V
Sbjct: 77 EYMFLQAADFLLLYETECDIHLGGSDQLG-HIELGLELLKKAGGPARP--FGLTFGRVMG 133
Query: 278 NNNEKMSKSL 287
+ KMSKS
Sbjct: 134 ADGTKMSKSK 143
>gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA
synthetases. Leucyl tRNA synthetase (LeuRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. In Aquifex
aeolicus, the gene encoding LeuRS is split in two, just
before the KMSKS motif. Consequently, LeuRS is a
heterodimer, which likely superimposes with the LeuRS
monomer found in most other organisms. LeuRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements and thus differs between
prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This
editing region hydrolyzes mischarged cognate tRNAs and
thus prevents the incorporation of chemically similar
amino acids.
Length = 314
Score = 51.5 bits (124), Expect = 4e-07
Identities = 23/90 (25%), Positives = 32/90 (35%), Gaps = 23/90 (25%)
Query: 237 FDIHGGGIDLI--------FPHHENEIAQSCAACQDSN--VSYW----MHNGHVTNNNEK 282
DI+ GG + F H A D + G V EK
Sbjct: 225 VDIYIGGKEHAPNHLLYSRFNHK---------ALFDEGLVTDEPPKGLIVQGMVLLEGEK 275
Query: 283 MSKSLGNFFTIRQITERYHPLALRHFLISA 312
MSKS GN T + ++Y A R +++ A
Sbjct: 276 MSKSKGNVVTPDEAIKKYGADAARLYILFA 305
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 51.1 bits (123), Expect = 1e-06
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 311
+G +T +KMSKS GN ++ E+Y ALR++L
Sbjct: 324 HGFLTLEGQKMSKSRGNVVDPDELLEQYGVDALRYYLAR 362
Score = 29.6 bits (67), Expect = 5.1
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 54 HLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDD---KIIRRANDLGENPLSLSNRY 109
HLGH ++ D+ RYL EV ++ T D+ KI +A G P L ++
Sbjct: 21 HLGHLYTYLAADVYARYLRLRGYEVFFL---TGTDEHGTKIELKAEKEGITPQELVDKN 76
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 49.9 bits (120), Expect = 2e-06
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
+G +T KMSKS GN ++ +RY ALR++L
Sbjct: 315 HGWLTVEGGKMSKSRGNVVDPDELLDRYGVDALRYYLARE 354
Score = 34.9 bits (81), Expect = 0.086
Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 54 HLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDD---KIIRRANDLGENPLSLSNRYC 110
H+GH + D+ RYL +V +V T D+ KI A G P L +RY
Sbjct: 15 HIGHLYTTIPADVYARYLRLRGYDVLFV---TGTDEHGTKIELAAEKEGVTPQELVDRYH 71
Query: 111 QEYLVDMADL 120
+E+
Sbjct: 72 EEFKELFKKF 81
>gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA
synthetases. Methionine tRNA synthetase (MetRS)
catalytic core domain. This class I enzyme aminoacylates
the 2'-OH of the nucleotide at the 3' of the appropriate
tRNA. MetRS, which consists of the core domain and an
anti-codon binding domain, functions as a monomer.
However, in some species the anti-codon binding domain
is followed by an EMAP domain. In this case, MetRS
functions as a homodimer. The core domain is based on
the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. As a result of a deletion event, MetRS has a
significantly shorter core domain insertion than IleRS,
ValRS, and LeuR. Consequently, the MetRS insertion
lacks the editing function.
Length = 319
Score = 47.9 bits (115), Expect = 6e-06
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
+G++T +KMSKS GN + ERY ALR++L+
Sbjct: 271 HGYLTVEGKKMSKSRGNVVDPDDLLERYGADALRYYLLRE 310
Score = 32.1 bits (74), Expect = 0.72
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 54 HLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDD---KIIRRANDLGENPLSLSNRYC 110
HLGH V D+ RY +V +V T D+ KI ++A + G P L ++Y
Sbjct: 16 HLGHLYGTVLADVFARYQRLRGYDVLFV---TGTDEHGTKIEQKAEEEGVTPQELCDKYH 72
Query: 111 QEY 113
+ +
Sbjct: 73 EIF 75
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 48.9 bits (117), Expect = 6e-06
Identities = 21/40 (52%), Positives = 25/40 (62%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
NGH+ N+EKMSKS GNF T+RQ E + A R L A
Sbjct: 709 NGHLMLNSEKMSKSTGNFLTLRQAIEEFSADATRFALADA 748
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 46.8 bits (112), Expect = 2e-05
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
NG V +KMSKS GN +R+ E Y +R +L S+
Sbjct: 568 NGFVLLEGKKMSKSKGNVIPLRKAIEEYGADVVRLYLTSS 607
>gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of
isoleucyl, leucyl, valyl and methioninyl tRNA
synthetases. Catalytic core domain of isoleucyl,
leucyl, valyl and methioninyl tRNA synthetases. These
class I enzymes are all monomers. However, in some
species, MetRS functions as a homodimer, as a result of
an additional C-terminal domain. These enzymes
aminoacylate the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. Enzymes in
this subfamily share an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids. MetRS has a significantly shorter
insertion, which lacks the editing function.
Length = 312
Score = 42.0 bits (99), Expect = 4e-04
Identities = 29/119 (24%), Positives = 40/119 (33%), Gaps = 16/119 (13%)
Query: 209 SWDSPWGPGRPGWHIEC-------SAMSAHYLSSKF--------DIHGGGIDLIFPHHEN 253
S WG P + S Y K D H G D++
Sbjct: 184 SRQRYWGTPLPEDVFDVWFDSGIGPLGSLGYPEEKEWFKDSYPADWHLIGKDILRGWANF 243
Query: 254 EIAQSCAACQDSNVSYWMHNGHVT-NNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 311
I A + + +G V +KMSKS GN + E+Y ALR++L S
Sbjct: 244 WITMLVALFGEIPPKNLLVHGFVLDEGGQKMSKSKGNVIDPSDVVEKYGADALRYYLTS 302
>gnl|CDD|232955 TIGR00395, leuS_arch, leucyl-tRNA synthetase, archaeal and
cytosolic family. The leucyl-tRNA synthetases belong to
two families so broadly different that they are
represented by separate models. This model includes both
archaeal and cytosolic eukaryotic leucyl-tRNA
synthetases; the eubacterial and mitochondrial forms
differ so substantially that some other tRNA ligases
score higher by this model than does any eubacterial
LeuS [Protein synthesis, tRNA aminoacylation].
Length = 938
Score = 42.9 bits (101), Expect = 5e-04
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
NG+V +KMSKS GN T+ Q E++ R ++ A
Sbjct: 611 NGYVMLEGKKMSKSKGNVLTLEQAVEKFGADVARLYIADA 650
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 41.9 bits (99), Expect = 0.001
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 273 NGHVT-NNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
G V EKMSKS GN + E+Y +R +++ A
Sbjct: 569 QGMVLGEEGEKMSKSKGNVVDPEEAVEKYGADTVRLYIMFA 609
>gnl|CDD|237012 PRK11893, PRK11893, methionyl-tRNA synthetase; Reviewed.
Length = 511
Score = 40.6 bits (96), Expect = 0.002
Identities = 40/205 (19%), Positives = 70/205 (34%), Gaps = 47/205 (22%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS----------------AHYRS 316
+G +T + EKMSKSLGN + + Y A+R+FL+ +
Sbjct: 290 HGFLTLDGEKMSKSLGNVIDPFDLVDEYGVDAVRYFLLREIPFGQDGDFSREAFINRINA 349
Query: 317 PLNYSVLQLDSASDAVFYIYQTLQDCEVAL-SPFQEHGKTARINPAAEDCINKLRDEFH- 374
L + L + ++ + + P + AA + ++R
Sbjct: 350 DLANDLGNLAQRTLSMIAKN-----FDGKVPEPGALTEADEALLEAAAALLERVRAAMDN 404
Query: 375 ARMSDDLNTSHILTGAFQDALKFINSSLNM-----LKKKQPKQQQLSLIESLRKIENEVK 429
L A ++ N ++ L K P E L + +
Sbjct: 405 LAFDKALE-------AILALVRAANKYIDEQAPWSLAKTDP--------ERLATVLYTLL 449
Query: 430 EVLRILGLL--P--PGAYSEVLQQL 450
EVLR + +L P P +++L QL
Sbjct: 450 EVLRGIAVLLQPVMPELAAKILDQL 474
Score = 28.7 bits (65), Expect = 9.0
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 54 HLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDD---KIIRRANDLGENPLSLSNRYC 110
H+GHA ++ D+L R+ L+ + T D+ KI R+A + G +P L++R
Sbjct: 17 HIGHAYTTLAADVLARFKR-LRGYDVFF--LTGTDEHGQKIQRKAEEAGISPQELADRNS 73
Query: 111 QEYLVDMADL 120
+ L
Sbjct: 74 AAFKRLWEAL 83
>gnl|CDD|232957 TIGR00398, metG, methionyl-tRNA synthetase. The methionyl-tRNA
synthetase (metG) is a class I amino acyl-tRNA ligase.
This model appears to recognize the methionyl-tRNA
synthetase of every species, including eukaryotic
cytosolic and mitochondrial forms. The UPGMA difference
tree calculated after search and alignment according to
This model shows an unusual deep split between two
families of MetG. One family contains forms from the
Archaea, yeast cytosol, spirochetes, and E. coli, among
others. The other family includes forms from yeast
mitochondrion, Synechocystis sp., Bacillus subtilis, the
Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori.
The E. coli enzyme is homodimeric, although monomeric
forms can be prepared that are fully active. Activity of
this enzyme in bacteria includes aminoacylation of
fMet-tRNA with Met; subsequent formylation of the Met to
fMet is catalyzed by a separate enzyme. Note that the
protein from Aquifex aeolicus is split into an alpha
(large) and beta (small) subunit; this model does not
include the C-terminal region corresponding to the beta
chain [Protein synthesis, tRNA aminoacylation].
Length = 530
Score = 40.4 bits (95), Expect = 0.002
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 274 GHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 311
G++T KMSKSLGN + R+ LR++L+
Sbjct: 319 GYLTVEGGKMSKSLGNVVDPSDLLARFGADILRYYLLK 356
Score = 32.7 bits (75), Expect = 0.52
Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 43 YVCGVTAYDLSHLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDD---KIIRRANDLG 99
Y G HLGHA + D+ RY EV +V D+ KI +A G
Sbjct: 9 YANGKP-----HLGHAYTTILADVYARYKRLRGYEVLFV---CGTDEHGTKIELKAEQEG 60
Query: 100 ENPLSLSNRYCQEY 113
P L ++Y +E+
Sbjct: 61 LTPKELVDKYHEEF 74
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 39.8 bits (94), Expect = 0.003
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
+ ++T K SKS G + ERY P LR++L +
Sbjct: 325 SEYLTLEGGKFSKSRGWGIWVDDALERYPPDYLRYYLAAN 364
>gnl|CDD|234829 PRK00750, lysK, lysyl-tRNA synthetase; Reviewed.
Length = 510
Score = 39.4 bits (93), Expect = 0.004
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 278 NNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 310
EK+SKS GN TI E P +LR F+
Sbjct: 276 KKGEKISKSKGNVITIEDWLEYAPPESLRLFMF 308
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 38.2 bits (90), Expect = 0.010
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 274 GHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 310
G + KMSKS GN ++ +RY ALR++L+
Sbjct: 291 GWWLMKDGKMSKSKGNVVDPEELVDRYGLDALRYYLL 327
>gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of class I
lysyl tRNA synthetase. Class I lysyl tRNA synthetase
(LysRS) catalytic core domain. This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. The class I LysRS is found only in archaea and
some bacteria and has evolved separately from class II
LysRS, as the two do not share structural or sequence
similarity.
Length = 353
Score = 37.7 bits (88), Expect = 0.011
Identities = 11/33 (33%), Positives = 12/33 (36%)
Query: 279 NNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 311
KMS S GN T E P LR+
Sbjct: 272 GGGKMSSSKGNVITPSDWLEVAPPEVLRYLYAR 304
>gnl|CDD|232956 TIGR00396, leuS_bact, leucyl-tRNA synthetase, eubacterial and
mitochondrial family. The leucyl-tRNA synthetases
belong to two families so broadly different that they
are represented by separate models. This model includes
both eubacterial and mitochondrial leucyl-tRNA
synthetases. It generates higher scores for some
valyl-tRNA synthetases than for any archaeal or
eukaryotic cytosolic leucyl-tRNA synthetase. Note that
the enzyme from Aquifex aeolicus is split into alpha and
beta chains; neither chain is long enough to score above
the trusted cutoff, but the alpha chain scores well
above the noise cutoff. The beta chain must be found by
a model and search designed for partial length matches
[Protein synthesis, tRNA aminoacylation].
Length = 842
Score = 37.8 bits (88), Expect = 0.014
Identities = 30/140 (21%), Positives = 56/140 (40%), Gaps = 8/140 (5%)
Query: 276 VTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYI 335
V EKMSKS GN ++I E Y ALR F++ + P+ S+ +S +
Sbjct: 599 VYVGYEKMSKSKGNGIDPQEIVESYGADALRLFIM---FMGPIAASLEWNESGLEGARRF 655
Query: 336 YQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFH---ARMSDDLNTSHILTGAFQ 392
+ + ++ E + A E+ +LR + H ++++DL A
Sbjct: 656 LDRVWNLVYEITG--ELDAASLTVTALEEAQKELRRDVHKFLKKVTEDLEKRESFNTAIS 713
Query: 393 DALKFINSSLNMLKKKQPKQ 412
++ +N K+ +
Sbjct: 714 AMMELLNKLYKAKKEALMLE 733
>gnl|CDD|216786 pfam01921, tRNA-synt_1f, tRNA synthetases class I (K). This family
includes only lysyl tRNA synthetases from prokaryotes.
Length = 357
Score = 37.6 bits (88), Expect = 0.015
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 281 EKMSKSLGNFFTIRQITERYHPLALRHFLI 310
KMS S GN TI E P +LR +
Sbjct: 278 GKMSSSKGNVITIEDWLEYAPPESLRFLMF 307
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 37.8 bits (89), Expect = 0.015
Identities = 17/41 (41%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 273 NGHVTNNN-EKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
+GHV + + +KMSKSLGN+ ++ ++Y ALR +L+S+
Sbjct: 582 HGHVLDEDGQKMSKSLGNYVDPFEVFDKYGADALRWYLLSS 622
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 37.6 bits (88), Expect = 0.016
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 279 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 313
KMSKS GN + ++Y ALR L S
Sbjct: 522 QGRKMSKSKGNVIDPLDVIDKYGADALRFTLASLA 556
>gnl|CDD|224302 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation,
ribosomal structure and biogenesis].
Length = 521
Score = 37.3 bits (87), Expect = 0.018
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 279 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 313
KMS S GN ++ E P LR +LI+
Sbjct: 274 GGGKMSSSKGNVISLSDWLEVAPPEVLR-YLIART 307
>gnl|CDD|185677 cd00817, ValRS_core, catalytic core domain of valyl-tRNA
synthetases. Valine amino-acyl tRNA synthetase (ValRS)
catalytic core domain. This enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. ValRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements. This editing region
hydrolyzes mischarged cognate tRNAs and thus prevents
the incorporation of chemically similar amino acids.
Length = 382
Score = 36.1 bits (84), Expect = 0.040
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 279 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 313
+ KMSKSLGN + + Y ALR L SA
Sbjct: 340 DGRKMSKSLGNVIDPLDVIDGYGADALRFTLASAA 374
>gnl|CDD|215739 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).
Other tRNA synthetase sub-families are too dissimilar to
be included.
Length = 606
Score = 35.4 bits (82), Expect = 0.069
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 1/86 (1%)
Query: 237 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNN-EKMSKSLGNFFTIRQ 295
D+ G D I A + + +G V + KMSKSLGN
Sbjct: 521 ADMLLEGSDQTRGWFYRMIVLGTALTGSAPYKNVLVHGLVRDEQGRKMSKSLGNVIDPLD 580
Query: 296 ITERYHPLALRHFLISAHYRSPLNYS 321
+ ++Y ALR +L S+ Y +N+S
Sbjct: 581 VIDKYGADALRLWLASSDYGRDINFS 606
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 35.0 bits (81), Expect = 0.083
Identities = 21/106 (19%), Positives = 48/106 (45%), Gaps = 12/106 (11%)
Query: 390 AFQDALKFINSSLNMLKKKQPKQ--QQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVL 447
A + L+ I+ L +K + K +L L+E R+ E+ R+ L +
Sbjct: 169 ALRQQLEVISEELEARRKLKEKGLVSRLELLELERERAEAQGELGRLEAELE-----VLK 223
Query: 448 QQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTR 493
+Q+ + L+R ++ + +++EE A+ ++ ++R L +
Sbjct: 224 RQIDELQLERQQIEQTFREEVLEELTEAQ-----ARLAELRERLNK 264
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 35.1 bits (82), Expect = 0.092
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 311
+G +T KMSKS G F R + P LR++L +
Sbjct: 320 HGFLTVEGAKMSKSRGTFIWARTYLDHLDPDYLRYYLAA 358
Score = 30.1 bits (69), Expect = 3.9
Identities = 22/71 (30%), Positives = 28/71 (39%), Gaps = 8/71 (11%)
Query: 54 HLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDDK----IIRRANDLGENPLSLSNRY 109
HLGH + D+ RY EV +V DD I+ +A G P L RY
Sbjct: 18 HLGHLVEYIQADIWVRYQRMRGHEVLFVCA----DDAHGTPIMLKAEKEGITPEELIARY 73
Query: 110 CQEYLVDMADL 120
E+ D A
Sbjct: 74 HAEHKRDFAGF 84
>gnl|CDD|214848 smart00840, DALR_2, This DALR domain is found in
cysteinyl-tRNA-synthetases.
Length = 56
Score = 30.2 bits (69), Expect = 0.24
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 372 EFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEV 431
F M DD NT L F + + IN L K ++ L + ++ +
Sbjct: 1 RFEEAMDDDFNTPEALAVLF-ELAREINR----LALKATDAEE------LAALAALLRAL 49
Query: 432 LRILGLL 438
+LGLL
Sbjct: 50 GGVLGLL 56
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 33.7 bits (78), Expect = 0.26
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 281 EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 321
KMSKSLGN + + ++Y LR ++ S+ Y L +S
Sbjct: 601 RKMSKSLGNVVDPQDVIDKYGADILRLWVASSDYWEDLRFS 641
>gnl|CDD|232969 TIGR00422, valS, valyl-tRNA synthetase. The valyl-tRNA synthetase
(ValS) is a class I amino acyl-tRNA ligase and is
particularly closely related to the isoleucyl tRNA
synthetase [Protein synthesis, tRNA aminoacylation].
Length = 861
Score = 32.7 bits (75), Expect = 0.51
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 279 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 313
KMSKSLGN + E+Y ALR L S
Sbjct: 522 QGRKMSKSLGNVIDPLDVIEKYGADALRFTLASLV 556
>gnl|CDD|181787 PRK09343, PRK09343, prefoldin subunit beta; Provisional.
Length = 121
Score = 30.8 bits (70), Expect = 0.59
Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 15/102 (14%)
Query: 403 NMLKKKQPKQQQLSLIESLR-KIE---NEVKEVLRILGLLPPGA--YSEV----LQQLKD 452
L + Q QQQL + + +I+ E+ + L L LP Y V ++ K
Sbjct: 11 AQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKIVGNLLVKVDKT 70
Query: 453 KALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRK 494
K K EL E +L+E R+ + ++ ++++ +L K
Sbjct: 71 KVEK--ELKER--KELLELRSRTLEKQEKKLREKLK-ELQAK 107
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 30.7 bits (70), Expect = 0.67
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 24/93 (25%)
Query: 403 NMLKKKQPKQQQLS-LIESLRKIENEVKE---VLRILGLLPPGA--------------YS 444
L + Q QQQL +I +++E ++KE L L L A
Sbjct: 10 AQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKE 69
Query: 445 EVLQQLKDKA------LKRAELTEEDVLQLIEE 471
E + +L+++ +K E EE + + +EE
Sbjct: 70 EAVDELEERKETLELRIKTLEKQEEKLQERLEE 102
>gnl|CDD|235046 PRK02507, PRK02507, proton extrusion protein PcxA; Provisional.
Length = 422
Score = 32.2 bits (74), Expect = 0.78
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 23/89 (25%)
Query: 385 HILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEV-------KEVLRI--- 434
L+ F ++ ++ P I ++E E KE L
Sbjct: 216 QQLSKTF-----IVSPLVD---HFFPALPFEIFINP--ELEEEALEELRRFKEELEFEAL 265
Query: 435 LGLLPPGAYSEVLQQLKDKALKRAELTEE 463
LGL PP + E+ ++LK+KA EL EE
Sbjct: 266 LGLAPPLSPEEIEEKLKEKA---EELAEE 291
>gnl|CDD|236000 PRK07360, PRK07360, FO synthase subunit 2; Reviewed.
Length = 371
Score = 31.8 bits (73), Expect = 0.79
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 442 AYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRAD 490
++ + + ++A K +L++ED L+L+E R + +D++R +
Sbjct: 2 MTDQIFEDILERARKGKDLSKEDALELLETTEPRRIFEILELADRLRKE 50
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 325
Score = 31.9 bits (73), Expect = 0.89
Identities = 16/41 (39%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 178 NNRAGE-RVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPG 217
AGE V V + NP D WK G P+W P PG
Sbjct: 24 GPGAGEVLVKVHAAGLNPVD---WKVIAWGPPAWSYPHVPG 61
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 31.5 bits (72), Expect = 1.2
Identities = 26/108 (24%), Positives = 37/108 (34%), Gaps = 34/108 (31%)
Query: 54 HLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEY 113
H+GHAR A+ + LY K +R D D + R E
Sbjct: 23 HIGHARTAL-LNYLYARKYGGKF---ILR-IEDTDPE-----------------RETPEA 60
Query: 114 LVDM--ADLQCL------PPTYQPRVSDHMEQIKDMITQIINNDCAYV 153
D DL+ L P YQ S+ + + ++I AYV
Sbjct: 61 -EDAILEDLEWLGLDWDEGPYYQ---SERFDIYYEYAEKLIEKGKAYV 104
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 31.6 bits (72), Expect = 1.3
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 273 NGHVTNNN-EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDA 331
+G + KMSKSLGN ++ +Y LR ++ S+ L +S L +
Sbjct: 601 HGFTLDEKGRKMSKSLGNVVDPLKVINKYGADILRLYVASSDPWEDLRFSDEILKQVVEK 660
Query: 332 VFYI 335
I
Sbjct: 661 YRKI 664
>gnl|CDD|233890 TIGR02486, RDH, reductive dehalogenase. This model represents a
family of corrin and 8-iron Fe-S cluster-containing
reductive dehalogenases found primarily in halorespiring
microorganisms such as dehalococcoides ethenogenes which
contains as many as 17 enzymes of this type with varying
substrate ranges. One example of a characterized species
is the tetrachloroethene reductive dehalogenase
(1.97.1.8) which also acts on trichloroethene converting
it to dichloroethene.
Length = 314
Score = 31.2 bits (71), Expect = 1.4
Identities = 21/104 (20%), Positives = 30/104 (28%), Gaps = 33/104 (31%)
Query: 193 NPADFALWK----------------AAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSK 236
P D + K +K GEP+WD G P + K
Sbjct: 197 KPIDAGMAKFCETCGKCADECPSGAISKGGEPTWDPEDSNGDP--------PGENNPGLK 248
Query: 237 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSY------WMHNG 274
+ G L NE C CQ + + W+H+
Sbjct: 249 WQYDGWRCLLFRC--YNEGGGGCGVCQ-AVCPFNKKPNSWIHDV 289
>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase.
Length = 616
Score = 31.2 bits (70), Expect = 1.5
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 273 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 310
+G +T + KM KSLGN ++ +++ P A+R+F +
Sbjct: 357 HGFLTKDGMKMGKSLGNTLEPFELVQKFGPDAVRYFFL 394
>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed.
Length = 800
Score = 31.3 bits (72), Expect = 1.6
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 281 EKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
+KMSKS GN T ++ E+Y A+R++ SA
Sbjct: 532 KKMSKSKGNVVTPEELLEKYGADAVRYWAASA 563
>gnl|CDD|131371 TIGR02318, phosphono_phnM, phosphonate metabolism protein PhnM.
This family consists of proteins from in the PhnM
family. PhnM is a a protein associated with phosphonate
utilization in a number of bacterial species. In
Pseudomonas stutzeri WM88, a protein that is part of a
system for the oxidation of phosphites (another form of
reduced phosphorous compound) scores between trusted and
noise cutoffs [Energy metabolism, Other].
Length = 376
Score = 30.8 bits (70), Expect = 1.7
Identities = 12/52 (23%), Positives = 27/52 (51%)
Query: 447 LQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIAL 498
L++ ++ + L++++ +++EER A R + +I A +GI L
Sbjct: 174 LEKYREYYRGKRGLSDDEFDEIVEERIARRAEYGLANRSEIAALARARGIPL 225
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. IleRS has an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids.
Length = 338
Score = 30.7 bits (70), Expect = 1.9
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 281 EKMSKSLGNFFTIRQITERYHPLALRHFLISA 312
KMSKSLGN+ +++ ++Y ALR ++ S+
Sbjct: 298 RKMSKSLGNYVDPQEVVDKYGADALRLWVASS 329
>gnl|CDD|197491 smart00053, DYNc, Dynamin, GTPase. Large GTPases that mediate
vesicle trafficking. Dynamin participates in the
endocytic uptake of receptors, associated ligands, and
plasma membrane following an exocytic event.
Length = 240
Score = 30.6 bits (69), Expect = 1.9
Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 70 YLEHLKCEVTYVRNFTDVDDKIIRRANDL------GENPLSLSNRYCQEY-----LVDMA 118
Y E L C+ +F +V ++I D G + + ++ R + L+D+
Sbjct: 75 YAEFLHCKGKKFTDFDEVRNEI-EAETDRVTGTNKGISGIPINLRVYSPHVLNLTLIDLP 133
Query: 119 DLQCLPPTYQPRVSDHMEQIKDMITQII 146
+ + QP D QIK MI Q I
Sbjct: 134 GITKVAVGDQPP--DIEYQIKKMIKQFI 159
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 30.6 bits (70), Expect = 2.1
Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 14/93 (15%)
Query: 395 LKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRIL--GLLPPGAYSEVLQQLKD 452
L+ L +K +++L ++E L K N++ V+ ++ + A E++++L +
Sbjct: 318 LEVYKRRKEYLLEK--LEERLHILEGLLKALNKIDFVIEVIRGSIDLKKAKKELIEELSE 375
Query: 453 K--------ALKRAELTEEDVLQLIEERAAARK 477
L+R LT+E++ +L +E K
Sbjct: 376 IQADYLLDMRLRR--LTKEEIEKLEKEIEELEK 406
>gnl|CDD|215492 PLN02907, PLN02907, glutamate-tRNA ligase.
Length = 722
Score = 30.8 bits (70), Expect = 2.4
Identities = 42/159 (26%), Positives = 63/159 (39%), Gaps = 46/159 (28%)
Query: 54 HLGHARAAVSFDLLYRYLEHLKCEVTYVRNFTDVDDKIIRRANDLGENPLSLSNRYCQEY 113
H+GHA+AA LL +Y Y K+I R +D NP S+ + +
Sbjct: 227 HIGHAKAA----LLNQYFARR-----Y-------KGKLIVRFDD--TNPSKESDEFVENI 268
Query: 114 LVDMADLQCLPP--TYQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRL 171
L D+ L TY SD+ Q+ +M ++I AYV +
Sbjct: 269 LKDIETLGIKYDAVTY---TSDYFPQLMEMAEKLIKEGKAYVDDTPR------------- 312
Query: 172 SGQRLENNRAGERVA-VDSRKRNPA---DFALWKAAKAG 206
E R ER+ ++S+ RN + + LWK AG
Sbjct: 313 -----EQMRK-ERMDGIESKCRNNSVEENLRLWKEMIAG 345
>gnl|CDD|226375 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication,
recombination, and repair].
Length = 1108
Score = 30.9 bits (70), Expect = 2.5
Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 421 LRKIENEVKEVLRILGLLP--PGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKN 478
KI E+K+ L++ G L G ++ + + K+ +L+ ED+ +E++ + +
Sbjct: 93 FYKILEELKKELKVYGSLADKSGFIEQLAELYTE--FKKYQLSVEDLEDTADEQSLKKLH 150
Query: 479 KDFSKSDQIRADL 491
++ A+L
Sbjct: 151 DLSLIYEEFEANL 163
>gnl|CDD|237967 PRK15446, PRK15446, phosphonate metabolism protein PhnM;
Provisional.
Length = 383
Score = 30.5 bits (70), Expect = 2.5
Identities = 12/52 (23%), Positives = 22/52 (42%)
Query: 447 LQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIAL 498
L++ ++ + L++E+ +EER A I A +GI L
Sbjct: 179 LEKYREYYAGKYGLSDEEFDAFVEERIALSARYAPPNRRAIAALARARGIPL 230
>gnl|CDD|239249 cd02951, SoxW, SoxW family; SoxW is a bacterial periplasmic TRX,
containing a redox active CXXC motif, encoded by a
genetic locus (sox operon) involved in thiosulfate
oxidation. Sulfur bacteria oxidize sulfur compounds to
provide reducing equivalents for carbon dioxide fixation
during autotrophic growth and the respiratory electron
transport chain. It is unclear what the role of SoxW is,
since it has been found to be dispensable in the
oxidation of thiosulfate to sulfate. SoxW is
specifically kept in the reduced state by SoxV, which is
essential in thiosulfate oxidation.
Length = 125
Score = 28.8 bits (65), Expect = 2.9
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 425 ENEVKEVLRILGLLPPGAYSEVLQQLKDKA 454
KE+ R+ G LPP + L+ +++KA
Sbjct: 93 PEGGKEIARLPGYLPPDEFLAYLEYVQEKA 122
>gnl|CDD|153102 cd01043, DPS, DPS protein, ferritin-like diiron-binding domain.
DPS (DNA Protecting protein under Starved conditions)
domain is a member of a broad superfamily of
ferritin-like diiron-carboxylate proteins. Some DPS
proteins nonspecifically bind DNA, protecting it from
cleavage caused by reactive oxygen species such as the
hydroxyl radicals produced during oxidation of Fe(II) by
hydrogen peroxide. These proteins assemble into
dodecameric structures, some form DPS-DNA co-crystalline
complexes, and possess iron and H2O2 detoxification
capabilities. Expression of DPS is induced by oxidative
or nutritional stress, including metal ion starvation.
Members of the DPS family are homopolymers formed by 12
four-helix bundle subunits that assemble with 23
symmetry into a hollow shell. The DPS ferroxidase site
is unusual in that it is not located in a four-helix
bundle as in ferritin, but is shared by 2-fold
symmetry-related subunits providing the iron ligands.
Many DPS sequences (e.g., E. coli) display an N-terminal
extension of variable length that contains two or three
positively charged lysine residues that extends into the
solvent and is thought to play an important role in the
stabilization of the complex with DNA. DPS Listeria Flp,
Bacillus anthracis Dlp-1 and Dlp-2, and Helicobacter
pylori HP-NAP which lack the N-terminal extension, do
not bind DNA. DPS proteins from Helicobacter pylori,
Treponema pallidum, and Borrelia burgdorferi are highly
immunogenic.
Length = 139
Score = 29.1 bits (66), Expect = 3.0
Identities = 13/54 (24%), Positives = 25/54 (46%)
Query: 416 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLI 469
L + LR+ +E+ E +R LG P G E + K L+ ++++ +
Sbjct: 38 ELYDELREAIDEIAERIRALGGKPLGTLKEYAELSTIKEEPAGVLSAKEMVAEL 91
>gnl|CDD|236513 PRK09431, asnB, asparagine synthetase B; Provisional.
Length = 554
Score = 29.9 bits (68), Expect = 3.7
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 334 YIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEF 373
Y +QT DCEV L+ +QE G D ++ L F
Sbjct: 92 YAFQTGSDCEVILALYQEKGP---------DFLDDLDGMF 122
>gnl|CDD|112953 pfam04163, Tht1, Tht1-like nuclear fusion protein.
Length = 554
Score = 30.1 bits (67), Expect = 3.7
Identities = 27/109 (24%), Positives = 43/109 (39%), Gaps = 22/109 (20%)
Query: 354 KTARINPAAEDCINKLRDEFHARMSDDLN-----TSHILTGAFQDALKFINSS------- 401
+ A N A I L+D+F A + D + + L + Q + F+NS
Sbjct: 287 EFASENAIALSAIGDLKDDFLAFLEDRIKNLIEMSEDSLKESVQRNIDFVNSGFQELEDF 346
Query: 402 -------LNMLKKKQPKQQQLSLIESLR---KIENEVKEVLRILGLLPP 440
L LKK +QQ L E L+ ++ K+ L+ +LP
Sbjct: 347 SIGLKEELGGLKKDLSEQQNLEAEEILQGFNDFLHDSKDHLKTDEILPE 395
>gnl|CDD|133062 cd06442, DPM1_like, DPM1_like represents putative enzymes similar
to eukaryotic DPM1. Proteins similar to eukaryotic
DPM1, including enzymes from bacteria and archaea; DPM1
is the catalytic subunit of eukaryotic
dolichol-phosphate mannose (DPM) synthase. DPM synthase
is required for synthesis of the
glycosylphosphatidylinositol (GPI) anchor, N-glycan
precursor, protein O-mannose, and C-mannose. In higher
eukaryotes,the enzyme has three subunits, DPM1, DPM2 and
DPM3. DPM is synthesized from dolichol phosphate and
GDP-Man on the cytosolic surface of the ER membrane by
DPM synthase and then is flipped onto the luminal side
and used as a donor substrate. In lower eukaryotes, such
as Saccharomyces cerevisiae and Trypanosoma brucei, DPM
synthase consists of a single component (Dpm1p and
TbDpm1, respectively) that possesses one predicted
transmembrane region near the C terminus for anchoring
to the ER membrane. In contrast, the Dpm1 homologues of
higher eukaryotes, namely fission yeast, fungi, and
animals, have no transmembrane region, suggesting the
existence of adapter molecules for membrane anchoring.
This family also includes bacteria and archaea DPM1_like
enzymes. However, the enzyme structure and mechanism of
function are not well understood. This protein family
belongs to Glycosyltransferase 2 superfamily.
Length = 224
Score = 29.4 bits (67), Expect = 4.3
Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 24/75 (32%)
Query: 88 DDKIIRRANDLGENPLSLSNRY-------CQEYLVDM-ADLQCLPPTYQPRVSDHMEQIK 139
++I R G L + Y + +V M ADL PP E I
Sbjct: 54 RVRLIVRPGKRG-----LGSAYIEGFKAARGDVIVVMDADLS-HPP----------EYIP 97
Query: 140 DMITQIINNDCAYVV 154
+++ + V+
Sbjct: 98 ELLEAQLEGGADLVI 112
>gnl|CDD|173925 cd02174, CCT, CTP:phosphocholine cytidylyltransferase.
CTP:phosphocholine cytidylyltransferase (CCT) catalyzes
the condensation of CTP and phosphocholine to form
CDP-choline as the rate-limiting and regulatory step in
the CDP-choline pathway. CCT is unique in that its
enzymatic activity is regulated by the extent of its
association with membrane structures. A current model
posts that the elastic stress of the bilayer curvature
is sensed by CCT and this governs the degree of
membrane association, thus providing a mechanism for
both positive and negative regulation of activity.
Length = 150
Score = 28.7 bits (65), Expect = 4.4
Identities = 10/18 (55%), Positives = 11/18 (61%), Gaps = 2/18 (11%)
Query: 43 YVCGVTAYDLSHLGHARA 60
YV G +DL H GHA A
Sbjct: 6 YVDGC--FDLFHYGHANA 21
>gnl|CDD|238955 cd01997, GMP_synthase_C, The C-terminal domain of GMP synthetase.
It contains two subdomains; the ATP pyrophosphatase
domain which closes to the N-termial and the
dimerization domain at C-terminal end. The ATP-PPase is
a twisted, five-stranded parallel beta-sheet sandwiched
between helical layers. It has a signature
nucleotide-binding motif, or P-loop, at the end of the
first-beta strand.The dimerization domain formed by the
C-terminal 115 amino acid for prokaryotic proteins. It
is adjacent to teh ATP-binding site of the ATP-PPase
subdomain. The largest difference between the primary
sequence of prokaryotic and eukaryotic GMP synthetase
map to the dimerization domain.Eukaryotic GMP synthetase
has several large insertions relative to prokaryotes.
Length = 295
Score = 29.4 bits (67), Expect = 4.5
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 409 QPKQQQLSLIESLRKI-ENEVKEVLRILGL 437
P+ +L LIE LR + ++EV+E+ R LGL
Sbjct: 135 LPEDMKLKLIEPLRDLFKDEVRELGRELGL 164
>gnl|CDD|173940 cd08181, PPD-like, 1,3-propanediol dehydrogenase-like (PPD).
1,3-propanediol dehydrogenase-like (PPD). This family is
a member of the iron-containing alcohol dehydrogenase
superfamily, and exhibits a dehydroquinate synthase-like
fold. Protein sequence similarity search and other
biochemical evidences suggest that they are close to the
iron-containing 1,3-propanediol dehydrogenase (EC
1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the
oxidation of propane-1,3-diol to 3-hydroxypropanal with
the simultaneous reduction of NADP+ to NADPH. The
protein structure of Thermotoga maritima TM0920 gene
contains one NADP+ and one iron ion.
Length = 357
Score = 29.5 bits (67), Expect = 4.5
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 417 LIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAAR 476
L E L + ++ E + IL LL G+ E L+ L +L++E++ + ERA +
Sbjct: 279 LPEYLELAKEQIPEKVFILKLLGFGSLDEFLKSLGLLLKVVIKLSDEEIEKWA-ERALSA 337
Query: 477 KNK 479
K+K
Sbjct: 338 KHK 340
>gnl|CDD|216047 pfam00656, Peptidase_C14, Caspase domain.
Length = 228
Score = 29.2 bits (66), Expect = 4.6
Identities = 23/116 (19%), Positives = 38/116 (32%), Gaps = 20/116 (17%)
Query: 140 DMITQIINND-CAYVVEG-DVFF-------AVEKSPNYGRLSGQRLENNRAGERVAVDSR 190
D + + N C + +F ++ S E+ E A S+
Sbjct: 90 DALDDVFNGLNCPSLKGKPKLFIIDACRGGPLDDGVKSDSGSSGESESVDDSEA-AGLSK 148
Query: 191 KRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDL 246
PADF + + G+ S+ G G W I+ L + G+DL
Sbjct: 149 IPAPADFLVAYSTTPGQVSYR---GTGSGSWFIQA-------LCQVLREYAPGLDL 194
>gnl|CDD|216083 pfam00724, Oxidored_FMN, NADH:flavin oxidoreductase / NADH oxidase
family.
Length = 336
Score = 29.6 bits (67), Expect = 4.6
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 15/76 (19%)
Query: 416 SLIESLRKIENEVKE-----VLRI--LGLLPPGAYSEVLQQLK------DKALKRAELTE 462
+E +K+ V E +++ LG P Y E L ++K ELT+
Sbjct: 76 EQVEGWKKLTEAVHENGSKIGVQLWHLGREAPPEYLEDLGLRPSDPSALPASIKVRELTK 135
Query: 463 EDVLQLIEE--RAAAR 476
E++ ++I+E +AA R
Sbjct: 136 EEIKEIIQEFVQAAKR 151
>gnl|CDD|220417 pfam09812, MRP-L28, Mitochondrial ribosomal protein L28. Members
of this family are components of the mitochondrial large
ribosomal subunit. Mature mitochondrial ribosomes
consist of a small (37S) and a large (54S) subunit. The
37S subunit contains at least 33 different proteins and
1 molecule of RNA (15S). The 54S subunit contains at
least 45 different proteins and 1 molecule of RNA (21S).
Length = 146
Score = 28.5 bits (64), Expect = 4.9
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 407 KKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRA----ELTE 462
KK+ K +++E +++ + L P V Q D+A +R +L+
Sbjct: 7 KKKKKVDPQREQRKRKRLEKFIRKRTKSARGLKPVEDRIVPQLSVDEAKRRQRKLLKLSP 66
Query: 463 EDVLQLIEERAAARK 477
ED+ E RA K
Sbjct: 67 EDL----ERRALIEK 77
>gnl|CDD|233454 TIGR01536, asn_synth_AEB, asparagine synthase
(glutamine-hydrolyzing). This model describes the
glutamine-hydrolysing asparagine synthase. A poorly
conserved C-terminal extension was removed from the
model. Bacterial members of the family tend to have a
long, poorly conserved insert lacking from archaeal and
eukaryotic sequences. Multiple isozymes have been
demonstrated, such as in Bacillus subtilis. Long-branch
members of the phylogenetic tree (which typically were
also second or third candidate members from their
genomes) were removed from the seed alignment and score
below trusted cutoff [Amino acid biosynthesis, Aspartate
family].
Length = 466
Score = 29.6 bits (67), Expect = 4.9
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 9/40 (22%)
Query: 334 YIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEF 373
Y +QT D EV L ++E G E+C+++L F
Sbjct: 91 YTFQTDSDTEVILHLYEEWG---------EECVDRLDGMF 121
>gnl|CDD|235427 PRK05354, PRK05354, arginine decarboxylase; Provisional.
Length = 634
Score = 29.7 bits (68), Expect = 5.2
Identities = 17/54 (31%), Positives = 33/54 (61%), Gaps = 9/54 (16%)
Query: 423 KIENEVK-----EVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE 471
+IE+ ++ +VL + P E+L++L++KA+K +L+ E+ QL+EE
Sbjct: 571 EIEHVIEGDTVADVLEYVQYDP----KELLERLREKAVKEGKLSPEERQQLLEE 620
>gnl|CDD|224585 COG1671, COG1671, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 150
Score = 28.4 bits (64), Expect = 5.6
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 19/51 (37%)
Query: 65 DLLYRYLEHLKCEVTYVRNF--------------TD-----VDDKIIRRAN 96
D +YR E + +VT+V NF D DD I+ A
Sbjct: 15 DEIYRVAERMGLKVTFVANFPHRVPPSPEIRTVVVDAGFDAADDWIVNLAE 65
>gnl|CDD|148159 pfam06385, Baculo_LEF-11, Baculovirus LEF-11 protein. This family
consists of several Baculovirus LEF-11 proteins. The
exact function of this family is unknown although it has
been shown that LEF-11 is required for viral DNA
replication during the infection cycle.
Length = 95
Score = 27.6 bits (62), Expect = 5.6
Identities = 9/64 (14%), Positives = 21/64 (32%), Gaps = 8/64 (12%)
Query: 365 CINKLRDEFHARMSDDLN--TSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLR 422
IN + F D +H+ F +I ++L+ + + +
Sbjct: 14 VINYRKHTF------DTKNVCAHVEDDGFATISDYIRANLDKAFIIVGDCSKKRVAPHRK 67
Query: 423 KIEN 426
++E
Sbjct: 68 RLER 71
>gnl|CDD|213366 cd12832, TmCorA-like_u3, Uncharacterized subfamily of the
Thermotoga maritima CorA-like family. This subfamily
belongs to the Thermotoga maritima CorA (TmCorA)-like
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes. Members of the
TmCorA-like family are found in all three kingdoms of
life. It is a functionally diverse family which includes
the CorA Co2+ transporter from the hyperthermophilic
Thermotoga maritima, and three Saccharomyces cerevisiae
proteins: two located in the plasma membrane: the Mg2+
transporter Alr1p/Swc3p and the putative Mg2+
transporter, Alr2p, and the vacuole membrane protein
Mnr2p, a putative Mg2+ transporter. Thermotoga maritima
CorA forms funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by a related protein, Saccharomyces cerevisiae
Alr1p. Natural variants in this signature sequence may
be associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 287
Score = 29.1 bits (66), Expect = 6.2
Identities = 20/116 (17%), Positives = 51/116 (43%), Gaps = 15/116 (12%)
Query: 364 DCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPK--------QQQL 415
+ I L++++ + M + + +L +DALK + L L ++ K +++
Sbjct: 88 EFIANLKEKWLSGMHKCESPTELLLRIVKDALKTYEAPLEKLSEELDKYEEEVFLKKRKG 147
Query: 416 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE 471
SL++ L ++ + + R+L L +V+ ++ +D+ L+ +
Sbjct: 148 SLLKRLYHLKRKASVIKRVLNLT-----QDVIDKIDTPLKSDPYT--QDLRDLLIK 196
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.4 bits (67), Expect = 6.2
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 9/75 (12%)
Query: 404 MLKKKQPKQQQLSLIESL-----RKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRA 458
+ KK++ +Q+ +E IE +++E+ RI GL A +L++++++A R
Sbjct: 112 LEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAKEILLEKVEEEA--RH 169
Query: 459 ELTEEDVLQLIEERA 473
E +++ IEE A
Sbjct: 170 EAAV--LIKEIEEEA 182
>gnl|CDD|152127 pfam11691, DUF3288, Protein of unknown function (DUF3288). This
family of proteins with unknown function appears to be
restricted to Cyanobacteria.
Length = 90
Score = 27.2 bits (61), Expect = 7.0
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 440 PGAYSEVLQQLKDKALKRAELTEEDVL---QLIEERAAARKNKDFSKSDQ 486
PGA E LQ+ +K LK LTEE++ + I + D S +
Sbjct: 42 PGA--EDLQRDLEKVLKLWGLTEEELFERTREIHAKGGVYSGFDTSDQED 89
>gnl|CDD|220640 pfam10234, Cluap1, Clusterin-associated protein-1. This protein is
conserved from worms to humans. The protein of 413 amino
acids contains a central coiled-coil domain, possibly
the region that binds to clusterin. Cluap1 expression is
highest in the nucleus and gradually increases during
late S to G2/M phases of the cell cycle and returns to
the basal level in the G0/G1 phases. In addition, it is
upregulated in colon cancer tissues compared to
corresponding non-cancerous mucosa. It thus plays a
crucial role in the life of the cell.
Length = 269
Score = 28.8 bits (65), Expect = 7.2
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 14/79 (17%)
Query: 428 VKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQI 487
VKE+L+I +L KA+K + EE+ + + + K D + Q+
Sbjct: 81 VKELLKITSVLY-------------KAMKSTDGDEEENTRSLAKFDLGSKISDLKAARQL 127
Query: 488 RADLTRKGIALMDM-GKET 505
+++T +G AL D+ GKE
Sbjct: 128 ASEITERGAALYDLLGKEL 146
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 28.9 bits (66), Expect = 7.8
Identities = 7/11 (63%), Positives = 7/11 (63%)
Query: 279 NNEKMSKSLGN 289
KMSKS GN
Sbjct: 517 QGRKMSKSKGN 527
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 8.1
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 412 QQQLSLIES----LRKIENEVKEVLRILGLLPPGA--YSEVLQQLKDKALKRAELTEEDV 465
++++ +E L +++ ++KE+ + L L Y E + ++ + LT
Sbjct: 327 EERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTP 386
Query: 466 LQLIEERAAARKNK 479
+L +E K K
Sbjct: 387 EKLEKELEELEKAK 400
>gnl|CDD|146204 pfam03448, MgtE_N, MgtE intracellular N domain. This domain is
found at the N-terminus of eubacterial magnesium
transporters of the MgtE family pfam01769. This domain
is an intracellular domain that has an alpha-helical
structure. The crystal structure of the MgtE transporter
shows two of 5 magnesium ions are in the interface
between the N domain and the CBS domains. In the absence
of magnesium there is a large shift between the N and
CBS domains.
Length = 102
Score = 27.1 bits (61), Expect = 8.3
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 417 LIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKR--AELTEEDVLQLIEE 471
L+E L +E L +L LLPP +EVL++L + L E++ +L+EE
Sbjct: 9 LLEEL-----PPEERLALLRLLPPERAAEVLEELDEDVQAELLEALPPEELAELLEE 60
>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 28.9 bits (66), Expect = 8.5
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 281 EKMSKSLGN 289
KMSKSLGN
Sbjct: 591 RKMSKSLGN 599
>gnl|CDD|217630 pfam03592, Terminase_2, Terminase small subunit. Packaging of
double-stranded viral DNA concatemers requires
interaction of the prohead with virus DNA. This process
is mediated by a phage-encoded DNA recognition and
terminase protein. The terminase enzymes described so
far, which are hetero-oligomers composed of a small and
a large subunit, do not have a significant level of
sequence homology. The small terminase subunit is
thought to form a nucleoprotein structure that helps to
position the terminase large subunit at the packaging
initiation site.
Length = 141
Score = 27.6 bits (62), Expect = 9.1
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 460 LTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWRPCVLVEQEQEA 519
LT+ + I+E R+ + +D++ +LT IA D + + ++ E
Sbjct: 40 LTKPKIKAYIDELMKEREKRTIITADEVLEELTE--IARGDETELVLVGTKEGEVEKIEK 97
Query: 520 PPAEKEKKPAA 530
K++ A
Sbjct: 98 KVKLKDRLKAL 108
>gnl|CDD|129369 TIGR00268, TIGR00268, TIGR00268 family protein. The N-terminal
region of the model shows similarity to
Argininosuccinate synthase proteins using PSI-blast and
using the recognize protein identification server
[Hypothetical proteins, Conserved].
Length = 252
Score = 28.2 bits (63), Expect = 9.2
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 418 IESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKD-KALKRAELTEEDVLQLIEERAAAR 476
E L+ ++ E +EVLR G +V ++++ L E+ E+++ +L+ E R
Sbjct: 181 EEKLKMVD-EAEEVLRNAG------VGQV--RVRNYDNLAVIEVPEDELSKLLNEAEEVR 231
Query: 477 KN-KDF 481
KD
Sbjct: 232 DKFKDI 237
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 28.9 bits (64), Expect = 9.5
Identities = 36/171 (21%), Positives = 60/171 (35%), Gaps = 23/171 (13%)
Query: 367 NKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLK-----KKQPKQQQLSLIESL 421
+ L +E R+ L T A QDA + + S +N+L P Q S E L
Sbjct: 278 DMLPEERKLRLLKALAEMSPYTTA-QDARQRLPSIVNLLLEYMPLGDTPPSFQFSHAECL 336
Query: 422 RKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDF 481
L LG P A + + L E+ + KNKDF
Sbjct: 337 LY-------ALHTLGKKHPNATNSLCGYKIVTGQPSDRLGEDF----------SEKNKDF 379
Query: 482 SKSDQIRADLTRKGIALMDMGKETIWRPCVLVEQEQEAPPAEKEKKPAATG 532
++ DLT+ + + G + + ++E + +++ TG
Sbjct: 380 TERLTYVEDLTKATMKKLTQGMSEHSKAMSTAKTDEEKEELKTKEQLTTTG 430
>gnl|CDD|223070 PHA03391, p47, viral transcription regulator p47; Provisional.
Length = 395
Score = 28.7 bits (65), Expect = 9.5
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 14/50 (28%)
Query: 279 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSA 328
N++K K L + +I I +R ++ Y VL+LD+
Sbjct: 180 NDKKFEKFLSSITSISDIIKR--------------HKFSKKYIVLELDAN 215
>gnl|CDD|219783 pfam08297, U3_snoRNA_assoc, U3 snoRNA associated. This family of
proteins is associated with U3 snoRNA. U3 snoRNA is
required for nucleolar processing of pre-18S ribosomal
RNA.
Length = 87
Score = 26.6 bits (59), Expect = 9.9
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 9/67 (13%)
Query: 400 SSLNMLKKKQPKQQQLSLIESLRKIENEVKE---VLRILG-----LLPPGAYSEVLQQLK 451
S KKQ K+ +L ++ L K +VK+ +R+L LPP A +++ K
Sbjct: 22 ESYEEELKKQKKKNKLRFLKKLEKRPKDVKKGPVTVRVLSDNNSRKLPPKAEKKIV-NSK 80
Query: 452 DKALKRA 458
DK L R
Sbjct: 81 DKWLNRK 87
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
0.317 0.132 0.392
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,339,043
Number of extensions: 2676020
Number of successful extensions: 3202
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3149
Number of HSP's successfully gapped: 138
Length of query: 537
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 435
Effective length of database: 6,413,494
Effective search space: 2789869890
Effective search space used: 2789869890
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.1 bits)