RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014658
(421 letters)
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 603 bits (1556), Expect = 0.0
Identities = 258/405 (63%), Positives = 311/405 (76%), Gaps = 9/405 (2%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRL 60
MA L CLPP+ +PRVSDH+ QI DMI QI++N CAY V+GDV+F+V+K P YG+LSG++L
Sbjct: 158 MAYLHCLPPSVEPRVSDHIPQIIDMIKQILDNGCAYRVDGDVYFSVDKFPEYGKLSGRKL 217
Query: 61 ENNRAGERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSK 120
E+NRAGERVAVDSRK+NPADFALWKAAK GEP WDSPWGPGRPGWHIECSAMSA YL
Sbjct: 218 EDNRAGERVAVDSRKKNPADFALWKAAKEGEPFWDSPWGPGRPGWHIECSAMSAAYLGHS 277
Query: 121 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQI 180
FDIHGGG+DL+FPHHENEIAQSCAAC DSN+SYW+HNG VT ++EKMSKSLGNFFTIRQ+
Sbjct: 278 FDIHGGGMDLVFPHHENEIAQSCAACCDSNISYWIHNGFVTVDSEKMSKSLGNFFTIRQV 337
Query: 181 TERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTA 240
+ YHPLALR FL+ HYRSP+NYS +QL+SAS+ +FYIYQTL DCE +L +
Sbjct: 338 IDLYHPLALRLFLLGTHYRSPINYSDVQLESASERIFYIYQTLHDCEESLQQHDSTFEKD 397
Query: 241 RINPAAEDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLK-KKQPKQQQL 299
+ P +CINK DEF MSDDL+T + A + LK IN L+ K KKQ K+
Sbjct: 398 SVPPDTLNCINKFHDEFVTSMSDDLHTP-VALAALSEPLKTINDLLHTRKGKKQEKR--- 453
Query: 300 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAA 359
+ESL +E ++++VL +LGL+P +YSE LQQL++KAL+RA+LTEE VLQ IEER A
Sbjct: 454 --LESLAALEKKIRDVLSVLGLMPT-SYSEALQQLREKALRRAKLTEEQVLQKIEERTVA 510
Query: 360 RKNKDFSKSDQIRADLTRKGIALMDMGKETIWRPCV-LVEQEQEA 403
RKNK++ KSD IR DL GIALMD T WRP + L QEQ A
Sbjct: 511 RKNKEYEKSDAIRKDLAAVGIALMDSPDGTTWRPAIPLALQEQVA 555
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 505 bits (1304), Expect = e-178
Identities = 174/393 (44%), Positives = 225/393 (57%), Gaps = 33/393 (8%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRL 60
M L LPP +PR ++H+ +I ++I ++I+ AY +GDV+F V K P+YG+LSG+ L
Sbjct: 101 MDALNVLPPDIEPRATEHIPEIIELIERLIDKGHAYEADGDVYFDVRKFPDYGKLSGRNL 160
Query: 61 ENNRAGERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSK 120
+ +AG RV V KR+P DFALWKAAK GEPSW+SPWG GRPGWHIECSAMS YL
Sbjct: 161 DELQAGARVEVAEEKRDPLDFALWKAAKPGEPSWESPWGKGRPGWHIECSAMSTKYLGET 220
Query: 121 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQI 180
FDIHGGG DLIFPHHENEIAQS AA +YWMHNG VT N EKMSKSLGNFFTIR +
Sbjct: 221 FDIHGGGADLIFPHHENEIAQSEAATGKPFANYWMHNGFVTVNGEKMSKSLGNFFTIRDL 280
Query: 181 TERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTA 240
++Y P LR FL+SAHYRSPLN+S L+ A A+ +Y L + +
Sbjct: 281 LKKYDPEVLRFFLLSAHYRSPLNFSEEALEQAKKALERLYNALAETALGEDD-------- 332
Query: 241 RINPAAEDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLS 300
A + + ++ F M DD NT L + + IN +L K
Sbjct: 333 ---EALLAELEEFKERFIEAMDDDFNTPEALA-VLFELAREINRALETKDK--------- 379
Query: 301 LIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAAR 360
E+ + ++ + +LGL + EL + ++ LIEER AR
Sbjct: 380 --EAAAALAALLRALADVLGLEQ--------DEEALFEAAADELLDAEIEALIEERQEAR 429
Query: 361 KNKDFSKSDQIRADLTRKGIALMDMGKE-TIWR 392
K KDF+ +D IR +L GI L D + T WR
Sbjct: 430 KAKDFALADAIRDELAALGIVLED-TPDGTTWR 461
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 446 bits (1149), Expect = e-155
Identities = 174/395 (44%), Positives = 221/395 (55%), Gaps = 35/395 (8%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVE-GDVFFAVEKSPNYGRLSG-Q 58
M L LPP +PR ++H+++I + I ++I AYV + GDV+F V K +YG+LSG
Sbjct: 100 MDALNVLPPDIEPRATEHIDEIIEFIEKLIEKGYAYVADDGDVYFDVSKFKDYGKLSGRD 159
Query: 59 RLENNRAGERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLS 118
LE +AG RV VD KRNP DF LWKAAK GEPSWDSPWG GRPGWHIECSAMS YL
Sbjct: 160 SLEELQAGARVEVDEEKRNPLDFVLWKAAKPGEPSWDSPWGKGRPGWHIECSAMSTKYLG 219
Query: 119 SKFDIHGGGIDLIFPHHENEIAQSCAACQDSN-VSYWMHNGHVTNNNEKMSKSLGNFFTI 177
FDIHGGG DLIFPHHENEIAQS AA YWMHNG + + EKMSKSLGNF T+
Sbjct: 220 ETFDIHGGGSDLIFPHHENEIAQSEAATGVKPFAKYWMHNGFLNIDGEKMSKSLGNFITV 279
Query: 178 RQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHG 237
R + ++Y P LR FL+S+HYRSPL++S L+ A A+ +Y L+
Sbjct: 280 RDLLKKYDPEVLRLFLLSSHYRSPLDFSEELLEEAKKALERLYNALRRLRDLA------- 332
Query: 238 KTARINPAAEDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQ 297
A + + F + DD NT L + K IN L + K +
Sbjct: 333 -----GDAELADLKEFEARFREALDDDFNTPKALA-VLFELAKEINRLLE--EGKSDAKA 384
Query: 298 QLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERA 357
LS + K +L ILGL G + + Q E +E++ LIEER
Sbjct: 385 VLSAL----------KALLAILGLKVLGLFPQSGAQE-------DESDDEEIEALIEERL 427
Query: 358 AARKNKDFSKSDQIRADLTRKGIALMDMGKETIWR 392
ARK K+++ +D+IR +L GI L D T WR
Sbjct: 428 EARKAKNWALADEIRDELLALGIILEDTPDGTTWR 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 = 379 bits (975), Expect = e-129
Identities = 177/393 (45%), Positives = 232/393 (59%), Gaps = 29/393 (7%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVE-GDVFFAVEKSPNYGRLSGQR 59
M L LPP +PR ++H+++I + I Q+I AYV + GDV+F V K +YG+LS Q
Sbjct: 99 MKALNVLPPDLEPRATEHIDEIIEFIEQLIEKGYAYVSDNGDVYFDVSKFKDYGKLSKQD 158
Query: 60 LENNRAGERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSS 119
L+ AG RV VD KRN DF LWK++K GEP WDSPWG GRPGWHIECSAM+ YL
Sbjct: 159 LDQLEAGARVDVDEAKRNKLDFVLWKSSKEGEPKWDSPWGKGRPGWHIECSAMNDKYLGD 218
Query: 120 KFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQ 179
+ DIHGGG+DLIFPHHENEIAQS AA YWMHNG + +NEKMSKSLGNFFT+R
Sbjct: 219 QIDIHGGGVDLIFPHHENEIAQSEAAFGKQLAKYWMHNGFLMIDNEKMSKSLGNFFTVRD 278
Query: 180 ITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKT 239
+ + Y P LR+FL+S HYRSPL++S L++A +A+ +Y+ L+ + +L+
Sbjct: 279 VLKNYDPEILRYFLLSVHYRSPLDFSEELLEAAKNALERLYKALRVLDTSLAYSGNQSLN 338
Query: 240 ARINPAAEDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQL 299
+ + F M DDLNT++ L F + K IN + K
Sbjct: 339 KFPDE------KEFEARFVEAMDDDLNTANALAVLF-ELAKSINLTF------VSKADAA 385
Query: 300 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAA 359
LIE L +E L +L LP S+ +Q + L E LIEER+ A
Sbjct: 386 LLIEHLIFLE----SRLGLLLGLP----SKPVQAGSNDDLGEIE-------ALIEERSIA 430
Query: 360 RKNKDFSKSDQIRADLTRKGIALMDMGKETIWR 392
RK KDF+K+D+IR +L +KGI L D + T WR
Sbjct: 431 RKEKDFAKADEIRDELAKKGIVLEDTPQGTTWR 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 = 323 bits (831), Expect = e-109
Identities = 124/206 (60%), Positives = 150/206 (72%), Gaps = 1/206 (0%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVE-GDVFFAVEKSPNYGRLSGQR 59
M L LPP +PRV++H+++I + I ++I AYV + GDV+F V P+YG+LSGQ
Sbjct: 87 MDALNVLPPDLEPRVTEHIDEIIEFIERLIKKGYAYVSDNGDVYFDVSSFPDYGKLSGQN 146
Query: 60 LENNRAGERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSS 119
LE AG R V KR+P DFALWKA+K GEPSWDSPWG GRPGWHIECSAM+ YL S
Sbjct: 147 LEQLEAGARGEVGEGKRDPLDFALWKASKEGEPSWDSPWGKGRPGWHIECSAMARKYLGS 206
Query: 120 KFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQ 179
+ DIHGGG+DL FPHHENEIAQS AA YW+HNGH+ EKMSKSLGNF TIR
Sbjct: 207 QIDIHGGGVDLKFPHHENEIAQSEAAFDQQLAKYWLHNGHLMIEGEKMSKSLGNFLTIRD 266
Query: 180 ITERYHPLALRHFLISAHYRSPLNYS 205
+ +RY P LR+FL+S HYRSPL++S
Sbjct: 267 VLKRYDPRILRYFLLSVHYRSPLDFS 292
>gnl|CDD|173001 PRK14535, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 699
Score = 282 bits (723), Expect = 1e-88
Identities = 165/406 (40%), Positives = 220/406 (54%), Gaps = 54/406 (13%)
Query: 4 LQCLPPTYQPRVSDHMEQIKDMITQIINNDCAY-VVEGDVFFAVEKSPNYGRLSGQRLEN 62
L L P +P+ ++++ Q+ MI +I N AY GDV++AV + YG+LSG+ L++
Sbjct: 329 LGVLRPDIEPKATENIPQMIAMIETLIQNGKAYPAANGDVYYAVREFAAYGQLSGKSLDD 388
Query: 63 NRAGERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFD 122
RAGERV VD KR+P DF LWKAAKAGEP+W+SPWG GRPGWHIECSAMS + FD
Sbjct: 389 LRAGERVEVDGFKRDPLDFVLWKAAKAGEPAWESPWGNGRPGWHIECSAMSENLFGDTFD 448
Query: 123 IHGGGIDLIFPHHENEIAQSCAACQD----------------SNVSYWMHNGHVTNNNEK 166
IHGGG DL FPHHENEIAQS A S+V YW+HNG + + EK
Sbjct: 449 IHGGGADLQFPHHENEIAQSVGATGHTCGHHHAQTHHGQSIASHVKYWLHNGFIRVDGEK 508
Query: 167 MSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDC 226
MSKSLGNFFTIR++ ++Y P +R F++ AHYRSPLNYS LD A A+ +Y TL++
Sbjct: 509 MSKSLGNFFTIREVLKQYDPEVVRFFILRAHYRSPLNYSDAHLDDAKGALTRLYTTLKNT 568
Query: 227 EVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSL 286
A + +N F+A M+DD T + F+ A +
Sbjct: 569 PAA-------------EFMLSENVNDYTRRFYAAMNDDFGTVEAVAVLFELA-----GEV 610
Query: 287 NMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTE 346
N Q + +K + I+GLL +E LQ L+
Sbjct: 611 NKTNDAQ--------------LAGCLKALGGIIGLLQRDP-TEFLQ----GGAASDGLSN 651
Query: 347 EDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWR 392
E++ LI R AR +K++++SD+IR L I L D T WR
Sbjct: 652 EEIEDLIARRKQARADKNWAESDRIRDLLNEHKIILEDNAGGTTWR 697
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 269 bits (691), Expect = 3e-84
Identities = 149/463 (32%), Positives = 214/463 (46%), Gaps = 65/463 (14%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEK----SPNYGRL- 55
M L PP RVS+++ +I D I +II+N AY G V+F VE Y +L
Sbjct: 140 MKALNVRPPDVITRVSEYVPEIVDFIQKIIDNGFAYESNGSVYFDVEAFRKAGHVYPKLE 199
Query: 56 --SGQRLENNRAGERV--AVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSA 111
S + GE V KR+P DFALWKA+K GEPSWDSPWG GRPGWHIECSA
Sbjct: 200 PESVADEDRIAEGEGALGKVSGEKRSPNDFALWKASKPGEPSWDSPWGKGRPGWHIECSA 259
Query: 112 MSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSN--VSYWMHNGHVTNNNEKMSK 169
M+++ L DIH GGIDL FPHH+NE+AQS A D + V+Y++H+GH+ KMSK
Sbjct: 260 MASNILGDPIDIHSGGIDLKFPHHDNELAQS-EAYFDKHQWVNYFLHSGHLHIKGLKMSK 318
Query: 170 SLGNFFTIRQITERYHPLALR-HFLISAHYRSPLNYSVLQLDSA--SDAVFYIYQTLQDC 226
SL NF TIRQ +Y +R FL+ + P+NYS +D A D VF+ + +
Sbjct: 319 SLKNFITIRQALSKYTARQIRLLFLLH-KWDKPMNYSDESMDEAIEKDKVFFNF--FANV 375
Query: 227 EVALSPFQEHGKTARINPAAEDCINKLR---DEFHARMSDDLNTSHILTGAFQDALKFIN 283
++ L + + + HA + D+ +T L A Q + N
Sbjct: 376 KIKLRESEL-TSPQKWTQHDFELNELFEETKSAVHAALLDNFDTPEALQ-ALQKLISATN 433
Query: 284 SSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAE 343
+ LN +QP LR + V ++L I GL+ Q
Sbjct: 434 TYLN--SGEQPSAPL------LRSVAQYVTKILSIFGLVEGSDGLGSQGQNS-------- 477
Query: 344 LTEEDVLQLIEE--------RAAARKNKD-----------FSKSDQIRAD-LTRKGIALM 383
T E+ L+E R AA+ D++R + L GI +
Sbjct: 478 -TSENFKPLLEALLRFRDEVRDAAKAEMKLISLDKKKKQLLQLCDKLRDEWLPNLGIRIE 536
Query: 384 DM-GKETIWRPC----VLVEQEQEAPPAEKEKKPAATGEEQKA 421
D ++W+ + E+E++ E+++ +E+K
Sbjct: 537 DKPDGPSVWKLDDKEELQREKEEKEALKEQKRLRKLKKQEEKK 579
>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 490
Score = 258 bits (661), Expect = 2e-81
Identities = 138/409 (33%), Positives = 192/409 (46%), Gaps = 64/409 (15%)
Query: 9 PTYQPRVSDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRLENNRAGER 68
P+ ++H++ + +I ++ Y G+V+F + P+YG L+ +E+ +AG R
Sbjct: 119 PSIVCNATEHIQDMIALIKRLEARGHTYCAGGNVYFDIRTFPSYGSLASAAVEDLQAGAR 178
Query: 69 VAVDSRKRNPADFALWKAAKAGEP---SWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHG 125
+ D+ KRNP DF LW E +WDSPWG G PGWHIECSAMS YL + DIH
Sbjct: 179 IEHDTNKRNPHDFVLWFTRSKFENHALTWDSPWGRGYPGWHIECSAMSMKYLGEQCDIHI 238
Query: 126 GGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQITER-Y 184
GG+D I HH NEIAQ AA V YW+H+ + N KMSKS G F T+ + E+ +
Sbjct: 239 GGVDHIRVHHTNEIAQCEAATGKPWVRYWLHHEFLLMNKGKMSKSAGQFLTLSSLQEKGF 298
Query: 185 HPLALRHFLISAHYRSPLNYS------------------VLQLDSASDAVFYIYQTLQDC 226
PL R FL+ HYRS L +S +D+A + TL +C
Sbjct: 299 QPLDYRFFLLGGHYRSQLAFSWEALKTAKAARRSLVRRVARVVDAARATTGSVRGTLAEC 358
Query: 227 ---EVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNTSHILTGAFQDALKFIN 283
VA S +E + +F A + DD +T L
Sbjct: 359 AAERVAESR----------ASESELLL----TDFRAALEDDFSTPKAL------------ 392
Query: 284 SSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAE 343
S L L K L L + ++ + +LGL G E L + A
Sbjct: 393 SELQKLVKDTSVPPSLCL--------SVLQAMDTVLGL---GLIQEATASLSAQV--PAG 439
Query: 344 LTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWR 392
+EE++ QLIE RA AR+ KDF +D+IR L +GI L D TIW+
Sbjct: 440 PSEEEIGQLIEARAHARQTKDFPLADEIRDKLKAEGIELEDTHLGTIWK 488
>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 = 196 bits (501), Expect = 5e-61
Identities = 64/101 (63%), Positives = 76/101 (75%)
Query: 105 WHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNN 164
WHIECSAM+ YL FDIHGGG+DLIFPHHENEIAQS AA YW+H GH+T +
Sbjct: 113 WHIECSAMAMKYLGETFDIHGGGVDLIFPHHENEIAQSEAATGKPFARYWLHTGHLTIDG 172
Query: 165 EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 205
EKMSKSLGNF T+R ++Y P LR L+S+HYRSPL++S
Sbjct: 173 EKMSKSLGNFITVRDALKKYDPEVLRLALLSSHYRSPLDFS 213
>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 = 193 bits (492), Expect = 3e-57
Identities = 100/281 (35%), Positives = 154/281 (54%), Gaps = 37/281 (13%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVEG----DVFFAVEKSPNYGRLS 56
M L+ LPP + ++++ +M+ +++ + AY+VEG DV+F+++ + +G S
Sbjct: 114 MEALRVLPPRDYIGAVESIDEVVEMVEKLLASGAAYIVEGPEYPDVYFSIDATEQFGYES 173
Query: 57 G------QRLENNRAG--ERVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIE 108
G L R G +R KR+P D LW+AA+ GEPSWDSP+G GRPGWHIE
Sbjct: 174 GYDRATMLELFAERGGDPDRPG----KRDPLDALLWRAAREGEPSWDSPFGRGRPGWHIE 229
Query: 109 CSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVS-YWMHNGHVTNNNEKM 167
CSA++ + L + FDI GGG DLIFPHHE A + AA ++ +++H G + + EKM
Sbjct: 230 CSAIALNRLGAGFDIQGGGSDLIFPHHEFSAAHAEAATGVRRMARHYVHAGMIGLDGEKM 289
Query: 168 SKSLGNFFTIRQIT-ERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDC 226
SKSLGN + ++ P A+R L++ HYR ++ +DAV L +
Sbjct: 290 SKSLGNLVFVSKLRAAGVDPAAIRLGLLAGHYRQDRDW--------TDAV------LAEA 335
Query: 227 EVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNT 267
E L+ ++ P A D I +LR +++DL+T
Sbjct: 336 EARLARWRA-ALALPDAPDATDLIARLRQH----LANDLDT 371
>gnl|CDD|183518 PRK12418, PRK12418, cysteinyl-tRNA synthetase; Provisional.
Length = 384
Score = 185 bits (473), Expect = 8e-55
Identities = 96/277 (34%), Positives = 144/277 (51%), Gaps = 29/277 (10%)
Query: 1 MADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVEG----DVFFAVEKSPNYGRLS 56
M L+ LPP + + ++ +++ +++ + AYVV+ DV+F+V+ +P +G S
Sbjct: 87 MEALRVLPPRDYVGAVESIPEVVELVEKLLASGAAYVVDDEEYPDVYFSVDATPQFGYES 146
Query: 57 GQRLENNRA--GERVAVDSR--KRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAM 112
G ER R KR+P D LW+AA+ GEPSW SP+GPGRPGWHIECSA+
Sbjct: 147 GYDRATMLELFAERGGDPDRPGKRDPLDALLWRAARPGEPSWPSPFGPGRPGWHIECSAI 206
Query: 113 SAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAAC-QDSNVSYWMHNGHVTNNNEKMSKSL 171
+ + L S FDI GGG DLIFPHHE A + AA + +++H G + + EKMSKS
Sbjct: 207 ALNRLGSGFDIQGGGSDLIFPHHEFSAAHAEAATGERRFARHYVHAGMIGLDGEKMSKSR 266
Query: 172 GNFFTIRQIT-ERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVAL 230
GN + ++ P A+R L++ HYR+ ++ L A L A
Sbjct: 267 GNLVFVSRLRAAGVDPAAIRLALLAGHYRADREWTDAVLAEAEA-------RLARWRAAA 319
Query: 231 SPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNT 267
+ P A D + ++R ++DDL+T
Sbjct: 320 A--------LPAGPDAADVVARVRA----ALADDLDT 344
>gnl|CDD|173000 PRK14534, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 481
Score = 173 bits (440), Expect = 3e-49
Identities = 115/387 (29%), Positives = 183/387 (47%), Gaps = 47/387 (12%)
Query: 16 SDHMEQIKDMITQIINNDCAYVVEGDVFFAVEKSPNYGRLSGQRLENNR--AGERVAVDS 73
S+++ + +++ + N Y V G+V+F +YG+++G L + + + RV +D
Sbjct: 124 SEYIPIMIEVVKVLEENGFTYFVNGNVYFDTSCFKSYGQMAGINLNDFKDMSVSRVEIDK 183
Query: 74 RKRNPADFALW---KAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDL 130
KRN +DF LW K E WDSPWG G P WH+EC+AM+ Y S DIH GG+D
Sbjct: 184 SKRNKSDFVLWFTNSKFKDQEMKWDSPWGFGYPSWHLECAAMNLEYFKSTLDIHLGGVDH 243
Query: 131 IFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQI-TERYHPLAL 189
I HH NEIA + ++H + EKMSKS NF TI+ + + + PL
Sbjct: 244 IGVHHINEIAIAECYLNKKWCDMFVHGEFLIMEYEKMSKSNNNFITIKDLEDQGFSPLDF 303
Query: 190 RHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDC 249
R+F ++AHYR+ L ++ L + A + L +L F +N +D
Sbjct: 304 RYFCLTAHYRTQLKFTFNNLKACKIARENMLNKLTYFYSSLDQFD-------LNLLNKDL 356
Query: 250 IN-------KLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLI 302
N + D F +++ DLN L L K LS +
Sbjct: 357 ENIEFSLEKEYYDSFLEKIAFDLNIPQGLA----------------LLWDIIKDDNLSFL 400
Query: 303 ESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKN 362
LR + + EVL + G E+L+++++ + + ++++ LIEER A+
Sbjct: 401 SKLR-LAFKFDEVLSL------GLREEILREIENHRI----VIDDNMKSLIEERRLAKCE 449
Query: 363 KDFSKSDQIRADLTRKGIALMDMGKET 389
KDF ++D+IR KG L+D + T
Sbjct: 450 KDFKRADEIREYFASKGFVLIDTEEGT 476
>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 = 89.5 bits (223), Expect = 3e-21
Identities = 50/188 (26%), Positives = 78/188 (41%), Gaps = 38/188 (20%)
Query: 208 QLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNT 267
L+ A A+ +Y L+ D + F A M DD NT
Sbjct: 3 NLEDARAALERLYTALRGVPPT--------------TVDIDWGEPFAERFIAAMDDDFNT 48
Query: 268 SHILTGAFQDALKF-INSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLL--PP 324
A A+ F + +N LKK+ ++ +L L+ + +LGLL P
Sbjct: 49 P----EAL--AVLFELAREINRLKKEDIEKAA-ALAALLKALGG-------VLGLLQQDP 94
Query: 325 GAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMD 384
A+ LQ L+ ++ LI +R ARK KD++++D+IR +L +GI L D
Sbjct: 95 EAF---LQG----GTGEGGLSVAEIEALIAQRNQARKAKDWAEADRIRDELAAQGIILED 147
Query: 385 MGKETIWR 392
+ T WR
Sbjct: 148 SPEGTTWR 155
>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 = 51.9 bits (125), Expect = 3e-07
Identities = 23/90 (25%), Positives = 32/90 (35%), Gaps = 23/90 (25%)
Query: 121 FDIHGGGIDLI--------FPHHENEIAQSCAACQDSN--VSYW----MHNGHVTNNNEK 166
DI+ GG + F H A D + G V EK
Sbjct: 225 VDIYIGGKEHAPNHLLYSRFNHK---------ALFDEGLVTDEPPKGLIVQGMVLLEGEK 275
Query: 167 MSKSLGNFFTIRQITERYHPLALRHFLISA 196
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 = 7e-07
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 195
+G +T +KMSKS GN ++ E+Y ALR++L
Sbjct: 324 HGFLTLEGQKMSKSRGNVVDPDELLEQYGVDALRYYLAR 362
>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 = 1e-06
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
+G +T KMSKS GN ++ +RY ALR++L
Sbjct: 315 HGWLTVEGGKMSKSRGNVVDPDELLDRYGVDALRYYLARE 354
>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 = 48.3 bits (116), Expect = 4e-06
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
+G++T +KMSKS GN + ERY ALR++L+
Sbjct: 271 HGYLTVEGKKMSKSRGNVVDPDDLLERYGADALRYYLLRE 310
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 48.5 bits (116), Expect = 5e-06
Identities = 21/40 (52%), Positives = 25/40 (62%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
NGH+ N+EKMSKS GNF T+RQ E + A R L A
Sbjct: 709 NGHLMLNSEKMSKSTGNFLTLRQAIEEFSADATRFALADA 748
>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 = 44.0 bits (104), Expect = 2e-05
Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 104 GWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQS-CAACQDSNVSYWMHNGHVT- 161
+ +A ++ DIH GG D + H E + A + + G V
Sbjct: 77 EYMFLQAADFLLLYETECDIHLGGSDQLG-HIELGLELLKKAGGPARP--FGLTFGRVMG 133
Query: 162 NNNEKMSKSL 171
+ KMSKS
Sbjct: 134 ADGTKMSKSK 143
>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: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
NG V +KMSKS GN +R+ E Y +R +L S+
Sbjct: 568 NGFVLLEGKKMSKSKGNVIPLRKAIEEYGADVVRLYLTSS 607
>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 = 42.5 bits (100), Expect = 3e-04
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
NG+V +KMSKS GN T+ Q E++ R ++ A
Sbjct: 611 NGYVMLEGKKMSKSKGNVLTLEQAVEKFGADVARLYIADA 650
>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 = 41.6 bits (98), Expect = 4e-04
Identities = 29/119 (24%), Positives = 40/119 (33%), Gaps = 16/119 (13%)
Query: 93 SWDSPWGPGRPGWHIEC-------SAMSAHYLSSKF--------DIHGGGIDLIFPHHEN 137
S WG P + S Y K D H G D++
Sbjct: 184 SRQRYWGTPLPEDVFDVWFDSGIGPLGSLGYPEEKEWFKDSYPADWHLIGKDILRGWANF 243
Query: 138 EIAQSCAACQDSNVSYWMHNGHVT-NNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 195
I A + + +G V +KMSKS GN + E+Y ALR++L S
Sbjct: 244 WITMLVALFGEIPPKNLLVHGFVLDEGGQKMSKSKGNVIDPSDVVEKYGADALRYYLTS 302
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 41.5 bits (98), Expect = 7e-04
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 157 NGHVT-NNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
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 = 0.001
Identities = 40/205 (19%), Positives = 70/205 (34%), Gaps = 47/205 (22%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS----------------AHYRS 200
+G +T + EKMSKSLGN + + Y A+R+FL+ +
Sbjct: 290 HGFLTLDGEKMSKSLGNVIDPFDLVDEYGVDAVRYFLLREIPFGQDGDFSREAFINRINA 349
Query: 201 PLNYSVLQLDSASDAVFYIYQTLQDCEVAL-SPFQEHGKTARINPAAEDCINKLRDEFH- 258
L + L + ++ + + P + AA + ++R
Sbjct: 350 DLANDLGNLAQRTLSMIAKN-----FDGKVPEPGALTEADEALLEAAAALLERVRAAMDN 404
Query: 259 ARMSDDLNTSHILTGAFQDALKFINSSLNM-----LKKKQPKQQQLSLIESLRKIENEVK 313
L A ++ N ++ L K P E L + +
Sbjct: 405 LAFDKALE-------AILALVRAANKYIDEQAPWSLAKTDP--------ERLATVLYTLL 449
Query: 314 EVLRILGLL--P--PGAYSEVLQQL 334
EVLR + +L P P +++L QL
Sbjct: 450 EVLRGIAVLLQPVMPELAAKILDQL 474
>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 = 0.001
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 158 GHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 195
G++T KMSKSLGN + R+ LR++L+
Sbjct: 319 GYLTVEGGKMSKSLGNVVDPSDLLARFGADILRYYLLK 356
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 39.8 bits (94), Expect = 0.002
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
+ ++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 = 0.003
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 162 NNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 194
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 = 0.007
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 158 GHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 194
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 = 0.008
Identities = 11/33 (33%), Positives = 12/33 (36%)
Query: 163 NNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 195
KMS S GN T E P LR+
Sbjct: 272 GGGKMSSSKGNVITPSDWLEVAPPEVLRYLYAR 304
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 37.8 bits (89), Expect = 0.010
Identities = 17/41 (41%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 157 NGHVTNNN-EKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
+GHV + + +KMSKSLGN+ ++ ++Y ALR +L+S+
Sbjct: 582 HGHVLDEDGQKMSKSLGNYVDPFEVFDKYGADALRWYLLSS 622
>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 = 0.010
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 165 EKMSKSLGNFFTIRQITERYHPLALRHFLI 194
KMS S GN TI E P +LR +
Sbjct: 278 GKMSSSKGNVITIEDWLEYAPPESLRFLMF 307
>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 = 0.012
Identities = 30/140 (21%), Positives = 56/140 (40%), Gaps = 8/140 (5%)
Query: 160 VTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYI 219
V EKMSKS GN ++I E Y ALR F++ + P+ S+ +S +
Sbjct: 599 VYVGYEKMSKSKGNGIDPQEIVESYGADALRLFIM---FMGPIAASLEWNESGLEGARRF 655
Query: 220 YQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFH---ARMSDDLNTSHILTGAFQ 276
+ + ++ E + A E+ +LR + H ++++DL A
Sbjct: 656 LDRVWNLVYEITG--ELDAASLTVTALEEAQKELRRDVHKFLKKVTEDLEKRESFNTAIS 713
Query: 277 DALKFINSSLNMLKKKQPKQ 296
++ +N K+ +
Sbjct: 714 AMMELLNKLYKAKKEALMLE 733
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 37.6 bits (88), Expect = 0.012
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 163 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 197
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 = 0.013
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 163 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 197
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 = 0.032
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 163 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 197
+ 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 = 0.053
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 1/86 (1%)
Query: 121 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNN-EKMSKSLGNFFTIRQ 179
D+ G D I A + + +G V + KMSKSLGN
Sbjct: 521 ADMLLEGSDQTRGWFYRMIVLGTALTGSAPYKNVLVHGLVRDEQGRKMSKSLGNVIDPLD 580
Query: 180 ITERYHPLALRHFLISAHYRSPLNYS 205
+ ++Y ALR +L S+ Y +N+S
Sbjct: 581 VIDKYGADALRLWLASSDYGRDINFS 606
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 35.1 bits (82), Expect = 0.067
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 195
+G +T KMSKS G F R + P LR++L +
Sbjct: 320 HGFLTVEGAKMSKSRGTFIWARTYLDHLDPDYLRYYLAA 358
>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 = 0.077
Identities = 21/106 (19%), Positives = 48/106 (45%), Gaps = 12/106 (11%)
Query: 274 AFQDALKFINSSLNMLKKKQPKQ--QQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVL 331
A + L+ I+ L +K + K +L L+E R+ E+ R+ L +
Sbjct: 169 ALRQQLEVISEELEARRKLKEKGLVSRLELLELERERAEAQGELGRLEAELE-----VLK 223
Query: 332 QQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTR 377
+Q+ + L+R ++ + +++EE A+ ++ ++R L +
Sbjct: 224 RQIDELQLERQQIEQTFREEVLEELTEAQ-----ARLAELRERLNK 264
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 33.7 bits (78), Expect = 0.19
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 165 EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 205
KMSKSLGN + + ++Y LR ++ S+ Y L +S
Sbjct: 601 RKMSKSLGNVVDPQDVIDKYGADILRLWVASSDYWEDLRFS 641
>gnl|CDD|214848 smart00840, DALR_2, This DALR domain is found in
cysteinyl-tRNA-synthetases.
Length = 56
Score = 30.2 bits (69), Expect = 0.21
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 256 EFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEV 315
F M DD NT L F + + IN L K ++ L + ++ +
Sbjct: 1 RFEEAMDDDFNTPEALAVLF-ELAREINR----LALKATDAEE------LAALAALLRAL 49
Query: 316 LRILGLL 322
+LGLL
Sbjct: 50 GGVLGLL 56
>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 = 0.41
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 163 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 197
KMSKSLGN + E+Y ALR L S
Sbjct: 522 QGRKMSKSLGNVIDPLDVIEKYGADALRFTLASLV 556
>gnl|CDD|236000 PRK07360, PRK07360, FO synthase subunit 2; Reviewed.
Length = 371
Score = 31.8 bits (73), Expect = 0.59
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 326 AYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRAD 374
++ + + ++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 = 0.64
Identities = 16/41 (39%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 62 NNRAGE-RVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPG 101
AGE V V + NP D WK G P+W P PG
Sbjct: 24 GPGAGEVLVKVHAAGLNPVD---WKVIAWGPPAWSYPHVPG 61
>gnl|CDD|181787 PRK09343, PRK09343, prefoldin subunit beta; Provisional.
Length = 121
Score = 30.0 bits (68), Expect = 0.82
Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 15/102 (14%)
Query: 287 NMLKKKQPKQQQLSLIESLR-KIE---NEVKEVLRILGLLPPGA--YSEV----LQQLKD 336
L + Q QQQL + + +I+ E+ + L L LP Y V ++ K
Sbjct: 11 AQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKIVGNLLVKVDKT 70
Query: 337 KALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRK 378
K K EL E +L+E R+ + ++ ++++ +L K
Sbjct: 71 KVEK--ELKER--KELLELRSRTLEKQEKKLREKLK-ELQAK 107
>gnl|CDD|235046 PRK02507, PRK02507, proton extrusion protein PcxA; Provisional.
Length = 422
Score = 31.4 bits (72), Expect = 0.83
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 23/89 (25%)
Query: 269 HILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEV-------KEVLRI--- 318
L+ F ++ ++ P I ++E E KE L
Sbjct: 216 QQLSKTF-----IVSPLVD---HFFPALPFEIFINP--ELEEEALEELRRFKEELEFEAL 265
Query: 319 LGLLPPGAYSEVLQQLKDKALKRAELTEE 347
LGL PP + E+ ++LK+KA EL EE
Sbjct: 266 LGLAPPLSPEEIEEKLKEKA---EELAEE 291
>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 = 0.94
Identities = 21/104 (20%), Positives = 30/104 (28%), Gaps = 33/104 (31%)
Query: 77 NPADFALWK----------------AAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSK 120
P D + K +K GEP+WD G P + K
Sbjct: 197 KPIDAGMAKFCETCGKCADECPSGAISKGGEPTWDPEDSNGDP--------PGENNPGLK 248
Query: 121 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSY------WMHNG 158
+ G L NE C CQ + + W+H+
Sbjct: 249 WQYDGWRCLLFRC--YNEGGGGCGVCQ-AVCPFNKKPNSWIHDV 289
>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 = 0.98
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 157 NGHVTNNN-EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDA 215
+G + KMSKSLGN ++ +Y LR ++ S+ L +S L +
Sbjct: 601 HGFTLDEKGRKMSKSLGNVVDPLKVINKYGADILRLYVASSDPWEDLRFSDEILKQVVEK 660
Query: 216 VFYI 219
I
Sbjct: 661 YRKI 664
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 29.6 bits (67), Expect = 1.1
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 24/93 (25%)
Query: 287 NMLKKKQPKQQQLS-LIESLRKIENEVKE---VLRILGLLPPGA--------------YS 328
L + Q QQQL +I +++E ++KE L L L A
Sbjct: 10 AQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKE 69
Query: 329 EVLQQLKDKA------LKRAELTEEDVLQLIEE 355
E + +L+++ +K E EE + + +EE
Sbjct: 70 EAVDELEERKETLELRIKTLEKQEEKLQERLEE 102
>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase.
Length = 616
Score = 31.2 bits (70), Expect = 1.1
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 157 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 194
+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 = 1.2
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 165 EKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
+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 = 1.3
Identities = 12/52 (23%), Positives = 27/52 (51%)
Query: 331 LQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIAL 382
L++ ++ + L++++ +++EER A R + +I A +GI L
Sbjct: 174 LEKYREYYRGKRGLSDDEFDEIVEERIARRAEYGLANRSEIAALARARGIPL 225
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 30.6 bits (70), Expect = 1.5
Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 14/93 (15%)
Query: 279 LKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRIL--GLLPPGAYSEVLQQLKD 336
L+ L +K +++L ++E L K N++ V+ ++ + A E++++L +
Sbjct: 318 LEVYKRRKEYLLEK--LEERLHILEGLLKALNKIDFVIEVIRGSIDLKKAKKELIEELSE 375
Query: 337 K--------ALKRAELTEEDVLQLIEERAAARK 361
L+R LT+E++ +L +E K
Sbjct: 376 IQADYLLDMRLRR--LTKEEIEKLEKEIEELEK 406
>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 = 1.5
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 165 EKMSKSLGNFFTIRQITERYHPLALRHFLISA 196
KMSKSLGN+ +++ ++Y ALR ++ S+
Sbjct: 298 RKMSKSLGNYVDPQEVVDKYGADALRLWVASS 329
>gnl|CDD|237967 PRK15446, PRK15446, phosphonate metabolism protein PhnM;
Provisional.
Length = 383
Score = 30.1 bits (69), Expect = 1.9
Identities = 12/52 (23%), Positives = 22/52 (42%)
Query: 331 LQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIAL 382
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 = 29.2 bits (66), Expect = 2.0
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 309 ENEVKEVLRILGLLPPGAYSEVLQQLKDKA 338
KE+ R+ G LPP + L+ +++KA
Sbjct: 93 PEGGKEIARLPGYLPPDEFLAYLEYVQEKA 122
>gnl|CDD|226375 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication,
recombination, and repair].
Length = 1108
Score = 30.5 bits (69), Expect = 2.0
Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 305 LRKIENEVKEVLRILGLLP--PGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKN 362
KI E+K+ L++ G L G ++ + + K+ +L+ ED+ +E++ + +
Sbjct: 93 FYKILEELKKELKVYGSLADKSGFIEQLAELYTE--FKKYQLSVEDLEDTADEQSLKKLH 150
Query: 363 KDFSKSDQIRADL 375
++ A+L
Sbjct: 151 DLSLIYEEFEANL 163
>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 = 2.3
Identities = 13/54 (24%), Positives = 25/54 (46%)
Query: 300 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLI 353
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 = 2.6
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 218 YIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEF 257
Y +QT DCEV L+ +QE G D ++ L F
Sbjct: 92 YAFQTGSDCEVILALYQEKGP---------DFLDDLDGMF 122
>gnl|CDD|216047 pfam00656, Peptidase_C14, Caspase domain.
Length = 228
Score = 29.6 bits (67), Expect = 2.7
Identities = 23/116 (19%), Positives = 38/116 (32%), Gaps = 20/116 (17%)
Query: 24 DMITQIINND-CAYVVEG-DVFF-------AVEKSPNYGRLSGQRLENNRAGERVAVDSR 74
D + + N C + +F ++ S E+ E A S+
Sbjct: 90 DALDDVFNGLNCPSLKGKPKLFIIDACRGGPLDDGVKSDSGSSGESESVDDSEA-AGLSK 148
Query: 75 KRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDL 130
PADF + + G+ S+ G G W I+ L + G+DL
Sbjct: 149 IPAPADFLVAYSTTPGQVSYR---GTGSGSWFIQA-------LCQVLREYAPGLDL 194
>gnl|CDD|112953 pfam04163, Tht1, Tht1-like nuclear fusion protein.
Length = 554
Score = 30.1 bits (67), Expect = 2.9
Identities = 27/109 (24%), Positives = 43/109 (39%), Gaps = 22/109 (20%)
Query: 238 KTARINPAAEDCINKLRDEFHARMSDDLN-----TSHILTGAFQDALKFINSS------- 285
+ A N A I L+D+F A + D + + L + Q + F+NS
Sbjct: 287 EFASENAIALSAIGDLKDDFLAFLEDRIKNLIEMSEDSLKESVQRNIDFVNSGFQELEDF 346
Query: 286 -------LNMLKKKQPKQQQLSLIESLR---KIENEVKEVLRILGLLPP 324
L LKK +QQ L E L+ ++ K+ L+ +LP
Sbjct: 347 SIGLKEELGGLKKDLSEQQNLEAEEILQGFNDFLHDSKDHLKTDEILPE 395
>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 = 3.0
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 301 LIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAAR 360
L E L + ++ E + IL LL G+ E L+ L +L++E++ + ERA +
Sbjct: 279 LPEYLELAKEQIPEKVFILKLLGFGSLDEFLKSLGLLLKVVIKLSDEEIEKWA-ERALSA 337
Query: 361 KNK 363
K+K
Sbjct: 338 KHK 340
>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 = 3.3
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 293 QPKQQQLSLIESLRKI-ENEVKEVLRILGL 321
P+ +L LIE LR + ++EV+E+ R LGL
Sbjct: 135 LPEDMKLKLIEPLRDLFKDEVRELGRELGL 164
>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 = 3.4
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 9/40 (22%)
Query: 218 YIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEF 257
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 = 3.7
Identities = 17/54 (31%), Positives = 33/54 (61%), Gaps = 9/54 (16%)
Query: 307 KIENEVK-----EVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE 355
+IE+ ++ +VL + P E+L++L++KA+K +L+ E+ QL+EE
Sbjct: 571 EIEHVIEGDTVADVLEYVQYDP----KELLERLREKAVKEGKLSPEERQQLLEE 620
>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 = 3.9
Identities = 9/64 (14%), Positives = 21/64 (32%), Gaps = 8/64 (12%)
Query: 249 CINKLRDEFHARMSDDLN--TSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLR 306
IN + F D +H+ F +I ++L+ + + +
Sbjct: 14 VINYRKHTF------DTKNVCAHVEDDGFATISDYIRANLDKAFIIVGDCSKKRVAPHRK 67
Query: 307 KIEN 310
++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 = 3.9
Identities = 20/116 (17%), Positives = 51/116 (43%), Gaps = 15/116 (12%)
Query: 248 DCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPK--------QQQL 299
+ I L++++ + M + + +L +DALK + L L ++ K +++
Sbjct: 88 EFIANLKEKWLSGMHKCESPTELLLRIVKDALKTYEAPLEKLSEELDKYEEEVFLKKRKG 147
Query: 300 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE 355
SL++ L ++ + + R+L L +V+ ++ +D+ L+ +
Sbjct: 148 SLLKRLYHLKRKASVIKRVLNLT-----QDVIDKIDTPLKSDPYT--QDLRDLLIK 196
>gnl|CDD|216083 pfam00724, Oxidored_FMN, NADH:flavin oxidoreductase / NADH oxidase
family.
Length = 336
Score = 29.2 bits (66), Expect = 4.1
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 15/76 (19%)
Query: 300 SLIESLRKIENEVKE-----VLRI--LGLLPPGAYSEVLQQLK------DKALKRAELTE 346
+E +K+ V E +++ LG P Y E L ++K ELT+
Sbjct: 76 EQVEGWKKLTEAVHENGSKIGVQLWHLGREAPPEYLEDLGLRPSDPSALPASIKVRELTK 135
Query: 347 EDVLQLIEE--RAAAR 360
E++ ++I+E +AA R
Sbjct: 136 EEIKEIIQEFVQAAKR 151
>gnl|CDD|223070 PHA03391, p47, viral transcription regulator p47; Provisional.
Length = 395
Score = 28.7 bits (65), Expect = 5.6
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 14/50 (28%)
Query: 163 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSA 212
N++K K L + +I I +R ++ Y VL+LD+
Sbjct: 180 NDKKFEKFLSSITSISDIIKR--------------HKFSKKYIVLELDAN 215
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.0 bits (66), Expect = 6.1
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 9/75 (12%)
Query: 288 MLKKKQPKQQQLSLIESL-----RKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRA 342
+ KK++ +Q+ +E IE +++E+ RI GL A +L++++++A R
Sbjct: 112 LEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAKEILLEKVEEEA--RH 169
Query: 343 ELTEEDVLQLIEERA 357
E +++ IEE A
Sbjct: 170 EAAV--LIKEIEEEA 182
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 28.9 bits (66), Expect = 6.1
Identities = 7/11 (63%), Positives = 7/11 (63%)
Query: 163 NNEKMSKSLGN 173
KMSKS GN
Sbjct: 517 QGRKMSKSKGN 527
>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 = 27.7 bits (62), Expect = 6.2
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 291 KKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRA----ELTE 346
KK+ K +++E +++ + L P V Q D+A +R +L+
Sbjct: 7 KKKKKVDPQREQRKRKRLEKFIRKRTKSARGLKPVEDRIVPQLSVDEAKRRQRKLLKLSP 66
Query: 347 EDVLQLIEERAAARK 361
ED+ E RA K
Sbjct: 67 EDL----ERRALIEK 77
>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 28.9 bits (66), Expect = 6.4
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 165 EKMSKSLGN 173
KMSKSLGN
Sbjct: 591 RKMSKSLGN 599
>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 = 28.4 bits (64), Expect = 6.5
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 14/79 (17%)
Query: 312 VKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQI 371
VKE+L+I +L KA+K + EE+ + + + K D + Q+
Sbjct: 81 VKELLKITSVLY-------------KAMKSTDGDEEENTRSLAKFDLGSKISDLKAARQL 127
Query: 372 RADLTRKGIALMDM-GKET 389
+++T +G AL D+ GKE
Sbjct: 128 ASEITERGAALYDLLGKEL 146
>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 = 7.2
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 302 IESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKD-KALKRAELTEEDVLQLIEERAAAR 360
E L+ ++ E +EVLR G +V ++++ L E+ E+++ +L+ E R
Sbjct: 181 EEKLKMVD-EAEEVLRNAG------VGQV--RVRNYDNLAVIEVPEDELSKLLNEAEEVR 231
Query: 361 KN-KDF 365
KD
Sbjct: 232 DKFKDI 237
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 28.5 bits (64), Expect = 7.2
Identities = 10/66 (15%), Positives = 25/66 (37%)
Query: 276 QDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLK 335
+ + + + + ++ ++ + + V++ L LP E L +L
Sbjct: 255 KLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLELA 314
Query: 336 DKALKR 341
D +KR
Sbjct: 315 DFIIKR 320
>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 = 7.5
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 344 LTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWRPCVLVEQEQEA 403
LT+ + I+E R+ + +D++ +LT IA D + + ++ E
Sbjct: 40 LTKPKIKAYIDELMKEREKRTIITADEVLEELTE--IARGDETELVLVGTKEGEVEKIEK 97
Query: 404 PPAEKEKKPAA 414
K++ A
Sbjct: 98 KVKLKDRLKAL 108
>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 = 26.9 bits (60), Expect = 7.6
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 324 PGAYSEVLQQLKDKALKRAELTEEDVL---QLIEERAAARKNKDFSKSDQ 370
PGA E LQ+ +K LK LTEE++ + I + D S +
Sbjct: 42 PGA--EDLQRDLEKVLKLWGLTEEELFERTREIHAKGGVYSGFDTSDQED 89
>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 = 26.7 bits (60), Expect = 7.9
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 301 LIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKR--AELTEEDVLQLIEE 355
L+E L +E L +L LLPP +EVL++L + L E++ +L+EE
Sbjct: 9 LLEEL-----PPEERLALLRLLPPERAAEVLEELDEDVQAELLEALPPEELAELLEE 60
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 28.5 bits (64), Expect = 8.1
Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 9/79 (11%)
Query: 287 NMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTE 346
P ++ L L E + +E E+KEV L + +++ + L E
Sbjct: 58 GGKPDVPPSKEFLDLEEEILDLEAEIKEVEENLE--------SLEKEINELEEWLNVLDE 109
Query: 347 EDVLQLIEERAAARKNKDF 365
E L E + +
Sbjct: 110 EKSF-LDENLEELSELSNL 127
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.5 bits (64), Expect = 8.1
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 296 QQQLSLIES----LRKIENEVKEVLRILGLLPPGA--YSEVLQQLKDKALKRAELTEEDV 349
++++ +E L +++ ++KE+ + L L Y E + ++ + LT
Sbjct: 327 EERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTP 386
Query: 350 LQLIEERAAARKNK 363
+L +E K K
Sbjct: 387 EKLEKELEELEKAK 400
>gnl|CDD|233396 TIGR01399, hrcV, type III secretion protein, HrcV family. Members
of this family are closely homologous to the flagellar
biosynthesis protein FlhA (TIGR01398) and should all
participate in type III secretion systems. Examples
include InvA (Salmonella enterica), LcrD (Yersinia
enterocolitica), HrcV (Xanthomonas), etc. Type III
secretion systems resemble flagellar biogenesis systems,
and may share the property of translocating special
classes of peptides through the membrane [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 677
Score = 28.5 bits (64), Expect = 8.1
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 16/72 (22%)
Query: 296 QQQLSLIESLRKIENE-VKEVLRILGLLPPGAYSEVLQQLKDK------------ALKRA 342
Q+ L++ + + E VKEV R+ LP +EVLQ+L + L
Sbjct: 491 QETRYLLDQMEREYPELVKEVQRV---LPLQRIAEVLQRLVSEQVSIRNLRLILETLIEW 547
Query: 343 ELTEEDVLQLIE 354
E+DV+ L E
Sbjct: 548 AQREKDVVMLTE 559
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 28.5 bits (64), Expect = 8.2
Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 289 LKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEED 348
K Q K + + + L++++ E+ E+ A + +L+DK L + E
Sbjct: 62 KAKGQKKDKIEEIKKELKELKEELTEL--------SAALKALEAELQDKLLSIPNIPHES 113
Query: 349 V 349
V
Sbjct: 114 V 114
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 28.4 bits (64), Expect = 8.5
Identities = 8/30 (26%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 8 PPTYQPRVSDHMEQIKDMITQIINNDCAYV 37
P YQ S+ + + ++I AYV
Sbjct: 78 GPYYQ---SERFDIYYEYAEKLIEKGKAYV 104
>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 = 28.5 bits (63), Expect = 8.6
Identities = 36/171 (21%), Positives = 60/171 (35%), Gaps = 23/171 (13%)
Query: 251 NKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLK-----KKQPKQQQLSLIESL 305
+ L +E R+ L T A QDA + + S +N+L P Q S E L
Sbjct: 278 DMLPEERKLRLLKALAEMSPYTTA-QDARQRLPSIVNLLLEYMPLGDTPPSFQFSHAECL 336
Query: 306 RKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDF 365
L LG P A + + L E+ + KNKDF
Sbjct: 337 LY-------ALHTLGKKHPNATNSLCGYKIVTGQPSDRLGEDF----------SEKNKDF 379
Query: 366 SKSDQIRADLTRKGIALMDMGKETIWRPCVLVEQEQEAPPAEKEKKPAATG 416
++ DLT+ + + G + + ++E + +++ TG
Sbjct: 380 TERLTYVEDLTKATMKKLTQGMSEHSKAMSTAKTDEEKEELKTKEQLTTTG 430
>gnl|CDD|221838 pfam12896, Apc4, Anaphase-promoting complex, cyclosome, subunit 4.
Apc4 is one of the larger of the subunits of the
anaphase-promoting complex or cyclosome. This family
represents the long domain downstream of the WD40
repeat/s that are present on the Apc4 subunits. The
anaphase-promoting complex is a multiprotein subunit E3
ubiquitin ligase complex that controls segregation of
chromosomes and exit from mitosis in eukaryotes. Results
in C.elegans show that the primary essential role of the
spindle assembly checkpoint is not in the chromosome
segregation process itself but rather in delaying
anaphase onset until all chromosomes are properly
attached to the spindle. the APC/C is likely to be
required for all metaphase-to-anaphase transitions in a
multicellular organism.
Length = 208
Score = 28.0 bits (63), Expect = 8.6
Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 12/83 (14%)
Query: 270 ILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENE------VKEVLRILGLLP 323
+ Q L++IN +L ++K++ +L L + +E V + LL
Sbjct: 24 RKSSQLQSLLEYINETLRLIKEEWKPALEL-FDRKLTNLADELTDQVGGDLVAELYDLLL 82
Query: 324 PGAYSEVLQ-----QLKDKALKR 341
G S L+ QL ++ LKR
Sbjct: 83 TGIISPALKDFLLNQLGERGLKR 105
>gnl|CDD|163144 TIGR03123, one_C_unchar_1, probable H4MPT-linked C1 transfer
pathway protein. This protein family was identified, by
the method of partial phylogenetic profiling, as related
to the use of tetrahydromethanopterin (H4MPT) as a C-1
carrier. Characteristic markers of the H4MPT-linked C1
transfer pathway include formylmethanofuran
dehydrogenase subunits, methenyltetrahydromethanopterin
cyclohydrolase, etc. Tetrahydromethanopterin, a
tetrahydrofolate analog, occurs in methanogenic archaea,
bacterial methanotrophs, planctomycetes, and a few other
lineages [Central intermediary metabolism, One-carbon
metabolism].
Length = 318
Score = 28.1 bits (63), Expect = 9.0
Identities = 23/107 (21%), Positives = 38/107 (35%), Gaps = 26/107 (24%)
Query: 314 EVLRILGLLPPGAYSEVLQQLKDKALK-------------RAELTEEDVLQLIEERAAAR 360
+V R+LG + Y+ K K+++ EL EEDV L + A+
Sbjct: 202 DVYRLLGEITEEDYTCDTPDGKGKSIEECMRRLARMVCADLEELGEEDVRNLAKYYYEAQ 261
Query: 361 KNKDFSKSDQIRADLTRKGIA----------LMDMGKETIWRPCVLV 397
+ ++ I L R G+ L + R C+ V
Sbjct: 262 LEQ---LTEAIEEVLERYGLKTVVAAGAGEFLAKEAAARLGRECIDV 305
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 28.4 bits (64), Expect = 9.5
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 16/72 (22%)
Query: 296 QQQLSLIESLRKIENE-VKEVLRILGLLPPGAYSEVLQQLKDKALK----RAEL------ 344
Q+ L++ + + ++ VKEV R + L +E+LQ+L ++ + R L
Sbjct: 500 QETRYLLDQMERKYSDLVKEVQRQIPL---QRIAEILQRLVEERISIRNMRLILEALVEW 556
Query: 345 --TEEDVLQLIE 354
E+DV+ L E
Sbjct: 557 APKEKDVVMLTE 568
>gnl|CDD|217253 pfam02854, MIF4G, MIF4G domain. MIF4G is named after Middle domain
of eukaryotic initiation factor 4G (eIF4G). Also occurs
in NMD2p and CBP80. The domain is rich in alpha-helices
and may contain multiple alpha-helical repeats. In
eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.
Length = 198
Score = 27.7 bits (62), Expect = 9.8
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 279 LKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRIL 319
LK + LN L ++ L++ +N +K +L ++
Sbjct: 1 LKKVKGLLNKLSPSNFEKIIDELLKLNMSDKNLLKYILELI 41
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 0.391
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: 21,444,240
Number of extensions: 2074576
Number of successful extensions: 2723
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2679
Number of HSP's successfully gapped: 134
Length of query: 421
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 322
Effective length of database: 6,546,556
Effective search space: 2107991032
Effective search space used: 2107991032
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 (21.6 bits)
S2: 60 (26.8 bits)