RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013130
(449 letters)
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 645 bits (1665), Expect = 0.0
Identities = 276/432 (63%), Positives = 335/432 (77%), Gaps = 9/432 (2%)
Query: 2 QIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINND 61
+II RAN+LGE+P+SLS RYC+E+L DMA L CLPP+ +PRVSDH+ QI DMI QI++N
Sbjct: 131 KIIARANELGEDPISLSRRYCEEFLSDMAYLHCLPPSVEPRVSDHIPQIIDMIKQILDNG 190
Query: 62 CAYVVEGDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFALWKAAKAGEPS 121
CAY V+GDV+F+V+K P YG+LSG++LE+NRAGERVAVDSRK+NPADFALWKAAK GEP
Sbjct: 191 CAYRVDGDVYFSVDKFPEYGKLSGRKLEDNRAGERVAVDSRKKNPADFALWKAAKEGEPF 250
Query: 122 WDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSY 181
WDSPWGPGRPGWHIECSAMSA YL FDIHGGG+DL+FPHHENEIAQSCAAC DSN+SY
Sbjct: 251 WDSPWGPGRPGWHIECSAMSAAYLGHSFDIHGGGMDLVFPHHENEIAQSCAACCDSNISY 310
Query: 182 WMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSAS 241
W+HNG VT ++EKMSKSLGNFFTIRQ+ + YHPLALR FL+ HYRSP+NYS +QL+SAS
Sbjct: 311 WIHNGFVTVDSEKMSKSLGNFFTIRQVIDLYHPLALRLFLLGTHYRSPINYSDVQLESAS 370
Query: 242 DAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNTSHILTG 301
+ +FYIYQTL DCE +L + + P +CINK DEF MSDDL+T +
Sbjct: 371 ERIFYIYQTLHDCEESLQQHDSTFEKDSVPPDTLNCINKFHDEFVTSMSDDLHTP-VALA 429
Query: 302 AFQDALKFINSSLNMLK-KKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQ 360
A + LK IN L+ K KKQ K+ +ESL +E ++++VL +LGL+P +YSE LQ
Sbjct: 430 ALSEPLKTINDLLHTRKGKKQEKR-----LESLAALEKKIRDVLSVLGLMPT-SYSEALQ 483
Query: 361 QLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWR 420
QL++KAL+RA+LTEE VLQ IEER ARKNK++ KSD IR DL GIALMD T WR
Sbjct: 484 QLREKALRRAKLTEEQVLQKIEERTVARKNKEYEKSDAIRKDLAAVGIALMDSPDGTTWR 543
Query: 421 PCV-LVEQEQEA 431
P + L QEQ A
Sbjct: 544 PAIPLALQEQVA 555
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 536 bits (1385), Expect = 0.0
Identities = 185/419 (44%), Positives = 241/419 (57%), Gaps = 33/419 (7%)
Query: 3 IIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDC 62
II+RAN+ GE+ L+ RY + DM L LPP +PR ++H+ +I ++I ++I+
Sbjct: 75 IIKRANEEGESIKELTERYIAAFHEDMDALNVLPPDIEPRATEHIPEIIELIERLIDKGH 134
Query: 63 AYVVEGDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFALWKAAKAGEPSW 122
AY +GDV+F V K P+YG+LSG+ L+ +AG RV V KR+P DFALWKAAK GEPSW
Sbjct: 135 AYEADGDVYFDVRKFPDYGKLSGRNLDELQAGARVEVAEEKRDPLDFALWKAAKPGEPSW 194
Query: 123 DSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYW 182
+SPWG GRPGWHIECSAMS YL FDIHGGG DLIFPHHENEIAQS AA +YW
Sbjct: 195 ESPWGKGRPGWHIECSAMSTKYLGETFDIHGGGADLIFPHHENEIAQSEAATGKPFANYW 254
Query: 183 MHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASD 242
MHNG VT N EKMSKSLGNFFTIR + ++Y P LR FL+SAHYRSPLN+S L+ A
Sbjct: 255 MHNGFVTVNGEKMSKSLGNFFTIRDLLKKYDPEVLRFFLLSAHYRSPLNFSEEALEQAKK 314
Query: 243 AVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNTSHILTGA 302
A+ +Y L + + A + + ++ F M DD NT L
Sbjct: 315 ALERLYNALAETALGEDD-----------EALLAELEEFKERFIEAMDDDFNTPEALA-V 362
Query: 303 FQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQL 362
+ + IN +L K E+ + ++ + +LGL +
Sbjct: 363 LFELAREINRALETKDK-----------EAAAALAALLRALADVLGLEQ--------DEE 403
Query: 363 KDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKE-TIWR 420
EL + ++ LIEER ARK KDF+ +D IR +L GI L D + T WR
Sbjct: 404 ALFEAAADELLDAEIEALIEERQEARKAKDFALADAIRDELAALGIVLED-TPDGTTWR 461
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 472 bits (1217), Expect = e-165
Identities = 182/421 (43%), Positives = 234/421 (55%), Gaps = 35/421 (8%)
Query: 3 IIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDC 62
II RA + G + ++ RY + DM L LPP +PR ++H+++I + I ++I
Sbjct: 74 IINRAREEGLSIREVAERYIAAFFEDMDALNVLPPDIEPRATEHIDEIIEFIEKLIEKGY 133
Query: 63 AYVVE-GDVFFAVEKSPNYGRLSG-QRLENNRAGERVAVDSRKRNPADFALWKAAKAGEP 120
AYV + GDV+F V K +YG+LSG LE +AG RV VD KRNP DF LWKAAK GEP
Sbjct: 134 AYVADDGDVYFDVSKFKDYGKLSGRDSLEELQAGARVEVDEEKRNPLDFVLWKAAKPGEP 193
Query: 121 SWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSN-V 179
SWDSPWG GRPGWHIECSAMS YL FDIHGGG DLIFPHHENEIAQS AA
Sbjct: 194 SWDSPWGKGRPGWHIECSAMSTKYLGETFDIHGGGSDLIFPHHENEIAQSEAATGVKPFA 253
Query: 180 SYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDS 239
YWMHNG + + EKMSKSLGNF T+R + ++Y P LR FL+S+HYRSPL++S L+
Sbjct: 254 KYWMHNGFLNIDGEKMSKSLGNFITVRDLLKKYDPEVLRLFLLSSHYRSPLDFSEELLEE 313
Query: 240 ASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNTSHIL 299
A A+ +Y L+ A + + F + DD NT L
Sbjct: 314 AKKALERLYNALRRLRDLA------------GDAELADLKEFEARFREALDDDFNTPKAL 361
Query: 300 TGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVL 359
+ K IN L + K + LS + K +L ILGL G + +
Sbjct: 362 A-VLFELAKEINRLLE--EGKSDAKAVLSAL----------KALLAILGLKVLGLFPQSG 408
Query: 360 QQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIW 419
Q E +E++ LIEER ARK K+++ +D+IR +L GI L D T W
Sbjct: 409 AQE-------DESDDEEIEALIEERLEARKAKNWALADEIRDELLALGIILEDTPDGTTW 461
Query: 420 R 420
R
Sbjct: 462 R 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 = 399 bits (1027), Expect = e-136
Identities = 187/419 (44%), Positives = 248/419 (59%), Gaps = 29/419 (6%)
Query: 3 IIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDC 62
II+RA + GE+ +S R+ + Y DM L LPP +PR ++H+++I + I Q+I
Sbjct: 73 IIKRARENGESVYEVSERFIEAYFEDMKALNVLPPDLEPRATEHIDEIIEFIEQLIEKGY 132
Query: 63 AYVVE-GDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFALWKAAKAGEPS 121
AYV + GDV+F V K +YG+LS Q L+ AG RV VD KRN DF LWK++K GEP
Sbjct: 133 AYVSDNGDVYFDVSKFKDYGKLSKQDLDQLEAGARVDVDEAKRNKLDFVLWKSSKEGEPK 192
Query: 122 WDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSY 181
WDSPWG GRPGWHIECSAM+ YL + DIHGGG+DLIFPHHENEIAQS AA Y
Sbjct: 193 WDSPWGKGRPGWHIECSAMNDKYLGDQIDIHGGGVDLIFPHHENEIAQSEAAFGKQLAKY 252
Query: 182 WMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSAS 241
WMHNG + +NEKMSKSLGNFFT+R + + Y P LR+FL+S HYRSPL++S L++A
Sbjct: 253 WMHNGFLMIDNEKMSKSLGNFFTVRDVLKNYDPEILRYFLLSVHYRSPLDFSEELLEAAK 312
Query: 242 DAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNTSHILTG 301
+A+ +Y+ L+ + +L+ + + F M DDLNT++ L
Sbjct: 313 NALERLYKALRVLDTSLAYSGNQSLNKFPDE------KEFEARFVEAMDDDLNTANALAV 366
Query: 302 AFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQ 361
F + K IN + K LIE L +E L +L LP S+ +Q
Sbjct: 367 LF-ELAKSINLTF------VSKADAALLIEHLIFLE----SRLGLLLGLP----SKPVQA 411
Query: 362 LKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWR 420
+ L E LIEER+ ARK KDF+K+D+IR +L +KGI L D + T WR
Sbjct: 412 GSNDDLGEIE-------ALIEERSIARKEKDFAKADEIRDELAKKGIVLEDTPQGTTWR 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 = 343 bits (882), Expect = e-116
Identities = 134/232 (57%), Positives = 164/232 (70%), Gaps = 1/232 (0%)
Query: 3 IIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDC 62
II+RA GE+ L+ R+ Y DM L LPP +PRV++H+++I + I ++I
Sbjct: 61 IIKRAQQQGESFRELAARFITAYTKDMDALNVLPPDLEPRVTEHIDEIIEFIERLIKKGY 120
Query: 63 AYVVE-GDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFALWKAAKAGEPS 121
AYV + GDV+F V P+YG+LSGQ LE AG R V KR+P DFALWKA+K GEPS
Sbjct: 121 AYVSDNGDVYFDVSSFPDYGKLSGQNLEQLEAGARGEVGEGKRDPLDFALWKASKEGEPS 180
Query: 122 WDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSY 181
WDSPWG GRPGWHIECSAM+ YL S+ DIHGGG+DL FPHHENEIAQS AA Y
Sbjct: 181 WDSPWGKGRPGWHIECSAMARKYLGSQIDIHGGGVDLKFPHHENEIAQSEAAFDQQLAKY 240
Query: 182 WMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 233
W+HNGH+ EKMSKSLGNF TIR + +RY P LR+FL+S HYRSPL++S
Sbjct: 241 WLHNGHLMIEGEKMSKSLGNFLTIRDVLKRYDPRILRYFLLSVHYRSPLDFS 292
>gnl|CDD|173001 PRK14535, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 699
Score = 294 bits (753), Expect = 1e-92
Identities = 175/436 (40%), Positives = 234/436 (53%), Gaps = 54/436 (12%)
Query: 2 QIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINND 61
+II RA + GE L+ R+ Q D L L P +P+ ++++ Q+ MI +I N
Sbjct: 299 KIIARAAENGETIGELTARFIQAMHEDADALGVLRPDIEPKATENIPQMIAMIETLIQNG 358
Query: 62 CAY-VVEGDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFALWKAAKAGEP 120
AY GDV++AV + YG+LSG+ L++ RAGERV VD KR+P DF LWKAAKAGEP
Sbjct: 359 KAYPAANGDVYYAVREFAAYGQLSGKSLDDLRAGERVEVDGFKRDPLDFVLWKAAKAGEP 418
Query: 121 SWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQD---- 176
+W+SPWG GRPGWHIECSAMS + FDIHGGG DL FPHHENEIAQS A
Sbjct: 419 AWESPWGNGRPGWHIECSAMSENLFGDTFDIHGGGADLQFPHHENEIAQSVGATGHTCGH 478
Query: 177 ------------SNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
S+V YW+HNG + + EKMSKSLGNFFTIR++ ++Y P +R F++ A
Sbjct: 479 HHAQTHHGQSIASHVKYWLHNGFIRVDGEKMSKSLGNFFTIREVLKQYDPEVVRFFILRA 538
Query: 225 HYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDE 284
HYRSPLNYS LD A A+ +Y TL++ A + +N
Sbjct: 539 HYRSPLNYSDAHLDDAKGALTRLYTTLKNTPAA-------------EFMLSENVNDYTRR 585
Query: 285 FHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVL 344
F+A M+DD T + F+ A +N Q + +K +
Sbjct: 586 FYAAMNDDFGTVEAVAVLFELA-----GEVNKTNDAQ--------------LAGCLKALG 626
Query: 345 RILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLT 404
I+GLL +E LQ L+ E++ LI R AR +K++++SD+IR L
Sbjct: 627 GIIGLLQRDP-TEFLQ----GGAASDGLSNEEIEDLIARRKQARADKNWAESDRIRDLLN 681
Query: 405 RKGIALMDMGKETIWR 420
I L D T WR
Sbjct: 682 EHKIILEDNAGGTTWR 697
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 286 bits (734), Expect = 4e-90
Identities = 157/490 (32%), Positives = 229/490 (46%), Gaps = 66/490 (13%)
Query: 3 IIRRANDLG-ENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINND 61
II+RA + L L+ ++ +E+ DM L PP RVS+++ +I D I +II+N
Sbjct: 113 IIKRAREEKLSIFLELARKWEKEFFEDMKALNVRPPDVITRVSEYVPEIVDFIQKIIDNG 172
Query: 62 CAYVVEGDVFFAVEK----SPNYGRL---SGQRLENNRAGERV--AVDSRKRNPADFALW 112
AY G V+F VE Y +L S + GE V KR+P DFALW
Sbjct: 173 FAYESNGSVYFDVEAFRKAGHVYPKLEPESVADEDRIAEGEGALGKVSGEKRSPNDFALW 232
Query: 113 KAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCA 172
KA+K GEPSWDSPWG GRPGWHIECSAM+++ L DIH GGIDL FPHH+NE+AQS
Sbjct: 233 KASKPGEPSWDSPWGKGRPGWHIECSAMASNILGDPIDIHSGGIDLKFPHHDNELAQS-E 291
Query: 173 ACQDSN--VSYWMHNGHVTNNNEKMSKSLGNFFTIRQITERYHPLALR-HFLISAHYRSP 229
A D + V+Y++H+GH+ KMSKSL NF TIRQ +Y +R FL+ + P
Sbjct: 292 AYFDKHQWVNYFLHSGHLHIKGLKMSKSLKNFITIRQALSKYTARQIRLLFLLH-KWDKP 350
Query: 230 LNYSVLQLDSA--SDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLR---DE 284
+NYS +D A D VF+ + + ++ L + + +
Sbjct: 351 MNYSDESMDEAIEKDKVFFNF--FANVKIKLRESEL-TSPQKWTQHDFELNELFEETKSA 407
Query: 285 FHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVL 344
HA + D+ +T L A Q + N+ LN +QP LR + V ++L
Sbjct: 408 VHAALLDNFDTPEALQ-ALQKLISATNTYLN--SGEQPSAPL------LRSVAQYVTKIL 458
Query: 345 RILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE--------RAAARKNKD---- 392
I GL+ Q T E+ L+E R AA+
Sbjct: 459 SIFGLVEGSDGLGSQGQNS---------TSENFKPLLEALLRFRDEVRDAAKAEMKLISL 509
Query: 393 -------FSKSDQIRAD-LTRKGIALMDM-GKETIWRPC----VLVEQEQEAPPAEKEKK 439
D++R + L GI + D ++W+ + E+E++ E+++
Sbjct: 510 DKKKKQLLQLCDKLRDEWLPNLGIRIEDKPDGPSVWKLDDKEELQREKEEKEALKEQKRL 569
Query: 440 PAATGEEQKA 449
+E+K
Sbjct: 570 RKLKKQEEKK 579
>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 490
Score = 266 bits (682), Expect = 3e-84
Identities = 145/444 (32%), Positives = 209/444 (47%), Gaps = 64/444 (14%)
Query: 2 QIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINND 61
++++ A + G++ L ++ Y + D A L P+ ++H++ + +I ++
Sbjct: 84 KMVKSAQEHGKSVLEIAAHYTAAFFRDTARLNIERPSIVCNATEHIQDMIALIKRLEARG 143
Query: 62 CAYVVEGDVFFAVEKSPNYGRLSGQRLENNRAGERVAVDSRKRNPADFALWKAAKAGEP- 120
Y G+V+F + P+YG L+ +E+ +AG R+ D+ KRNP DF LW E
Sbjct: 144 HTYCAGGNVYFDIRTFPSYGSLASAAVEDLQAGARIEHDTNKRNPHDFVLWFTRSKFENH 203
Query: 121 --SWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSN 178
+WDSPWG G PGWHIECSAMS YL + DIH GG+D I HH NEIAQ AA
Sbjct: 204 ALTWDSPWGRGYPGWHIECSAMSMKYLGEQCDIHIGGVDHIRVHHTNEIAQCEAATGKPW 263
Query: 179 VSYWMHNGHVTNNNEKMSKSLGNFFTIRQITER-YHPLALRHFLISAHYRSPLNYS---- 233
V YW+H+ + N KMSKS G F T+ + E+ + PL R FL+ HYRS L +S
Sbjct: 264 VRYWLHHEFLLMNKGKMSKSAGQFLTLSSLQEKGFQPLDYRFFLLGGHYRSQLAFSWEAL 323
Query: 234 --------------VLQLDSASDAVFYIYQTLQDC---EVALSPFQEHGKTARINPAAED 276
+D+A + TL +C VA S +E
Sbjct: 324 KTAKAARRSLVRRVARVVDAARATTGSVRGTLAECAAERVAESR----------ASESEL 373
Query: 277 CINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKI 336
+ +F A + DD +T L S L L K L L
Sbjct: 374 LL----TDFRAALEDDFSTPKAL------------SELQKLVKDTSVPPSLCL------- 410
Query: 337 ENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKS 396
+ ++ + +LGL G E L + A +EE++ QLIE RA AR+ KDF +
Sbjct: 411 -SVLQAMDTVLGL---GLIQEATASLSAQV--PAGPSEEEIGQLIEARAHARQTKDFPLA 464
Query: 397 DQIRADLTRKGIALMDMGKETIWR 420
D+IR L +GI L D TIW+
Sbjct: 465 DEIRDKLKAEGIELEDTHLGTIWK 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 = 1e-60
Identities = 64/101 (63%), Positives = 76/101 (75%)
Query: 133 WHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNN 192
WHIECSAM+ YL FDIHGGG+DLIFPHHENEIAQS AA YW+H GH+T +
Sbjct: 113 WHIECSAMAMKYLGETFDIHGGGVDLIFPHHENEIAQSEAATGKPFARYWLHTGHLTIDG 172
Query: 193 EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 233
EKMSKSLGNF T+R ++Y P LR L+S+HYRSPL++S
Sbjct: 173 EKMSKSLGNFITVRDALKKYDPEVLRLALLSSHYRSPLDFS 213
Score = 48.0 bits (115), Expect = 2e-06
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 3 IIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRV 43
II+RA + G + +++ Y +E+ DM L LPP PRV
Sbjct: 72 IIKRAREEGLSWKEVADYYTKEFFEDMKALNVLPPDVVPRV 112
>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 = 198 bits (504), Expect = 9e-59
Identities = 105/304 (34%), Positives = 161/304 (52%), Gaps = 37/304 (12%)
Query: 6 RANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYV 65
RA G + L + DM L+ LPP + ++++ +M+ +++ + AY+
Sbjct: 91 RAERDGVDWRELGTSQIDLFREDMEALRVLPPRDYIGAVESIDEVVEMVEKLLASGAAYI 150
Query: 66 VEG----DVFFAVEKSPNYGRLSG------QRLENNRAG--ERVAVDSRKRNPADFALWK 113
VEG DV+F+++ + +G SG L R G +R KR+P D LW+
Sbjct: 151 VEGPEYPDVYFSIDATEQFGYESGYDRATMLELFAERGGDPDRPG----KRDPLDALLWR 206
Query: 114 AAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAA 173
AA+ GEPSWDSP+G GRPGWHIECSA++ + L + FDI GGG DLIFPHHE A + AA
Sbjct: 207 AAREGEPSWDSPFGRGRPGWHIECSAIALNRLGAGFDIQGGGSDLIFPHHEFSAAHAEAA 266
Query: 174 CQDSNVS-YWMHNGHVTNNNEKMSKSLGNFFTIRQIT-ERYHPLALRHFLISAHYRSPLN 231
++ +++H G + + EKMSKSLGN + ++ P A+R L++ HYR +
Sbjct: 267 TGVRRMARHYVHAGMIGLDGEKMSKSLGNLVFVSKLRAAGVDPAAIRLGLLAGHYRQDRD 326
Query: 232 YSVLQLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSD 291
+ +DAV L + E L+ ++ P A D I +LR +++
Sbjct: 327 W--------TDAV------LAEAEARLARWRA-ALALPDAPDATDLIARLRQH----LAN 367
Query: 292 DLNT 295
DL+T
Sbjct: 368 DLDT 371
>gnl|CDD|183518 PRK12418, PRK12418, cysteinyl-tRNA synthetase; Provisional.
Length = 384
Score = 189 bits (482), Expect = 7e-56
Identities = 97/278 (34%), Positives = 145/278 (52%), Gaps = 29/278 (10%)
Query: 28 DMADLQCLPPTYQPRVSDHMEQIKDMITQIINNDCAYVVEG----DVFFAVEKSPNYGRL 83
DM L+ LPP + + ++ +++ +++ + AYVV+ DV+F+V+ +P +G
Sbjct: 86 DMEALRVLPPRDYVGAVESIPEVVELVEKLLASGAAYVVDDEEYPDVYFSVDATPQFGYE 145
Query: 84 SGQRLENNRA--GERVAVDSR--KRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSA 139
SG ER R KR+P D LW+AA+ GEPSW SP+GPGRPGWHIECSA
Sbjct: 146 SGYDRATMLELFAERGGDPDRPGKRDPLDALLWRAARPGEPSWPSPFGPGRPGWHIECSA 205
Query: 140 MSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAAC-QDSNVSYWMHNGHVTNNNEKMSKS 198
++ + L S FDI GGG DLIFPHHE A + AA + +++H G + + EKMSKS
Sbjct: 206 IALNRLGSGFDIQGGGSDLIFPHHEFSAAHAEAATGERRFARHYVHAGMIGLDGEKMSKS 265
Query: 199 LGNFFTIRQIT-ERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYIYQTLQDCEVA 257
GN + ++ P A+R L++ HYR+ ++ L A L A
Sbjct: 266 RGNLVFVSRLRAAGVDPAAIRLALLAGHYRADREWTDAVLAEAEA-------RLARWRAA 318
Query: 258 LSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNT 295
+ P A D + ++R ++DDL+T
Sbjct: 319 AA--------LPAGPDAADVVARVRA----ALADDLDT 344
>gnl|CDD|173000 PRK14534, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 481
Score = 176 bits (448), Expect = 5e-50
Identities = 121/429 (28%), Positives = 199/429 (46%), Gaps = 47/429 (10%)
Query: 2 QIIRRANDLGENPLSLSNRYCQEYLVDMADLQCLPPTYQPRVSDHMEQIKDMITQIINND 61
++++ A + G +S + + + D L + P S+++ + +++ + N
Sbjct: 82 KVVKAARERGLTVYEISRFFTEAFFDDCKKLNIVYPDKVLVASEYIPIMIEVVKVLEENG 141
Query: 62 CAYVVEGDVFFAVEKSPNYGRLSGQRLENNR--AGERVAVDSRKRNPADFALW---KAAK 116
Y V G+V+F +YG+++G L + + + RV +D KRN +DF LW K
Sbjct: 142 FTYFVNGNVYFDTSCFKSYGQMAGINLNDFKDMSVSRVEIDKSKRNKSDFVLWFTNSKFK 201
Query: 117 AGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQSCAACQD 176
E WDSPWG G P WH+EC+AM+ Y S DIH GG+D I HH NEIA +
Sbjct: 202 DQEMKWDSPWGFGYPSWHLECAAMNLEYFKSTLDIHLGGVDHIGVHHINEIAIAECYLNK 261
Query: 177 SNVSYWMHNGHVTNNNEKMSKSLGNFFTIRQI-TERYHPLALRHFLISAHYRSPLNYSVL 235
++H + EKMSKS NF TI+ + + + PL R+F ++AHYR+ L ++
Sbjct: 262 KWCDMFVHGEFLIMEYEKMSKSNNNFITIKDLEDQGFSPLDFRYFCLTAHYRTQLKFTFN 321
Query: 236 QLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCIN-------KLRDEFHAR 288
L + A + L +L F +N +D N + D F +
Sbjct: 322 NLKACKIARENMLNKLTYFYSSLDQFD-------LNLLNKDLENIEFSLEKEYYDSFLEK 374
Query: 289 MSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILG 348
++ DLN L L K LS + LR + + EVL +
Sbjct: 375 IAFDLNIPQGLA----------------LLWDIIKDDNLSFLSKLR-LAFKFDEVLSL-- 415
Query: 349 LLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGI 408
G E+L+++++ + + ++++ LIEER A+ KDF ++D+IR KG
Sbjct: 416 ----GLREEILREIENHRI----VIDDNMKSLIEERRLAKCEKDFKRADEIREYFASKGF 467
Query: 409 ALMDMGKET 417
L+D + T
Sbjct: 468 VLIDTEEGT 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 = 89.2 bits (222), Expect = 4e-21
Identities = 50/188 (26%), Positives = 78/188 (41%), Gaps = 38/188 (20%)
Query: 236 QLDSASDAVFYIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFHARMSDDLNT 295
L+ A A+ +Y L+ D + F A M DD NT
Sbjct: 3 NLEDARAALERLYTALRGVPPT--------------TVDIDWGEPFAERFIAAMDDDFNT 48
Query: 296 SHILTGAFQDALKF-INSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLL--PP 352
A A+ F + +N LKK+ ++ +L L+ + +LGLL P
Sbjct: 49 P----EAL--AVLFELAREINRLKKEDIEKAA-ALAALLKALGG-------VLGLLQQDP 94
Query: 353 GAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMD 412
A+ LQ L+ ++ LI +R ARK KD++++D+IR +L +GI L D
Sbjct: 95 EAF---LQG----GTGEGGLSVAEIEALIAQRNQARKAKDWAEADRIRDELAAQGIILED 147
Query: 413 MGKETIWR 420
+ 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: 149 FDIHGGGIDLI--------FPHHENEIAQSCAACQDSN--VSYW----MHNGHVTNNNEK 194
DI+ GG + F H A D + G V EK
Sbjct: 225 VDIYIGGKEHAPNHLLYSRFNHK---------ALFDEGLVTDEPPKGLIVQGMVLLEGEK 275
Query: 195 MSKSLGNFFTIRQITERYHPLALRHFLISA 224
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 = 8e-07
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 223
+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: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
+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: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
+G++T +KMSKS GN + ERY ALR++L+
Sbjct: 271 HGYLTVEGKKMSKSRGNVVDPDDLLERYGADALRYYLLRE 310
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 48.9 bits (117), Expect = 5e-06
Identities = 21/40 (52%), Positives = 25/40 (62%)
Query: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
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 = 44.4 bits (105), Expect = 2e-05
Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 132 GWHIECSAMSAHYLSSKFDIHGGGIDLIFPHHENEIAQS-CAACQDSNVSYWMHNGHVT- 189
+ +A ++ DIH GG D + H E + A + + G V
Sbjct: 77 EYMFLQAADFLLLYETECDIHLGGSDQLG-HIELGLELLKKAGGPARP--FGLTFGRVMG 133
Query: 190 NNNEKMSKSL 199
+ 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: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
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 = 42.9 bits (101), Expect = 4e-04
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
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 = 42.0 bits (99), Expect = 4e-04
Identities = 29/119 (24%), Positives = 40/119 (33%), Gaps = 16/119 (13%)
Query: 121 SWDSPWGPGRPGWHIEC-------SAMSAHYLSSKF--------DIHGGGIDLIFPHHEN 165
S WG P + S Y K D H G D++
Sbjct: 184 SRQRYWGTPLPEDVFDVWFDSGIGPLGSLGYPEEKEWFKDSYPADWHLIGKDILRGWANF 243
Query: 166 EIAQSCAACQDSNVSYWMHNGHVT-NNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 223
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 = 41.9 bits (99), Expect = 7e-04
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 185 NGHVT-NNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
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: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS----------------AHYRS 228
+G +T + EKMSKSLGN + + Y A+R+FL+ +
Sbjct: 290 HGFLTLDGEKMSKSLGNVIDPFDLVDEYGVDAVRYFLLREIPFGQDGDFSREAFINRINA 349
Query: 229 PLNYSVLQLDSASDAVFYIYQTLQDCEVAL-SPFQEHGKTARINPAAEDCINKLRDEFH- 286
L + L + ++ + + P + AA + ++R
Sbjct: 350 DLANDLGNLAQRTLSMIAKN-----FDGKVPEPGALTEADEALLEAAAALLERVRAAMDN 404
Query: 287 ARMSDDLNTSHILTGAFQDALKFINSSLNM-----LKKKQPKQQQLSLIESLRKIENEVK 341
L A ++ N ++ L K P E L + +
Sbjct: 405 LAFDKALE-------AILALVRAANKYIDEQAPWSLAKTDP--------ERLATVLYTLL 449
Query: 342 EVLRILGLL--P--PGAYSEVLQQL 362
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 = 0.002
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 186 GHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 223
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 = 0.003
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
+ ++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: 190 NNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 222
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: 186 GHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 222
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 = 38.1 bits (89), Expect = 0.008
Identities = 11/33 (33%), Positives = 12/33 (36%)
Query: 191 NNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 223
KMS S GN T E P LR+
Sbjct: 272 GGGKMSSSKGNVITPSDWLEVAPPEVLRYLYAR 304
>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 = 0.011
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 193 EKMSKSLGNFFTIRQITERYHPLALRHFLI 222
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 = 0.011
Identities = 17/41 (41%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 185 NGHVTNNN-EKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
+GHV + + +KMSKSLGN+ ++ ++Y ALR +L+S+
Sbjct: 582 HGHVLDEDGQKMSKSLGNYVDPFEVFDKYGADALRWYLLSS 622
>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: 188 VTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDAVFYI 247
V EKMSKS GN ++I E Y ALR F++ + P+ S+ +S +
Sbjct: 599 VYVGYEKMSKSKGNGIDPQEIVESYGADALRLFIM---FMGPIAASLEWNESGLEGARRF 655
Query: 248 YQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEFH---ARMSDDLNTSHILTGAFQ 304
+ + ++ E + A E+ +LR + H ++++DL A
Sbjct: 656 LDRVWNLVYEITG--ELDAASLTVTALEEAQKELRRDVHKFLKKVTEDLEKRESFNTAIS 713
Query: 305 DALKFINSSLNMLKKKQPKQ 324
++ +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 = 0.013
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 191 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 225
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 = 0.014
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 191 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 225
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 = 0.034
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 191 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 225
+ 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 = 0.054
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 1/86 (1%)
Query: 149 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSYWMHNGHVTNNN-EKMSKSLGNFFTIRQ 207
D+ G D I A + + +G V + KMSKSLGN
Sbjct: 521 ADMLLEGSDQTRGWFYRMIVLGTALTGSAPYKNVLVHGLVRDEQGRKMSKSLGNVIDPLD 580
Query: 208 ITERYHPLALRHFLISAHYRSPLNYS 233
+ ++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 = 0.070
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLIS 223
+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 = 34.6 bits (80), Expect = 0.090
Identities = 21/106 (19%), Positives = 48/106 (45%), Gaps = 12/106 (11%)
Query: 302 AFQDALKFINSSLNMLKKKQPKQ--QQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVL 359
A + L+ I+ L +K + K +L L+E R+ E+ R+ L +
Sbjct: 169 ALRQQLEVISEELEARRKLKEKGLVSRLELLELERERAEAQGELGRLEAELE-----VLK 223
Query: 360 QQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTR 405
+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 = 0.20
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 193 EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYS 233
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: 284 EFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEV 343
F M DD NT L F + + IN L K ++ L + ++ +
Sbjct: 1 RFEEAMDDDFNTPEALAVLF-ELAREINR----LALKATDAEE------LAALAALLRAL 49
Query: 344 LRILGLL 350
+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 = 0.43
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 191 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAH 225
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 = 0.63
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 354 AYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRAD 402
++ + + ++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 = 0.63
Identities = 16/41 (39%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 90 NNRAGE-RVAVDSRKRNPADFALWKAAKAGEPSWDSPWGPG 129
AGE V V + NP D WK G P+W P PG
Sbjct: 24 GPGAGEVLVKVHAAGLNPVD---WKVIAWGPPAWSYPHVPG 61
>gnl|CDD|235046 PRK02507, PRK02507, proton extrusion protein PcxA; Provisional.
Length = 422
Score = 31.4 bits (72), Expect = 0.93
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 23/89 (25%)
Query: 297 HILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEV-------KEVLRI--- 346
L+ F ++ ++ P I ++E E KE L
Sbjct: 216 QQLSKTF-----IVSPLVD---HFFPALPFEIFINP--ELEEEALEELRRFKEELEFEAL 265
Query: 347 LGLLPPGAYSEVLQQLKDKALKRAELTEE 375
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 = 0.95
Identities = 21/104 (20%), Positives = 30/104 (28%), Gaps = 33/104 (31%)
Query: 105 NPADFALWK----------------AAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSK 148
P D + K +K GEP+WD G P + K
Sbjct: 197 KPIDAGMAKFCETCGKCADECPSGAISKGGEPTWDPEDSNGDP--------PGENNPGLK 248
Query: 149 FDIHGGGIDLIFPHHENEIAQSCAACQDSNVSY------WMHNG 186
+ 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 = 1.0
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 185 NGHVTNNN-EKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSASDA 243
+G + KMSKSLGN ++ +Y LR ++ S+ L +S L +
Sbjct: 601 HGFTLDEKGRKMSKSLGNVVDPLKVINKYGADILRLYVASSDPWEDLRFSDEILKQVVEK 660
Query: 244 VFYI 247
I
Sbjct: 661 YRKI 664
>gnl|CDD|181787 PRK09343, PRK09343, prefoldin subunit beta; Provisional.
Length = 121
Score = 29.7 bits (67), Expect = 1.1
Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 15/102 (14%)
Query: 315 NMLKKKQPKQQQLSLIESLR-KIE---NEVKEVLRILGLLPPGA--YSEV----LQQLKD 364
L + Q QQQL + + +I+ E+ + L L LP Y V ++ K
Sbjct: 11 AQLAQLQQLQQQLERLLQQKSQIDLELREINKALEELEKLPDDTPIYKIVGNLLVKVDKT 70
Query: 365 KALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRK 406
K K EL E +L+E R+ + ++ ++++ +L K
Sbjct: 71 KVEK--ELKER--KELLELRSRTLEKQEKKLREKLK-ELQAK 107
>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase.
Length = 616
Score = 31.2 bits (70), Expect = 1.2
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 185 NGHVTNNNEKMSKSLGNFFTIRQITERYHPLALRHFLI 222
+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: 193 EKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
+KMSKS GN T ++ E+Y A+R++ SA
Sbjct: 532 KKMSKSKGNVVTPEELLEKYGADAVRYWAASA 563
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 29.6 bits (67), Expect = 1.3
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 24/93 (25%)
Query: 315 NMLKKKQPKQQQLS-LIESLRKIENEVKE---VLRILGLLPPGA--------------YS 356
L + Q QQQL +I +++E ++KE L L L A
Sbjct: 10 AQLAQLQQLQQQLQKVILQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKE 69
Query: 357 EVLQQLKDKA------LKRAELTEEDVLQLIEE 383
E + +L+++ +K E EE + + +EE
Sbjct: 70 EAVDELEERKETLELRIKTLEKQEEKLQERLEE 102
>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 = 1.4
Identities = 12/52 (23%), Positives = 27/52 (51%)
Query: 359 LQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIAL 410
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 = 1.6
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 193 EKMSKSLGNFFTIRQITERYHPLALRHFLISA 224
KMSKSLGN+ +++ ++Y ALR ++ S+
Sbjct: 298 RKMSKSLGNYVDPQEVVDKYGADALRLWVASS 329
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 30.6 bits (70), Expect = 1.7
Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 14/93 (15%)
Query: 307 LKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRIL--GLLPPGAYSEVLQQLKD 364
L+ L +K +++L ++E L K N++ V+ ++ + A E++++L +
Sbjct: 318 LEVYKRRKEYLLEK--LEERLHILEGLLKALNKIDFVIEVIRGSIDLKKAKKELIEELSE 375
Query: 365 K--------ALKRAELTEEDVLQLIEERAAARK 389
L+R LT+E++ +L +E K
Sbjct: 376 IQADYLLDMRLRR--LTKEEIEKLEKEIEELEK 406
>gnl|CDD|237967 PRK15446, PRK15446, phosphonate metabolism protein PhnM;
Provisional.
Length = 383
Score = 30.5 bits (70), Expect = 2.0
Identities = 12/52 (23%), Positives = 22/52 (42%)
Query: 359 LQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIAL 410
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 = 2.1
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 337 ENEVKEVLRILGLLPPGAYSEVLQQLKDKA 366
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 = 2.3
Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 333 LRKIENEVKEVLRILGLLP--PGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKN 390
KI E+K+ L++ G L G ++ + + K+ +L+ ED+ +E++ + +
Sbjct: 93 FYKILEELKKELKVYGSLADKSGFIEQLAELYTE--FKKYQLSVEDLEDTADEQSLKKLH 150
Query: 391 KDFSKSDQIRADL 403
++ 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 = 2.4
Identities = 13/54 (24%), Positives = 25/54 (46%)
Query: 328 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLI 381
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 = 2.8
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 246 YIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEF 285
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 = 3.2
Identities = 23/116 (19%), Positives = 38/116 (32%), Gaps = 20/116 (17%)
Query: 52 DMITQIINND-CAYVVEG-DVFF-------AVEKSPNYGRLSGQRLENNRAGERVAVDSR 102
D + + N C + +F ++ S E+ E A S+
Sbjct: 90 DALDDVFNGLNCPSLKGKPKLFIIDACRGGPLDDGVKSDSGSSGESESVDDSEA-AGLSK 148
Query: 103 KRNPADFALWKAAKAGEPSWDSPWGPGRPGWHIECSAMSAHYLSSKFDIHGGGIDL 158
PADF + + G+ S+ G G W I+ L + G+DL
Sbjct: 149 IPAPADFLVAYSTTPGQVSYR---GTGSGSWFIQA-------LCQVLREYAPGLDL 194
>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 = 3.2
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 329 LIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAAR 388
L E L + ++ E + IL LL G+ E L+ L +L++E++ + ERA +
Sbjct: 279 LPEYLELAKEQIPEKVFILKLLGFGSLDEFLKSLGLLLKVVIKLSDEEIEKWA-ERALSA 337
Query: 389 KNK 391
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 = 3.5
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 321 QPKQQQLSLIESLRKI-ENEVKEVLRILGL 349
P+ +L LIE LR + ++EV+E+ R LGL
Sbjct: 135 LPEDMKLKLIEPLRDLFKDEVRELGRELGL 164
>gnl|CDD|112953 pfam04163, Tht1, Tht1-like nuclear fusion protein.
Length = 554
Score = 29.7 bits (66), Expect = 3.5
Identities = 27/109 (24%), Positives = 43/109 (39%), Gaps = 22/109 (20%)
Query: 266 KTARINPAAEDCINKLRDEFHARMSDDLN-----TSHILTGAFQDALKFINSS------- 313
+ A N A I L+D+F A + D + + L + Q + F+NS
Sbjct: 287 EFASENAIALSAIGDLKDDFLAFLEDRIKNLIEMSEDSLKESVQRNIDFVNSGFQELEDF 346
Query: 314 -------LNMLKKKQPKQQQLSLIESLR---KIENEVKEVLRILGLLPP 352
L LKK +QQ L E L+ ++ K+ L+ +LP
Sbjct: 347 SIGLKEELGGLKKDLSEQQNLEAEEILQGFNDFLHDSKDHLKTDEILPE 395
>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 = 3.7
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 9/40 (22%)
Query: 246 YIYQTLQDCEVALSPFQEHGKTARINPAAEDCINKLRDEF 285
Y +QT D EV L ++E G E+C+++L F
Sbjct: 91 YTFQTDSDTEVILHLYEEWG---------EECVDRLDGMF 121
>gnl|CDD|216083 pfam00724, Oxidored_FMN, NADH:flavin oxidoreductase / NADH oxidase
family.
Length = 336
Score = 29.2 bits (66), Expect = 4.2
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 15/76 (19%)
Query: 328 SLIESLRKIENEVKE-----VLRI--LGLLPPGAYSEVLQQLK------DKALKRAELTE 374
+E +K+ V E +++ LG P Y E L ++K ELT+
Sbjct: 76 EQVEGWKKLTEAVHENGSKIGVQLWHLGREAPPEYLEDLGLRPSDPSALPASIKVRELTK 135
Query: 375 EDVLQLIEE--RAAAR 388
E++ ++I+E +AA R
Sbjct: 136 EEIKEIIQEFVQAAKR 151
>gnl|CDD|235427 PRK05354, PRK05354, arginine decarboxylase; Provisional.
Length = 634
Score = 29.3 bits (67), Expect = 4.3
Identities = 17/54 (31%), Positives = 33/54 (61%), Gaps = 9/54 (16%)
Query: 335 KIENEVK-----EVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE 383
+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 = 4.4
Identities = 9/64 (14%), Positives = 21/64 (32%), Gaps = 8/64 (12%)
Query: 277 CINKLRDEFHARMSDDLN--TSHILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLR 334
IN + F D +H+ F +I ++L+ + + +
Sbjct: 14 VINYRKHTF------DTKNVCAHVEDDGFATISDYIRANLDKAFIIVGDCSKKRVAPHRK 67
Query: 335 KIEN 338
++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 = 4.5
Identities = 20/116 (17%), Positives = 51/116 (43%), Gaps = 15/116 (12%)
Query: 276 DCINKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLKKKQPK--------QQQL 327
+ I L++++ + M + + +L +DALK + L L ++ K +++
Sbjct: 88 EFIANLKEKWLSGMHKCESPTELLLRIVKDALKTYEAPLEKLSEELDKYEEEVFLKKRKG 147
Query: 328 SLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEE 383
SL++ L ++ + + R+L L +V+ ++ +D+ L+ +
Sbjct: 148 SLLKRLYHLKRKASVIKRVLNLT-----QDVIDKIDTPLKSDPYT--QDLRDLLIK 196
>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 = 6.3
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 319 KKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRA----ELTE 374
KK+ K +++E +++ + L P V Q D+A +R +L+
Sbjct: 7 KKKKKVDPQREQRKRKRLEKFIRKRTKSARGLKPVEDRIVPQLSVDEAKRRQRKLLKLSP 66
Query: 375 EDVLQLIEERAAARK 389
ED+ E RA K
Sbjct: 67 EDL----ERRALIEK 77
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.0 bits (66), Expect = 6.4
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 9/75 (12%)
Query: 316 MLKKKQPKQQQLSLIESL-----RKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRA 370
+ KK++ +Q+ +E IE +++E+ RI GL A +L++++++A R
Sbjct: 112 LEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAKEILLEKVEEEA--RH 169
Query: 371 ELTEEDVLQLIEERA 385
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 = 6.4
Identities = 7/11 (63%), Positives = 7/11 (63%)
Query: 191 NNEKMSKSLGN 201
KMSKS GN
Sbjct: 517 QGRKMSKSKGN 527
>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 28.9 bits (66), Expect = 6.8
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 193 EKMSKSLGN 201
KMSKSLGN
Sbjct: 591 RKMSKSLGN 599
>gnl|CDD|223070 PHA03391, p47, viral transcription regulator p47; Provisional.
Length = 395
Score = 28.7 bits (65), Expect = 6.9
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 14/50 (28%)
Query: 191 NNEKMSKSLGNFFTIRQITERYHPLALRHFLISAHYRSPLNYSVLQLDSA 240
N++K K L + +I I +R ++ Y VL+LD+
Sbjct: 180 NDKKFEKFLSSITSISDIIKR--------------HKFSKKYIVLELDAN 215
>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 = 7.3
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 14/79 (17%)
Query: 340 VKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDFSKSDQI 399
VKE+L+I +L KA+K + EE+ + + + K D + Q+
Sbjct: 81 VKELLKITSVLY-------------KAMKSTDGDEEENTRSLAKFDLGSKISDLKAARQL 127
Query: 400 RADLTRKGIALMDM-GKET 417
+++T +G AL D+ GKE
Sbjct: 128 ASEITERGAALYDLLGKEL 146
>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 = 7.8
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 372 LTEEDVLQLIEERAAARKNKDFSKSDQIRADLTRKGIALMDMGKETIWRPCVLVEQEQEA 431
LT+ + I+E R+ + +D++ +LT IA D + + ++ E
Sbjct: 40 LTKPKIKAYIDELMKEREKRTIITADEVLEELTE--IARGDETELVLVGTKEGEVEKIEK 97
Query: 432 PPAEKEKKPAA 442
K++ A
Sbjct: 98 KVKLKDRLKAL 108
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 28.5 bits (64), Expect = 8.1
Identities = 10/66 (15%), Positives = 25/66 (37%)
Query: 304 QDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLK 363
+ + + + + ++ ++ + + V++ L LP E L +L
Sbjct: 255 KLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLELA 314
Query: 364 DKALKR 369
D +KR
Sbjct: 315 DFIIKR 320
>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 = 27.9 bits (63), Expect = 8.4
Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 24/72 (33%)
Query: 3 IIRRANDLGENPLSLSNRY-------CQEYLVDM-ADLQCLPPTYQPRVSDHMEQIKDMI 54
+I R G L + Y + +V M ADL PP E I +++
Sbjct: 57 LIVRPGKRG-----LGSAYIEGFKAARGDVIVVMDADLS-HPP----------EYIPELL 100
Query: 55 TQIINNDCAYVV 66
+ V+
Sbjct: 101 EAQLEGGADLVI 112
>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 = 8.5
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 330 IESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKD-KALKRAELTEEDVLQLIEERAAAR 388
E L+ ++ E +EVLR G +V ++++ L E+ E+++ +L+ E R
Sbjct: 181 EEKLKMVD-EAEEVLRNAG------VGQV--RVRNYDNLAVIEVPEDELSKLLNEAEEVR 231
Query: 389 KN-KDF 393
KD
Sbjct: 232 DKFKDI 237
>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 = 26.5 bits (59), Expect = 8.6
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 352 PGAYSEVLQQLKDKALKRAELTEEDVL---QLIEERAAARKNKDFSKSDQ 398
PGA E LQ+ +K LK LTEE++ + I + D S +
Sbjct: 42 PGA--EDLQRDLEKVLKLWGLTEEELFERTREIHAKGGVYSGFDTSDQED 89
>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 = 8.8
Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 9/79 (11%)
Query: 315 NMLKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTE 374
P ++ L L E + +E E+KEV L + +++ + L E
Sbjct: 58 GGKPDVPPSKEFLDLEEEILDLEAEIKEVEENLE--------SLEKEINELEEWLNVLDE 109
Query: 375 EDVLQLIEERAAARKNKDF 393
E L E + +
Sbjct: 110 EKSF-LDENLEELSELSNL 127
>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 = 8.9
Identities = 36/171 (21%), Positives = 60/171 (35%), Gaps = 23/171 (13%)
Query: 279 NKLRDEFHARMSDDLNTSHILTGAFQDALKFINSSLNMLK-----KKQPKQQQLSLIESL 333
+ L +E R+ L T A QDA + + S +N+L P Q S E L
Sbjct: 278 DMLPEERKLRLLKALAEMSPYTTA-QDARQRLPSIVNLLLEYMPLGDTPPSFQFSHAECL 336
Query: 334 RKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEEDVLQLIEERAAARKNKDF 393
L LG P A + + L E+ + KNKDF
Sbjct: 337 LY-------ALHTLGKKHPNATNSLCGYKIVTGQPSDRLGEDF----------SEKNKDF 379
Query: 394 SKSDQIRADLTRKGIALMDMGKETIWRPCVLVEQEQEAPPAEKEKKPAATG 444
++ DLT+ + + G + + ++E + +++ TG
Sbjct: 380 TERLTYVEDLTKATMKKLTQGMSEHSKAMSTAKTDEEKEELKTKEQLTTTG 430
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.5 bits (64), Expect = 8.9
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 324 QQQLSLIES----LRKIENEVKEVLRILGLLPPGA--YSEVLQQLKDKALKRAELTEEDV 377
++++ +E L +++ ++KE+ + L L Y E + ++ + LT
Sbjct: 327 EERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTP 386
Query: 378 LQLIEERAAARKNK 391
+L +E K K
Sbjct: 387 EKLEKELEELEKAK 400
>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 = 9.1
Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 317 LKKKQPKQQQLSLIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKRAELTEED 376
K Q K + + + L++++ E+ E+ A + +L+DK L + E
Sbjct: 62 KAKGQKKDKIEEIKKELKELKEELTEL--------SAALKALEAELQDKLLSIPNIPHES 113
Query: 377 V 377
V
Sbjct: 114 V 114
>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 = 9.2
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 16/72 (22%)
Query: 324 QQQLSLIESLRKIENE-VKEVLRILGLLPPGAYSEVLQQLKDK------------ALKRA 370
Q+ L++ + + E VKEV R+ LP +EVLQ+L + L
Sbjct: 491 QETRYLLDQMEREYPELVKEVQRV---LPLQRIAEVLQRLVSEQVSIRNLRLILETLIEW 547
Query: 371 ELTEEDVLQLIE 382
E+DV+ L E
Sbjct: 548 AQREKDVVMLTE 559
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 28.4 bits (64), Expect = 9.3
Identities = 8/30 (26%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 36 PPTYQPRVSDHMEQIKDMITQIINNDCAYV 65
P YQ S+ + + ++I AYV
Sbjct: 78 GPYYQ---SERFDIYYEYAEKLIEKGKAYV 104
>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 = 9.5
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 329 LIESLRKIENEVKEVLRILGLLPPGAYSEVLQQLKDKALKR--AELTEEDVLQLIEE 383
L+E L +E L +L LLPP +EVL++L + L E++ +L+EE
Sbjct: 9 LLEEL-----PPEERLALLRLLPPERAAEVLEELDEDVQAELLEALPPEELAELLEE 60
>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 = 9.5
Identities = 23/107 (21%), Positives = 38/107 (35%), Gaps = 26/107 (24%)
Query: 342 EVLRILGLLPPGAYSEVLQQLKDKALK-------------RAELTEEDVLQLIEERAAAR 388
+V R+LG + Y+ K K+++ EL EEDV L + A+
Sbjct: 202 DVYRLLGEITEEDYTCDTPDGKGKSIEECMRRLARMVCADLEELGEEDVRNLAKYYYEAQ 261
Query: 389 KNKDFSKSDQIRADLTRKGIA----------LMDMGKETIWRPCVLV 425
+ ++ I L R G+ L + R C+ V
Sbjct: 262 LEQ---LTEAIEEVLERYGLKTVVAAGAGEFLAKEAAARLGRECIDV 305
>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 = 27.6 bits (62), Expect = 9.9
Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 12/83 (14%)
Query: 298 ILTGAFQDALKFINSSLNMLKKKQPKQQQLSLIESLRKIENE------VKEVLRILGLLP 351
+ Q L++IN +L ++K++ +L L + +E V + LL
Sbjct: 24 RKSSQLQSLLEYINETLRLIKEEWKPALEL-FDRKLTNLADELTDQVGGDLVAELYDLLL 82
Query: 352 PGAYSEVLQ-----QLKDKALKR 369
G S L+ QL ++ LKR
Sbjct: 83 TGIISPALKDFLLNQLGERGLKR 105
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: 22,880,005
Number of extensions: 2217612
Number of successful extensions: 2796
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2752
Number of HSP's successfully gapped: 130
Length of query: 449
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 349
Effective length of database: 6,502,202
Effective search space: 2269268498
Effective search space used: 2269268498
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)