RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8372
(883 letters)
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 313 bits (804), Expect = 3e-96
Identities = 109/206 (52%), Positives = 141/206 (68%), Gaps = 10/206 (4%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTR 359
EV+AS + VLNK+ +PF I + E+LRLK+RYLD R PEMQ NL+ RSK R
Sbjct: 94 EVLASELEVLNKSKT-LPFPIDDEEDVSEELRLKYRYLDLRRPEMQKNLKLRSKVTSAIR 152
Query: 360 EFLATHRDFVEVETPTLFKRTPGGAREFVVP--THEPNKFYSLVQSPQQLKQLLMVGSVD 417
FL + F+E+ETP L K TP GAR+++VP H P KFY+L QSPQ KQLLMV D
Sbjct: 153 NFLDDN-GFLEIETPILTKSTPEGARDYLVPSRVH-PGKFYALPQSPQLFKQLLMVAGFD 210
Query: 418 RYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCY----CLNIP-TRT 472
RY+QIARC+RDE R DRQPEFTQ+DIE+SF T++DVM L+E L+ + L +
Sbjct: 211 RYYQIARCFRDEDLRADRQPEFTQIDIEMSFVTQEDVMALMEGLIRHVFKEVLGVDLPTP 270
Query: 473 FSRISYNDAISLYGSDKPDLRYDCKI 498
F R++Y +A+ YGSDKPDLR+ ++
Sbjct: 271 FPRMTYAEAMRRYGSDKPDLRFGLEL 296
Score = 239 bits (612), Expect = 7e-69
Identities = 97/258 (37%), Positives = 133/258 (51%), Gaps = 27/258 (10%)
Query: 630 STNKKITEYKNLAKK------AFNDVKMSTVKVQDSLEWTNKLTKILPDLNVEEFRNKEN 683
+ K+I E AK A+ +KV + + K L + + +
Sbjct: 333 LSRKQIDELTEFAKIYGAKGLAY-------IKVNED-GLKGPIAKFLSEEELAALLERTG 384
Query: 684 LEEGDLIVVSWGKQEDVLSLLGMIRSESHKIKVKNTLPLEFDNPKSFSIFWVVDFPLFLP 743
++GDLI K + V LG +R +K+ L L + F+ WVVDFP+F
Sbjct: 385 AKDGDLIFFGADKAKVVNDALGALR-----LKLGKELGLI--DEDKFAFLWVVDFPMFEY 437
Query: 744 S-DSGTLESAHHPFTQPHPEDEH-LLSSNPLEVRGLHYDLVLNGNEIGGGSIRIHSSELQ 801
+ G +AHHPFT P ED L +++P + R YDLVLNG E+GGGSIRIH E+Q
Sbjct: 438 DEEEGRWVAAHHPFTMPKDEDLDELETTDPGKARAYAYDLVLNGYELGGGSIRIHRPEIQ 497
Query: 802 ESILHFLNIETSSLQ----HMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFPK 857
E + L I + ++ A KYG PPHGGIA G+DRL+ +L G SIRDVIAFPK
Sbjct: 498 EKVFEILGISEEEAEEKFGFLLDALKYGAPPHGGIAFGLDRLVMLLAGADSIRDVIAFPK 557
Query: 858 GFGGKDHLSGAPCDIPEA 875
+D L+GAP + E
Sbjct: 558 TQSAQDLLTGAPSPVDEK 575
Score = 68.9 bits (170), Expect = 6e-12
Identities = 25/49 (51%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 9 RSHTCGALRLSDVDKTVTLCGWLQNQRVDM----FALLRDAYGQVQVIV 53
R+H CG LR S V +TVTLCGW+ +R D F LRD G VQV+
Sbjct: 4 RTHYCGELRESHVGQTVTLCGWVHRRR-DHGGLIFIDLRDREGIVQVVF 51
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 294 bits (755), Expect = 3e-89
Identities = 110/206 (53%), Positives = 139/206 (67%), Gaps = 10/206 (4%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTR 359
EV+A I VLN + +PF I++ A E++RLK+RYLD R PEMQ NL+ RSK R
Sbjct: 94 EVLAEEIEVLNASK-TLPFQIEDETNASEEIRLKYRYLDLRRPEMQKNLKLRSKVTKAIR 152
Query: 360 EFLATHRDFVEVETPTLFKRTPGGAREFVVPT--HEPNKFYSLVQSPQQLKQLLMVGSVD 417
FL F+E+ETP L K TP GAR+F+VP+ H P KFY+L QSPQ KQLLMV D
Sbjct: 153 NFLDDQ-GFLEIETPILTKSTPEGARDFLVPSRVH-PGKFYALPQSPQLFKQLLMVAGFD 210
Query: 418 RYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCY----CLNI-PTRT 472
RY+QIARC+RDE R DRQPEFTQ+D+E+SF +DVM LIE+LL Y I
Sbjct: 211 RYYQIARCFRDEDLRADRQPEFTQIDLEMSFVDEEDVMELIEKLLRYVFKEVKGIELKTP 270
Query: 473 FSRISYNDAISLYGSDKPDLRYDCKI 498
F R++Y +A+ YGSDKPDLR+ ++
Sbjct: 271 FPRMTYAEAMRRYGSDKPDLRFPLEL 296
Score = 244 bits (624), Expect = 1e-70
Identities = 103/269 (38%), Positives = 147/269 (54%), Gaps = 14/269 (5%)
Query: 620 RILILPKDLDSTNKKITEYKNLAKKAFNDVKMSTVKVQDSLEWTNKLTKILPDLNVEEFR 679
+ +++P + K+I E AK + ++ +KV++ + K L + +EE
Sbjct: 322 KAIVVPGGASLSRKQIDELTEFAKI-YGAKGLAYIKVEED-GLKGPIAKFLSEEILEELI 379
Query: 680 NKENLEEGDLIVVSWGKQEDVLSLLGMIRSESHKIKVKNTLPLEFDNPKSFSIFWVVDFP 739
+ E+GD+I K++ V LG +R + K L + F WVVDFP
Sbjct: 380 ERLGAEDGDIIFFVADKKKVVNKALGALRLKLGKE-------LGLIDKDQFKFLWVVDFP 432
Query: 740 LFLPSD-SGTLESAHHPFTQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSIRIHSS 798
LF + G +AHHPFT P PED LL ++P VR YDLVLNG E+GGGSIRIH
Sbjct: 433 LFEWDEEEGRYVAAHHPFTMPKPEDLELLEADPESVRARAYDLVLNGYELGGGSIRIHDP 492
Query: 799 ELQESILHFLNIETSSLQ----HMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIA 854
E+QE + L I + +++AFKYG PPHGGIA G+DRL+ +L G +SIRDVIA
Sbjct: 493 EIQEKVFEILGISPEEAEEKFGFLLEAFKYGAPPHGGIAFGLDRLVMLLTGAESIRDVIA 552
Query: 855 FPKGFGGKDHLSGAPCDIPEAERNYYNLK 883
FPK D L+ AP ++ E + ++K
Sbjct: 553 FPKTQQAADLLTNAPSEVDEKQLKELSIK 581
Score = 62.2 bits (152), Expect = 7e-10
Identities = 25/60 (41%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 9 RSHTCGALRLSDVDKTVTLCGWLQNQRVDM----FALLRDAYGQVQVIVPNHQVPNIYRT 64
R+H CG LR S V +TVTL GW+ +R D F LRD G VQV+ P +
Sbjct: 2 RTHYCGELRESHVGQTVTLSGWVHRRR-DHGGLIFIDLRDREGIVQVVFDPEDSPEAFEV 60
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 245 bits (628), Expect = 3e-71
Identities = 102/204 (50%), Positives = 142/204 (69%), Gaps = 13/204 (6%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTR 359
E++A +IT+LNK+ P I+ + A+E++RLK+RYLD R PEMQ L+ R K R
Sbjct: 92 EILAESITLLNKSKT-PPLIIEKTD-AEEEVRLKYRYLDLRRPEMQQRLKLRHKVTKAVR 149
Query: 360 EFLATHRDFVEVETPTLFKRTPGGAREFVVPT--HEPNKFYSLVQSPQQLKQLLMVGSVD 417
FL F+E+ETP L K TP GAR+++VP+ H+ +FY+L QSPQ KQLLMV VD
Sbjct: 150 NFLDQQ-GFLEIETPMLTKSTPEGARDYLVPSRVHKG-EFYALPQSPQLFKQLLMVSGVD 207
Query: 418 RYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCYC------LNIPTR 471
RY+QIARC+RDE R DRQPEFTQ+D+E+SF T++DVM LIE+L+ + +++ +
Sbjct: 208 RYYQIARCFRDEDLRADRQPEFTQIDMEMSFMTQEDVMELIEKLVSHVFLEVKGIDLK-K 266
Query: 472 TFSRISYNDAISLYGSDKPDLRYD 495
F ++Y +A+ YGSDKPDLR+
Sbjct: 267 PFPVMTYAEAMERYGSDKPDLRFP 290
Score = 204 bits (521), Expect = 2e-56
Identities = 98/258 (37%), Positives = 141/258 (54%), Gaps = 15/258 (5%)
Query: 631 TNKKITEYKNLAKKAFNDVK-MSTVKVQDSLEWTNKLTKILPDLNVEEFRNKENLEEGDL 689
+ K I E + AK+ K ++ +KV + + + K L + + + + + GD+
Sbjct: 331 SRKSIKELRKFAKE--YGAKGLAYLKVNED-GINSPIKKFLDEKKGKILLERTDAQNGDI 387
Query: 690 IVVSWGKQEDVLSLLGMIRSESHKIKVKNTLPLEFDNPKSFSIFWVVDFPLFLPSDSGTL 749
++ G ++ VL LG +R +K+ L L +P FS WVVDFP+F G L
Sbjct: 388 LLFGAGSKKIVLDALGALR-----LKLGKDLGLV--DPDLFSFLWVVDFPMFEKDKEGRL 440
Query: 750 ESAHHPFTQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSIRIHSSELQESILHFLN 809
+AHHPFT P ED L + P E YDLVLNG E+GGGSIRIH E+Q+ + L
Sbjct: 441 CAAHHPFTMPKDEDLENLEAAPEEALAEAYDLVLNGVELGGGSIRIHDPEVQKKVFEILG 500
Query: 810 IETSSLQ----HMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFPKGFGGKDHL 865
I+ + +++AFKYG PPH G ALG+DRLM +L GT +IRDVIAFPK +
Sbjct: 501 IDPEEAREKFGFLLEAFKYGTPPHAGFALGLDRLMMLLTGTDNIRDVIAFPKTTAAACLM 560
Query: 866 SGAPCDIPEAERNYYNLK 883
+ AP I E + ++K
Sbjct: 561 TEAPSFIDEKQLEELSIK 578
Score = 46.7 bits (111), Expect = 4e-05
Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 5/48 (10%)
Query: 9 RSHTCGALRLSDVDKTVTLCGWLQNQRVDM----FALLRDAYGQVQVI 52
R+H CG LR + +TVTL GW+ +R D+ F LRD G VQV+
Sbjct: 2 RTHYCGQLRTEHLGQTVTLAGWVNRRR-DLGGLIFIDLRDRSGIVQVV 48
>gnl|CDD|238400 cd00777, AspRS_core, Asp tRNA synthetase (aspRS) class II core
domain. Class II assignment is based upon its structure
and the presence of three characteristic sequence
motifs. AspRS is a homodimer, which attaches a specific
amino acid to the 3' OH group of ribose of the
appropriate tRNA. The catalytic core domain is primarily
responsible for the ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. AspRS in this family
differ from those found in the AsxRS family by a GAD
insert in the core domain.
Length = 280
Score = 231 bits (591), Expect = 2e-69
Identities = 80/145 (55%), Positives = 99/145 (68%), Gaps = 7/145 (4%)
Query: 348 LRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGGAREFVVPT-HEPNKFYSLVQSPQQ 406
LR RS+ + R FL + FVE+ETP L K TP GAR+F+VP+ P KFY+L QSPQ
Sbjct: 1 LRLRSRVIKAIRNFL-DEQGFVEIETPILTKSTPEGARDFLVPSRLHPGKFYALPQSPQL 59
Query: 407 LKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCY-- 464
KQLLMV DRYFQIARC+RDE R DRQPEFTQ+DIE+SF ++D+M LIE LL Y
Sbjct: 60 FKQLLMVSGFDRYFQIARCFRDEDLRADRQPEFTQIDIEMSFVDQEDIMSLIEGLLKYVF 119
Query: 465 --CLNIP-TRTFSRISYNDAISLYG 486
L + T F R++Y +A+ YG
Sbjct: 120 KEVLGVELTTPFPRMTYAEAMERYG 144
Score = 213 bits (546), Expect = 4e-63
Identities = 81/179 (45%), Positives = 112/179 (62%), Gaps = 13/179 (7%)
Query: 692 VSWGKQEDVLSLL-GMIRS---ESHKIKVKNTLP-LEFDNPKS---FSIFWVVDFPLFLP 743
+S+ QED++SL+ G+++ E +++ P + + F W+VDFPLF
Sbjct: 99 MSFVDQEDIMSLIEGLLKYVFKEVLGVELTTPFPRMTYAEAMERYGFKFLWIVDFPLFEW 158
Query: 744 SD-SGTLESAHHPFTQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSIRIHSSELQE 802
+ G L SAHHPFT P ED LL +P + R YDLVLNG E+GGGSIRIH ++QE
Sbjct: 159 DEEEGRLVSAHHPFTAPKEEDLDLLEKDPEDARAQAYDLVLNGVELGGGSIRIHDPDIQE 218
Query: 803 SILHFLNIETSSLQ----HMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFPK 857
+ L + + +++AFKYG PPHGGIALG+DRL+ +L G++SIRDVIAFPK
Sbjct: 219 KVFEILGLSEEEAEEKFGFLLEAFKYGAPPHGGIALGLDRLVMLLTGSESIRDVIAFPK 277
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 227 bits (581), Expect = 3e-67
Identities = 97/190 (51%), Positives = 117/190 (61%), Gaps = 16/190 (8%)
Query: 328 EDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGG-ARE 386
E+ RLK+RYLD R P+MQ NL+ RSK + REFL R F+EVETP L K TP G AR+
Sbjct: 2 EETRLKYRYLDLRRPKMQANLKLRSKIIKAIREFLDE-RGFLEVETPILTKSTPEGGARD 60
Query: 387 FVVPTHEPNKFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDESTRPDRQP-EFTQLDIE 445
F+VP+ K L QSPQ KQLLMV DR FQIA C+RDE R DR P EFTQLD+E
Sbjct: 61 FLVPSKFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAPCFRDEDLRTDRHPPEFTQLDLE 120
Query: 446 LSFTTRDDVMRLIEELLCYC-------------LNIPTRTFSRISYNDAISLYGSDKPDL 492
+SF +DVM L E+L+ Y L I F RI+Y +AI YGSDKPDL
Sbjct: 121 MSFVDYEDVMDLTEDLIKYVFKKVLGKREELELLGIELPEFPRITYAEAIERYGSDKPDL 180
Query: 493 RYDCKIMIAI 502
R+ ++
Sbjct: 181 RFGLELKDVT 190
Score = 156 bits (397), Expect = 6e-42
Identities = 69/199 (34%), Positives = 90/199 (45%), Gaps = 32/199 (16%)
Query: 664 NKLTKILPDL-NVEEFRNKENLEEGDLIVVSWGKQEDVLSLLGMIRSESHKIKVKNTLPL 722
+ PDL E ++ + +G V + V LG +RSE + + +
Sbjct: 171 ERYGSDKPDLRFGLELKDVTEIFKGSEFKVFAEAGDVVDKALGALRSELGEENLGD---- 226
Query: 723 EFDNPKSFSIFWVVDFPLFLPSDSGTLESAHHPFTQPHPEDEHLLSSNPLEVRGLHYDLV 782
+ +V DFPLF HPF P ED +DLV
Sbjct: 227 ----KDKDNPVFVTDFPLFE-----------HPFYMPKDEDP--------PGLAERFDLV 263
Query: 783 LNGNEIGGGSIRIHSSELQESILHFLNIETSS----LQHMIQAFKYGCPPHGGIALGIDR 838
LNG EIGGGSIRIH E Q L ++ + A KYG PPHGGI LG+DR
Sbjct: 264 LNGGEIGGGSIRIHDPEEQRKRFEELGLDPEEAEEKFGFYLDALKYGMPPHGGIGLGLDR 323
Query: 839 LMSILCGTQSIRDVIAFPK 857
L+ +L G +SIR+VIAFPK
Sbjct: 324 LVMLLTGLESIREVIAFPK 342
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 235 bits (602), Expect = 6e-67
Identities = 96/207 (46%), Positives = 138/207 (66%), Gaps = 12/207 (5%)
Query: 300 EVIASNITVLNKADVNIPFHI----KNYNKAKEDLRLKHRYLDFRFPEMQHNLRFRSKFL 355
EV+A ++ +LN ++PF + + + KE++RL++R LD R P+M NLR R + +
Sbjct: 151 EVVAESVDILNVVTKSLPFLVTTADEQKDSIKEEVRLRYRVLDLRRPQMNANLRLRHRVV 210
Query: 356 MRTREFLATHRDFVEVETPTLFKRTPGGAREFVVPTH-EPNKFYSLVQSPQQLKQLLMVG 414
R +L FVE+ETP L + TP GAR+++VP+ +P FY+L QSPQ KQ+LMV
Sbjct: 211 KLIRRYLEDVHGFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQMLMVS 270
Query: 415 SVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCYC------LNI 468
DRY+QIARC+RDE R DRQPEFTQLD+EL+FT +D+++L E+L+ + +
Sbjct: 271 GFDRYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLEDMLKLNEDLIRQVFKEIKGVQL 330
Query: 469 PTRTFSRISYNDAISLYGSDKPDLRYD 495
P F R++Y +A+S YGSDKPDLRY
Sbjct: 331 P-NPFPRLTYAEAMSKYGSDKPDLRYG 356
Score = 159 bits (404), Expect = 9e-41
Identities = 88/230 (38%), Positives = 123/230 (53%), Gaps = 18/230 (7%)
Query: 654 VKVQD--SLEWTNKLTKILPDLNVEEFRNKENLEEGDLIVVSWGKQEDVLSLLGMIRSES 711
+KV D LE L + L E+ GDLI+ + G V L +R
Sbjct: 421 LKVLDDGELEGIKALVESLSPEQAEQLLAACGAGPGDLILFAAGPTSSVNKTLDRLRQ-- 478
Query: 712 HKIKVKNTLPLEFDNPKSFSIFWVVDFPLF-LPSDSGTLESAHHPFTQPHPEDEHLLSSN 770
+ TL L +P SI WV DFP+F D LE+ HHPFT P+PED LSS
Sbjct: 479 ---FIAKTLDL--IDPSRHSILWVTDFPMFEWNEDEQRLEALHHPFTAPNPEDMGDLSS- 532
Query: 771 PLEVRGLHYDLVLNGNEIGGGSIRIHSSELQESILHFLNIETSSLQ----HMIQAFKYGC 826
R L YD+V NG EIGGGS+RI+ ++Q+ +L + + + ++++A G
Sbjct: 533 ---ARALAYDMVYNGVEIGGGSLRIYRRDVQQKVLEAIGLSPEEAESKFGYLLEALDMGA 589
Query: 827 PPHGGIALGIDRLMSILCGTQSIRDVIAFPKGFGGKDHLSGAPCDIPEAE 876
PPHGGIA G+DRL+ +L G +SIRDVIAFPK + L+ AP ++ + +
Sbjct: 590 PPHGGIAYGLDRLVMLLAGAKSIRDVIAFPKTTTAQCALTRAPSEVDDKQ 639
Score = 56.3 bits (136), Expect = 5e-08
Identities = 28/63 (44%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 6 YTTRSHTCGALRLSDVDKTVTLCGWLQNQRVDM----FALLRDAYGQVQVIVPNHQVPNI 61
+ +RSH CGAL ++DV VTLCGW+ R DM F +RD G VQV+ + P
Sbjct: 56 WPSRSHLCGALSVNDVGSRVTLCGWVDLHR-DMGGLTFLDVRDHTGIVQVVTLPDEFPEA 114
Query: 62 YRT 64
+RT
Sbjct: 115 HRT 117
>gnl|CDD|218798 pfam05891, Methyltransf_PK, AdoMet dependent proline
di-methyltransferase. This protein is expressed in the
tail neuron PVT and in uterine cells in C. elegans
[worm-base]. In Saccharomyces cerevisiae this is AdoMet
dependent proline di-methyltransferase. This enzyme
catalyzes the di-methylation of ribosomal proteins Rpl12
and Rps25 at N-terminal proline residues. The
methyltransferases described here specifically recognise
the N-terminal X-Pro-Lys sequence motif, and they may
account for nearly all previously described eukaryotic
protein N-terminal methylation reactions. A number of
other yeast and human proteins also share the
recognition motif and may be similarly modified. As with
other methyltransferases, this family carries the
characteristic GxGxG motif.
Length = 217
Score = 204 bits (520), Expect = 2e-60
Identities = 91/209 (43%), Positives = 125/209 (59%), Gaps = 8/209 (3%)
Query: 86 YSEVTEYYSNVPPTIDGMLNGYSSISDLDIQTSNQFLSSLYCQKKSDPGKTRV---LDVG 142
YS+ Y+ V T+DGML GY +SD+D+ S FL L ++ PGK R LD G
Sbjct: 6 YSKAIAYWEGVSATVDGMLGGYGHVSDIDVNGSRNFLRRL--LRERLPGKRRHLVALDCG 63
Query: 143 AGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQDFKPEDLNI 202
AGIGR++K LL F K+DL+E F+ +AKE + + K+ + VG+QDF PE+
Sbjct: 64 AGIGRVTKNLLLPLFSKVDLVEPVEDFLAKAKEYLAEGKKKVGNFFCVGLQDFTPEEG-- 121
Query: 203 KYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIIIKDNVASGVKNEYDDEDSSVVRS 262
+YD+IWIQW + + DED++ FL CK L NG I++K+NVA +D EDSSV RS
Sbjct: 122 RYDLIWIQWCIGHLTDEDLVAFLKRCKGGLKPNGFIVVKENVAQ-NGFVFDKEDSSVTRS 180
Query: 263 LPQFCLLFSKANLKCVKSEKGEFSPMDLW 291
F LF KA LK V E+ + P +L+
Sbjct: 181 EAYFKKLFKKAGLKLVAEERQKGLPQELY 209
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 207 bits (528), Expect = 1e-56
Identities = 97/216 (44%), Positives = 132/216 (61%), Gaps = 18/216 (8%)
Query: 300 EVIASNITVLNKADVNIPFHIKN-----------YNKAKEDLRLKHRYLDFRFPEMQHNL 348
EV +++L ++ +PF I + + EDLRL++RYLD R P MQ +L
Sbjct: 98 EVFVRELSILAASEA-LPFAISDKAMTAGAGSAGADAVNEDLRLQYRYLDIRRPAMQDHL 156
Query: 349 RFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGGAREFVVPTH-EPNKFYSLVQSPQQL 407
R + + R+FL + R F+E+ETP L K TP GAR+++VP+ P +FY+L QSPQ
Sbjct: 157 AKRHRIIKCARDFLDS-RGFLEIETPILTKSTPEGARDYLVPSRIHPKEFYALPQSPQLF 215
Query: 408 KQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCYCLN 467
KQLLM+ +RYFQ+ARC+RDE RP+RQPEFTQLDIE SF + + LIEEL
Sbjct: 216 KQLLMIAGFERYFQLARCFRDEDLRPNRQPEFTQLDIEASFIDEEFIFELIEELTARMFA 275
Query: 468 IP----TRTFSRISYNDAISLYGSDKPDLRYDCKIM 499
I R F R+ Y +A+ GSD+PDLR+D K
Sbjct: 276 IGGIALPRPFPRMPYAEAMDTTGSDRPDLRFDLKFA 311
Score = 141 bits (357), Expect = 1e-34
Identities = 80/225 (35%), Positives = 122/225 (54%), Gaps = 32/225 (14%)
Query: 672 DLNVEEFRNKENL---------EEGD-LIVVSWGKQEDVLSLLGMIRSESHKIKVKNTLP 721
D N+ +F + + E+GD +I+++ VLS LG +R + + + L
Sbjct: 380 DSNIVQFFSADEKEALKRRFHAEDGDVIIMIADASCAIVLSALGQLR-----LHLADRLG 434
Query: 722 LEFDNPKSFSIFWVVDFPLFLPSDSGTLESAHHPFTQPHPEDEHLLSSNPLEVRGL---- 777
L F W+ DFPLF +D G + S+HHPFT P ED +P ++ L
Sbjct: 435 L--IPEGVFHPLWITDFPLFEATDDGGVTSSHHPFTAPDRED-----FDPGDIEELLDLR 487
Query: 778 --HYDLVLNGNEIGGGSIRIHSSELQESILHFLNIETSSLQH----MIQAFKYGCPPHGG 831
YDLV+NG E+GGGSIRI+ ++Q I L + ++ ++AF + PPHGG
Sbjct: 488 SRAYDLVVNGEELGGGSIRINDKDIQLRIFAALGLSEEDIEDKFGFFLRAFDFAAPPHGG 547
Query: 832 IALGIDRLMSILCGTQSIRDVIAFPKGFGGKDHLSGAPCDIPEAE 876
IALG+DR++S++ T SIR+VIAFPK L+GAP ++ + +
Sbjct: 548 IALGLDRVVSMILQTPSIREVIAFPKNRSAACPLTGAPSEVAQEQ 592
Score = 35.0 bits (80), Expect = 0.20
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 13 CGALRLSDVDKTVTLCGWLQNQRVD---MFALLRDAYGQVQVIV-PNHQVPNIYRTST 66
CG L L D + V L GW+ R +F LRD G +Q + P ++Y +
Sbjct: 9 CGHLSLDDTGREVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAA 66
>gnl|CDD|238358 cd00669, Asp_Lys_Asn_RS_core, Asp_Lys_Asn_tRNA synthetase class II
core domain. This domain is the core catalytic domain of
class II aminoacyl-tRNA synthetases of the subgroup
containing aspartyl, lysyl, and asparaginyl tRNA
synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. Nearly all class II tRNA synthetases
are dimers and enzymes in this subgroup are homodimers.
These enzymes attach a specific amino acid to the 3' OH
group of ribose of the appropriate tRNA.
Length = 269
Score = 129 bits (327), Expect = 2e-33
Identities = 57/155 (36%), Positives = 81/155 (52%), Gaps = 17/155 (10%)
Query: 348 LRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPG-GAREFVVPTHEPNKFYSLVQSPQQ 406
+ RSK + R+F+ F+EVETP L K T G GAR F+V + Y L SPQ
Sbjct: 1 FKVRSKIIKAIRDFMDDR-GFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRISPQL 59
Query: 407 LKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCYCL 466
K+ LMVG +DR F+I R +R+E R QPEFT +D+E++F +DV+ L E L+ +
Sbjct: 60 FKKRLMVGGLDRVFEINRNFRNEDLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHLA 119
Query: 467 N---------------IPTRTFSRISYNDAISLYG 486
F R++Y +A+ YG
Sbjct: 120 REVLGVTAVTYGFELEDFGLPFPRLTYREALERYG 154
Score = 105 bits (264), Expect = 4e-25
Identities = 39/128 (30%), Positives = 62/128 (48%), Gaps = 23/128 (17%)
Query: 734 WVVDFPLFLPSDSGTLESAHHPFTQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSI 793
++ D+P H P PH + +DL +NG E+G GS
Sbjct: 158 FLTDYPAE----------MHSPLASPHDVNP---------EIADAFDLFINGVEVGNGSS 198
Query: 794 RIHSSELQESILHFLNI----ETSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSI 849
R+H ++Q + I + ++A +YG PPHGG+ +GIDRL+ ++ + +I
Sbjct: 199 RLHDPDIQAEVFQEQGINKEAGMEYFEFYLKALEYGLPPHGGLGIGIDRLIMLMTNSPTI 258
Query: 850 RDVIAFPK 857
R+VIAFPK
Sbjct: 259 REVIAFPK 266
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 118 bits (298), Expect = 3e-28
Identities = 69/206 (33%), Positives = 99/206 (48%), Gaps = 24/206 (11%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTR 359
EVI I VLNKA+ +P I A+ D RL +R+LD R P ++ + RS+ L R
Sbjct: 88 EVIPEEIEVLNKAEEPLPLDISGKVLAELDTRLDNRFLDLRRPRVRAIFKIRSEVLRAFR 147
Query: 360 EFLATHRDFVEVETPTLFKR-TPGGAREFVVPTHEPNKFYSLVQSPQQLKQLLMVGSVDR 418
EFL + F E+ TP + T GGA F + E + L QSPQ KQ+++ +R
Sbjct: 148 EFLYEN-GFTEIFTPKIVASGTEGGAELFPIDYFEKEAY--LAQSPQLYKQMMVGAGFER 204
Query: 419 YFQIARCYRDESTRPDRQ-PEFTQLDIELSFTTRD-DVMRLIEELLCYCLN--------- 467
F+I +R E R E+T +D+E+ F DVM L+E LL Y
Sbjct: 205 VFEIGPVFRAEEHNTSRHLNEYTSIDVEMGFIDDHEDVMDLLENLLRYMYEDVAENCEKE 264
Query: 468 ---------IPTRTFSRISYNDAISL 484
+P RI+Y++AI +
Sbjct: 265 LELLGIELPVPETPIPRITYDEAIEI 290
Score = 83.7 bits (208), Expect = 7e-17
Identities = 43/105 (40%), Positives = 56/105 (53%), Gaps = 14/105 (13%)
Query: 755 PF-TQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSIRIHS-SELQESILHF-LNIE 811
PF T P +D + S +DL+ G EI G RIH L ESI LN E
Sbjct: 336 PFYTMPDEDDPEISKS---------FDLLFRGLEITSGGQRIHRYDMLVESIKEKGLNPE 386
Query: 812 TSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
S + ++AFKYG PPHGG LG++RL L G ++IR+ + FP
Sbjct: 387 --SFEFYLEAFKYGMPPHGGFGLGLERLTMKLLGLENIREAVLFP 429
Score = 41.7 bits (99), Expect = 0.001
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 23 KTVTLCGWLQNQRVDM----FALLRDAYGQVQVIVPNHQVPNIYRTS 65
+ VTL GW+ R D+ F +LRD G +QV+V ++ T
Sbjct: 17 EEVTLAGWVHEIR-DLGGIAFLILRDRSGIIQVVVKKKVDEELFETI 62
>gnl|CDD|129550 TIGR00458, aspS_nondisc, nondiscriminating aspartyl-tRNA
synthetase. In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_arch, represents
aspartyl-tRNA synthetases from the eukaryotic cytosol
and from the Archaea. In some species, this enzyme
aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn)
is subsequently transamidated to Asn-tRNA(asn) [Protein
synthesis, tRNA aminoacylation].
Length = 428
Score = 115 bits (289), Expect = 3e-27
Identities = 72/205 (35%), Positives = 98/205 (47%), Gaps = 23/205 (11%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTR 359
E+I + I V+N+A +P A+ D RL +R+LD R P +Q R RS L R
Sbjct: 85 EIIPTKIEVINEAKEPLPLDPTEKVPAELDTRLDYRFLDLRRPTVQAIFRIRSGVLESVR 144
Query: 360 EFLATHRDFVEVETPTLFKR-TPGGAREFVVPTHEPNKFYSLVQSPQQLKQLLMVGSVDR 418
EFLA F+EV TP L T GG F + E F L QSPQ KQ LM +R
Sbjct: 145 EFLAE-EGFIEVHTPKLVASATEGGTELFPITYFEREAF--LGQSPQLYKQQLMAAGFER 201
Query: 419 YFQIARCYRDESTRPDRQ-PEFTQLDIELSFTTRDDVMRLIEEL---------------- 461
++I +R E R E T +DIE++F DVM ++EEL
Sbjct: 202 VYEIGPIFRAEEHNTHRHLNEATSIDIEMAFEDHHDVMDILEELVVRVFEDVPERCAHQL 261
Query: 462 --LCYCLNIPTRTFSRISYNDAISL 484
L + L P F R++Y++AI +
Sbjct: 262 ETLEFKLEKPEGKFVRLTYDEAIEM 286
Score = 67.2 bits (164), Expect = 1e-11
Identities = 38/128 (29%), Positives = 60/128 (46%), Gaps = 25/128 (19%)
Query: 733 FWVVDFPLFLPSDSGTLESAHHPF-TQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGG 791
+++ D+P + PF T P ++ + S +DL+ EI G
Sbjct: 316 YFITDWP-----------TEIRPFYTMPDEDNPEISKS---------FDLMYRDLEISSG 355
Query: 792 SIRIHSSE-LQESI-LHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSI 849
+ RIH + L E I LN E + ++AF YG PPH G LG +R + L G ++I
Sbjct: 356 AQRIHLHDLLVERIKAKGLNPE--GFKDYLEAFSYGMPPHAGWGLGAERFVMFLLGLKNI 413
Query: 850 RDVIAFPK 857
R+ + FP+
Sbjct: 414 REAVLFPR 421
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 114 bits (287), Expect = 7e-27
Identities = 63/212 (29%), Positives = 90/212 (42%), Gaps = 30/212 (14%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTR 359
E+ I VL +AD P K ++ + L +R+LD R P++Q + RS L R
Sbjct: 88 ELQVEKIEVLGEADPPYPIDKKE--HSELETLLDNRHLDLRTPKIQAVFKIRSSILRAIR 145
Query: 360 EFLATHRDFVEVETPTLFKRTPGGARE-FVVPTHEPNKFYSLVQSPQQLKQLLMVGSVDR 418
EF F EV TP + G E F V + + L QSPQ K+ L +++R
Sbjct: 146 EFFYE-NGFTEVHTPIITASATEGGGELFKVDYFDKEAY--LTQSPQLYKEALA-AALER 201
Query: 419 YFQIARCYRDESTRPDRQ-PEFTQLDIELSFTTRDDVMRLIEELLCYCLN---------- 467
F I +R E + R EF LD E++F +DVM L EEL+ Y
Sbjct: 202 VFTIGPTFRAEKSNTRRHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVLEECADEL 261
Query: 468 ------------IPTRTFSRISYNDAISLYGS 487
+ F RI+Y +AI +
Sbjct: 262 EFLGRDNSELKRPESAPFPRITYKEAIEILEE 293
Score = 90.0 bits (224), Expect = 7e-19
Identities = 54/211 (25%), Positives = 78/211 (36%), Gaps = 50/211 (23%)
Query: 657 QDSLEWTNKLTKILPDLNVEEFRN------KENLEEGDLIVVSWG--KQEDVLSLLGMIR 708
D LE+ + L F E LEE V WG + LG
Sbjct: 258 ADELEFLGRDNSELKRPESAPFPRITYKEAIEILEEKGFEKVEWGDDLGTEHERYLGE-- 315
Query: 709 SESHKIKVKNTLPLEFDNPKSFSIFWVVDFPLFLPSDSGTLESAHHPF-TQPHPEDEHLL 767
E+ P +V ++P PF +P P+
Sbjct: 316 --------------EYFKP----PVFVTNYP-----------KEIKPFYMRPDPD----- 341
Query: 768 SSNPLEVRGLHYDLVLNGN-EIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGC 826
NP V +DL+ G EI GGS R H +L + ++ S + + KYG
Sbjct: 342 --NPGTVAS--FDLLAPGGGEIIGGSQREHDYDLLVERIKEKGLDPESYEWYLDLRKYGM 397
Query: 827 PPHGGIALGIDRLMSILCGTQSIRDVIAFPK 857
PPH G LG++RL+ + G +IR+ I FP+
Sbjct: 398 PPHAGFGLGLERLVMYILGLDNIREAIPFPR 428
Score = 36.4 bits (85), Expect = 0.063
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 5/45 (11%)
Query: 20 DVDKTVTLCGWLQNQRVDM----FALLRDAYGQVQVIVPNHQVPN 60
+ VT+ GW+ N+R D+ F +LRD G +Q +VP ++V
Sbjct: 14 VGGQEVTVRGWVHNKR-DLGKIIFLVLRDGSGFIQAVVPKNKVYE 57
>gnl|CDD|238399 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II
core domain. Assignment to class II aminoacyl-tRNA
synthetases (aaRS) based upon its structure and the
presence of three characteristic sequence motifs in the
core domain. This family includes AsnRS as well as a
subgroup of AspRS. AsnRS and AspRS are homodimers,
which attach either asparagine or aspartate to the 3'OH
group of ribose of the appropriate tRNA. While archaea
lack asnRS, they possess a non-discriminating aspRS,
which can mischarge Asp-tRNA with Asn. Subsequently, a
tRNA-dependent aspartate amidotransferase converts the
bound aspartate to asparagine. The catalytic core domain
is primarily responsible for the ATP-dependent formation
of the enzyme bound aminoacyl-adenylate.
Length = 322
Score = 88.4 bits (220), Expect = 6e-19
Identities = 61/184 (33%), Positives = 90/184 (48%), Gaps = 28/184 (15%)
Query: 325 KAKEDLRLKHRYLDFRFPEMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKR-TPGG 383
A + L +R+LD R P++Q R RS+ L REFL + F EV TP + T GG
Sbjct: 1 DANLETLLDNRHLDLRTPKVQAIFRIRSEVLRAFREFLREN-GFTEVHTPKITSTDTEGG 59
Query: 384 AREFVVPTHEPNKFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDESTRPDRQ-PEFTQL 442
A F V + L QSPQ K+ +++ +++R ++I +R E + R EF L
Sbjct: 60 AELFKVSYFGKPAY--LAQSPQLYKE-MLIAALERVYEIGPVFRAEKSNTRRHLSEFWML 116
Query: 443 DIELSF-TTRDDVMRLIEELLCY--------C-------------LNIPTRTFSRISYND 480
+ E++F ++VM LIEEL+ Y C L P F RI+Y++
Sbjct: 117 EAEMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNRELLKPLEPFPRITYDE 176
Query: 481 AISL 484
AI L
Sbjct: 177 AIEL 180
Score = 84.5 bits (210), Expect = 1e-17
Identities = 39/106 (36%), Positives = 57/106 (53%), Gaps = 13/106 (12%)
Query: 755 PF-TQPHPEDEHLLSSNPLEVRGLHYDLVLNGN-EIGGGSIRIHS-SELQESILHFLNIE 811
PF +P ++ + S +DL++ G EI GGS RIH EL+E I ++
Sbjct: 224 PFYMKPDDDNPETVES---------FDLLMPGVGEIVGGSQRIHDYDELEERIKE-HGLD 273
Query: 812 TSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFPK 857
S + + KYG PPHGG LG++RL+ L G +IR+ I FP+
Sbjct: 274 PESFEWYLDLRKYGMPPHGGFGLGLERLVMWLLGLDNIREAILFPR 319
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 86.2 bits (214), Expect = 2e-17
Identities = 68/226 (30%), Positives = 101/226 (44%), Gaps = 48/226 (21%)
Query: 279 KSEKGEFSPMDLWEDWGLLSKEVIASNITVLNKADVNIPFHIKNYNKAKE-DLRLKHRYL 337
K++KGE S + ++ VL K + +P Y+ + + R + RYL
Sbjct: 175 KTKKGELS--------------IFPTSFEVLTKCLLMLP---DKYHGLTDQETRYRQRYL 217
Query: 338 DFRF-PEMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGGA--REFVVPTHEP 394
D PE++ R R+K + R FL R F+EVETP L GGA R FV TH
Sbjct: 218 DLIANPEVRDIFRTRAKIISYIRRFLDD-RGFLEVETPML-NMIAGGAAARPFV--THHN 273
Query: 395 N---KFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDE--STRPDRQPEFTQLDIELSFT 449
+ Y + + LK+L+ VG +R ++I R +R+E STR PEFT + ++
Sbjct: 274 DLNMDLYLRIATELHLKRLV-VGGFERVYEIGRQFRNEGISTR--HNPEFTTCEFYQAYA 330
Query: 450 TRDDVMRLIEELLCYC-------LNIP--------TRTFSRISYND 480
+D+M L EE++ I T F RIS
Sbjct: 331 DYNDMMELTEEMVSGMVKELTGSYKIKYHGIEIDFTPPFRRISMIS 376
Score = 58.5 bits (142), Expect = 9e-09
Identities = 23/38 (60%), Positives = 27/38 (71%)
Query: 819 IQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
A +YG PP GG LGIDRL+ +L + SIRDVIAFP
Sbjct: 510 CTALEYGLPPTGGWGLGIDRLVMLLTDSASIRDVIAFP 547
>gnl|CDD|238398 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core
domain. Class II LysRS is a dimer which attaches a
lysine to the 3' OH group of ribose of the appropriate
tRNA. Its assignment to class II aaRS is based upon its
structure and the presence of three characteristic
sequence motifs in the core domain. It is found in
eukaryotes as well as some prokaryotes and archaea.
However, LysRS belongs to class I aaRS's in some
prokaryotes and archaea. The catalytic core domain is
primarily responsible for the ATP-dependent formation of
the enzyme bound aminoacyl-adenylate.
Length = 329
Score = 79.2 bits (196), Expect = 7e-16
Identities = 59/203 (29%), Positives = 89/203 (43%), Gaps = 44/203 (21%)
Query: 347 NLRFRSKFLMRT------REFLATHRDFVEVETPTLFKRTPGGA--REFVVPTHEPN--- 395
N R F++R+ R+FL R F+EVETP L + GGA R F+ TH N
Sbjct: 1 NEEVRQTFIVRSKIISYIRKFLDD-RGFLEVETPML-QPIAGGAAARPFI--THH-NALD 55
Query: 396 -KFYSLVQSPQ-QLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDD 453
Y L +P+ LK+L+ VG +R ++I R +R+E PEFT ++ ++ +D
Sbjct: 56 MDLY-LRIAPELYLKRLI-VGGFERVYEIGRNFRNEGIDLTHNPEFTMIEFYEAYADYND 113
Query: 454 VMRLIEELLCYCLN-------IP--------TRTFSRISYNDAISLY-GSDKP------- 490
+M L E+L + I T F R++ DA+ G D P
Sbjct: 114 MMDLTEDLFSGLVKKINGKTKIEYGGKELDFTPPFKRVTMVDALKEKTGIDFPELDLEQP 173
Query: 491 -DLRYDCKIMIAIKEQPPWPSGY 512
+L +I K + P G
Sbjct: 174 EELAKLLAKLIKEKIEKPRTLGK 196
Score = 59.9 bits (146), Expect = 2e-09
Identities = 21/38 (55%), Positives = 28/38 (73%)
Query: 819 IQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
+ A +YG PP GG+ +GIDRL+ +L + SIRDVI FP
Sbjct: 288 VTALEYGMPPTGGLGIGIDRLVMLLTDSNSIRDVILFP 325
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 79.7 bits (198), Expect = 2e-15
Identities = 73/237 (30%), Positives = 110/237 (46%), Gaps = 58/237 (24%)
Query: 279 KSEKGEFSPMDLWEDWGLLSKEVIASNITVLNKADVNIP--FH-IKNYNKAKEDLRLKHR 335
K++ GE S V A+ +T+L K+ +P FH + + + R + R
Sbjct: 118 KTKTGELS--------------VKATELTLLTKSLRPLPDKFHGLTD-----VETRYRQR 158
Query: 336 YLDF--RFPEMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGG--AREFVVPT 391
Y+D PE + R RSK + R FL +R F+EVETP L + GG AR F+ T
Sbjct: 159 YVDLIVN-PESRETFRKRSKIISAIRRFL-DNRGFLEVETPML-QPIAGGAAARPFI--T 213
Query: 392 HEPN----KFYSLVQSPQ-QLKQLLMVGSVDRYFQIARCYRDE--STRPDRQPEFTQLDI 444
H N Y L +P+ LK+L+ VG +R ++I R +R+E TR PEFT L+
Sbjct: 214 HH-NALDIDLY-LRIAPELYLKRLI-VGGFERVYEIGRNFRNEGIDTR--HNPEFTMLEF 268
Query: 445 ELSFTTRDDVMRLIEELLCYC-------LNIP--------TRTFSRISYNDAISLYG 486
++ +D+M L EEL+ + + F R++ DAI Y
Sbjct: 269 YQAYADYNDMMDLTEELIRHLAQAVLGTTKVTYQGTEIDFGPPFKRLTMVDAIKEYT 325
Score = 61.6 bits (151), Expect = 9e-10
Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 819 IQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
++A +YG PP GG+ +GIDRL+ +L + SIRDVI FP
Sbjct: 448 LRALEYGMPPTGGLGIGIDRLVMLLTDSPSIRDVILFP 485
>gnl|CDD|239812 cd04317, EcAspRS_like_N, EcAspRS_like_N: N-terminal, anticodon
recognition domain of the type found in Escherichia
coli aspartyl-tRNA synthetase (AspRS), the human
mitochondrial (mt) AspRS-2, the discriminating (D)
Thermus thermophilus AspRS-1, and the nondiscriminating
(ND) Helicobacter pylori AspRS. These homodimeric
enzymes are class2b aminoacyl-tRNA synthetases (aaRSs).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. aaRSs
catalyze the specific attachment of amino acids (AAs)
to their cognate tRNAs during protein biosynthesis.
This 2-step reaction involves i) the activation of the
AA by ATP in the presence of magnesium ions, followed
by ii) the transfer of the activated AA to the
terminal ribose of tRNA. In the case of the class2b
aaRSs, the activated AA is attached to the 3'OH of the
terminal ribose. Eukaryotes contain 2 sets of aaRSs,
both of which are encoded by the nuclear genome. One
set concerns with cytoplasmic synthesis, whereas the
other exclusively with mitochondrial protein synthesis.
Human mtAspRS participates in mitochondrial
biosynthesis; this enzyme been shown to charge E.coli
native tRNAsp in addition to in vitro transcribed human
mitochondrial tRNAsp. T. thermophilus is rare among
bacteria in having both a D_AspRS and a ND_AspRS.
H.pylori ND-AspRS can charge both tRNAASp and tRNAAsn,
it is fractionally more efficient at aminoacylating
tRNAAsp over tRNAAsn. The H.pylori genome does not
contain AsnRS.
Length = 135
Score = 72.2 bits (178), Expect = 6e-15
Identities = 27/62 (43%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 9 RSHTCGALRLSDVDKTVTLCGWLQNQRVD---MFALLRDAYGQVQVIVPNHQVPNIYRTS 65
R+H CG LR S V + VTLCGW+Q +R +F LRD YG VQV+ + P
Sbjct: 1 RTHYCGELRESHVGQEVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAE 60
Query: 66 TL 67
L
Sbjct: 61 KL 62
Score = 67.9 bits (167), Expect = 2e-13
Identities = 24/45 (53%), Positives = 31/45 (68%), Gaps = 1/45 (2%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRFPEM 344
EV+AS + VLNKA +PF I + E+LRLK+RYLD R P+M
Sbjct: 92 EVVASELEVLNKAK-TLPFEIDDDVNVSEELRLKYRYLDLRRPKM 135
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 78.5 bits (193), Expect = 6e-15
Identities = 50/176 (28%), Positives = 84/176 (47%), Gaps = 14/176 (7%)
Query: 300 EVIASNITVLNKADVNIPFHIKNYNKAKE--------DLRLKHRYLDFRFPEMQHNLRFR 351
E+ I + ++ +PF +++ ++ + D RL R++D R P R +
Sbjct: 157 ELKVKKIHTVTESLRTLPFTLEDASRKESDEGAKVNFDTRLNSRWMDLRTPASGAIFRLQ 216
Query: 352 SKFLMRTREFLATHRDFVEVETPTLFKR-TPGGAREFVVPTHEPNKFYSLVQSPQQLKQL 410
S+ R+FL DF E+ +P + + GGA F + N+F L QSPQ KQ+
Sbjct: 217 SRVCQYFRQFLIDS-DFCEIHSPKIINAPSEGGANVFKLEYF--NRFAYLAQSPQLYKQM 273
Query: 411 LMVGSVDRYFQIARCYRDESTRPDRQ-PEFTQLDIELSFTTR-DDVMRLIEELLCY 464
++ G V R F++ +R E++ R EF LD+E+ +V+ L E L Y
Sbjct: 274 VLQGDVPRVFEVGPVFRSENSNTHRHLTEFVGLDVEMRINEHYYEVLDLAESLFNY 329
Score = 63.5 bits (154), Expect = 3e-10
Identities = 32/113 (28%), Positives = 57/113 (50%), Gaps = 10/113 (8%)
Query: 746 SGTLESAHHPF-TQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSIRIHSSELQESI 804
S S+ PF T +DE +S YD+ + G EI G+ RIH +L +
Sbjct: 440 SDRFPSSARPFYTMECKDDERFTNS---------YDMFIRGEEISSGAQRIHDPDLLLAR 490
Query: 805 LHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFPK 857
LN++ + ++ + +F+ G PHGG +G++R++ + G ++R FP+
Sbjct: 491 AKMLNVDLTPIKEYVDSFRLGAWPHGGFGVGLERVVMLYLGLSNVRLASLFPR 543
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 75.3 bits (186), Expect = 4e-14
Identities = 73/269 (27%), Positives = 113/269 (42%), Gaps = 62/269 (23%)
Query: 279 KSEKGEFSPMDLWEDWGLLSKEVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLD 338
K++ GE S V + +L+K+ P K + +++R + RYLD
Sbjct: 126 KTKTGELS--------------VSVEELRLLSKS--LRPLPEKFHGLTDKEIRYRQRYLD 169
Query: 339 FRFPEMQHNLRFRSKFLMRT------REFLATHRDFVEVETPTLFKRTPGGA--REFVVP 390
+ N R F+ R+ REFL R F+EVETP L + PGGA R F+
Sbjct: 170 -----LIVNPESRQTFIKRSKIIRAIREFLDD-RGFLEVETPML-QPIPGGAAARPFI-- 220
Query: 391 THEPNKF---YSLVQSPQ-QLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIEL 446
TH N L +P+ LK+L+ VG +R F+I R +R+E PEFT L+
Sbjct: 221 THH-NALDMDLYLRIAPELYLKRLI-VGGFERVFEIGRNFRNEGIDTTHNPEFTMLEFYQ 278
Query: 447 SFTTRDDVMRLIEEL-------LCYCLNIP--------TRTFSRISYNDAISLYGS---- 487
++ +D+M L EEL + + ++ F RI+ DA+ Y
Sbjct: 279 AYADYEDLMDLTEELIKELAKEVNGTTKVTYGGQEIDFSKPFKRITMVDALKEYLGVDFD 338
Query: 488 ---DKPDLRYDCKIMIAIKEQPPWPSGYP 513
D + + K I+ + G
Sbjct: 339 DLFDDEEAKELAK-KHGIEVEKYGTWGLG 366
Score = 59.5 bits (145), Expect = 4e-09
Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 819 IQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
++A +YG PP GG+ +GIDRL+ +L + SIRDVI FP
Sbjct: 459 VEALEYGMPPTGGLGIGIDRLVMLLTNSPSIRDVILFP 496
>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
Length = 505
Score = 75.1 bits (184), Expect = 5e-14
Identities = 45/149 (30%), Positives = 76/149 (51%), Gaps = 5/149 (3%)
Query: 317 PFHIKNYNKAKEDLRLKHRYLDF-RFPEMQHNLRFRSKFLMRTREFLATHRDFVEVETPT 375
P K + +++R + RYLD + + RSK L R+F+ R F+EVETP
Sbjct: 152 PLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVA-RGFMEVETP- 209
Query: 376 LFKRTPGGA--REFVVPTHEPNKFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDESTRP 433
+ + PGGA R F+ + + L +P+ + L+VG +R F+I R +R+E
Sbjct: 210 MMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISV 269
Query: 434 DRQPEFTQLDIELSFTTRDDVMRLIEELL 462
PEFT +++ +++ D++ L E L
Sbjct: 270 RHNPEFTMMELYMAYADYHDLIELTESLF 298
Score = 48.5 bits (115), Expect = 1e-05
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 8/86 (9%)
Query: 779 YDLVLNGNEIGGGSIRIHSSELQ-ESILHFLNIETSSL-------QHMIQAFKYGCPPHG 830
++ + G EIG G ++ +E Q E +N + + + + A +YG PP
Sbjct: 414 FEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTA 473
Query: 831 GIALGIDRLMSILCGTQSIRDVIAFP 856
G+ +GIDR++ + + +IRDVI FP
Sbjct: 474 GLGIGIDRMIMLFTNSHTIRDVILFP 499
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 74.4 bits (183), Expect = 1e-13
Identities = 36/108 (33%), Positives = 56/108 (51%), Gaps = 10/108 (9%)
Query: 751 SAHHPF-TQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSIRIHSSELQESILHFLN 809
A PF T P P+D +S +D+ + G EI G+ R+H EL E
Sbjct: 425 LAVRPFYTMPCPDDPKYSNS---------FDVFIRGEEIISGAQRVHDPELLEKRAEECG 475
Query: 810 IETSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFPK 857
I+ ++ I +F+YG PPHGG +G++R++ + CG +IR FP+
Sbjct: 476 IDVKTISTYIDSFRYGAPPHGGFGVGLERVVMLFCGLNNIRKTSLFPR 523
Score = 71.3 bits (175), Expect = 9e-13
Identities = 54/187 (28%), Positives = 82/187 (43%), Gaps = 27/187 (14%)
Query: 300 EVIASNITVLNKADVNIPFHI-----------------KNYNKAKEDLRLKHRYLDFRFP 342
E+ I ++KA +PF++ + + +D RL +R LD R P
Sbjct: 160 EIQVRKIYCVSKALATLPFNVEDAARSESEIEKALQTGEQLVRVGQDTRLNNRVLDLRTP 219
Query: 343 EMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGGARE---FVVPTHEPNKFYS 399
Q R +S+ REFL + + FVE+ TP L GA E V +
Sbjct: 220 ANQAIFRIQSQVCNLFREFLLS-KGFVEIHTPKLI----AGASEGGSAVFRLDYKGQPAC 274
Query: 400 LVQSPQQLKQLLMVGSVDRYFQIARCYRDESTRPDRQ-PEFTQLDIELSFTTR-DDVMRL 457
L QSPQ KQ+ + G R F+I +R E + R EFT LD+E+ +V+ +
Sbjct: 275 LAQSPQLHKQMAICGDFRRVFEIGPVFRAEDSFTHRHLCEFTGLDLEMEIKEHYSEVLDV 334
Query: 458 IEELLCY 464
++EL
Sbjct: 335 VDELFVA 341
>gnl|CDD|232998 TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and
non-spirochete bacterial. This model represents the
lysyl-tRNA synthetases that are class II amino-acyl tRNA
synthetases. It includes all eukaryotic and most
bacterial examples of the enzyme, but not archaeal or
spirochete forms [Protein synthesis, tRNA
aminoacylation].
Length = 496
Score = 73.9 bits (182), Expect = 1e-13
Identities = 69/236 (29%), Positives = 106/236 (44%), Gaps = 35/236 (14%)
Query: 295 GLLSKEVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLDFRF-PEMQHNLRFRSK 353
G LS V + + +L KA +P K + ++ R + RYLD P+ + RSK
Sbjct: 122 GELS--VHVTELQILTKALRPLP--DKFHGLTDQETRYRQRYLDLIVNPDSRQTFLVRSK 177
Query: 354 FLMRTREFLATHRDFVEVETPTLFKRTPGGA--REFVVPTHEPNK----FYSLVQSPQQL 407
+ R FL R F+EVETP L + PGGA R F+ TH N Y + L
Sbjct: 178 IIKAIRRFL-DDRGFIEVETPML-QVIPGGANARPFI--THH-NALDMDLYLRIAPELYL 232
Query: 408 KQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEEL---LCY 464
K+L+ VG ++ ++I R +R+E PEFT ++ ++ +D+M L E L L
Sbjct: 233 KRLI-VGGFEKVYEIGRNFRNEGVDTTHNPEFTMIEFYQAYADYEDLMDLTENLFKFLAQ 291
Query: 465 CLNIPT------------RTFSRISYNDAISLYGSDKP---DLRYDCKIMIAIKEQ 505
L T + F RI+ +AI Y + D D + A+ ++
Sbjct: 292 ELLGTTKITYGELEIDFKKPFKRITMVEAIKKYDMETGIDFDDLKDFETAKALAKK 347
Score = 55.8 bits (135), Expect = 6e-08
Identities = 21/38 (55%), Positives = 30/38 (78%)
Query: 819 IQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
++A +YG PP GG+ +GIDRL+ +L ++SIRDVI FP
Sbjct: 453 VEALEYGMPPTGGLGIGIDRLVMLLTDSKSIRDVILFP 490
>gnl|CDD|238391 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl
synthetase-like catalytic core domain. Class II amino
acyl-tRNA synthetases (aaRS) share a common fold and
generally attach an amino acid to the 3' OH of ribose of
the appropriate tRNA. PheRS is an exception in that it
attaches the amino acid at the 2'-OH group, like class I
aaRSs. These enzymes are usually homodimers. This domain
is primarily responsible for ATP-dependent formation of
the enzyme bound aminoacyl-adenylate. The substrate
specificity of this reaction is further determined by
additional domains. Intererestingly, this domain is also
found is asparagine synthase A (AsnA), in the accessory
subunit of mitochondrial polymerase gamma and in the
bacterial ATP phosphoribosyltransferase regulatory
subunit HisZ.
Length = 211
Score = 68.7 bits (168), Expect = 5e-13
Identities = 34/129 (26%), Positives = 54/129 (41%), Gaps = 18/129 (13%)
Query: 351 RSKFLMRTREFLATHRDFVEVETP-----TLFKRTPGGAREFVVPTHEPNKFYSLVQSPQ 405
RSK + R F+A F EVETP L ++ ++ + E + L + +
Sbjct: 2 RSKIEQKLRRFMAEL-GFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLE 60
Query: 406 QLKQLLMVGSV----DRYFQIARCYRDESTR--PDRQPEFTQLDIELSFTTRDD------ 453
L V + R +I +R+E R R EFTQL+ E+ ++
Sbjct: 61 PGLVRLFVSHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGEEASEFEE 120
Query: 454 VMRLIEELL 462
++ L EELL
Sbjct: 121 LIELTEELL 129
Score = 32.5 bits (74), Expect = 0.63
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 11/61 (18%)
Query: 779 YDLVLNGNEIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDR 838
G EIG G R + L + +A +Y PP G LG++R
Sbjct: 162 DHPEGRGLEIGSGGYRQDEQARA-----------ADLYFLDEALEYRYPPTIGFGLGLER 210
Query: 839 L 839
L
Sbjct: 211 L 211
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 70.8 bits (174), Expect = 5e-13
Identities = 57/206 (27%), Positives = 84/206 (40%), Gaps = 36/206 (17%)
Query: 342 PEMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRT----PGGAREFV-VPTHE-PN 395
+ + L+ +S L TREFL R FVEV P + T G+ V + +
Sbjct: 24 EKYRKVLKVQSSILRYTREFL-DGRGFVEVLPPIISPSTDPLMGLGSDLPVKQISIDFYG 82
Query: 396 KFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDESTRPDRQP---EFTQLDIELSFTTRD 452
Y L S KQL + + + F ++ +R E D EFTQLDIE+ D
Sbjct: 83 VEYYLADSMILHKQL-ALRMLGKIFYLSPNFRLEPVDKDTGRHLYEFTQLDIEIEGADLD 141
Query: 453 DVMRLIEELLCYC------------------LNIPTRTFSRISYNDAISL------YGSD 488
+VM LIE+L+ Y L R F RI++ +A+ + G D
Sbjct: 142 EVMDLIEDLIKYLVKELLEEHEDELEFFGRDLPHLKRPFKRITHKEAVEILNEEGCRGID 201
Query: 489 KPDLRYDC-KIMIAIKEQPPWPSGYP 513
+L + K + E+P W P
Sbjct: 202 LEELGSEGEKSLSEHFEEPFWIIDIP 227
Score = 35.4 bits (82), Expect = 0.10
Identities = 32/132 (24%), Positives = 50/132 (37%), Gaps = 27/132 (20%)
Query: 731 SIFWVVDFPLFLPSDSGTLESAHHPFTQ-PHPE-DEHLLSSNPLEVRGLHYDLVLN---G 785
FW++D P F PE L + YDL+L G
Sbjct: 219 EPFWIIDIPKGS-----------REFYDREDPERPGVLRN----------YDLLLPEGYG 257
Query: 786 NEIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCG 845
+ GG E+ E I ++ + ++ K G P G +G++RL +CG
Sbjct: 258 EAVSGGEREYEYEEIVERI-REHGVDPEKYKWYLEMAKEGPLPSAGFGIGVERLTRYICG 316
Query: 846 TQSIRDVIAFPK 857
+ IR+V FP+
Sbjct: 317 LRHIREVQPFPR 328
>gnl|CDD|232984 TIGR00462, genX, EF-P lysine aminoacylase GenX. Many Gram-negative
bacteria have a protein closely homologous to the
C-terminal region of lysyl-tRNA synthetase (LysS).
Multiple sequence alignment of these proteins with the
homologous regions of collected LysS proteins shows that
these proteins form a distinct set rather than just
similar truncations of LysS. The protein is termed GenX
after its designation in E. coli. Interestingly, genX
often is located near a homolog of
lysine-2,3-aminomutase. Its function is unknown [Unknown
function, General].
Length = 290
Score = 67.2 bits (165), Expect = 5e-12
Identities = 40/126 (31%), Positives = 55/126 (43%), Gaps = 15/126 (11%)
Query: 366 RDFVEVETPTLFKRTPGGARE---------FVVPTHEPNKFYSLVQSPQ-QLKQLLMVGS 415
R +EVETP L +P + FV P + Y L SP+ +K+LL GS
Sbjct: 5 RGVLEVETPLL---SPAPVTDPHLDAFATEFVGPDGQGRPLY-LQTSPEYAMKRLLAAGS 60
Query: 416 VDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLIEELLCYCLNIPTRTFSR 475
FQI + +R+ PEFT L+ D+M +E LL L P R
Sbjct: 61 G-PIFQICKVFRNGERGRRHNPEFTMLEWYRPGFDYHDLMDEVEALLQELLGDPFAPAER 119
Query: 476 ISYNDA 481
+SY +A
Sbjct: 120 LSYQEA 125
Score = 50.6 bits (122), Expect = 1e-06
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 816 QHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIA 854
+ + A + G P G+ALG+DRL+ + G SI DV+A
Sbjct: 252 ERFLAALEAGLPECSGVALGVDRLLMLALGADSIDDVLA 290
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge tRNA(asn)
by misacylation with Asp, followed by transamidation of
Asp to Asn [Protein synthesis, tRNA aminoacylation].
Length = 453
Score = 66.2 bits (162), Expect = 3e-11
Identities = 26/71 (36%), Positives = 41/71 (57%)
Query: 787 EIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGT 846
EI GGS R + E+ + + ++T +L + KYG PH G LG +RL++ + G
Sbjct: 376 EIIGGSEREDDLDKLENRMKEMGLDTDALNWYLDLRKYGSVPHSGFGLGFERLLAYITGL 435
Query: 847 QSIRDVIAFPK 857
++IRD I FP+
Sbjct: 436 ENIRDAIPFPR 446
Score = 51.2 bits (123), Expect = 2e-06
Identities = 50/203 (24%), Positives = 74/203 (36%), Gaps = 47/203 (23%)
Query: 328 EDLRLKHRYLDFRFPEMQHNLRFRSKFL---MRTREFL--ATHR-----DFVEVETPTLF 377
+D L+ + F +LR R+ L MR R L A HR F V P L
Sbjct: 105 DDYPLQKKEHSLEFLRDIAHLRLRTNTLGAVMRVRNALSQAIHRYFQENGFTWVSPPILT 164
Query: 378 KRTPGGARE-FVVPTHEP-------NKFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDE 429
GA E F V T K L S QL ++ + + +R E
Sbjct: 165 SNDCEGAGELFRVSTGNIDFSQDFFGKEAYLTVS-GQLYLETYALALSKVYTFGPTFRAE 223
Query: 430 STRPDRQ-PEFTQLDIELSFTTRDDVMRLIEELLCYCL---------------------- 466
+ R EF ++ E++F +D+++L E L+ Y +
Sbjct: 224 KSNTSRHLSEFWMIEPEMAFANLNDLLQLAETLIKYIIKAVLENCSQELKFLEKNFDKDL 283
Query: 467 -----NIPTRTFSRISYNDAISL 484
NI F+RI+Y DAI +
Sbjct: 284 IKRLENIINNKFARITYTDAIEI 306
>gnl|CDD|225178 COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA
synthetase (class II) [Translation, ribosomal structure
and biogenesis].
Length = 322
Score = 65.1 bits (159), Expect = 4e-11
Identities = 51/164 (31%), Positives = 69/164 (42%), Gaps = 25/164 (15%)
Query: 347 NLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGG-------AREFVVPTHEPNKFYS 399
NL R+ + R F A R +EVETP L P EF+ P K
Sbjct: 15 NLLKRAAIIAAIRRFFA-ERGVLEVETPAL-SVAPVTDIHLHPFETEFLGPGGAKGKPLW 72
Query: 400 LVQSPQ-QLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDVMRLI 458
L SP+ +K+LL GS FQ+ + +R+E PEFT L+ + D RL+
Sbjct: 73 LHTSPEYHMKRLLAAGSGP-IFQLGKVFRNEEMGRLHNPEFTMLEW---YRVGCDYYRLM 128
Query: 459 EE---LLCYCLNIPTRTFSRISYNDA------ISLYGSDKPDLR 493
E LL L R+SY +A I +DK +LR
Sbjct: 129 NEVDDLLQLVLE--CVEAERLSYQEAFLRYLGIDPLSADKTELR 170
Score = 47.3 bits (113), Expect = 2e-05
Identities = 18/30 (60%), Positives = 22/30 (73%)
Query: 827 PPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
PP G+ALG DRL+ + G +SI DVIAFP
Sbjct: 289 PPCSGVALGFDRLVMLALGAESIDDVIAFP 318
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 66.9 bits (164), Expect = 4e-11
Identities = 57/142 (40%), Positives = 76/142 (53%), Gaps = 19/142 (13%)
Query: 331 RLKHRYLDFRF-PEMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGG--AREF 387
R++ RYLD PE + LR RS + RE L R F+EVETP L ++ GG AR F
Sbjct: 752 RVRQRYLDLAVNPEARDLLRARSAVVRAVRETL-VARGFLEVETPIL-QQVHGGANARPF 809
Query: 388 VVPTHEPNKF----YSLVQSPQ-QLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQL 442
V TH N + Y L +P+ LK+ L VG V+R F++ R +R+E PEFT L
Sbjct: 810 V--TH-INAYDMDLY-LRIAPELYLKR-LCVGGVERVFELGRNFRNEGVDATHNPEFTLL 864
Query: 443 DIELSFTTRD-DVMR-LIEELL 462
+ + D D MR L EL+
Sbjct: 865 EAYQAHA--DYDTMRDLTRELI 884
Score = 55.0 bits (133), Expect = 2e-07
Identities = 41/133 (30%), Positives = 58/133 (43%), Gaps = 39/133 (29%)
Query: 737 DFPLFLPSDSGTLESAHHPFTQPHPEDEHLLSSNPLEVRGLHYDLVLNGNEIGGGSIRIH 796
DFP S S P T+PH D L +DLV G E+G
Sbjct: 982 DFPT---SVS--------PLTRPHRSDPGLAE---------RWDLVAWGVELGTAY---- 1017
Query: 797 SSELQESILHFLNIETSSL-------QHM------IQAFKYGCPPHGGIALGIDRLMSIL 843
SEL + + + SL + M +QA +Y PP GG+ +G+DRL+ +L
Sbjct: 1018 -SELTDPVEQRRRLTEQSLLAAGGDPEAMELDEDFLQALEYAMPPTGGLGMGVDRLVMLL 1076
Query: 844 CGTQSIRDVIAFP 856
G +SIR+ + FP
Sbjct: 1077 TG-RSIRETLPFP 1088
Score = 34.2 bits (79), Expect = 0.37
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 13/53 (24%)
Query: 9 RSHTCGALRLSDVDKTVTLCGWLQNQRVD--------MFALLRDAYGQVQVIV 53
+HT + + V++ G RV +FA LRD G++QV++
Sbjct: 638 PTHTVAEALDAPTGEEVSVSG-----RVLRIRDYGGVLFADLRDWSGELQVLL 685
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 63.1 bits (153), Expect = 4e-10
Identities = 43/143 (30%), Positives = 72/143 (50%), Gaps = 13/143 (9%)
Query: 328 EDLRLKHRYLDFRFPEMQHN------LRFRSKFLMRTREFLATHRDFVEVETPTLFKRTP 381
+D +K+RY RF +M N ++ R L R++ R+FVEVETP L
Sbjct: 210 QDNDVKYRY---RFTDMMTNPCVIETIKKRHVMLQALRDYF-NERNFVEVETPVLHTVAS 265
Query: 382 GG-AREFVVPTHEPNKFYSLVQSPQ-QLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEF 439
G A+ FV + L +P+ LKQ + VG ++R ++I + +R+E PEF
Sbjct: 266 GANAKSFVTHHNANAMDLFLRVAPELHLKQCI-VGGMERIYEIGKVFRNEDADRSHNPEF 324
Query: 440 TQLDIELSFTTRDDVMRLIEELL 462
T + ++ T +D+M + E++
Sbjct: 325 TSCEFYAAYHTYEDLMPMTEDIF 347
Score = 40.4 bits (94), Expect = 0.004
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 819 IQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
+++ + G PP G +GIDR + +L + +IRD I FP
Sbjct: 523 LKSLQVGLPPTAGWGMGIDRALMLLTNSSNIRDGIIFP 560
Score = 30.0 bits (67), Expect = 6.2
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 22/87 (25%)
Query: 76 FTEKDGNRSHYSEVT--EYYSNVPPTIDGMLNGYSSISDLDIQTSNQFL---------SS 124
F +D +RSH E T E+Y+ Y + DL T + F +
Sbjct: 311 FRNEDADRSHNPEFTSCEFYA-----------AYHTYEDLMPMTEDIFRQLAMRVNGTTV 359
Query: 125 LYCQKKSDPGKTRVLDVGAGIGRISKY 151
+ ++ G +D+G R+S Y
Sbjct: 360 VQIYPENAHGNPVTVDLGKPFRRVSVY 386
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 61.9 bits (150), Expect = 8e-10
Identities = 64/235 (27%), Positives = 101/235 (42%), Gaps = 37/235 (15%)
Query: 279 KSEKGEFSPMDLWEDWGLLSKEVIASNITVLNKADVNIPFHIKNYNKAKEDLRLKHRYLD 338
KS+KGE S + KE I +L+ +P Y ++R + RYLD
Sbjct: 200 KSKKGELS---------IFPKETI-----ILSPCLHMLPM---KYGLKDTEIRYRQRYLD 242
Query: 339 FRFPE-MQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGGAREFVVPTHEPN-- 395
E + R+K + R FL R F+EVETPT+ GGA TH +
Sbjct: 243 LMINESTRSTFITRTKIINYLRNFL-NDRGFIEVETPTM-NLVAGGANARPFITHHNDLD 300
Query: 396 -KFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDDV 454
Y + + LK +L+VG +D+ ++I + +R+E PEFT + ++ D+
Sbjct: 301 LDLYLRIATELPLK-MLIVGGIDKVYEIGKVFRNEGIDNTHNPEFTSCEFYWAYADFYDL 359
Query: 455 MRLIEELLCYCLNIPTRTFSRISYNDAISLYGSDKPDLRYDCKIMIAIKEQPPWP 509
++ E+ + T+ +I YN D P+ K I I PP+P
Sbjct: 360 IKWSEDFFSQLVMHLFGTY-KILYN-------KDGPE-----KDPIEIDFTPPYP 401
Score = 44.6 bits (105), Expect = 2e-04
Identities = 18/36 (50%), Positives = 23/36 (63%)
Query: 821 AFKYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFP 856
+ +YG PP GG+ LGIDR+ L I+DVI FP
Sbjct: 544 SLEYGLPPTGGLGLGIDRITMFLTNKNCIKDVILFP 579
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 55.0 bits (133), Expect = 3e-09
Identities = 22/108 (20%), Positives = 43/108 (39%), Gaps = 14/108 (12%)
Query: 137 RVLDVGAGIGRISKYLLAKHFD-KIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQD- 194
RVLD+G G G ++ L ++ ++ S + +E A+E KL +
Sbjct: 4 RVLDIGCGTGSLAIELARLFPGARVTGVDLSPEMLELARENA-----KLALGPRITFVQG 58
Query: 195 --FKPEDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIII 240
DL +D ++I +L+ L+ +L G +++
Sbjct: 59 DAPDALDLLEGFDAVFIGGGGGDLLE-----LLDALASLLKPGGRLVL 101
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.).
Length = 107
Score = 54.4 bits (131), Expect = 5e-09
Identities = 25/107 (23%), Positives = 51/107 (47%), Gaps = 6/107 (5%)
Query: 137 RVLDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQDFK 196
RVLD+G G G ++ L + ++ ++ S +E A++ L V D +
Sbjct: 1 RVLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAA---LLADNVEVLKGDAE 57
Query: 197 --PEDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIIIK 241
P + + +DVI L ++ ED+ +FL +++L G++++
Sbjct: 58 ELPPEADESFDVIISDPPLHHLV-EDLARFLEEARRLLKPGGVLVLT 103
>gnl|CDD|219760 pfam08242, Methyltransf_12, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 98
Score = 53.1 bits (128), Expect = 1e-08
Identities = 20/101 (19%), Positives = 39/101 (38%), Gaps = 4/101 (3%)
Query: 139 LDVGAGIGRISKYLLAK-HFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQDFKP 197
LD+G G G + + LL + ++ S +E A E + + + D
Sbjct: 1 LDIGCGTGTLLRALLEALPGLEYTGVDISPAALEAAAERLAALGLLDAVRVRLDVLDA-I 59
Query: 198 EDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGII 238
+ +DV+ VL + D L +++L G++
Sbjct: 60 DLDPGSFDVVVASNVLHHL--ADPRAVLRNLRRLLKPGGVL 98
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 50.7 bits (122), Expect = 7e-08
Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 16/105 (15%)
Query: 139 LDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQDFKPE 198
LDVG G G +++ L + ++ ++ S + + A++ E
Sbjct: 1 LDVGCGTGLLAEALARRGGARVTGVDLSPEMLALARKR-----------APRKFVVGDAE 49
Query: 199 DLNIK---YDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIII 240
DL +DV+ VL + D + L ++L G ++I
Sbjct: 50 DLPFPDESFDVVVSSLVLHHL--PDPERALREIARVLKPGGKLVI 92
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 55.1 bits (134), Expect = 8e-08
Identities = 25/70 (35%), Positives = 37/70 (52%)
Query: 787 EIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLMSILCGT 846
EI GGS R ++ E+ + L + + +YG PH G LG +RL++ + G
Sbjct: 373 EIIGGSQREERLDVLEARIKELGLNKEDYWWYLDLRRYGSVPHSGFGLGFERLVAYITGL 432
Query: 847 QSIRDVIAFP 856
+IRDVI FP
Sbjct: 433 DNIRDVIPFP 442
Score = 31.2 bits (72), Expect = 2.9
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 21 VDKTVTLCGWLQNQRVD---MFALLRD--AYGQVQVIVPN 55
V + VT+ GW++ +R F LRD + Q+QV+ N
Sbjct: 15 VGQEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDN 54
>gnl|CDD|236474 PRK09350, PRK09350, poxB regulator PoxA; Provisional.
Length = 306
Score = 54.5 bits (132), Expect = 9e-08
Identities = 44/148 (29%), Positives = 62/148 (41%), Gaps = 23/148 (15%)
Query: 347 NLRFRSKFLMRTREFLATHRDFVEVETPTL------------FKRTPGGAREFVVPTHEP 394
NL R+K + R F A R +EVETP L F+ FV P
Sbjct: 4 NLLKRAKIIAEIRRFFA-DRGVLEVETPILSQATVTDIHLVPFET------RFVGPGASQ 56
Query: 395 NKFYSLVQSPQ-QLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQLDIELSFTTRDD 453
K L+ SP+ +K+LL GS FQI + +R+E PEFT L+
Sbjct: 57 GKTLWLMTSPEYHMKRLLAAGSGP-IFQICKSFRNEEAGRYHNPEFTMLEWYRPHYDMYR 115
Query: 454 VMRLIEELLCYCLNIPTRTFSRISYNDA 481
+M +++LL L+ +SY A
Sbjct: 116 LMNEVDDLLQQVLD--CEPAESLSYQQA 141
Score = 44.5 bits (106), Expect = 1e-04
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 816 QHMIQAFKYGCPPHGGIALGIDRLMSILCGTQSIRDV 852
+++I A + G P G+ALG+DRL+ + G +SI +V
Sbjct: 270 ENLIAALEAGLPDCSGVALGVDRLIMLALGAESISEV 306
>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G,
H, P, S and T). Other tRNA synthetase sub-families are
too dissimilar to be included. This domain is the core
catalytic domain of tRNA synthetases and includes
glycyl, histidyl, prolyl, seryl and threonyl tRNA
synthetases.
Length = 171
Score = 48.8 bits (117), Expect = 2e-06
Identities = 36/132 (27%), Positives = 51/132 (38%), Gaps = 39/132 (29%)
Query: 359 REFLATHRDFVEVETPT-----LFKRTPG---------------GAREFV-VPTHEP--- 394
RE L + EV+TP L++ + G E PT E
Sbjct: 10 RELL-KRYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGEELYLRPTAEVGIT 68
Query: 395 NKFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDESTRPD----RQPEFTQLDIELSFTT 450
F + + S ++L + +QI C+R E RP R EFTQ+D E F T
Sbjct: 69 RLFKNEILSYRELPL--------KLYQIGPCFRYE-ARPRRGLGRVREFTQVDAE-IFGT 118
Query: 451 RDDVMRLIEELL 462
+ +EELL
Sbjct: 119 PEQSEEELEELL 130
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 50.7 bits (121), Expect = 2e-06
Identities = 28/77 (36%), Positives = 37/77 (48%)
Query: 781 LVLNGNEIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLM 840
LV E+ GGS R E E+ L L + S + +YG PH G LG +RL+
Sbjct: 482 LVPRVGELIGGSQREERLEYLEARLDELKLNKESYWWYLDLRRYGSVPHAGFGLGFERLV 541
Query: 841 SILCGTQSIRDVIAFPK 857
G +IRD I FP+
Sbjct: 542 QFATGIDNIRDAIPFPR 558
>gnl|CDD|234556 TIGR04345, ovoA_Cterm, putative 4-mercaptohistidine
N1-methyltranferase. Ovothiol A is
N1-methyl-4-mercaptohistidine. In the absence of
S-adenosylmethione, a methyl donor, the intermediate
produced is 4-mercaptohistidine. In both Erwinia
tasmaniensis and Trypanosoma cruzi, a protein occurs
with 5-histidylcysteine sulfoxide synthase activity, but
these two enzymes and most homologs share an additional
C-terminal methyltransferase domain. Thus OvoA may be a
bifunctional enzyme with 5-histidylcysteine sulfoxide
synthase and 4-mercaptohistidine N1-methyltranferase
activity. This model describes C-terminal putative
4-mercaptohistidine N1-methyltranferase domain
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 242
Score = 47.2 bits (113), Expect = 1e-05
Identities = 39/138 (28%), Positives = 61/138 (44%), Gaps = 40/138 (28%)
Query: 134 GKTRVLDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQA-------------------- 173
+ R LD+G +GR S + LA++FD++D ++ S++FI A
Sbjct: 41 SRKRALDIGCAVGRAS-FELARYFDEVDGIDFSARFIRPAVALKERGSLRYALKEEGELV 99
Query: 174 --KEEILKDCDKLDKCY-NVGIQDFKPED-LNIK-----YDVIWIQWVLMFILDE--DII 222
KE L D LD+ V F D N+K YD+I + +LD D
Sbjct: 100 SFKEVTLSDL-GLDEVRDRV---SFFQGDACNLKPHFTGYDLI----LAANLLDRLYDPA 151
Query: 223 KFLNLCKQILNKNGIIII 240
FL+ + LN G+++I
Sbjct: 152 AFLSSIHERLNPGGLLVI 169
>gnl|CDD|239766 cd04100, Asp_Lys_Asn_RS_N, Asp_Lys_Asn_RS_N: N-terminal,
anticodon recognition domain of class 2b aminoacyl-tRNA
synthetases (aaRSs). This domain is a beta-barrel
domain (OB fold) involved in binding the tRNA anticodon
stem-loop. Class 2b aaRSs include the homodimeric
aspartyl-, asparaginyl-, and lysyl-tRNA synthetases
(AspRS, AsnRS, and LysRS). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Eukaryotes contain 2 sets of aaRSs, both of which are
encoded by the nuclear genome. One set concerns with
cytoplasmic protein synthesis, whereas the other
exclusively with mitochondrial protein synthesis.
Included in this group are archeal and archeal-like
AspRSs which are non-discriminating and can charge both
tRNAAsp and tRNAAsn. E. coli cells have two isoforms of
LysRSs (LysS and LysU) encoded by two distinct genes,
which are differentially regulated. The cytoplasmic and
the mitochondrial isoforms of human LysRS are encoded
by a single gene. Yeast cytoplasmic and mitochondrial
LysRSs participate in mitochondrial import of
cytoplasmic tRNAlysCUU. In addition to their
housekeeping role, human LysRS may function as a
signaling molecule that activates immune cells. Tomato
LysRS may participate in a process possibly connected
to conditions of oxidative-stress conditions or heavy
metal uptake. It is known that human tRNAlys and LysRS
are specifically packaged into HIV-1 suggesting a role
for LysRS in tRNA packaging. AsnRS is immunodominant
antigen of the filarial nematode Brugia malayai and is
of interest as a target for anti-parasitic drug design.
Human AsnRS has been shown to be a pro-inflammatory
chemokine which interacts with CCR3 chemokine receptors
on T cells, immature dendritic cells and macrophages.
Length = 85
Score = 43.7 bits (104), Expect = 1e-05
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 24 TVTLCGWLQNQRVD---MFALLRDAYGQVQVIVPNHQVPNIYRT 64
VTL GW+ ++R +F LRD G VQV+V ++ +
Sbjct: 1 EVTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEE 44
>gnl|CDD|183450 PRK12335, PRK12335, tellurite resistance protein TehB; Provisional.
Length = 287
Score = 45.3 bits (108), Expect = 8e-05
Identities = 37/121 (30%), Positives = 56/121 (46%), Gaps = 17/121 (14%)
Query: 125 LYCQKKSDPGKTRVLDVGAGIGRISKYLLAKHFD--KIDLLEQSSKFIEQAKEEILKDCD 182
L + PGK LD+G G GR S YL FD +D+ +QS + +++ E+ +
Sbjct: 113 LEAVQTVKPGKA--LDLGCGQGRNSLYLALLGFDVTAVDINQQSLENLQEIAEK-----E 165
Query: 183 KLDKCYNVGIQDFKPEDLNIKYDVIWIQWVLMFILDE---DIIKFLNLCKQILNKNGIII 239
L+ G+ D + +YD I VLMF+ E IIK N+ + N G +
Sbjct: 166 NLN--IRTGLYDINSASIQEEYDFILSTVVLMFLNRERIPAIIK--NMQEHT-NPGGYNL 220
Query: 240 I 240
I
Sbjct: 221 I 221
>gnl|CDD|240414 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional.
Length = 586
Score = 45.4 bits (107), Expect = 1e-04
Identities = 25/77 (32%), Positives = 39/77 (50%)
Query: 781 LVLNGNEIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLM 840
LV E+ GGS R + E + ++ + S Q K+G PH G LG +RL+
Sbjct: 503 LVPKIGEVIGGSQREDNLERLDKMIKEKKLNMESYWWYRQLRKFGSHPHAGFGLGFERLI 562
Query: 841 SILCGTQSIRDVIAFPK 857
++ G +I+D I FP+
Sbjct: 563 MLVTGVDNIKDTIPFPR 579
>gnl|CDD|173391 PTZ00098, PTZ00098, phosphoethanolamine N-methyltransferase;
Provisional.
Length = 263
Score = 44.2 bits (104), Expect = 2e-04
Identities = 40/151 (26%), Positives = 77/151 (50%), Gaps = 12/151 (7%)
Query: 106 GYSSISDLDIQTSNQFLSSLYCQKKSDPGKTRVLDVGAGIGRISKYLLAKHFDKIDLLEQ 165
G IS I+ + + LS + + S +VLD+G+G+G KY+ K+ + ++
Sbjct: 29 GEDYISSGGIEATTKILSDIELNENS-----KVLDIGSGLGGGCKYINEKYGAHVHGVDI 83
Query: 166 SSKFIEQAKEEILKDCDKLD-KCYNVGIQDFKPEDLNIKYDVIWIQWVLMFILDEDIIKF 224
K + AK D +K++ + ++ +DF PE+ +D+I+ + ++ + D K
Sbjct: 84 CEKMVNIAKLRN-SDKNKIEFEANDILKKDF-PEN---TFDMIYSRDAILHLSYADKKKL 138
Query: 225 LNLCKQILNKNGIIIIKDNVASGVKNEYDDE 255
C + L NGI++I D A ++N +D+E
Sbjct: 139 FEKCYKWLKPNGILLITDYCADKIEN-WDEE 168
>gnl|CDD|223574 COG0500, SmtA, SAM-dependent methyltransferases [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 257
Score = 43.7 bits (100), Expect = 2e-04
Identities = 23/133 (17%), Positives = 46/133 (34%), Gaps = 5/133 (3%)
Query: 133 PGKTRVLDVGAGIGRISKYL-LAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVG 191
PG VLD+G G GR++ L + ++ S + + A+ L
Sbjct: 47 PGGLGVLDIGCGTGRLALLARLGGRGAYVVGVDLSPEMLALARARAEGAGLGLVDFVVAD 106
Query: 192 IQDFK-PEDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIIIKDNVASGVKN 250
P + + +D++ VL + K L ++L G +++ D + G+
Sbjct: 107 ALGGVLPFEDSASFDLVISLLVLHLL---PPAKALRELLRVLKPGGRLVLSDLLRDGLLE 163
Query: 251 EYDDEDSSVVRSL 263
+
Sbjct: 164 GRLAALLGFGDPV 176
>gnl|CDD|145868 pfam02938, GAD, GAD domain. This domain is found in some members
of the GatB and aspartyl tRNA synthetases.
Length = 94
Score = 39.9 bits (94), Expect = 4e-04
Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 3/96 (3%)
Query: 609 SETKSSGEDVYRILILPKDLDSTNKKITEYKNLAKKAFNDVKMSTVKVQDSLEWTNKLTK 668
SE G V + L +P + K+I E + AK+ F ++ +KV+ T + K
Sbjct: 2 SEALKKGGSV-KALCVPGGAGLSRKQIDELERFAKE-FGAKGLAWIKVEG-GGHTGPIAK 58
Query: 669 ILPDLNVEEFRNKENLEEGDLIVVSWGKQEDVLSLL 704
L + VEE + + GD+++ K++ V L
Sbjct: 59 FLTEEEVEELLERVGAQNGDILLFVADKEKVVNKAL 94
>gnl|CDD|177970 PLN02336, PLN02336, phosphoethanolamine N-methyltransferase.
Length = 475
Score = 40.5 bits (95), Expect = 0.003
Identities = 39/123 (31%), Positives = 60/123 (48%), Gaps = 18/123 (14%)
Query: 103 MLNGYSSISDLDIQTSNQFLSSLYCQKKSDPGKTRVLDVGAGIGRISKYLL--AKHFDKI 160
ML+ S SDLD + + LS L GK+ VL++GAGIGR + L A +
Sbjct: 13 MLD--SKASDLDKEERPEILSLL----PPYEGKS-VLELGAGIGRFTGELAKKAGQVIAL 65
Query: 161 DLLEQSSKFIEQAKEEILKDCDKLDK--CYNVGIQDFKPEDLNIKYDVIWIQWVLMFILD 218
D +E K K E + K K C +V D D ++ D+I+ W+LM++ D
Sbjct: 66 DFIESVIK-----KNESINGHYKNVKFMCADVTSPDLNISDGSV--DLIFSNWLLMYLSD 118
Query: 219 EDI 221
+++
Sbjct: 119 KEV 121
>gnl|CDD|239818 cd04323, AsnRS_cyto_like_N, AsnRS_cyto_like_N: N-terminal,
anticodon recognition domain of the type found in human
and Saccharomyces cerevisiae cytoplasmic
asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai
AsnRs and, in various putative bacterial AsnRSs. This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. The enzymes in
this group are homodimeric class2b aminoacyl-tRNA
synthetases (aaRSs). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Eukaryotes contain 2 sets of aaRSs, both of which are
encoded by the nuclear genome. One set concerns with
cytoplasmic synthesis, whereas the other exclusively
with mitochondrial protein synthesis. AsnRS is
immunodominant antigen of the filarial nematode B.
malayai and of interest as a target for anti-parasitic
drug design. Human AsnRS has been shown to be a
pro-inflammatory chemokine which interacts with CCR3
chemokine receptors on T cells, immature dendritic
cells and macrophages.
Length = 84
Score = 36.8 bits (86), Expect = 0.004
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 24 TVTLCGWLQNQRVD---MFALLRDAYGQVQVIVPNHQVPNIYRTSTL---ASLPIF 73
V + GW+ R MF +LRD G +Q ++ V Y +L +S+ +
Sbjct: 1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVT 56
>gnl|CDD|222287 pfam13649, Methyltransf_25, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 97
Score = 37.3 bits (87), Expect = 0.004
Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 10/103 (9%)
Query: 138 VLDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQDFKP 197
+LD+G G GR+ + L + ++ S + +E AKE + + D
Sbjct: 1 ILDLGCGTGRVLRALARAGPSSVTGVDISKEALELAKERL----RDKGPKVRFVVADA-- 54
Query: 198 EDL---NIKYDVIWIQWVLMFIL-DEDIIKFLNLCKQILNKNG 236
DL +D++ + + L + + L ++L G
Sbjct: 55 RDLPFEEGSFDLVICAGLSLDYLSPKQLRALLREAARLLRPGG 97
>gnl|CDD|223434 COG0357, GidB, Predicted S-adenosylmethionine-dependent
methyltransferase involved in bacterial cell division
[Cell envelope biogenesis, outer membrane].
Length = 215
Score = 39.2 bits (92), Expect = 0.004
Identities = 33/160 (20%), Positives = 61/160 (38%), Gaps = 25/160 (15%)
Query: 121 FLSSLYCQKKSDPGKTRVLDVGAGIG------RISKYLLAKHFDKIDLLEQSSKFIEQAK 174
L SL D RVLD+G+G G I+ ++ L + F+ + K
Sbjct: 54 ILDSLVLLPYLDGKAKRVLDIGSGAGFPGIPLAIA--FPDLKVTLLESLGKKIAFLREVK 111
Query: 175 EEILKDCDKLD--KCYNVGIQDFKPEDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQIL 232
+E+ L+ + + ++F E +YDV+ + V + L LC +L
Sbjct: 112 KEL-----GLENVEIVHGRAEEFGQEKK--QYDVVTSRAV------ASLNVLLELCLPLL 158
Query: 233 NKNGIIIIKDNVASGVKNEYDDEDSSVVRSLPQFCLLFSK 272
G + K+E + + +++ Q +FS
Sbjct: 159 KVGGGFLAY--KGLAGKDELPEAEKAILPLGGQVEKVFSL 196
>gnl|CDD|219793 pfam08320, PIG-X, PIG-X / PBN1. Mammalian PIG-X and yeast PBN1 are
essential components of
glycosylphosphatidylinositol-mannosyltransferase I.
These enzymes are involved in the transfer of sugar
molecules.
Length = 206
Score = 38.1 bits (89), Expect = 0.009
Identities = 22/73 (30%), Positives = 27/73 (36%), Gaps = 12/73 (16%)
Query: 718 NTLPLEFDNPKSFSIFWVVDFPLFL----PSDSGTLESAHHPFTQPH------PEDEHLL 767
+ L E S W V PL L PS+ S P ED LL
Sbjct: 76 SELLFELAPDASCPDCWNVTIPLHLRYLRPSEGSGYTSV--EVPNPKVFWACDVEDGPLL 133
Query: 768 SSNPLEVRGLHYD 780
S NP + +GL Y+
Sbjct: 134 SCNPFDRKGLGYE 146
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 39.2 bits (91), Expect = 0.010
Identities = 24/83 (28%), Positives = 39/83 (46%)
Query: 781 LVLNGNEIGGGSIRIHSSELQESILHFLNIETSSLQHMIQAFKYGCPPHGGIALGIDRLM 840
LV E+ GGS R ++ + + + + + + +YG H G LG +R++
Sbjct: 489 LVPKVGELIGGSQREERYDVIKQRIEEMGLPIEPYEWYLDLRRYGTVKHCGFGLGFERMI 548
Query: 841 SILCGTQSIRDVIAFPKGFGGKD 863
G +IRDVI FP+ G D
Sbjct: 549 LFATGIDNIRDVIPFPRYPGKAD 571
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 37.4 bits (87), Expect = 0.010
Identities = 27/112 (24%), Positives = 47/112 (41%), Gaps = 9/112 (8%)
Query: 134 GKTRVLDVGAGIGRISKYLLAKHFDKIDL--LEQSSKFIEQAKEEILKDCDKLDKC--YN 189
+VLD+G G G ++ L K ++ ++ S + IE+AKE K +
Sbjct: 3 SGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKK--LGYENVEFIQ 60
Query: 190 VGIQDFKPEDLN-IKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIII 240
I++ L +DV+ VL D K L ++L G++I+
Sbjct: 61 GDIEELPQLQLEDNSFDVVISNEVLN--HLPDPDKVLEEIIRVLKPGGVLIV 110
>gnl|CDD|218506 pfam05219, DREV, DREV methyltransferase. This family contains DREV
protein homologues from several eukaryotes. The function
of this protein is unknown. However, these proteins
appear to be related to other methyltransferases
(Bateman A pers obs).
Length = 265
Score = 38.3 bits (89), Expect = 0.011
Identities = 36/143 (25%), Positives = 61/143 (42%), Gaps = 23/143 (16%)
Query: 104 LNGYSSISDLDIQTSNQFLSSLYCQKKS-DPGKT--RVLDVGAGIGRISKYLLAKHFDKI 160
+NG+ + I + QF L G+ +LD+GAG G I+ +A F+++
Sbjct: 61 INGFLGRGSMFIFSEEQFRKLLVIGGFQPASGQEPVTLLDLGAGDGEITLR-MAPTFEEV 119
Query: 161 DLLEQSSKFIEQAKEEILKDCDKLDKCYNV-GIQDFKPEDLNIKYDVIWIQWVLMFILDE 219
E S ++ K+ K YNV +++ D+N D+I + + +LD
Sbjct: 120 YATELSWTMRDRLKK----------KNYNVLTEIEWQETDVN--LDLI----LCLNLLDR 163
Query: 220 --DIIKFLNLCKQILNKNGIIII 240
D K L L NG +I+
Sbjct: 164 CFDPFKLLEDIHLALAPNGRVIV 186
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 154
Score = 37.1 bits (86), Expect = 0.013
Identities = 29/153 (18%), Positives = 51/153 (33%), Gaps = 34/153 (22%)
Query: 137 RVLDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQDFK 196
RVLD+G G G + + L + FD + ++ S + D L
Sbjct: 25 RVLDIGCGTGILLRLLRERGFD-VTGVDPSPAAVLIFSLFDAPDPAVLAG---------- 73
Query: 197 PEDLNIKYDVIW----IQWVLMFILDEDIIKFLNLCKQILNKNGIIIIKDNVASGVKNEY 252
KYD+I ++ + D L +++L G+++I +A +
Sbjct: 74 ------KYDLITAFEVLEHL------PDPPALLQQLRELLKPGGVLLISTPLADDDARLF 121
Query: 253 DDEDSSVVR-------SLPQFCLLFSKANLKCV 278
+ R S L KA + V
Sbjct: 122 ANWHYLRPRNTHISFYSEESLKRLLEKAGFELV 154
>gnl|CDD|225137 COG2227, UbiG,
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol
methylase [Coenzyme metabolism].
Length = 243
Score = 36.2 bits (84), Expect = 0.046
Identities = 35/123 (28%), Positives = 55/123 (44%), Gaps = 13/123 (10%)
Query: 121 FLSSLYCQKKSDPGKTRVLDVGAGIGRISKYL--LAKHFDKIDLLEQSSKFIEQAKEEIL 178
++ + + PG RVLDVG G G +S+ L L ID E K IE AK L
Sbjct: 47 YIREVARLRFDLPGL-RVLDVGCGGGILSEPLARLGASVTGIDASE---KPIEVAKLHAL 102
Query: 179 KDCDKLDKCYNVG-IQDFKPEDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGI 237
+ +D Y ++D ++DV+ VL + D + FL C +++ GI
Sbjct: 103 ESGVNID--YRQATVEDL--ASAGGQFDVVTCMEVLEHVPDPE--SFLRACAKLVKPGGI 156
Query: 238 III 240
+ +
Sbjct: 157 LFL 159
>gnl|CDD|233668 TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase. This
model represents an O-methyltransferase believed to act
at two points in the ubiquinone biosynthetic pathway in
bacteria (UbiG) and fungi (COQ3). A separate methylase
(MenG/UbiE) catalyzes the single C-methylation step. The
most commonly used names for genes in this family do not
indicate whether this gene is an O-methyl, or C-methyl
transferase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 224
Score = 35.3 bits (82), Expect = 0.079
Identities = 35/120 (29%), Positives = 52/120 (43%), Gaps = 16/120 (13%)
Query: 127 CQKKSDPGKTRVLDVGAGIGRISKYLLAKHFD--KIDLLEQSSKFIEQAKEEILKD-CDK 183
+ K RVLDVG G G +S+ L + ID E++ IE AK KD K
Sbjct: 38 RKNKKPLFGLRVLDVGCGGGLLSEPLARLGANVTGIDASEEN---IEVAKLHAKKDPLLK 94
Query: 184 LDKCYNV-GIQDFKPEDLNIKYDVIWIQWVLMFILD--EDIIKFLNLCKQILNKNGIIII 240
++ Y ++D E +DV+ M +L+ D F+ C Q+L GI+
Sbjct: 95 IE--YRCTSVEDL-AEKGAKSFDVV----TCMEVLEHVPDPQAFIRACAQLLKPGGILFF 147
>gnl|CDD|202783 pfam03848, TehB, Tellurite resistance protein TehB.
Length = 192
Score = 34.4 bits (79), Expect = 0.13
Identities = 29/91 (31%), Positives = 41/91 (45%), Gaps = 11/91 (12%)
Query: 133 PGKTRVLDVGAGIGRISKYLLAKHFD--KIDLLEQSSKFIEQAKEEILKDCDKLDKCYNV 190
PGK LD+G G GR S +L +D +D E S ++ KE+ + LD
Sbjct: 31 PGKA--LDLGCGQGRNSLFLSLLGYDVTAVDHNENSIANLQDIKEK-----ENLD--IPT 81
Query: 191 GIQDFKPEDLNIKYDVIWIQWVLMFILDEDI 221
+ D ++ YD I VLMF+ E I
Sbjct: 82 ALYDINSASIDENYDFILSTVVLMFLQAERI 112
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. This domain is also found at the
C-terminus of eukaryotic GCN2 protein kinase and at the
N-terminus of the ATP phosphoribosyltransferase
accessory subunit, HisZ. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding domain.
Length = 261
Score = 34.9 bits (81), Expect = 0.14
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 418 RYFQIARCYRDESTRPDRQPEFTQLDIEL 446
+ + I +R E + R EF Q+ +E+
Sbjct: 84 KLYYIGPVFRYERPQKGRYREFYQVGVEI 112
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 35.3 bits (82), Expect = 0.16
Identities = 28/120 (23%), Positives = 44/120 (36%), Gaps = 23/120 (19%)
Query: 369 VEVETPTLFKRTPGGAREFVV-PTHEPNKFYSLVQSPQQL---KQLLMVGSVDRYFQIAR 424
E P LF+ G R + PT E + + + + K L + + +QI
Sbjct: 86 WEGFGPELFRVKDRGDRPLALRPTSEEV-ITDMFR--KWIRSYKDLPL-----KLYQIQS 137
Query: 425 CYRDESTRPDRQP-----EFTQLDIELSFTTRDDVMRLIEELLCYCLNIPTRTFSRISYN 479
+RDE RP R EF D +D E++ L+ +R F R+
Sbjct: 138 KFRDE-KRP-RFGLLRGREFLMKDAYSFHADEEDAEETYEKM----LDAYSRIFLRLPLI 191
>gnl|CDD|225136 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 34.5 bits (80), Expect = 0.16
Identities = 40/163 (24%), Positives = 67/163 (41%), Gaps = 30/163 (18%)
Query: 88 EVTEYYSNVPPTIDGMLNGYSSISDLDIQ-TSNQFLSSLYCQKKSDPGKTRVLDVGAGIG 146
+V + + V D M + + + + L SL K D +VLDV G G
Sbjct: 12 KVQKVFDKVAKKYDLM----NDLMSFGLHRLWRRALISLLGIKPGD----KVLDVACGTG 63
Query: 147 RISKYLLAKHFD--KIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGIQDFKPEDLNIK- 203
++ LLAK ++ L+ S +E A+E+ LK + + VG D E+L
Sbjct: 64 DMA-LLLAKSVGTGEVVGLDISESMLEVAREK-LKKKGVQNVEFVVG--DA--ENLPFPD 117
Query: 204 --YDVIWI----QWVLMFILDEDIIKFLNLCKQILNKNGIIII 240
+D + I + V DI K L ++L G +++
Sbjct: 118 NSFDAVTISFGLRNV------TDIDKALKEMYRVLKPGGRLLV 154
>gnl|CDD|239814 cd04319, PhAsnRS_like_N, PhAsnRS_like_N: N-terminal, anticodon
recognition domain of the type found in Pyrococcus
horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. The archeal
enzymes in this group are homodimeric class2b
aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the
specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Length = 103
Score = 32.5 bits (74), Expect = 0.19
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 25 VTLCGWLQNQRV---DMFALLRDAYGQVQVIVPNHQVPNIYR 63
VTL GW+ +R F +LRD+ G VQ + YR
Sbjct: 2 VTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKDLNEEAYR 43
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding
domain of lysyl, aspartyl, and asparaginyl -tRNA
synthetases (See pfam00152). Aminoacyl-tRNA synthetases
catalyze the addition of an amino acid to the
appropriate tRNA molecule EC:6.1.1.-. This family also
includes part of RecG helicase involved in DNA repair.
Replication factor A is a heterotrimeric complex, that
contains a subunit in this family. This domain is also
found at the C-terminus of bacterial DNA polymerase III
alpha chain.
Length = 75
Score = 31.1 bits (71), Expect = 0.32
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 25 VTLCGWLQNQRVDM----FALLRDAYGQVQVIVPNHQVPNIYRT 64
VT+ G + + R F LRD G +QV++ + + +
Sbjct: 1 VTVAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLFKEEAEKLAKK 44
>gnl|CDD|214812 smart00769, WHy, Water Stress and Hypersensitive response.
Length = 100
Score = 31.9 bits (73), Expect = 0.37
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 771 PLEVRGLHYDLVLNGNEIG------GGSIRIHSSELQE 802
P+ V GL YDL LNG E+G G++ + + +
Sbjct: 30 PIPVNGLSYDLYLNGVELGSGEIPDSGTLPGNGRTVLD 67
>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme,
which is found in biotin biosynthetic gene clusters in
proteobacteria, firmicutes, green-sulfur bacteria,
fusobacterium and bacteroides, is believed to carry out
an enzymatic step prior to the formation of pimeloyl-CoA
(although attribution of this annotation is not
traceable). The enzyme appears related to
methyltransferases by homology [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 240
Score = 33.4 bits (77), Expect = 0.41
Identities = 28/148 (18%), Positives = 58/148 (39%), Gaps = 33/148 (22%)
Query: 104 LNGYSSISDLDIQTSNQFLSSLYCQKKSDPGKTRVLDVGAGIGRISKYLLAKH-FDKIDL 162
Y + + + + + L+ L + P VLD+G G G +++ LL + +
Sbjct: 6 AKTYDRHAKIQREMAKRLLALLKEKGIFIP--ASVLDIGCGTGYLTRALLKRFPQAEFIA 63
Query: 163 LEQSSKFIEQAKEE-------ILKDCDKLDKCYNVGIQDFKPEDLNIKYDVIW----IQW 211
+ S+ + QAK + I D +KL + +D+I +QW
Sbjct: 64 NDISAGMLAQAKTKLSENVQFICGDAEKLPLEDS-------------SFDLIVSNLALQW 110
Query: 212 VLMFILDEDIIKFLNLCKQILNKNGIII 239
+D+ + L+ ++L G++
Sbjct: 111 C------DDLSQALSELARVLKPGGLLA 132
>gnl|CDD|223498 COG0421, SpeE, Spermidine synthase [Amino acid transport and
metabolism].
Length = 282
Score = 33.1 bits (76), Expect = 0.54
Identities = 29/119 (24%), Positives = 47/119 (39%), Gaps = 24/119 (20%)
Query: 137 RVLDVGAGIGRISKYLLAKHFD--KIDLLEQSSKFIEQAKEEI-LKDCDKLDKCYNVGIQ 193
RVL +G G G + +L KH +I ++E IE A++ + D + I
Sbjct: 79 RVLIIGGGDGGTLREVL-KHLPVERITMVEIDPAVIELARKYLPEPSGGADDPRVEIIID 137
Query: 194 DFKP--EDLNIKYDVIWIQWVLMFILD----EDIIK------FLNLCKQILNKNGIIII 240
D D K+DVI I+D + F C++ L ++GI +
Sbjct: 138 DGVEFLRDCEEKFDVI--------IVDSTDPVGPAEALFTEEFYEGCRRALKEDGIFVA 188
>gnl|CDD|239811 cd04316, ND_PkAspRS_like_N, ND_PkAspRS_like_N: N-terminal,
anticodon recognition domain of the type found in the
homodimeric non-discriminating (ND) Pyrococcus
kodakaraensis aspartyl-tRNA synthetase (AspRS). This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. P. kodakaraensis
AspRS is a class 2b aaRS. aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation the AA by ATP in the
presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose. P.
kodakaraensis ND-AspRS can charge both tRNAAsp and
tRNAAsn. Some of the enzymes in this group may be
discriminating, based on the presence of homologs of
asparaginyl-tRNA synthetase (AsnRS) in their completed
genomes.
Length = 108
Score = 31.1 bits (71), Expect = 0.59
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 23 KTVTLCGWLQNQRVDM----FALLRDAYGQVQVIVPNHQVP 59
+ VT+ GW+ R D+ F +LRD G VQV P +V
Sbjct: 13 EEVTVAGWVHEIR-DLGGIKFVILRDREGIVQVTAPKKKVD 52
>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
alpha chain catalytic core domain. PheRS belongs to
class II aminoacyl-tRNA synthetases (aaRS) based upon
its structure and the presence of three characteristic
sequence motifs. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. While class II aaRSs generally
aminoacylate the 3'-OH ribose of the appropriate tRNA,
PheRS is an exception in that it attaches the amino acid
at the 2'-OH group, like class I aaRSs. PheRS is an
alpha-2/ beta-2 tetramer.
Length = 218
Score = 32.5 bits (75), Expect = 0.67
Identities = 23/82 (28%), Positives = 32/82 (39%), Gaps = 8/82 (9%)
Query: 403 SPQQLKQLLMVGSVDRYFQIARCYRDESTRPDRQPEFTQL-----DIELSFTTRDDVMRL 457
S Q + L + R F I R YR++ PEF Q+ D L+F D+
Sbjct: 67 SAVQARALAKLKPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFA---DLKGT 123
Query: 458 IEELLCYCLNIPTRTFSRISYN 479
+EE T+ R SY
Sbjct: 124 LEEFAKELFGPITKVRFRPSYF 145
>gnl|CDD|211555 TIGR00138, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase
GidB. GidB (glucose-inhibited division protein B)
appears to be present and in a single copy in nearly all
complete eubacterial genomes. It is missing only from
some obligate intracellular species of various lineages
(Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera,
etc.). GidB shows a methytransferase fold in its the
crystal structure, and acts as a 7-methylguanosine
(m(7)G) methyltransferase, apparently specific to 16S
rRNA [Protein synthesis, tRNA and rRNA base
modification].
Length = 181
Score = 32.2 bits (74), Expect = 0.75
Identities = 32/128 (25%), Positives = 52/128 (40%), Gaps = 24/128 (18%)
Query: 119 NQFLSSLYCQKKSDPGKTRVLDVGAGIGRISKYLLAKHFD--KIDLLEQSSK---FIEQA 173
L SL + D RV+D+G+G G LA K+ LLE + K F+ +
Sbjct: 29 RHILDSLALLEYLD--GKRVIDIGSGAG-FPGIPLAIARPELKLTLLESNHKKVAFLREV 85
Query: 174 KEEILKDCDKLDKCYNVGIQDFKPEDLN--IKYDVIWIQWVLMFILDEDIIKFLNLCKQI 231
K E+ L+ NV I + + ED ++D+I + + + L L +
Sbjct: 86 KAEL-----GLN---NVEIVNGRAEDFQHEEQFDIITSRAL------ASLNVLLELTLNL 131
Query: 232 LNKNGIII 239
L G +
Sbjct: 132 LKVGGYFL 139
>gnl|CDD|226608 COG4123, COG4123, Predicted O-methyltransferase [General function
prediction only].
Length = 248
Score = 32.6 bits (75), Expect = 0.77
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 133 PGKTRVLDVGAGIGRISKYLLAKHFDK--IDLLEQSSKFIEQAKEEI-LKDCDKLDKCYN 189
P K R+LD+GAG G + LLA+ +K I +E + E A+ + L ++ +
Sbjct: 43 PKKGRILDLGAGNGALG-LLLAQRTEKAKIVGVEIQEEAAEMAQRNVALNPLEERIQVIE 101
Query: 190 VGIQDFKPEDLNIKYDVI 207
I++F + +D+I
Sbjct: 102 ADIKEFLKALVFASFDLI 119
>gnl|CDD|188054 TIGR00477, tehB, tellurite resistance protein TehB. Part of a
tellurite-reducing operon tehA and tehB [Cellular
processes, Toxin production and resistance].
Length = 195
Score = 32.2 bits (73), Expect = 0.89
Identities = 27/86 (31%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 133 PGKTRVLDVGAGIGRISKYLLAKHFD--KIDLLEQSSKFIEQAKEEILKDCDKLDKCYNV 190
P KT LD+G G GR S YL +D D E S F+ + KE+ + L+ +
Sbjct: 31 PCKT--LDLGCGQGRNSLYLSLLGYDVTAWDHNENSIAFVNETKEK-----ENLN--LST 81
Query: 191 GIQDFKPEDLNIKYDVIWIQWVLMFI 216
+ D ++ YD I V MF+
Sbjct: 82 ALYDINAANIQENYDFIVSTVVFMFL 107
>gnl|CDD|181902 PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase;
Provisional.
Length = 342
Score = 32.2 bits (74), Expect = 1.1
Identities = 24/59 (40%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 104 LNGYSSISDLDIQTSNQFLSSLYCQKKSDPGKTRVLDVGAGIGRISKYLLAKHFDKIDL 162
L G S LD+ S LS+L + K +VLDVG G G +S LA+H KI L
Sbjct: 172 LPGVFSRDGLDV-GSQLLLSTL-----TPHTKGKVLDVGCGAGVLSAV-LARHSPKIRL 223
>gnl|CDD|216573 pfam01564, Spermine_synth, Spermine/spermidine synthase. Spermine
and spermidine are polyamines. This family includes
spermidine synthase that catalyzes the fifth (last) step
in the biosynthesis of spermidine from arginine, and
spermine synthase.
Length = 240
Score = 31.9 bits (73), Expect = 1.1
Identities = 32/126 (25%), Positives = 54/126 (42%), Gaps = 28/126 (22%)
Query: 131 SDPGKTRVLDVGAGIG----RISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDC-DKLD 185
S P +VL +G G G + K+ +KI L+E K IE +K+ + D
Sbjct: 72 SHPNPKKVLIIGGGDGGALREVVKH---PSVEKITLVEIDEKVIEFSKKFLPSLAGGFDD 128
Query: 186 KCYNVGIQDFKP--EDLNIKYDVIWIQWVLMFILDE-DII---------KFLNLCKQILN 233
V I D +D +++DVI I+D D + +F +L K+ L
Sbjct: 129 PRVKVVIGDGFKFLKDYLVEFDVI--------IVDSTDPVGPAENLFSKEFYDLLKRALK 180
Query: 234 KNGIII 239
++G+ +
Sbjct: 181 EDGVFV 186
>gnl|CDD|237852 PRK14896, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Provisional.
Length = 258
Score = 31.8 bits (73), Expect = 1.2
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 132 DPGKTRVLDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKD 180
D VL++G G G ++ LAK K+ +E + E +++ +
Sbjct: 27 DTDGDPVLEIGPGKGALTDE-LAKRAKKVYAIELDPRLAEFLRDDEIAA 74
>gnl|CDD|221347 pfam11968, DUF3321, Putative methyltransferase (DUF3321). This
family is broadly conserved, being found in fungi,
plants, arthropods and up to primates. it may be a
methyltransferase.
Length = 220
Score = 31.8 bits (73), Expect = 1.2
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 122 LSSLYCQKKSDPGKTRVLDVGA--GIGRISKYLLAKHFD--KIDLLEQSSKFIEQ 172
L L + K GK R L+VGA SK FD +IDL Q ++Q
Sbjct: 40 LKPLNVRLKLGEGKLRALEVGALSTKNACSKS---GLFDVTRIDLNSQHPGILQQ 91
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 32.1 bits (73), Expect = 1.3
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 418 RYFQIARCYRDESTRPDRQPEFTQLDI--ELSFTTRDDVMRLIEELLCYCLNI 468
+ F+I CYR ES + EFT ++ S TR+++ +I++ L + L I
Sbjct: 284 KIFEIGPCYRKESDGKEHLEEFTMVNFCQMGSGCTRENLENIIDDFLKH-LGI 335
>gnl|CDD|218199 pfam04665, Pox_A32, Poxvirus A32 protein. The A32 protein is
thought to be involved in viral DNA packaging.
Length = 241
Score = 31.6 bits (72), Expect = 1.4
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 219 EDIIKFLNLCKQILNKNGIIIIKDNVASGVKNE--YDDEDSSVVRSLPQFCLL---FS-- 271
+ +++ +N+ + K + II+D+V + YD D V+ +L FS
Sbjct: 176 KLLLRAVNIMRSAEKKRRVYIIEDSVFCEGEQRICYDSADERVIARNLDPDILLTQFSHM 235
Query: 272 KANLK 276
K+NL
Sbjct: 236 KSNLL 240
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 32.1 bits (74), Expect = 1.5
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 418 RYFQIARCYRDESTRPDRQPEFTQLD 443
+YF I R +R ++ PEF QL+
Sbjct: 352 KYFSIGRVFRPDTIDATHLPEFYQLE 377
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 31.4 bits (72), Expect = 1.6
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 8/67 (11%)
Query: 418 RYFQIARCYRDESTRPDRQPEFTQL-----DIELSFTTRDDVMRLIEELLCYCLNIPTRT 472
+ F I R +R + PEF Q+ D +SF D+ ++EE L +
Sbjct: 104 KIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVSF---ADLKGVLEEFLRKFFGFEVKV 160
Query: 473 FSRISYN 479
R SY
Sbjct: 161 RFRPSYF 167
>gnl|CDD|215291 PLN02532, PLN02532, asparagine-tRNA synthetase.
Length = 633
Score = 32.1 bits (73), Expect = 1.7
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 823 KYGCPPHGGIALGIDRLMSILCGTQSIRDVIAFPKGFG 860
++G H G +LG + ++ G +RD I FP+ +G
Sbjct: 592 RHGTVKHSGFSLGFELMVLFATGLPDVRDAIPFPRSWG 629
>gnl|CDD|237872 PRK14968, PRK14968, putative methyltransferase; Provisional.
Length = 188
Score = 31.0 bits (71), Expect = 1.8
Identities = 33/138 (23%), Positives = 50/138 (36%), Gaps = 38/138 (27%)
Query: 130 KSDPGKTRVLDVGAGIGRISKYLLAKHFD--KIDLLEQSSKFIEQAKEEILKDCDKLDKC 187
G RVL+VG G G ++ +D+ + +E AK KL+
Sbjct: 20 VDKKGD-RVLEVGTGSGIVAIVAAKNGKKVVGVDI---NPYAVECAKCNA-----KLNNI 70
Query: 188 YNVGIQDFKPEDL-----NIKYDVI--------------WIQWVLMFILD------EDII 222
N G++ DL K+DVI W W L + L E I
Sbjct: 71 RNNGVE-VIRSDLFEPFRGDKFDVILFNPPYLPTEEEEEWDDW-LNYALSGGKDGREVID 128
Query: 223 KFLNLCKQILNKNGIIII 240
+FL+ + L G I++
Sbjct: 129 RFLDEVGRYLKPGGRILL 146
>gnl|CDD|225999 COG3468, AidA, Type V secretory pathway, adhesin AidA [Cell
envelope biogenesis, outer membrane / Intracellular
trafficking and secretion].
Length = 592
Score = 31.7 bits (72), Expect = 2.2
Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 7/75 (9%)
Query: 597 QIKNVDNFRSNRSETKSSG-----EDVYRILILPKDLDSTNKKITEYKNLAKKAFNDVKM 651
+ ++DN ++ SSG E YR L+ L + Y+ + F D
Sbjct: 420 GVNSLDNTGAD--GYLSSGYTASLEGGYRFLLGEASLTLQPQAQLTYQGVTVDDFTDSNG 477
Query: 652 STVKVQDSLEWTNKL 666
S V + +L
Sbjct: 478 SEVSGDNGDSLQGRL 492
>gnl|CDD|217086 pfam02527, GidB, rRNA small subunit methyltransferase G. This is a
family of bacterial glucose inhibited division proteins
these are probably involved in the regulation of cell
devision. GidB has been shown to be a methyltransferase
G specific to the rRNA small subunit. Previously
identified as a glucose-inhibited division protein B
that appears to be present and in a single copy in all
complete eubacterial genomes so far sequenced. GidB
specifically methylates the N7 position of a guanosine
in 16S rRNA.
Length = 184
Score = 30.7 bits (70), Expect = 2.5
Identities = 28/128 (21%), Positives = 50/128 (39%), Gaps = 20/128 (15%)
Query: 119 NQFLSSLYCQKKSDPGKTRVLDVGAGIG----RISKYLLAKHFDKIDLLEQSSKFIEQAK 174
L SL + D + +V DVG+G G ++ K ++ L + F+E+ K
Sbjct: 33 RHLLDSLVVLEYLDNIRIKVADVGSGAGFPGIPLAIAFPDKKLTLLESLLKKINFLEELK 92
Query: 175 EEILKDCDKLDKCYNVGIQDFKPEDLNIK--YDVIWIQWVLMFILDEDIIKFLNLCKQIL 232
+E+ L+ NV I + E+ + YDVI + V + + +L
Sbjct: 93 KEL-----NLE---NVTIVHARAEEYQHEEQYDVITSRAV------ASLNELTEWALPLL 138
Query: 233 NKNGIIII 240
G +
Sbjct: 139 KPGGYFLA 146
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 31.3 bits (72), Expect = 2.6
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 418 RYFQIARCYRDESTRPD--RQPEFTQLDIEL 446
+ + I +R E RP R +F Q +E+
Sbjct: 99 KLYYIGPMFRYE--RPQKGRYRQFHQFGVEV 127
>gnl|CDD|216177 pfam00891, Methyltransf_2, O-methyltransferase. This family
includes a range of O-methyltransferases. These enzymes
utilise S-adenosyl methionine.
Length = 239
Score = 30.7 bits (70), Expect = 2.9
Identities = 28/117 (23%), Positives = 48/117 (41%), Gaps = 25/117 (21%)
Query: 133 PGKTRVLDVGAGIGRISKYLLAKH-------FDKIDLLEQSSKFIEQAKEEILKDCDKLD 185
G + ++DVG G G ++ ++ + FD I A D+++
Sbjct: 100 SGLSSLVDVGGGTGALAAAIVRAYPHIKGIVFD-------LPHVIADAPSA-----DRVE 147
Query: 186 KCYNVGIQDFKPEDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIIIKD 242
VG F+ + D I ++WVL DED +K L C + L G +I+ +
Sbjct: 148 ---FVGGDFFES---VPEADAILLKWVLHDWSDEDCVKILKRCYEALPPGGKVIVVE 198
>gnl|CDD|218286 pfam04840, Vps16_C, Vps16, C-terminal region. This protein forms
part of the Class C vacuolar protein sorting (Vps)
complex. Vps16 is essential for vacuolar protein
sorting, which is essential for viability in plants, but
not yeast. The Class C Vps complex is required for
SNARE-mediated membrane fusion at the lysosome-like
yeast vacuole. It is thought to play essential roles in
membrane docking and fusion at the Golgi-to-endosome and
endosome-to-vacuole stages of transport. The role of
VPS16 in this complex is not known.
Length = 319
Score = 30.5 bits (69), Expect = 3.3
Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 14/99 (14%)
Query: 338 DFRFPEMQHNLRFRSKFLMRTREFLATHRDFVEVETPTLFKRTPGGAREFVVP------T 391
DF+ P+ + + L + + E+E K++P G FV
Sbjct: 202 DFKIPD--------KRLWWLKIKTLVEAKKWEELEQLAQSKKSPIGYMPFVTYCLSQGNK 253
Query: 392 HEPNKFYSLVQSPQQLKQLLMVGSVDRYFQIARCYRDES 430
E K+ + +++K + VG ++A RD
Sbjct: 254 DEAKKYIPRLSYQEKVKAYVEVGDFREAIELAGKERDIP 292
>gnl|CDD|221146 pfam11597, Med13_N, Mediator complex subunit 13 N-terminal.
Mediator is a large complex of up to 33 proteins that is
conserved from plants through fungi to humans - the
number and representation of individual subunits varying
with species. It is arranged into four different
sections, a core, a head, a tail and a kinase-activity
part, and the number of subunits within each of these is
what varies with species. Overall, Mediator regulates
the transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Med13 is part of the
ancillary kinase module, together with Med12, CDK8 and
CycC, which in yeast is implicated in transcriptional
repression, though most of this activity is likely
attributable to the CDK8 kinase. The large Med12 and
Med13 proteins are required for specific developmental
processes in Drosophila, zebrafish, and Caenorhabditis
elegans but their biochemical functions are not
understood.
Length = 370
Score = 30.6 bits (69), Expect = 3.3
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 81 GNRSHYSEVTEYYSNVPPTIDGMLNGYSSISDLDIQ 116
+R+H + + P ++G L G S +SDL +
Sbjct: 182 LSRTHLTPAQKQVYLSPGGLNGTLTGQSYLSDLQVD 217
>gnl|CDD|183040 PRK11207, PRK11207, tellurite resistance protein TehB; Provisional.
Length = 197
Score = 30.1 bits (68), Expect = 3.5
Identities = 32/90 (35%), Positives = 44/90 (48%), Gaps = 7/90 (7%)
Query: 133 PGKTRVLDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLDKCYNVGI 192
PGKT LD+G G GR S YL A FD + +++ I A E +K + LD + +
Sbjct: 31 PGKT--LDLGCGNGRNSLYLAANGFD-VTAWDKNPMSI--ANLERIKAAENLDNLHTA-V 84
Query: 193 QDFKPEDLNIKYDVIWIQWVLMFILDEDII 222
D + +YD I VLMF L+ I
Sbjct: 85 VDLNNLTFDGEYDFILSTVVLMF-LEAKTI 113
>gnl|CDD|234786 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed.
Length = 250
Score = 30.5 bits (70), Expect = 3.6
Identities = 33/130 (25%), Positives = 54/130 (41%), Gaps = 27/130 (20%)
Query: 130 KSDPGKTRVLDVGAGIGRI----SKYLLAKHFDKIDLLEQSSKFIEQAKEEILKDCDKLD 185
K VLDVG G G I + L AK +D+ Q+ +E A+E +
Sbjct: 115 KLVLPGKTVLDVGCGSG-ILAIAAAKLGAKKVLAVDIDPQA---VEAARENAELN----- 165
Query: 186 KCYNVGIQDFKPEDLNIKYDVIWIQWVLMFILDEDIIKFLNLCKQILNKNGIIIIKDNVA 245
V + + P+ ++K DVI + IL +++ ++L G +I+
Sbjct: 166 ---GVELNVYLPQG-DLKADVI-----VANILANPLLELAPDLARLLKPGGRLIL----- 211
Query: 246 SGVKNEYDDE 255
SG+ E DE
Sbjct: 212 SGILEEQADE 221
>gnl|CDD|227895 COG5608, COG5608, LEA14-like dessication related protein [Defense
mechanisms].
Length = 161
Score = 29.3 bits (66), Expect = 5.0
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 771 PLEVRGLHYDLVLNGNEIGGGSI 793
P+ V GL Y + +N +IG G I
Sbjct: 65 PIPVTGLQYAVYMNDIKIGEGEI 87
>gnl|CDD|203189 pfam05175, MTS, Methyltransferase small domain. This domain is
found in ribosomal RNA small subunit methyltransferase C
as well as other methyltransferases .
Length = 170
Score = 29.5 bits (67), Expect = 5.2
Identities = 10/40 (25%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 137 RVLDVGAGIGRISKYLLAKHFD-KIDLLEQSSKFIEQAKE 175
+VLD+G G G + L + D ++ +++ +++ +E A+
Sbjct: 34 KVLDLGCGYGVLGAALAKRSPDLEVTMVDINARALESARA 73
>gnl|CDD|182918 PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 255
Score = 29.9 bits (68), Expect = 5.5
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 7/62 (11%)
Query: 116 QTSNQFLSSLYCQKKSDPGKTRVLDVGAGIGRISKYLLAKHFDKIDLLEQSSKFIEQAKE 175
Q ++ L+ L P RVLD G G G+ + LA+ ++ L + S++ I++AK+
Sbjct: 32 QDLDRLLAEL------PPRPLRVLDAGGGEGQTAI-KLAELGHQVILCDLSAEMIQRAKQ 84
Query: 176 EI 177
Sbjct: 85 AA 86
>gnl|CDD|221748 pfam12741, SusD-like, Susd and RagB outer membrane lipoprotein.
This is a family of SusD-like proteins, one member of
which, BT1043, is an outer membrane lipoprotein involved
in host glycan metabolism. The structures of this and
SusD-homologues in the family are dominated by
tetratrico peptide repeats that may facilitate
association with outer membrane beta-barrel transporters
required for glycan uptake. The structure of BT1043
complexed with N-acetyllactosamine reveals that
recognition is mediated via hydrogen bonding
interactions with the reducing end of
beta-N-acetylglucosamine, suggesting a role in binding
glycans liberated from the mucin polypeptide. Mammalian
distal gut bacteria have an expanded capacity to utilize
glycans. In the absence of dietary sources, some species
rely on host-derived mucosal glycans. The ability of
Bacteroides thetaiotaomicron, a prominent human gut
symbiont, to forage host glycans contributes to both its
ability to persist within an individual host and its
ability to be transmitted naturally to new hosts at
birth.
Length = 529
Score = 30.2 bits (68), Expect = 6.1
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 614 SGEDVYRILILPKDLDSTNKKITEYKNLAKKAFNDVKM 651
S E+VY K+LD + +T+Y N +AF +
Sbjct: 179 SQEEVYTSFF--KELDEAVQVLTDYINAGSEAFPSFDI 214
>gnl|CDD|215509 PLN02943, PLN02943, aminoacyl-tRNA ligase.
Length = 958
Score = 29.9 bits (67), Expect = 6.9
Identities = 13/44 (29%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 138 VLDVGAGIGRISKYL--LAKHFDKIDLLEQSSKFIEQAKEEILK 179
++D+ A + R+SK L + +D + S KF+E+A E++++
Sbjct: 884 MVDISAEVERLSKRLSKMQTEYDALAARLSSPKFVEKAPEDVVR 927
>gnl|CDD|234456 TIGR04074, bacter_Hen1, 3' terminal RNA ribose
2'-O-methyltransferase Hen1. Members of this protein
family are bacterial Hen1, a 3' terminal RNA ribose
2'-O-methyltransferase that acts in bacterial RNA
repair. All members of the seed alignment belong to a
cassette with the RNA repair enzyme polynucleotide
kinase-phosphatase (Pnkp). Chemically similar Hen1 in
eukaryotes acts instead on small regulatory RNAs
[Transcription, RNA processing, Protein synthesis, tRNA
and rRNA base modification].
Length = 462
Score = 29.6 bits (67), Expect = 8.0
Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 134 GKTRVLDVGAGIGRISKYLLA-KHFDKIDLLEQSSKFIEQAKE 175
G VLD+G G G++ + LLA K F++I ++ S++ +E A
Sbjct: 282 GARSVLDLGCGEGKLLRLLLAEKQFERIAGVDVSARELEIAAR 324
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 29.4 bits (66), Expect = 8.5
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 740 LFLPSDSGTLESAHHPFTQPHPEDEHLLSSNPLEVRGLH 778
L LP GT + HPE + +SNP+E G+H
Sbjct: 134 LELPGKRGT-----SRYVDVHPEFRVIFTSNPVEYAGVH 167
>gnl|CDD|233775 TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase.
This family consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 314
Score = 29.2 bits (66), Expect = 8.7
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 142 GAG-IGR-ISKYLLAKHFDKI---DLLEQSSKFIEQAKEEILKDCDK 183
GAG IG + K L + I D L KF+ A I DK
Sbjct: 6 GAGFIGSNLVKALNERGITDILVVDNLRDGHKFLNLADLVIADYIDK 52
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 29.3 bits (67), Expect = 9.3
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 418 RYFQIARCYRDESTRPD--RQPEFTQLDIEL 446
+ + I +R E RP R +F Q +E+
Sbjct: 100 KLYYIGPMFRYE--RPQKGRYRQFHQFGVEV 128
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
0.320 0.138 0.416
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 45,313,733
Number of extensions: 4540300
Number of successful extensions: 4284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4159
Number of HSP's successfully gapped: 156
Length of query: 883
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 778
Effective length of database: 6,280,432
Effective search space: 4886176096
Effective search space used: 4886176096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (28.0 bits)