Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_017549340.1 C792_RS0110175 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000330705.1:WP_017549340.1 Length = 491 Score = 556 bits (1434), Expect = e-163 Identities = 271/486 (55%), Positives = 367/486 (75%), Gaps = 1/486 (0%) Query: 1 MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60 M++ + + EL + I KEIK S++V ++RI+A D+ + +FL +++E A+ELD Sbjct: 1 MNIHELTVEELYEKIQAKEIKPSEVVGALFERIEASDETIGSFLFVNKEEGLKRAEELDR 60 Query: 61 AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120 G LFG+P+G+KDNI TK + TTC+S++LE+F+P+YDATV+ +L + V +G Sbjct: 61 LQAEDRMDGALFGIPMGIKDNICTKDILTTCASRMLEDFNPVYDATVMDKLNEENPVMMG 120 Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180 K NMDEFAMG STENS +K +NPW+ VPGGSSGGSAAAVAAG VPFSLGSDTGGS+R Sbjct: 121 KQNMDEFAMGGSTENSYFKPARNPWDTKAVPGGSSGGSAAAVAAGYVPFSLGSDTGGSVR 180 Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240 QP++FCGVVG+KPTYGRVSRYGLVAFASSLDQIGPITR V DNA +L+ ISG DSTS Sbjct: 181 QPSAFCGVVGMKPTYGRVSRYGLVAFASSLDQIGPITRNVRDNAKILEIISGSHGKDSTS 240 Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300 +FL + D+ G+KIA+PKE++GEG+ E SV + ++ E LGAT +EVS+P Sbjct: 241 MPGVEAEFLEGIDRDLSGMKIALPKEFIGEGIDDEVSASVRRSAEIFESLGATVDEVSIP 300 Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360 H+KY ++ YYL++SSEASANLARFDGIRYGY+ + A L + YK+TR+EGFG+EVKRRI+ Sbjct: 301 HTKYGVSAYYLIASSEASANLARFDGIRYGYKAEGAQTLEEHYKKTRSEGFGSEVKRRIL 360 Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420 LGTF LS+G+YD +Y +AQK+R+L++ + +++F +YD+I+GPTTPT A+ IGE ++D L Sbjct: 361 LGTFVLSAGHYDQHYIRAQKLRSLLEGEMKELFSEYDLIIGPTTPTAAYDIGEKSEDSLQ 420 Query: 421 MYANDILTIPVNLAGVPGISVPCGLA-DGLPLGLQIIGKHFDESTVYRVAHAFEQATDHH 479 MY +DILT+P NL G+P +S+P GL+ DG P+GLQ+I HFDE +Y A FE+ + H Sbjct: 421 MYKDDILTVPANLTGMPALSIPSGLSRDGRPIGLQLIANHFDEKKIYNAAFKFEEKFNLH 480 Query: 480 KAKPEL 485 + +L Sbjct: 481 EELKKL 486 Lambda K H 0.315 0.134 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 724 Number of extensions: 31 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 485 Length of database: 491 Length adjustment: 34 Effective length of query: 451 Effective length of database: 457 Effective search space: 206107 Effective search space used: 206107 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
Align candidate WP_017549340.1 C792_RS0110175 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00132.hmm # target sequence database: /tmp/gapView.980619.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00132 [M=466] Accession: TIGR00132 Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-189 616.6 0.0 1.7e-189 616.4 0.0 1.0 1 NCBI__GCF_000330705.1:WP_017549340.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017549340.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 616.4 0.0 1.7e-189 1.7e-189 3 465 .. 13 478 .. 11 479 .. 0.98 Alignments for each domain: == domain 1 score: 616.4 bits; conditional E-value: 1.7e-189 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kek.klagipiavKdniavk 72 e++++ke++ +ev+ ++ eriea +++i +fl v+ke+ lk+a++ld+ a + + l+gip+++Kdni++k NCBI__GCF_000330705.1:WP_017549340.1 13 EKIQAKEIKPSEVVGALFERIEASDETIGSFLFVNKEEGLKRAEELDRLQAedRMDgALFGIPMGIKDNICTK 85 68999******************************************9877543356**************** PP TIGR00132 73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGs 145 di ttcaS++Le+++++ydatV+ +l+e++ +++Gk N+DEFamG+ste+S+f++ +nP++++ vpGGSsgGs NCBI__GCF_000330705.1:WP_017549340.1 86 DILTTCASRMLEDFNPVYDATVMDKLNEENPVMMGKQNMDEFAMGGSTENSYFKPARNPWDTKAVPGGSSGGS 158 ************************************************************************* PP TIGR00132 146 aaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvis 218 aaavaa+ vp++lgsDTGgS+RqP +fcgvvG+KPtYG+vSRyGlva+asSldqiG+++++v d a++l++is NCBI__GCF_000330705.1:WP_017549340.1 159 AAAVAAGYVPFSLGSDTGGSVRQPSAFCGVVGMKPTYGRVSRYGLVAFASSLDQIGPITRNVRDNAKILEIIS 231 ************************************************************************* PP TIGR00132 219 gkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkl 291 g+ kDsts+ ++e+le + +dl g+k+++ ke+++e++d+ev++++++ e +e+lga++ evs+p+ k+ NCBI__GCF_000330705.1:WP_017549340.1 232 GSHGKDSTSMPGVEAEFLEGIDRDLSGMKIALPKEFIGEGIDDEVSASVRRSAEIFESLGATVDEVSIPHTKY 304 ************999********************************************************** PP TIGR00132 292 alaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykk 364 +++Yy+i++sEas+nlar+dgiryG+++e ++ l+e y+ktRsegfg+evkrRi+lG+++ls++ yd++y++ NCBI__GCF_000330705.1:WP_017549340.1 305 GVSAYYLIASSEASANLARFDGIRYGYKAEGAQTLEEHYKKTRSEGFGSEVKRRILLGTFVLSAGHYDQHYIR 377 ************************************************************************* PP TIGR00132 365 AqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekgl 437 Aqk+r+l+ e+++lf+e+D+i++pt+pt a +gek ed+l+my +D+ltvpanl+G+pa+s+P g +++g NCBI__GCF_000330705.1:WP_017549340.1 378 AQKLRSLLEGEMKELFSEYDLIIGPTTPTAAYDIGEKSEDSLQMYKDDILTVPANLTGMPALSIPSGLSRDGR 450 ************************************************************************* PP TIGR00132 438 piGlqiigkafddkkllsvakaleqald 465 piGlq+i+++fd+kk++++a ++e++++ NCBI__GCF_000330705.1:WP_017549340.1 451 PIGLQLIANHFDEKKIYNAAFKFEEKFN 478 ************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (491 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 31.60 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory