Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_013538388.1 THEAM_RS08375 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000185805.1:WP_013538388.1 Length = 487 Score = 550 bits (1417), Expect = e-161 Identities = 279/476 (58%), Positives = 356/476 (74%), Gaps = 3/476 (0%) Query: 1 MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60 M L + + EL LI KKE+K S+LV + +RI+ ++K+ A++ + + A AK DE Sbjct: 1 MELLEKSLKELHTLIKKKELKPSELVQANIERIEQTEEKLNAYITVCAQEALEKAKVADE 60 Query: 61 AVDGRSEHGL--LFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVT 118 + SE + LFG+PI +KDNI +G+R TC+S++LE+F YDATV ++L++ A+ Sbjct: 61 ELLRLSEDEIPELFGIPIAIKDNINVEGIRMTCASRMLESFISPYDATVTKKLRERGAIF 120 Query: 119 IGKLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGS 178 IGK N+DEFAMGSSTE S + TKNPW+ VPGGSSGGSAAAVAA SLGSDTGGS Sbjct: 121 IGKNNLDEFAMGSSTETSYFGPTKNPWDFSRVPGGSSGGSAAAVAARSALASLGSDTGGS 180 Query: 179 IRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDS 238 IRQPA+FCGVVGLKPTYGRVSRYGL AFASSLDQIGPIT+ VED A+LL ISG+D D+ Sbjct: 181 IRQPAAFCGVVGLKPTYGRVSRYGLTAFASSLDQIGPITKNVEDAAYLLNIISGLDSKDA 240 Query: 239 TSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVS 298 TSA + VP+FL +L G++KGLK+ +PKEY EG+ E + V A + LE LGA EVS Sbjct: 241 TSAKLPVPNFLEALNGEVKGLKVGLPKEYFVEGIEPEVKALVEEAARKLEKLGAELVEVS 300 Query: 299 LPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRR 358 LP +KY++ TYY+++ +EAS+NL RFDG+RY YR N L+D+Y +TRAEGFG+EVKRR Sbjct: 301 LPTTKYSVETYYIIAPAEASSNLGRFDGVRYTYRAKNYKGLVDMYCKTRAEGFGDEVKRR 360 Query: 359 IMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDP 418 IM+GT+ LS+GYYDAYY KAQKVRTLI DF+ FE DV++ P TP AFKIGE T DP Sbjct: 361 IMIGTYTLSAGYYDAYYLKAQKVRTLIYNDFQKAFESVDVLLTPVTPEVAFKIGEKTDDP 420 Query: 419 LTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFE 473 + MY +D+ TI VNLAG+P +S+PCGL A LP+G+Q+IGK FDE T+ +VAHA E Sbjct: 421 IKMYLSDVFTIAVNLAGLPALSLPCGLTAQNLPVGVQLIGKAFDEETILKVAHALE 476 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: 612 Number of extensions: 30 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: 487 Length adjustment: 34 Effective length of query: 451 Effective length of database: 453 Effective search space: 204303 Effective search space used: 204303 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_013538388.1 THEAM_RS08375 (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.1182.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-204 666.5 0.0 1.2e-204 666.3 0.0 1.0 1 lcl|NCBI__GCF_000185805.1:WP_013538388.1 THEAM_RS08375 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185805.1:WP_013538388.1 THEAM_RS08375 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 666.3 0.0 1.2e-204 1.2e-204 2 465 .. 12 480 .. 11 481 .. 0.98 Alignments for each domain: == domain 1 score: 666.3 bits; conditional E-value: 1.2e-204 TIGR00132 2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva....ke.kklagipiav 65 ++l+kkke++ +e++++ +erie++++k+na+++v++++al+kak d+++ +e +l+gipia+ lcl|NCBI__GCF_000185805.1:WP_013538388.1 12 HTLIKKKELKPSELVQANIERIEQTEEKLNAYITVCAQEALEKAKVADEELLrlseDEiPELFGIPIAI 80 6789*********************************************987775434449******** PP TIGR00132 66 KdniavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPene 134 Kdni+v++i++tcaS++Le ++spydatV+++l+e ga+ iGk NlDEFamGsstetS+fg+tknP++ lcl|NCBI__GCF_000185805.1:WP_013538388.1 81 KDNINVEGIRMTCASRMLESFISPYDATVTKKLRERGAIFIGKNNLDEFAMGSSTETSYFGPTKNPWDF 149 ********************************************************************* PP TIGR00132 135 ervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGil 203 +rvpGGSsgGsaaavaa ++ +lgsDTGgSiRqPA+fcgvvGlKPtYG+vSRyGl+a+asSldqiG++ lcl|NCBI__GCF_000185805.1:WP_013538388.1 150 SRVPGGSSGGSAAAVAARSALASLGSDTGGSIRQPAAFCGVVGLKPTYGRVSRYGLTAFASSLDQIGPI 218 ********************************************************************* PP TIGR00132 204 akkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklle 272 +k+ved+a +l++isg D+kD ts++ +v+++le+l+ ++kglkvg+ ke++ e+++ evk+ +e++ + lcl|NCBI__GCF_000185805.1:WP_013538388.1 219 TKNVEDAAYLLNIISGLDSKDATSAKLPVPNFLEALNGEVKGLKVGLPKEYFVEGIEPEVKALVEEAAR 287 ********************************************************************* PP TIGR00132 273 kleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgee 341 kle+lgae+vevslp+ k+++ +Yyii+p+Eassnl r+dg+ry +r++++k l ++y ktR+egfg+e lcl|NCBI__GCF_000185805.1:WP_013538388.1 288 KLEKLGAELVEVSLPTTKYSVETYYIIAPAEASSNLGRFDGVRYTYRAKNYKGLVDMYCKTRAEGFGDE 356 ********************************************************************* PP TIGR00132 342 vkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemyl 410 vkrRim+G+y+ls++yyd+yy+kAqkvrtli ++f+k+fe+vDv+++p++p +afk+gek++dp++myl lcl|NCBI__GCF_000185805.1:WP_013538388.1 357 VKRRIMIGTYTLSAGYYDAYYLKAQKVRTLIYNDFQKAFESVDVLLTPVTPEVAFKIGEKTDDPIKMYL 425 ********************************************************************* PP TIGR00132 411 sDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 sDv+t+ +nlaGlpa+s+P+g + ++lp+G+q+igkafd++++l+va+ale++l+ lcl|NCBI__GCF_000185805.1:WP_013538388.1 426 SDVFTIAVNLAGLPALSLPCGLTAQNLPVGVQLIGKAFDEETILKVAHALEAELN 480 **************************************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (487 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.27 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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