Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011320446.1 AVA_RS18990 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000204075.1:WP_011320446.1 Length = 486 Score = 560 bits (1444), Expect = e-164 Identities = 279/482 (57%), Positives = 367/482 (76%), Gaps = 4/482 (0%) Query: 8 ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67 I EL + + KKE ++ E+ IQ ++ K+ +FL + ++A A+ +D + E Sbjct: 4 IRELHEQLVKKERSAVEITQETLDHIQELEPKLHSFLHITAQQALEQARAVDAKIAAGEE 63 Query: 68 HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127 GLL G+PIGVKDN+ TKG+ TTC+S+ILENF P Y++TV Q+L DA AV +GK N+DEF Sbjct: 64 IGLLAGIPIGVKDNMCTKGIPTTCASRILENFVPPYESTVTQKLLDAGAVVVGKTNLDEF 123 Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187 AMGSSTENSAY++T NPW+L VPGGSSGGSAAAVAA E +LGSDTGGSIRQPASFCG Sbjct: 124 AMGSSTENSAYQVTANPWDLSRVPGGSSGGSAAAVAAEECVVALGSDTGGSIRQPASFCG 183 Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247 VVGLKPTYG VSRYGLVA+ASSLDQIGP ++VED A LL+AI+G D DSTS V++PD Sbjct: 184 VVGLKPTYGLVSRYGLVAYASSLDQIGPFGKSVEDTAILLKAIAGYDPKDSTSLKVEIPD 243 Query: 248 FLSSLTGDIKG---LKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304 +++SL D+K L+I V KE GEG+ ++V A++ L+ LGA +S P+ +Y Sbjct: 244 YVASLKPDLKARGKLRIGVIKETFGEGLDSVVEQAVTKAIEQLQRLGAEIHVISCPNFRY 303 Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTF 364 + +YY+++ SEASANLAR+DG++YG+R DNL+ +YK+TRA GFG EVKRRIM+GT+ Sbjct: 304 GVPSYYIIAPSEASANLARYDGVKYGWRAPEGDNLLSMYKRTRATGFGAEVKRRIMIGTY 363 Query: 365 ALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAN 424 ALS+GYYDAYY KAQKVRTLIK+DFE+ F+ DV+V PT PT AFK GE T DP++MY N Sbjct: 364 ALSAGYYDAYYLKAQKVRTLIKQDFENAFKNVDVLVSPTAPTTAFKAGEKTADPISMYLN 423 Query: 425 DILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483 D++TIPVNLAG+PG+S+PCG + GLP+GLQ+IGK E + +VA+A+EQ+T H ++P Sbjct: 424 DLMTIPVNLAGLPGLSLPCGFDEQGLPIGLQLIGKVLREDQLLQVAYAYEQSTSWHLSQP 483 Query: 484 EL 485 ++ Sbjct: 484 KI 485 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: 656 Number of extensions: 23 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: 486 Length adjustment: 34 Effective length of query: 451 Effective length of database: 452 Effective search space: 203852 Effective search space used: 203852 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_011320446.1 AVA_RS18990 (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.10671.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-208 678.3 0.0 3e-208 678.2 0.0 1.0 1 lcl|NCBI__GCF_000204075.1:WP_011320446.1 AVA_RS18990 Asp-tRNA(Asn)/Glu-tR Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_011320446.1 AVA_RS18990 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 ! 678.2 0.0 3e-208 3e-208 2 464 .. 8 476 .. 7 478 .. 0.98 Alignments for each domain: == domain 1 score: 678.2 bits; conditional E-value: 3e-208 TIGR00132 2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 +e+l+kke s++e+++e+l++i++ + k+++fl++t+++al++a+++d+k+a +e +lagipi+vKd lcl|NCBI__GCF_000204075.1:WP_011320446.1 8 HEQLVKKERSAVEITQETLDHIQELEPKLHSFLHITAQQALEQARAVDAKIAagEEiGLLAGIPIGVKD 76 78999**********************************************9976656*********** PP TIGR00132 68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136 n+++k+i+ttcaS+iLen+v+py++tV+++l +aga+++GktNlDEFamGsste+Sa++vt+nP++ +r lcl|NCBI__GCF_000204075.1:WP_011320446.1 77 NMCTKGIPTTCASRILENFVPPYESTVTQKLLDAGAVVVGKTNLDEFAMGSSTENSAYQVTANPWDLSR 145 ********************************************************************* PP TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205 vpGGSsgGsaaavaa+++++algsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiG++ k lcl|NCBI__GCF_000204075.1:WP_011320446.1 146 VPGGSSGGSAAAVAAEECVVALGSDTGGSIRQPASFCGVVGLKPTYGLVSRYGLVAYASSLDQIGPFGK 214 ********************************************************************* PP TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlk...glkvgvvkelseesldkevkekfekll 271 +ved+a++l++i+g+D kDstsl+v++++++ +lk dlk +l++gv+ke ++e+ld+ v++++ k++ lcl|NCBI__GCF_000204075.1:WP_011320446.1 215 SVEDTAILLKAIAGYDPKDSTSLKVEIPDYVASLKPDLKargKLRIGVIKETFGEGLDSVVEQAVTKAI 283 ***********************************955533379************************* PP TIGR00132 272 ekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340 e+l++lgaei +s+p++++ ++ Yyii+psEas+nlarydg++yG r+ e ++l +y++tR+ gfg+ lcl|NCBI__GCF_000204075.1:WP_011320446.1 284 EQLQRLGAEIHVISCPNFRYGVPSYYIIAPSEASANLARYDGVKYGWRAPEGDNLLSMYKRTRATGFGA 352 ********************************************************************* PP TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemy 409 evkrRim+G+yals++yyd+yy+kAqkvrtli+++fe++f++vDv+vsptapt+afk gek++dp++my lcl|NCBI__GCF_000204075.1:WP_011320446.1 353 EVKRRIMIGTYALSAGYYDAYYLKAQKVRTLIKQDFENAFKNVDVLVSPTAPTTAFKAGEKTADPISMY 421 ********************************************************************* PP TIGR00132 410 lsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464 l+D++t+p+nlaGlp++s+P+g +e+glpiGlq+igk++ +++ll+va+a+eq + lcl|NCBI__GCF_000204075.1:WP_011320446.1 422 LNDLMTIPVNLAGLPGLSLPCGFDEQGLPIGLQLIGKVLREDQLLQVAYAYEQST 476 ****************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (486 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.79 // [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