Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_010529623.1 ON01_RS03495 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000224785.1:WP_010529623.1 Length = 489 Score = 727 bits (1876), Expect = 0.0 Identities = 358/487 (73%), Positives = 419/487 (86%), Gaps = 5/487 (1%) Query: 1 MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60 MSLFDH I +L+ ++HKKEI DLVD SY RI VDD+V+AFL LDEE+AR+ AK+LD Sbjct: 1 MSLFDHSIKQLEGMLHKKEISAEDLVDASYNRIHEVDDQVKAFLTLDEEQARSQAKQLDA 60 Query: 61 AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFD-PIYDATVVQRLQDAEAVTI 119 A D E+ LF +P G+KDNIVTKGLRTTC S+ L+NFD P+Y+ATVV++L + VT+ Sbjct: 61 APD---ENAQLFAIPAGIKDNIVTKGLRTTCGSQFLKNFDDPLYNATVVEKLNTEKTVTV 117 Query: 120 GKLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSI 179 GKLNMDEFAMGSSTEN++Y T+NPWN D VPGGSSGGSAA+VAAGEV FSLGSDTGGSI Sbjct: 118 GKLNMDEFAMGSSTENTSYTPTRNPWNTDYVPGGSSGGSAASVAAGEVLFSLGSDTGGSI 177 Query: 180 RQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDST 239 RQPASFCGVVG+KPTYGRVSR+GLVAFASSLDQIGPITR+VEDNA +L+ ISG DKMDST Sbjct: 178 RQPASFCGVVGMKPTYGRVSRFGLVAFASSLDQIGPITRSVEDNARILEIISGHDKMDST 237 Query: 240 SANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSL 299 SA+VDVP + LTGD+KG+KIAVPKEYL EGV E +E+V++ALKV E LGA WEEVSL Sbjct: 238 SADVDVPSYTDKLTGDVKGMKIAVPKEYLAEGVAPEVKEAVMSALKVYESLGAEWEEVSL 297 Query: 300 PHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRI 359 PHSKYA+A YYLL+SSEASANLARFDG+RYG R+D ADN++D++ +R+EGFG+EVKRRI Sbjct: 298 PHSKYAVAAYYLLASSEASANLARFDGVRYGVRSDKADNMMDMFTYSRSEGFGDEVKRRI 357 Query: 360 MLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPL 419 MLGTFALSSGYYDAYYKKAQKVRTLIK DF+++ + YDV++GPT PTPAFK+GE DPL Sbjct: 358 MLGTFALSSGYYDAYYKKAQKVRTLIKNDFDNILKDYDVVIGPTAPTPAFKVGEKIDDPL 417 Query: 420 TMYANDILTIPVNLAGVPGISVPCGLA-DGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478 TMYANDILTIPVNLAGVPGISVPCG + +GLP+GLQIIG F E TVYR AHA+EQATDH Sbjct: 418 TMYANDILTIPVNLAGVPGISVPCGFSEEGLPIGLQIIGNAFAEGTVYRAAHAYEQATDH 477 Query: 479 HKAKPEL 485 H +P+L Sbjct: 478 HTKRPQL 484 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: 747 Number of extensions: 26 Number of successful extensions: 4 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: 489 Length adjustment: 34 Effective length of query: 451 Effective length of database: 455 Effective search space: 205205 Effective search space used: 205205 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_010529623.1 ON01_RS03495 (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.3032861.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-204 665.7 0.2 2.1e-204 665.5 0.2 1.0 1 NCBI__GCF_000224785.1:WP_010529623.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010529623.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 665.5 0.2 2.1e-204 2.1e-204 3 465 .. 13 476 .. 11 477 .. 0.99 Alignments for each domain: == domain 1 score: 665.5 bits; conditional E-value: 2.1e-204 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvakekklagipiavKdniavkdie 75 +l+kke+s++++++++++ri++v+d+++afl++++e+a ++ak+ld++ +++ +l+ ip+++Kdni++k+++ NCBI__GCF_000224785.1:WP_010529623.1 13 GMLHKKEISAEDLVDASYNRIHEVDDQVKAFLTLDEEQARSQAKQLDAAPDENAQLFAIPAGIKDNIVTKGLR 85 5899********************************************997778******************* PP TIGR00132 76 ttcaSkiLenyv.spydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaa 147 ttc+S++L+n+ + y+atVve+l+++ ++++Gk N+DEFamGsste+ + +t+nP+n+++vpGGSsgGsaa NCBI__GCF_000224785.1:WP_010529623.1 86 TTCGSQFLKNFDdPLYNATVVEKLNTEKTVTVGKLNMDEFAMGSSTENTSYTPTRNPWNTDYVPGGSSGGSAA 158 ***********7356********************************************************** PP TIGR00132 148 avaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgk 220 +vaa++v ++lgsDTGgSiRqPAsfcgvvG+KPtYG+vSR+Glva+asSldqiG+++++ved a +l++isg+ NCBI__GCF_000224785.1:WP_010529623.1 159 SVAAGEVLFSLGSDTGGSIRQPASFCGVVGMKPTYGRVSRFGLVAFASSLDQIGPITRSVEDNARILEIISGH 231 ************************************************************************* PP TIGR00132 221 DkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklal 293 Dk+Dsts++v+v++++ +l+ d+kg+k++v ke+ e++ evke++ ++l++ e+lgae++evslp++k+a+ NCBI__GCF_000224785.1:WP_010529623.1 232 DKMDSTSADVDVPSYTDKLTGDVKGMKIAVPKEYLAEGVAPEVKEAVMSALKVYESLGAEWEEVSLPHSKYAV 304 ************************************************************************* PP TIGR00132 294 aiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAq 366 a+Yy++++sEas+nlar+dg+ryG r +++++++++++ +Rsegfg+evkrRimlG++als++yyd+yykkAq NCBI__GCF_000224785.1:WP_010529623.1 305 AAYYLLASSEASANLARFDGVRYGVRSDKADNMMDMFTYSRSEGFGDEVKRRIMLGTFALSSGYYDAYYKKAQ 377 ************************************************************************* PP TIGR00132 367 kvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpi 439 kvrtli+++f+++++++Dv+++ptapt afk+gek +dpl+my++D+lt+p+nlaG+p+isvP+g +e+glpi NCBI__GCF_000224785.1:WP_010529623.1 378 KVRTLIKNDFDNILKDYDVVIGPTAPTPAFKVGEKIDDPLTMYANDILTIPVNLAGVPGISVPCGFSEEGLPI 450 ************************************************************************* PP TIGR00132 440 Glqiigkafddkkllsvakaleqald 465 Glqiig+af++ +++++a+a+eqa+d NCBI__GCF_000224785.1:WP_010529623.1 451 GLQIIGNAFAEGTVYRAAHAYEQATD 476 ***********************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (489 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: 32.09 // [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