Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012757265.1 RLEG_RS08490 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000023185.1:WP_012757265.1 Length = 493 Score = 461 bits (1186), Expect = e-134 Identities = 245/477 (51%), Positives = 322/477 (67%), Gaps = 11/477 (2%) Query: 8 ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67 I E +Q + KEI +L + I A + ++ A++ + + AR AK DE + + Sbjct: 9 IAEARQKLRAKEITAIELTEAYISAIDAANGRLNAYIKVTPDLARVMAKNSDERI-AAGK 67 Query: 68 HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127 G L G+P+G+KD T G+ T S IL F+P Y++TV Q L D AV +GKLNMDEF Sbjct: 68 AGELEGIPLGIKDLFATVGVHTQACSHILNGFEPRYESTVTQNLWDDGAVMLGKLNMDEF 127 Query: 128 AMGSSTENSAYKLTKNPW-----NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182 AMGSS E S Y NPW N VPGGSSGGSAAAVAA + +DTGGSIRQP Sbjct: 128 AMGSSNETSHYGAVINPWRAAGSNQQLVPGGSSGGSAAAVAAHLCAGATATDTGGSIRQP 187 Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242 A+F G VG+KPTYGR SR+G VAFASSLDQ GPI R V D A LL++++ VD D+TS + Sbjct: 188 AAFTGTVGIKPTYGRCSRWGTVAFASSLDQAGPIARDVRDAAILLKSMASVDAKDTTSVD 247 Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302 + VPD+ ++L +KG+KI +P EY +G+ E + L+ GA ++SLPH+ Sbjct: 248 LPVPDYEAALGQSLKGMKIGIPNEYRVDGMPDEIETLWRQGIAWLKDAGAEIVDISLPHT 307 Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362 KYAL YY+++ +EAS+NLAR+DG+RYG R D D ++D+Y++TRA GFG EVKRRIM+G Sbjct: 308 KYALPAYYIVAPAEASSNLARYDGVRYGLRVDGKD-IVDMYEKTRAAGFGKEVKRRIMIG 366 Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEK-YDVIVGPTTPTPAFKIGEN--TKDPL 419 T+ LS+GYYDAYY +AQKVRTLIK+DFE F+ D I+ P TP+ AF + + DP+ Sbjct: 367 TYVLSAGYYDAYYIRAQKVRTLIKRDFELAFDAGVDAILTPATPSSAFGVADENLAADPV 426 Query: 420 TMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475 MY NDI T+ VN+AG+PGI+VP GL GLPLGLQ+IGK FDE T+++ AH EQA Sbjct: 427 KMYLNDIFTVTVNMAGLPGIAVPAGLDHKGLPLGLQLIGKPFDEETLFKTAHVIEQA 483 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: 620 Number of extensions: 32 Number of successful extensions: 5 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: 493 Length adjustment: 34 Effective length of query: 451 Effective length of database: 459 Effective search space: 207009 Effective search space used: 207009 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_012757265.1 RLEG_RS08490 (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.7905.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-172 559.5 0.0 3.3e-172 559.3 0.0 1.0 1 lcl|NCBI__GCF_000023185.1:WP_012757265.1 RLEG_RS08490 Asp-tRNA(Asn)/Glu-t Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_012757265.1 RLEG_RS08490 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 ! 559.3 0.0 3.3e-172 3.3e-172 2 463 .. 13 483 .. 12 486 .. 0.97 Alignments for each domain: == domain 1 score: 559.3 bits; conditional E-value: 3.3e-172 TIGR00132 2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 +++l +ke+++ e++e+++ +i+a + ++na+++vt++ a +ak++d+++a + +l gip+++Kd lcl|NCBI__GCF_000023185.1:WP_012757265.1 13 RQKLRAKEITAIELTEAYISAIDAANGRLNAYIKVTPDLARVMAKNSDERIAaGKaGELEGIPLGIKDL 81 688999*********************************************984536************ PP TIGR00132 69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP.....e 132 +a+ +++t + S+iL+++ + y++tV+++l ++ga+++Gk N+DEFamGss etS +g++ nP lcl|NCBI__GCF_000023185.1:WP_012757265.1 82 FATVGVHTQACSHILNGFEPRYESTVTQNLWDDGAVMLGKLNMDEFAMGSSNETSHYGAVINPwraagS 150 ***************************************************************666666 PP TIGR00132 133 neervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiG 201 n++ vpGGSsgGsaaavaa+l+ a ++DTGgSiRqPA+f+g+vG+KPtYG+ SR+G va+asSldq G lcl|NCBI__GCF_000023185.1:WP_012757265.1 151 NQQLVPGGSSGGSAAAVAAHLCAGATATDTGGSIRQPAAFTGTVGIKPTYGRCSRWGTVAFASSLDQAG 219 99******************************************************************* PP TIGR00132 202 ilakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekl 270 ++a++v d+a++l+ ++ +D+kD+ts++ +v+++ +l + lkg+k+g+ +e++ +++++e+++ +++ lcl|NCBI__GCF_000023185.1:WP_012757265.1 220 PIARDVRDAAILLKSMASVDAKDTTSVDLPVPDYEAALGQSLKGMKIGIPNEYRVDGMPDEIETLWRQG 288 ********************************************************************* PP TIGR00132 271 lekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfg 339 + l++ gaeiv++slp+ k+al++Yyi++p+Eassnlarydg+ryG rv+ ++ + ++y ktR++gfg lcl|NCBI__GCF_000023185.1:WP_012757265.1 289 IAWLKDAGAEIVDISLPHTKYALPAYYIVAPAEASSNLARYDGVRYGLRVDGKD-IVDMYEKTRAAGFG 356 **************************************************9888.************** PP TIGR00132 340 eevkrRimlGayalskeyydkyykkAqkvrtliidefeklfe.evDvivsptaptlafklgek..aedp 405 +evkrRim+G+y+ls++yyd+yy++Aqkvrtli+++fe +f+ vD i++p++p +af ++++ a+dp lcl|NCBI__GCF_000023185.1:WP_012757265.1 357 KEVKRRIMIGTYVLSAGYYDAYYIRAQKVRTLIKRDFELAFDaGVDAILTPATPSSAFGVADEnlAADP 425 *****************************************737**************9987622567* PP TIGR00132 406 lemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463 ++myl+D++tv++n+aGlp+i+vP+g ++kglp+Glq+igk fd+++l++ a+ +eqa lcl|NCBI__GCF_000023185.1:WP_012757265.1 426 VKMYLNDIFTVTVNMAGLPGIAVPAGLDHKGLPLGLQLIGKPFDEETLFKTAHVIEQA 483 *******************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (493 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.81 // [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