Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_101446556.1 BD749_RS17050 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_002846395.1:WP_101446556.1 Length = 478 Score = 412 bits (1059), Expect = e-119 Identities = 223/459 (48%), Positives = 307/459 (66%), Gaps = 5/459 (1%) Query: 6 HKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGR 65 H + +++ I ++ LV+ I+ ++ AFL + EE A A A +D+ + Sbjct: 5 HSLRDIRSDIANGQVSCRQLVEHYLHNIKQ-QPELNAFLEIFEEEAYAQADAVDKKL-AS 62 Query: 66 SEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMD 125 G L GM IG+KD + +G SS+IL F +Y AT VQRL +A+ IG+ N D Sbjct: 63 GHAGKLAGMVIGLKDVLAYEGHSLQASSQILNGFKSLYTATAVQRLLAEDAIIIGRQNCD 122 Query: 126 EFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASF 185 EFAMG+S ENS++ N + VPGGSSGGSA AV A S+GSDTGGS+RQPASF Sbjct: 123 EFAMGASNENSSFGPVLNADDKTRVPGGSSGGSAVAVQADLCLASIGSDTGGSVRQPASF 182 Query: 186 CGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDV 245 CGVVGLKPTY R+SRYGL+A+ASS DQIG I+++VED A LL+ ++G D+ DST ++ V Sbjct: 183 CGVVGLKPTYSRISRYGLIAYASSFDQIGVISKSVEDAALLLEVMAGSDEYDSTVSHRPV 242 Query: 246 PDFLSSLTGDIKGLKIAVPKE-YLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304 P + L D K KI ++ + EG+ E +ES+L +L+ G E V P+ Y Sbjct: 243 PAYSQMLQTD-KKYKIGYIRDCFESEGLDAEVKESILGVKDMLQEAGHEVEAVEFPYLDY 301 Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTF 364 + TYY+L+++EAS+NL RFDG++YGYR++NA +L LYK+TRAEGFG EV+RRIMLGTF Sbjct: 302 MVPTYYILTTAEASSNLGRFDGVKYGYRSENATDLTSLYKKTRAEGFGPEVQRRIMLGTF 361 Query: 365 ALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAN 424 LS+ YYDAYY KAQ+VR LIK+ +++ + YD ++ PT PT AF++ ENT +PL MY Sbjct: 362 VLSADYYDAYYTKAQRVRRLIKEKTDELLQNYDFLILPTAPTTAFRLEENTANPLAMYLA 421 Query: 425 DILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDE 462 DI T+ +LAGVP IS+P G A+GL +GLQ++ + F+E Sbjct: 422 DIFTVQASLAGVPAISIPVGRDANGLSIGLQLMTRSFEE 460 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: 598 Number of extensions: 35 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: 478 Length adjustment: 34 Effective length of query: 451 Effective length of database: 444 Effective search space: 200244 Effective search space used: 200244 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_101446556.1 BD749_RS17050 (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.1754402.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-175 570.4 0.2 1.7e-175 570.2 0.2 1.0 1 NCBI__GCF_002846395.1:WP_101446556.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101446556.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 570.2 0.2 1.7e-175 1.7e-175 3 463 .. 12 473 .. 10 476 .. 0.97 Alignments for each domain: == domain 1 score: 570.2 bits; conditional E-value: 1.7e-175 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkd 73 + + + +vs ++++e++l++i+++ + +nafle+ +e+a+++a+++dkk+a + klag++i++Kd++a ++ NCBI__GCF_002846395.1:WP_101446556.1 12 SDIANGQVSCRQLVEHYLHNIKQQPE-LNAFLEIFEEEAYAQADAVDKKLAsGHaGKLAGMVIGLKDVLAYEG 83 56788999**************9998.***********************974536***************** PP TIGR00132 74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146 ++ ++S+iL++++s y at v+rl +++a+iiG+ N DEFamG+s e+S fg++ n +++rvpGGSsgGsa NCBI__GCF_002846395.1:WP_101446556.1 84 HSLQASSQILNGFKSLYTATAVQRLLAEDAIIIGRQNCDEFAMGASNENSSFGPVLNADDKTRVPGGSSGGSA 156 ************************************************************************* PP TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219 av adl+ ++gsDTGgS+RqPAsfcgvvGlKPtY ++SRyGl+ayasS+dqiG+++k+ved+al+l+v++g NCBI__GCF_002846395.1:WP_101446556.1 157 VAVQADLCLASIGSDTGGSVRQPASFCGVVGLKPTYSRISRYGLIAYASSFDQIGVISKSVEDAALLLEVMAG 229 ************************************************************************* PP TIGR00132 220 kDkkDstslevkveelleelkkdlkglkvgvvkelse.esldkevkekfekllekleelgaeivevslpsvkl 291 +D+ Dst + +v+ + + l++ k+ k+g++++++e e+ld evke++ +++ l+e g+e++ v++p++++ NCBI__GCF_002846395.1:WP_101446556.1 230 SDEYDSTVSHRPVPAYSQMLQT-DKKYKIGYIRDCFEsEGLDAEVKESILGVKDMLQEAGHEVEAVEFPYLDY 301 ******************9999.9**********765278********************************* PP TIGR00132 292 alaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykk 364 ++++Yyi++++Eassnl r+dg++yG+r e++++l+ ly+ktR+egfg ev+rRimlG+++ls++yyd+yy+k NCBI__GCF_002846395.1:WP_101446556.1 302 MVPTYYILTTAEASSNLGRFDGVKYGYRSENATDLTSLYKKTRAEGFGPEVQRRIMLGTFVLSADYYDAYYTK 374 ************************************************************************* PP TIGR00132 365 AqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekgl 437 Aq+vr+li+++ ++l++++D+++ ptapt+af+l+e++++pl+myl+D++tv a+laG+pais+P+g + +gl NCBI__GCF_002846395.1:WP_101446556.1 375 AQRVRRLIKEKTDELLQNYDFLILPTAPTTAFRLEENTANPLAMYLADIFTVQASLAGVPAISIPVGRDANGL 447 ************************************************************************* PP TIGR00132 438 piGlqiigkafddkkllsvakaleqa 463 +iGlq+++++f++ +ll +++ + ++ NCBI__GCF_002846395.1:WP_101446556.1 448 SIGLQLMTRSFEEPQLLAFSNYILDK 473 *******************9887655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (478 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 25.51 // [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