Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_090448027.1 BLS63_RS22440 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_900100495.1:WP_090448027.1 Length = 483 Score = 513 bits (1320), Expect = e-150 Identities = 252/480 (52%), Positives = 346/480 (72%), Gaps = 3/480 (0%) Query: 6 HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63 H++T E+ + + KE +L +RI+ +D ++ +F+++ EE A A+ D Sbjct: 2 HRLTLAEIARALAAKEFSAEELTRSLLQRIRRLDPQLNSFISVTEELALQQAQAADSR-R 60 Query: 64 GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123 E+G L G PIG KD T+G+RT+C S +L+NF Y+ATVV++L A +VT+GK+N Sbjct: 61 AAGENGALLGAPIGHKDLFCTQGIRTSCGSLMLDNFKAPYNATVVEKLAAAGSVTLGKMN 120 Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183 MDEFAMGS+ E+S Y KNPWNL+ VPGGSSGGSAAA+AA +P + G+DTGGSIRQPA Sbjct: 121 MDEFAMGSANESSHYGAVKNPWNLERVPGGSSGGSAAAIAARLLPAATGTDTGGSIRQPA 180 Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243 + + GLKPTYGRVSR+G++A+ASSLDQ GP+ RT ED A +LQA++G D DSTS + Sbjct: 181 ALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCALMLQAMAGFDAKDSTSVDA 240 Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303 V D+L+SL + GL+I +PKEY G G+ + V+A++K LE LGA+ +E+SLP+ + Sbjct: 241 PVDDYLASLNQPLSGLRIGLPKEYFGAGLDSRIADVVMASVKQLEQLGASVKEISLPNMQ 300 Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363 +A+ YY+++ +EAS+NL+RFDG+R+GYR + +L DLYK++RAEGFG EVKRRIM+GT Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCEQPSDLTDLYKRSRAEGFGAEVKRRIMVGT 360 Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYA 423 +ALS+GYYDAYY KAQK+R LIK DF F + DVI+GPTTP PA+K+GE DP+ Y Sbjct: 361 YALSAGYYDAYYLKAQKIRRLIKNDFVSAFAEVDVILGPTTPNPAWKLGEKNNDPVAAYL 420 Query: 424 NDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483 DI TI NLAG+PGIS+P G DGLP+G+Q++ +F E + VAH ++ ATD H P Sbjct: 421 EDIYTITANLAGLPGISMPAGFVDGLPVGVQLLAPYFQEGRLLNVAHQYQLATDWHTHTP 480 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: 569 Number of extensions: 19 Number of successful extensions: 1 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: 483 Length adjustment: 34 Effective length of query: 451 Effective length of database: 449 Effective search space: 202499 Effective search space used: 202499 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_090448027.1 BLS63_RS22440 (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.10812.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-182 593.4 0.0 1.7e-182 593.2 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090448027.1 BLS63_RS22440 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090448027.1 BLS63_RS22440 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 ! 593.2 0.0 1.7e-182 1.7e-182 3 464 .. 11 473 .. 9 475 .. 0.98 Alignments for each domain: == domain 1 score: 593.2 bits; conditional E-value: 1.7e-182 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 ++l +ke+s++e+++++l+ri + + ++n+f++vt+e al++a++ d++ a e l g pi+ Kd + lcl|NCBI__GCF_900100495.1:WP_090448027.1 11 RALAAKEFSAEELTRSLLQRIRRLDPQLNSFISVTEELALQQAQAADSRRAaGEnGALLGAPIGHKDLF 79 568899*****************************************998875636************* PP TIGR00132 70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138 ++++i+t+c+S +L+n+++py+atVve+l +ag +++Gk N+DEFamGs+ e+S +g++knP+n ervp lcl|NCBI__GCF_900100495.1:WP_090448027.1 80 CTQGIRTSCGSLMLDNFKAPYNATVVEKLAAAGSVTLGKMNMDEFAMGSANESSHYGAVKNPWNLERVP 148 ********************************************************************* PP TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207 GGSsgGsaaa+aa l p a g+DTGgSiRqPA++++ GlKPtYG+vSR+G++ayasSldq G+la++ lcl|NCBI__GCF_900100495.1:WP_090448027.1 149 GGSSGGSAAAIAARLLPAATGTDTGGSIRQPAALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTA 217 ********************************************************************* PP TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276 ed al+l++++g D+kDsts++++v+++l +l++ l gl++g+ ke+++ +ld+++++ + + +++le+ lcl|NCBI__GCF_900100495.1:WP_090448027.1 218 EDCALMLQAMAGFDAKDSTSVDAPVDDYLASLNQPLSGLRIGLPKEYFGAGLDSRIADVVMASVKQLEQ 286 ********************************************************************* PP TIGR00132 277 lgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrR 345 lga ++e+slp+++ a+++Yy+i+p+Eassnl+r+dg+r+G+r e++++l++ly+++R+egfg+evkrR lcl|NCBI__GCF_900100495.1:WP_090448027.1 287 LGASVKEISLPNMQHAIPAYYVIAPAEASSNLSRFDGVRFGYRCEQPSDLTDLYKRSRAEGFGAEVKRR 355 ********************************************************************* PP TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414 im+G+yals++yyd+yy+kAqk+r+li+++f +f evDvi++pt+p a klgek++dp++ yl+D++ lcl|NCBI__GCF_900100495.1:WP_090448027.1 356 IMVGTYALSAGYYDAYYLKAQKIRRLIKNDFVSAFAEVDVILGPTTPNPAWKLGEKNNDPVAAYLEDIY 424 ********************************************************************* PP TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464 t++anlaGlp+is+P+g +glp+G+q+ + +f++ +ll+va++++ a+ lcl|NCBI__GCF_900100495.1:WP_090448027.1 425 TITANLAGLPGISMPAGFV-DGLPVGVQLLAPYFQEGRLLNVAHQYQLAT 473 *******************.7***********************998665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (483 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: 00:00:00.02 # Mc/sec: 10.76 // [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