Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_077244139.1 B1A74_RS06555 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_001995255.1:WP_077244139.1 Length = 478 Score = 488 bits (1257), Expect = e-142 Identities = 240/477 (50%), Positives = 337/477 (70%), Gaps = 3/477 (0%) Query: 1 MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60 M +ETVIGLE+H +L T SK+FS +P +GAEPN +DL PGVLPV+N+ V+ A+ Sbjct: 1 MEWETVIGLEIHAQLNTVSKIFSGAPTAYGAEPNRQACPVDLGMPGVLPVLNRGVVERAV 60 Query: 61 RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119 +AL+ E+A S F RKNYFYPD PK YQISQF+ PI +G++DIE+ DG TKRIG+T Sbjct: 61 MLGLALDAEVAGRSVFARKNYFYPDLPKGYQISQFELPIVASGHLDIELEDGSTKRIGVT 120 Query: 120 RLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177 R H+EEDAGKS H+G ++ +DLNR GTPL+EIVSEPD+RS KEA AY++KL S+++Y Sbjct: 121 RAHLEEDAGKSLHEGFEAMTGIDLNRAGTPLVEIVSEPDLRSAKEAVAYMKKLHSLVRYL 180 Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237 + D M+EGS RCDAN+S+RP GQ +FGT+AELKNLNSF +V + + +E +RQ + + Sbjct: 181 DICDGNMQEGSFRCDANVSIRPKGQAEFGTRAELKNLNSFRFVERAINFEIERQIDVIEG 240 Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297 GG + QETR +D +T MR KE ++DYRYFP+PD++P+ +D + E +R +PELPD Sbjct: 241 GGRVVQETRLYDPDRDETRSMRTKEEANDYRYFPDPDLLPVEVDQDFIEEIRGRLPELPD 300 Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357 ++ ++V E LP YDA VLT T+EM DF+E+ + KL +NW+MG + LN+++V Sbjct: 301 AKRERFVREYELPEYDAGVLTATREMGDFYEAVVRGCNAPKLAANWVMGEFSAALNRSEV 360 Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417 EL + + LAG++ I+D T+S KIAK+VF + G+A ++E GL QI+D Sbjct: 361 ELAEAPVDAGALAGLLARIQDETISGKIAKEVFEAMWNGEGDADSVIEAKGLKQITDTGA 420 Query: 418 LLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELDK 474 + ++E + NN + +E YK GK K GF VGQ+MKA++G+ANP VN+ LK+ LD+ Sbjct: 421 IDAIIDEVIANNPKQLEQYKGGKDKLFGFFVGQVMKATQGKANPAQVNERLKERLDQ 477 Lambda K H 0.313 0.133 0.373 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: 636 Number of extensions: 22 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: 475 Length of database: 478 Length adjustment: 33 Effective length of query: 442 Effective length of database: 445 Effective search space: 196690 Effective search space used: 196690 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 bits)
Align candidate WP_077244139.1 B1A74_RS06555 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm # target sequence database: /tmp/gapView.1774.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00133 [M=481] Accession: TIGR00133 Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-185 601.0 0.0 8.3e-185 600.8 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077244139.1 B1A74_RS06555 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_077244139.1 B1A74_RS06555 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 600.8 0.0 8.3e-185 8.3e-185 2 480 .. 1 475 [. 1 476 [. 0.99 Alignments for each domain: == domain 1 score: 600.8 bits; conditional E-value: 8.3e-185 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +e+e viGlE+H qlnt sK+F+ +++ + +pN++ cpv+lg+PG+lPvlN+ +v+ A++l+lal++ lcl|NCBI__GCF_001995255.1:WP_077244139.1 1 MEWETVIGLEIHAQLNTVSKIFSGAPTAYGA-EPNRQACPVDLGMPGVLPVLNRGVVERAVMLGLALDA 68 57899************************99.************************************* PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138 + v+ svF+RK+YfYpDlPkgyqi+q++lPi+ G+l+iele+++ k+ig++r hlEeD+gks +++ lcl|NCBI__GCF_001995255.1:WP_077244139.1 69 E-VAGRSVFARKNYFYPDLPKGYQISQFELPIVASGHLDIELEDGStKRIGVTRAHLEEDAGKSLHEGF 136 *.557************************************998766********************87 PP TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207 + ++ +D+NR+g+PL+EiV++Pdl+sakea+a++kkl++++ryl+i dg+++eGs+R+D+Nvsir+k lcl|NCBI__GCF_001995255.1:WP_077244139.1 137 E--AMTGIDLNRAGTPLVEIVSEPDLRSAKEAVAYMKKLHSLVRYLDICDGNMQEGSFRCDANVSIRPK 203 5..799*************************************************************** PP TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276 Gq ++gtr+E+KNlns++ +e+ai++EieRq+++++ g v+qetr +d + t s+R Kee++DYRY lcl|NCBI__GCF_001995255.1:WP_077244139.1 204 GQAEFGTRAELKNLNSFRFVERAINFEIERQIDVIEGGGRVVQETRLYDPDRDETRSMRTKEEANDYRY 272 ********************************************************************* PP TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345 fp+Pdl p+e+d+++++e ++++lpelP+akr+r+++ey+l e+da vl++ +e+ d +e vv+ + p lcl|NCBI__GCF_001995255.1:WP_077244139.1 273 FPDPDLLPVEVDQDFIEE-IRGRLPELPDAKRERFVREYELPEYDAGVLTATREMGDFYEAVVRGCNAP 340 ******************.************************************************** PP TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414 kla+nW++ e+ + Ln+++++laea +++ +la l++ i++++is+k+ake++e + + ++d++++ie+ lcl|NCBI__GCF_001995255.1:WP_077244139.1 341 KLAANWVMGEFSAALNRSEVELAEAPVDAGALAGLLARIQDETISGKIAKEVFEAMWNGEGDADSVIEA 409 ********************************************************************* PP TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 +gl qi+d+ ++ +i++evi++npk++e+yk gk+k+++f+vGqvmk t+g+a+p++v++ lke+l lcl|NCBI__GCF_001995255.1:WP_077244139.1 410 KGLKQITDTGAIDAIIDEVIANNPKQLEQYKGGKDKLFGFFVGQVMKATQGKANPAQVNERLKERL 475 ****************************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7.65 // [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