Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_010529624.1 ON01_RS03500 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= metacyc::MONOMER-13956 (476 letters) >NCBI__GCF_000224785.1:WP_010529624.1 Length = 476 Score = 765 bits (1976), Expect = 0.0 Identities = 380/476 (79%), Positives = 421/476 (88%) Query: 1 MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60 MNFET+IGLEVHVELKT+SKIFS SP FG E N+ + IDLGYPGVLPVLN+EAV +AM Sbjct: 1 MNFETIIGLEVHVELKTESKIFSPSPNAFGDEPNSNINPIDLGYPGVLPVLNEEAVNYAM 60 Query: 61 KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITR 120 KAA+ALNC+IAT+TKFDRKNYFYPDNPKAYQISQFD+PIGENGWIEIEV G+ KRIGITR Sbjct: 61 KAALALNCDIATNTKFDRKNYFYPDNPKAYQISQFDQPIGENGWIEIEVNGEKKRIGITR 120 Query: 121 LHLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTGV 180 LH+EEDAGKLTH DG+SLVDFNRQGTPL+EIVSEPDIRTPEEAYAYLEKLK+IIQYTGV Sbjct: 121 LHMEEDAGKLTHQDDGHSLVDFNRQGTPLIEIVSEPDIRTPEEAYAYLEKLKNIIQYTGV 180 Query: 181 SDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSGF 240 SDCKMEEGSLRCDAN+S+RPIGQEEFG KTELKNLNSF+FVQKGLE EEKRQE+ LLSG Sbjct: 181 SDCKMEEGSLRCDANLSIRPIGQEEFGVKTELKNLNSFSFVQKGLEFEEKRQEKELLSGG 240 Query: 241 FIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDER 300 I QETRRYDE TK+TILMRVKEGSDDYRYFPEPDLV LYID+EWKER++A IPELPD R Sbjct: 241 EILQETRRYDEKTKETILMRVKEGSDDYRYFPEPDLVPLYIDEEWKERIRAEIPELPDTR 300 Query: 301 RKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKEL 360 ++RYI EL YDA VLT +KEMADFFEE V GA+ KQASNWLMG+V AY+N KEL Sbjct: 301 KQRYINELELPEYDAAVLTSSKEMADFFEEAVNHGADIKQASNWLMGDVLAYMNKHYKEL 360 Query: 361 ADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVLL 420 ++ALTPE LA MIKLIE GTISSKIAKKVF EL+E GGD EKIVKEKGLVQISDEG L Sbjct: 361 NELALTPEALATMIKLIEDGTISSKIAKKVFAELVENGGDPEKIVKEKGLVQISDEGQLT 420 Query: 421 KLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKKR 476 +++T+ LD N QSI D+KNGKDRAI +LVGQ+MK +KGQANPPMVNKIL +EI KR Sbjct: 421 EIITKVLDENEQSIIDYKNGKDRAIKYLVGQVMKVTKGQANPPMVNKILQQEIDKR 476 Lambda K H 0.314 0.134 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: 863 Number of extensions: 32 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: 476 Length of database: 476 Length adjustment: 33 Effective length of query: 443 Effective length of database: 443 Effective search space: 196249 Effective search space used: 196249 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_010529624.1 ON01_RS03500 (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.947750.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-191 621.2 3.0 6e-191 621.0 3.0 1.0 1 NCBI__GCF_000224785.1:WP_010529624.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010529624.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 621.0 3.0 6e-191 6e-191 2 480 .. 1 473 [. 1 474 [. 0.98 Alignments for each domain: == domain 1 score: 621.0 bits; conditional E-value: 6e-191 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 +++e +iGlEvHv l t+sK+F+ ++n + + +pN+n++p++lg+PG+lPvlN+eav+ A+k alaln+ i NCBI__GCF_000224785.1:WP_010529624.1 1 MNFETIIGLEVHVELKTESKIFSPSPNAFGD-EPNSNINPIDLGYPGVLPVLNEEAVNYAMKAALALNCDIA- 71 689****************************.**************************************66. PP TIGR00133 75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslvD 147 ++FdRK+YfYpD Pk+yqi+q+d+Pi+e+G +eie+++++k+igi+rlh+EeD+gk++++ + +slvD NCBI__GCF_000224785.1:WP_010529624.1 72 TNTKFDRKNYFYPDNPKAYQISQFDQPIGENGWIEIEVNGEKKRIGITRLHMEEDAGKLTHQDD---GHSLVD 141 599**********************************************************955...59**** PP TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220 fNR g+PL+EiV++Pd+++++ea a+l+kl++i++y+++sd+++eeGs+R+D+N+sir+ Gqe++g + E+KN NCBI__GCF_000224785.1:WP_010529624.1 142 FNRQGTPLIEIVSEPDIRTPEEAYAYLEKLKNIIQYTGVSDCKMEEGSLRCDANLSIRPIGQEEFGVKTELKN 214 ************************************************************************* PP TIGR00133 221 lnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvk 293 lns++ ++k +e+E +Rq+k+l +g e+ qetr +dek++ t+ +R Ke s DYRYfpePdl+p+ idee+ + NCBI__GCF_000224785.1:WP_010529624.1 215 LNSFSFVQKGLEFEEKRQEKELLSGGEILQETRRYDEKTKETILMRVKEGSDDYRYFPEPDLVPLYIDEEWKE 287 **********************************************************************955 PP TIGR00133 294 ekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkis 366 ++++++pelP+++++r+ +e++l e+da vl+s +e++d fee+v+ ++ k+a nW++ ++l+++nk+ + NCBI__GCF_000224785.1:WP_010529624.1 288 -RIRAEIPELPDTRKQRYINELELPEYDAAVLTSSKEMADFFEEAVNHGADIKQASNWLMGDVLAYMNKHYKE 359 .5*********************************************************************** PP TIGR00133 367 laeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpk 439 l+e +l+pe+la++ikli++g+is+k+ak+++ el+en++dp+k+++++gl+qisde +l++i+ +v++en++ NCBI__GCF_000224785.1:WP_010529624.1 360 LNELALTPEALATMIKLIEDGTISSKIAKKVFAELVENGGDPEKIVKEKGLVQISDEGQLTEIITKVLDENEQ 432 ************************************************************************* PP TIGR00133 440 evekyksgkekalkflvGqvmkktkgradpkevekllkell 480 ++ +yk+gk++a+k+lvGqvmk tkg+a+p v+k+l++ + NCBI__GCF_000224785.1:WP_010529624.1 433 SIIDYKNGKDRAIKYLVGQVMKVTKGQANPPMVNKILQQEI 473 *************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (476 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: 00:00:00.00 # Mc/sec: 26.64 // [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