Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_090218450.1 CV091_RS00950 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_002796795.1:WP_090218450.1 Length = 503 Score = 392 bits (1007), Expect = e-113 Identities = 206/483 (42%), Positives = 307/483 (63%), Gaps = 15/483 (3%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E VIG+EVH ++ +++K+FS + FGAEPNSN +D A PG+LPV+N+ V+ +R Sbjct: 21 WELVIGMEVHAQVSSNAKLFSGASTKFGAEPNSNVAFVDAAMPGMLPVINEFCVEQTVRT 80 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121 + L EI S FDRKNYFYPD P+ YQISQ PI G + +E+ DG + + + R+ Sbjct: 81 GLGLKAEINLWSAFDRKNYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTARNVRVERI 140 Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179 HME+DAGKS H + S VDLNR G L+EIVS+PDIR P+EA AY+ KLR I+QY G Sbjct: 141 HMEQDAGKSIHDMDPNMSFVDLNRTGVCLMEIVSQPDIRGPEEAAAYIAKLRQIMQYLGT 200 Query: 180 SDVKMEEGSLRCDANISLRPYGQ-EKF---------GTKAELKNLNSFNYVRKGLEYEEK 229 D M+ G+LR D N+S+ GQ EKF GT+ E+KN+NS ++++ +E E + Sbjct: 201 CDGNMQNGNLRADVNVSVCLPGQYEKFQETGDFSHLGTRCEIKNMNSMRFIQQAIEVEAR 260 Query: 230 RQEEELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVR 289 RQ + +GG+I QETR +D G+T MR KE + DYRYFP+PD++PL I+ W + + Sbjct: 261 RQIAIIEAGGKIDQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLLPLEIEQDWVDDIA 320 Query: 290 QTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVN 349 +PELPD++K+++++E L YDA VLT + +FE + G KL +NW++ + Sbjct: 321 AKLPELPDQKKSRFISEFSLTDYDASVLTAEVAAASYFEE-VAQGRTGKLAANWVINELF 379 Query: 350 EYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGL 409 L K+ ++ ++ ++P L G+I LI +S KIAK +F + +GG+ +I+E+ G+ Sbjct: 380 GRLKKDDKDITESPVSPAQLGGIIDLISSDAISGKIAKDLFEIVYTEGGDPAEIVEERGM 439 Query: 410 VQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLK 469 Q++D + ++E + N VE K K G+ VGQ+MKA+ G+ANP+ VNQL+ Sbjct: 440 KQVTDTGAIEAALDEIIAANPAQVEKAKENP-KLAGWFVGQVMKATGGKANPKAVNQLVA 498 Query: 470 QEL 472 +L Sbjct: 499 AKL 501 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: 634 Number of extensions: 23 Number of successful extensions: 6 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: 503 Length adjustment: 34 Effective length of query: 441 Effective length of database: 469 Effective search space: 206829 Effective search space used: 206829 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: 52 (24.6 bits)
Align candidate WP_090218450.1 CV091_RS00950 (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.3077794.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-158 511.7 0.0 1e-157 511.5 0.0 1.0 1 NCBI__GCF_002796795.1:WP_090218450.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002796795.1:WP_090218450.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 511.5 0.0 1e-157 1e-157 3 480 .. 20 501 .. 18 502 .. 0.95 Alignments for each domain: == domain 1 score: 511.5 bits; conditional E-value: 1e-157 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 ++elviG+EvH q+ ++KlF+ +s+++ +pN+nv v+ ++PG lPv+N+ v++ + +l l+++i+ NCBI__GCF_002796795.1:WP_090218450.1 20 DWELVIGMEVHAQVSSNAKLFSGASTKFGA-EPNSNVAFVDAAMPGMLPVINEFCVEQTVRTGLGLKAEIN-L 90 789*************************99.**************************************76.5 PP TIGR00133 76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvD 147 s FdRK+YfYpDlP+gyqi+q + Pi+ +G++ +el ++ +++++er+h+E+D+gks + + +++s+vD NCBI__GCF_002796795.1:WP_090218450.1 91 WSAFDRKNYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTaRNVRVERIHMEQDAGKSIHDMD--PNMSFVD 161 ************************************9765449******************966..79***** PP TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq..........e 210 +NR+gv L+EiV++Pd++ ++ea+a++ klrqi++yl+ dg++++G++R+DvNvs+ l Gq + NCBI__GCF_002796795.1:WP_090218450.1 162 LNRTGVCLMEIVSQPDIRGPEEAAAYIAKLRQIMQYLGTCDGNMQNGNLRADVNVSVCLPGQyekfqetgdfS 234 *********************************************************9988733332222234 PP TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlp 283 + gtr EiKN+ns++ i++aie E Rq+++++ g ++ qetr +d k t s+R+Kee++DYRYfp+Pdl NCBI__GCF_002796795.1:WP_090218450.1 235 HLGTRCEIKNMNSMRFIQQAIEVEARRQIAIIEAGGKIDQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLL 307 5799********************************************************************* PP TIGR00133 284 pieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileel 356 p+ei++++v++ +++klpelP++k+ r+ +e+ l ++da vl++++ +++feev++ + kla+nW+++el NCBI__GCF_002796795.1:WP_090218450.1 308 PLEIEQDWVDD-IAAKLPELPDQKKSRFISEFSLTDYDASVLTAEVAAASYFEEVAQGRTG-KLAANWVINEL 378 ***********.*******************************************997776.*********** PP TIGR00133 357 lgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvki 429 g+L+k + +++e+ ++p +l +i+li+ + is+k+ak+l+e + ++++dp +++e++g+ q++d+ ++ ++ NCBI__GCF_002796795.1:WP_090218450.1 379 FGRLKKDDKDITESPVSPAQLGGIIDLISSDAISGKIAKDLFEIVYTEGGDPAEIVEERGMKQVTDTGAIEAA 451 ************************************************************************* PP TIGR00133 430 veevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 ++e+i+ np +vek k++ k+ +++vGqvmk t g+a+pk v++l+ +l NCBI__GCF_002796795.1:WP_090218450.1 452 LDEIIAANPAQVEKAKEN-PKLAGWFVGQVMKATGGKANPKAVNQLVAAKL 501 *************98875.56889**********************98877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (503 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 23.34 // [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