Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_012674285.1 SULAZ_RS07640 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_000021545.1:WP_012674285.1 Length = 482 Score = 479 bits (1234), Expect = e-140 Identities = 237/471 (50%), Positives = 332/471 (70%), Gaps = 1/471 (0%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 F+ VIGLE HV++ T +KMF FGA PN+N + LA+PG LPV+NK AV++A++A Sbjct: 11 FDVVIGLETHVQMSTKTKMFCGCEVEFGAPPNTNVCPVCLAHPGTLPVINKTAVEYAVKA 70 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122 A+ALN ++ S RKNYFYPD PK YQISQ+D+P+ +GYI+I+V K+I I RLH Sbjct: 71 ALALNCKVHNLSIMARKNYFYPDLPKGYQISQYDKPLATDGYIEIKVGDSFKKIRIHRLH 130 Query: 123 MEEDAGKSTHKGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVSDV 182 +EEDAGK+ H+G S VDLNR GTPL+EIV+EPDI S +EA YLEKLR+I++Y GVS+ Sbjct: 131 IEEDAGKTIHEGSKSYVDLNRAGTPLMEIVTEPDISSAEEARKYLEKLRNIMRYIGVSEA 190 Query: 183 KMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGEIG 242 ME+G LRCD NISL+P G + GTK ELKN+NSF ++ K +EYE +RQ + L G +I Sbjct: 191 DMEKGQLRCDVNISLKPKGSSQLGTKVELKNINSFRFIVKAIEYEIERQAKLLKKGEKII 250 Query: 243 QETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERKAK 302 QETR FD +GKT MR KE + DYRYFP+PD++P+ + D+ E ++ ++PELPD++ + Sbjct: 251 QETRLFDPDSGKTYTMRTKEEAHDYRYFPDPDLLPILLKDSQIEEIKNSLPELPDQKYYR 310 Query: 303 YVNELGLPAYDAHVLTLTKEMSDFFESTIE-HGADVKLTSNWLMGGVNEYLNKNQVELLD 361 Y+ LP YDA VLT K ++++FE ++ + KL SNW++ + LN+ +++ + Sbjct: 311 YIQSFNLPPYDAEVLTSDKNLANYFEEVVKLFPQNPKLVSNWILNELLGKLNEKGIDIEN 370 Query: 362 TKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLLKF 421 + ++ +LA ++ LI DGT+S KIAK+VF G + K I+E+ GL QIS+E + Sbjct: 371 SPISANSLAELVSLIADGTISGKIAKEVFDIAFETGKSPKTIVEEKGLKQISNEDEIRSI 430 Query: 422 VNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472 V L+ + VE YK+G K +GFLVGQIMK +KG+ANPQLVN++LK+EL Sbjct: 431 VKAVLERHPAEVEKYKSGNEKILGFLVGQIMKETKGKANPQLVNKILKEEL 481 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: 661 Number of extensions: 25 Number of successful extensions: 2 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: 482 Length adjustment: 34 Effective length of query: 441 Effective length of database: 448 Effective search space: 197568 Effective search space used: 197568 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_012674285.1 SULAZ_RS07640 (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.21102.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-196 639.3 2.9 2e-196 639.1 2.9 1.0 1 lcl|NCBI__GCF_000021545.1:WP_012674285.1 SULAZ_RS07640 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012674285.1 SULAZ_RS07640 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 ! 639.1 2.9 2e-196 2e-196 3 480 .. 10 481 .. 8 482 .] 0.98 Alignments for each domain: == domain 1 score: 639.1 bits; conditional E-value: 2e-196 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 e+++viGlE+Hvq+ tk+K+Fc c+ e+ +pNtnvcpvcl+ PG+lPv+Nk av+ A+k alaln+k lcl|NCBI__GCF_000021545.1:WP_012674285.1 10 EFDVVIGLETHVQMSTKTKMFCGCEVEFGA-PPNTNVCPVCLAHPGTLPVINKTAVEYAVKAALALNCK 77 89**************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140 v++ s+ +RK+YfYpDlPkgyqi+q+d+P+a+dG++ei++ ++ k+i+i+rlh+EeD+gk+ +++s lcl|NCBI__GCF_000021545.1:WP_012674285.1 78 -VHNLSIMARKNYFYPDLPKGYQISQYDKPLATDGYIEIKVGDSFKKIRIHRLHIEEDAGKTIHEGS-- 143 .668*************************************************************77.. PP TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209 s+vD+NR+g+PL+EiVt+Pd++sa+ear++l+klr+i+ry+++s++d+e+G +R+DvN+s+++kG+ lcl|NCBI__GCF_000021545.1:WP_012674285.1 144 --KSYVDLNRAGTPLMEIVTEPDISSAEEARKYLEKLRNIMRYIGVSEADMEKGQLRCDVNISLKPKGS 210 ..59***************************************************************** PP TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278 ++ gt+vE+KN+ns++ i kaieyEieRq kllkkge++ qetr fd + +t ++R Kee++DYRYfp lcl|NCBI__GCF_000021545.1:WP_012674285.1 211 SQLGTKVELKNINSFRFIVKAIEYEIERQAKLLKKGEKIIQETRLFDPDSGKTYTMRTKEEAHDYRYFP 279 ********************************************************************* PP TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep.k 346 +Pdl pi +++++++e +++ lpelP++k r+ + ++l +da+vl+sd++l+++feevvkl ++ k lcl|NCBI__GCF_000021545.1:WP_012674285.1 280 DPDLLPILLKDSQIEE-IKNSLPELPDQKYYRYIQSFNLPPYDAEVLTSDKNLANYFEEVVKLFPQNpK 347 ****************.9********************************************986555* PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 l+ nWil+ellg+Ln+k i+++++ +++++lael+ li +g+is+k+ake+++ +e++k+pk+++e++ lcl|NCBI__GCF_000021545.1:WP_012674285.1 348 LVSNWILNELLGKLNEKGIDIENSPISANSLAELVSLIADGTISGKIAKEVFDIAFETGKSPKTIVEEK 416 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 gl qis+e+e+ +iv++v++ +p evekyksg ek+l+flvGq+mk+tkg+a+p+ v+k+lke l lcl|NCBI__GCF_000021545.1:WP_012674285.1 417 GLKQISNEDEIRSIVKAVLERHPAEVEKYKSGNEKILGFLVGQIMKETKGKANPQLVNKILKEEL 481 ***************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (482 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: 00:00:00.02 # Mc/sec: 10.30 // [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