Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_012565271.1 RC1_RS00085 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_000016185.1:WP_012565271.1 Length = 484 Score = 446 bits (1146), Expect = e-129 Identities = 221/473 (46%), Positives = 327/473 (69%), Gaps = 5/473 (1%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E VIGLEVH ++ +++K+FS + FGA PNS + +D A+PG+LPV+N+ V+ A++ Sbjct: 12 WEIVIGLEVHAQVISNAKLFSGAATAFGAAPNSQVSFVDAAFPGMLPVINEVCVEQAVKT 71 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121 + L +I S FDRKNYFY D P YQISQF QP+ NG I +++ DG T+ +GI RL Sbjct: 72 GLGLKAQINLRSVFDRKNYFYADLPAGYQISQFQQPVVGNGTIVLDLADGSTREVGIERL 131 Query: 122 HMEEDAGKSTHKGEYS--LVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179 H+E DAGKS H S VDLNR G L+EIVS+PD+RSP+EA AYL KLR+I++Y G Sbjct: 132 HLEIDAGKSLHDQHPSKTYVDLNRAGVALMEIVSKPDMRSPEEAAAYLRKLRTILRYLGT 191 Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239 D MEEGS+RCD N+S+R GQ +GT+ E KN+NS YV++ +EYE +RQ E + GG Sbjct: 192 CDGNMEEGSMRCDVNVSVRKVGQP-YGTRTETKNVNSIRYVQQAIEYEAQRQVELIEGGG 250 Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299 + QETR +D + G+T MR KE + DYRYFP+PD++PL I+ +W +R+++T+PELPD++ Sbjct: 251 TVVQETRLWDPNKGETRSMRSKEEAHDYRYFPDPDLLPLEIEQSWVDRIKETLPELPDDK 310 Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359 KA+++ + GL AYDA +L + +DF+E T+ G D KL +N+++G + LNK ++ Sbjct: 311 KARFMADYGLSAYDAGILVAERARADFYE-TVAKGRDPKLAANYVIGDLLGALNKTGRDI 369 Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419 ++ + ++L G+I L+ DGT+S +IAK VF E+ G I+E GL Q++D + Sbjct: 370 TESPIAADDLGGLIDLVTDGTISGRIAKDVFAEMLETGEKPSLIVEKKGLRQVTDTGAID 429 Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472 K ++E + N V ++++GK K GF VGQ+M+A++G+ANP LVN++L +L Sbjct: 430 KAIDEVMAANADKVAEFRSGKEKLFGFFVGQVMRATQGKANPALVNEILATKL 482 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: 621 Number of extensions: 25 Number of successful extensions: 5 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: 484 Length adjustment: 34 Effective length of query: 441 Effective length of database: 450 Effective search space: 198450 Effective search space used: 198450 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_012565271.1 RC1_RS00085 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.24574.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-169 548.5 0.0 6.9e-169 548.3 0.0 1.0 1 lcl|NCBI__GCF_000016185.1:WP_012565271.1 RC1_RS00085 Asp-tRNA(Asn)/Glu-tR Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016185.1:WP_012565271.1 RC1_RS00085 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.3 0.0 6.9e-169 6.9e-169 3 480 .. 11 482 .. 9 483 .. 0.97 Alignments for each domain: == domain 1 score: 548.3 bits; conditional E-value: 6.9e-169 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 e+e+viGlEvH q+ ++KlF+ + + + pN++v+ v+ ++PG lPv+N+ v++A+k +l l+++ lcl|NCBI__GCF_000016185.1:WP_012565271.1 11 EWEIVIGLEVHAQVISNAKLFSGAATAFGA-APNSQVSFVDAAFPGMLPVINEVCVEQAVKTGLGLKAQ 78 6899************************99.9************************************* PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139 i+ svFdRK+YfY DlP gyqi+q+++P++ +G++ ++l +++ +e+gierlhlE D+gks + ++ lcl|NCBI__GCF_000016185.1:WP_012565271.1 79 IN-LRSVFDRKNYFYADLPAGYQISQFQQPVVGNGTIVLDLADGStREVGIERLHLEIDAGKSLHDQH- 145 77.59***********************************9876659******************966. PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 ++ ++vD+NR+gv L+EiV+kPd++s++ea+a+l+klr+ilryl+ dg++eeGsmR+DvNvs+r +G lcl|NCBI__GCF_000016185.1:WP_012565271.1 146 -PSKTYVDLNRAGVALMEIVSKPDMRSPEEAAAYLRKLRTILRYLGTCDGNMEEGSMRCDVNVSVRKVG 213 .79***************************************************************888 PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 q gtr E KN+ns++ +++aieyE +Rq++l++ g +v+qetr +d +k t s+R+Kee++DYRYf lcl|NCBI__GCF_000016185.1:WP_012565271.1 214 QP-YGTRTETKNVNSIRYVQQAIEYEAQRQVELIEGGGTVVQETRLWDPNKGETRSMRSKEEAHDYRYF 281 75.799*************************************************************** PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl p+ei++++v++ ++e+lpelP+ k++r++ +ygls++da +lv+++ +d +e+v+k + pk lcl|NCBI__GCF_000016185.1:WP_012565271.1 282 PDPDLLPLEIEQSWVDR-IKETLPELPDDKKARFMADYGLSAYDAGILVAERARADFYETVAKGRD-PK 348 ****************9.****************************************99998765.5* PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 la+n+++ +llg Lnk+ +++e+ +++++l li+l+++g+is+++ak+++ e+le++++p+ ++ek+ lcl|NCBI__GCF_000016185.1:WP_012565271.1 349 LAANYVIGDLLGALNKTGRDITESPIAADDLGGLIDLVTDGTISGRIAKDVFAEMLETGEKPSLIVEKK 417 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 gl q++d+ ++ k+++ev++ n+++v +++sgkek+++f+vGqvm+ t+g+a+p+ v+++l +l lcl|NCBI__GCF_000016185.1:WP_012565271.1 418 GLRQVTDTGAIDKAIDEVMAANADKVAEFRSGKEKLFGFFVGQVMRATQGKANPALVNEILATKL 482 ************************************************************99887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (484 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 7.96 // [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