Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_026606927.1 METAC_RS0110060 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Korea:Ga0059261_0351 (310 letters) >NCBI__GCF_000427445.1:WP_026606927.1 Length = 309 Score = 280 bits (716), Expect = 3e-80 Identities = 151/302 (50%), Positives = 192/302 (63%), Gaps = 4/302 (1%) Query: 1 MSVSVFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPD 60 M +FIDG AGTTGL I RLA + + L RKD + + D V+LCLPD Sbjct: 1 MPAKIFIDGEAGTTGLGIAARLAGEPGVERVSLAPELRKDPEAKKALLAGVDVVVLCLPD 60 Query: 61 DAAREAVALI---ANDTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCW 117 DAARE VAL+ + R++DASTAHRVA+GWTYGF EL Q+ AI AR VSNPGC+ Sbjct: 61 DAARETVALVDSLGDQGPRILDASTAHRVAEGWTYGFPELAKGQSDAIRTARRVSNPGCY 120 Query: 118 PTGFLALVRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFEDGSEPTGFRAYGLDLEH 177 TG +AL+RPLV AGLI PD+ + SGYSGGGK+MIA++E G P F AY L LEH Sbjct: 121 ATGAIALLRPLVDAGLISPDFSIAIHAVSGYSGGGKAMIADYESGHAP-AFEAYALGLEH 179 Query: 178 KHLPEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDS 237 KH+PE+Q++AR+D P+F P+V +GML+ PL L LP P A ++ +A Y Sbjct: 180 KHVPEIQRYARLDRRPVFTPSVGNFAQGMLVCAPLFLDELPGWPKAADLKAAIAAHYAAR 239 Query: 238 PIVRVLPSDDVSLVRIEDDAGTDRLTIRVFGNAERGQARLVATLDNLGKGAGGAAVQNLN 297 VR++ ++ + E GT+ L +RVF N Q LVA LDNLGKGA GAA+QNL Sbjct: 240 QYVRLVEAEPSGRIEPEALNGTNDLELRVFANEAYRQVVLVAKLDNLGKGASGAALQNLK 299 Query: 298 IM 299 +M Sbjct: 300 LM 301 Lambda K H 0.319 0.136 0.400 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: 272 Number of extensions: 14 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: 310 Length of database: 309 Length adjustment: 27 Effective length of query: 283 Effective length of database: 282 Effective search space: 79806 Effective search space used: 79806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_026606927.1 METAC_RS0110060 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
# 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/TIGR01851.hmm # target sequence database: /tmp/gapView.29471.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01851 [M=310] Accession: TIGR01851 Description: argC_other: N-acetyl-gamma-glutamyl-phosphate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-117 378.2 0.0 1.9e-117 377.9 0.0 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026606927.1 METAC_RS0110060 N-acetyl-gamma-g Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026606927.1 METAC_RS0110060 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 377.9 0.0 1.9e-117 1.9e-117 2 308 .. 3 302 .. 2 304 .. 0.96 Alignments for each domain: == domain 1 score: 377.9 bits; conditional E-value: 1.9e-117 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd 70 k+fidGeaGttGl i rla+ +e +s++++ rkd++++ ll +dv++lclpddaare+v+lvd lcl|NCBI__GCF_000427445.1:WP_026606927.1 3 AKIFIDGEAGTTGLGIAARLAGEPGVERVSLAPELRKDPEAKKALLAGVDVVVLCLPDDAARETVALVD 71 59******************************************************************9 PP TIGR01851 71 n...pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPad 136 + +ildasta+r+ae+w+yGfpela +q + i+ a+rv+nPGcyatgaiallrPlv+aG++ d lcl|NCBI__GCF_000427445.1:WP_026606927.1 72 SlgdQGPRILDASTAHRVAEGWTYGFPELAKGQSDAIRTARRVSNPGCYATGAIALLRPLVDAGLISPD 140 73324579************************************************************* PP TIGR01851 137 fPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdf 205 f ++i+avsGysGGGka+ia+ye s +++ af +y+l lehkh+pe++++++l ++P+ftP+vG+f lcl|NCBI__GCF_000427445.1:WP_026606927.1 141 FSIAIHAVSGYSGGGKAMIADYE--SGHAP---AFEAYALGLEHKHVPEIQRYARLDRRPVFTPSVGNF 204 ***********************..55555...89********************************** PP TIGR01851 206 aqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfv 274 aqG+lv pl l el + + a+d+++a+a +y+ +++v+++e++ + +++++lngtn lel v lcl|NCBI__GCF_000427445.1:WP_026606927.1 205 AQGMLVCAPLFLDELPGWPKAADLKAAIAAHYAARQYVRLVEAEPSG-----RIEPEALNGTNDLELRV 268 ****************************************9987665.....679************** PP TIGR01851 275 fgsddgerallvarldnlGkGasGaavqnlnial 308 f++++ ++++lva+ldnlGkGasGaa+qnl+++l lcl|NCBI__GCF_000427445.1:WP_026606927.1 269 FANEAYRQVVLVAKLDNLGKGASGAALQNLKLML 302 ********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (309 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: 00:00:00.01 # Mc/sec: 8.74 // [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