Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_057687249.1 ABB28_RS15365 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Dyella79:N515DRAFT_3769 (319 letters) >NCBI__GCF_001431535.1:WP_057687249.1 Length = 317 Score = 440 bits (1132), Expect = e-128 Identities = 214/316 (67%), Positives = 257/316 (81%) Query: 1 MSIDKKTIGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVAEHVDGYAGELRYA 60 M++ T+GIVGARGHTGAELI+L+A HP L+L FVSSRE GQR+A+H GE++Y Sbjct: 1 MNVKTFTLGIVGARGHTGAELIKLVAAHPNLQLAFVSSRERAGQRLADHHPEITGEVQYE 60 Query: 61 NLDPAAVAAQGADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFNERWYYGLPEL 120 NLD AVAA+G D V+LALPNG AAP+V A+++A+P+T+I+DLSADYRF WYYGLPEL Sbjct: 61 NLDADAVAAKGVDAVILALPNGLAAPFVAALESARPDTVIVDLSADYRFEGSWYYGLPEL 120 Query: 121 TRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAPPVSFGVSGYSGAGTTPSDKNNPEKL 180 TR ++ GE+ ISNPGCYATA+QL+I PL D+LA PP FGVSGYSGAGTTPSDKNNPE L Sbjct: 121 TRTQYNGEKHISNPGCYATAMQLAIHPLLDLLAGPPQCFGVSGYSGAGTTPSDKNNPELL 180 Query: 181 RDNLMPYSLTGHTHEQEASRHLGLPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQRF 240 DNLMPY+LT H HE+E S HL +PVEFMPHVAPHFRG+T+T NL+L + RE+I RF Sbjct: 181 ADNLMPYALTNHVHEREVSAHLRVPVEFMPHVAPHFRGITMTVNLWLNQVQTREQIAARF 240 Query: 241 RHAYDGEKLVKVVDEAPWVSQIAHRHHAEVGGFAVSVDGKRVVIVATLDNLLKGAATQAI 300 AY E LV VVD+APWVS+IA RH +VGGF V+ GKRVV+VATLDNLLKGAATQA+ Sbjct: 241 ADAYAAEPLVDVVDDAPWVSRIAGRHGVQVGGFTVAPGGKRVVVVATLDNLLKGAATQAM 300 Query: 301 QNINRAIGVDEYTSIP 316 QN+N A+G+DE TSIP Sbjct: 301 QNLNLALGIDELTSIP 316 Lambda K H 0.318 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: 351 Number of extensions: 9 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: 319 Length of database: 317 Length adjustment: 27 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_057687249.1 ABB28_RS15365 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01850 (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/TIGR01850.hmm # target sequence database: /tmp/gapView.3677429.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01850 [M=345] Accession: TIGR01850 Description: argC: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-101 325.2 0.0 2e-100 322.3 0.0 1.8 1 NCBI__GCF_001431535.1:WP_057687249.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001431535.1:WP_057687249.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 322.3 0.0 2e-100 2e-100 2 339 .. 7 316 .. 6 317 .] 0.95 Alignments for each domain: == domain 1 score: 322.3 bits; conditional E-value: 2e-100 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvd.lkleeleeeeileeadvvf 72 +++ivGa+G+tGaeL++l+a+Hp+++++ +vssre ag++l+++hp+++g+v+ ++l++ +++ ++ +d+v+ NCBI__GCF_001431535.1:WP_057687249.1 7 TLGIVGARGHTGAELIKLVAAHPNLQLA-FVSSRErAGQRLADHHPEITGEVQyENLDADAVA--AKGVDAVI 76 579*************************.8888888****************98888876665..679***** PP TIGR01850 73 lAlphgvsaelvpellekg..vkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkakl 143 lAlp+g +a++v++l +++ ++++dlSad+R++ +++YGlpEl+r ++++ k NCBI__GCF_001431535.1:WP_057687249.1 77 LALPNGLAAPFVAALESARpdTVIVDLSADYRFEG-------------------SWYYGLPELTRTQYNGEKH 130 ************999885445*************3...................489**************** PP TIGR01850 144 ianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieq 216 i+nPGCyaTa++La++Pll+ + p+ ++++sG+SgAG+++s+k++ + +++nl+pY++t+H H++E+++ NCBI__GCF_001431535.1:WP_057687249.1 131 ISNPGCYATAMQLAIHPLLDLLAGPPQ---CFGVSGYSGAGTTPSDKNNPELLADNLMPYALTNHVHEREVSA 200 *******************99999998...******************************************* PP TIGR01850 217 elsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgs 289 +l+ v v+f+ph++p++rGi++t++++l++ t+e++++ ++++Y+ ep+v+v++ ++P++++++g+ NCBI__GCF_001431535.1:WP_057687249.1 201 HLR------VPVEFMPHVAPHFRGITMTVNLWLNQVQTREQIAARFADAYAAEPLVDVVD--DAPWVSRIAGR 265 ***......88************************************************9..9********** PP TIGR01850 290 nfvdig.vavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLe 339 + v++g ++v+ krvvvv+++DNL+KGaa+qA+qnlNl+lg de ++++ NCBI__GCF_001431535.1:WP_057687249.1 266 HGVQVGgFTVAPGGKRVVVVATLDNLLKGAATQAMQNLNLALGIDELTSIP 316 *****99****************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (317 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: 00:00:00.00 # Mc/sec: 11.72 // [ok]
This GapMind analysis is from Jul 25 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