Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate N515DRAFT_3769 N515DRAFT_3769 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Dyella79:N515DRAFT_3769 (319 letters) >FitnessBrowser__Dyella79:N515DRAFT_3769 Length = 319 Score = 640 bits (1650), Expect = 0.0 Identities = 319/319 (100%), Positives = 319/319 (100%) Query: 1 MSIDKKTIGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVAEHVDGYAGELRYA 60 MSIDKKTIGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVAEHVDGYAGELRYA Sbjct: 1 MSIDKKTIGIVGARGHTGAELIRLIATHPALELGFVSSRELDGQRVAEHVDGYAGELRYA 60 Query: 61 NLDPAAVAAQGADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFNERWYYGLPEL 120 NLDPAAVAAQGADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFNERWYYGLPEL Sbjct: 61 NLDPAAVAAQGADVVVLALPNGKAAPYVEAIDAAKPETLILDLSADYRFNERWYYGLPEL 120 Query: 121 TRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAPPVSFGVSGYSGAGTTPSDKNNPEKL 180 TRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAPPVSFGVSGYSGAGTTPSDKNNPEKL Sbjct: 121 TRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAPPVSFGVSGYSGAGTTPSDKNNPEKL 180 Query: 181 RDNLMPYSLTGHTHEQEASRHLGLPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQRF 240 RDNLMPYSLTGHTHEQEASRHLGLPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQRF Sbjct: 181 RDNLMPYSLTGHTHEQEASRHLGLPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQRF 240 Query: 241 RHAYDGEKLVKVVDEAPWVSQIAHRHHAEVGGFAVSVDGKRVVIVATLDNLLKGAATQAI 300 RHAYDGEKLVKVVDEAPWVSQIAHRHHAEVGGFAVSVDGKRVVIVATLDNLLKGAATQAI Sbjct: 241 RHAYDGEKLVKVVDEAPWVSQIAHRHHAEVGGFAVSVDGKRVVIVATLDNLLKGAATQAI 300 Query: 301 QNINRAIGVDEYTSIPLEG 319 QNINRAIGVDEYTSIPLEG Sbjct: 301 QNINRAIGVDEYTSIPLEG 319 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: 505 Number of extensions: 8 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: 319 Length adjustment: 28 Effective length of query: 291 Effective length of database: 291 Effective search space: 84681 Effective search space used: 84681 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 N515DRAFT_3769 N515DRAFT_3769 (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.17102.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-96 307.3 0.0 3.7e-95 305.0 0.0 1.8 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 N515DRAFT_3769 N-acetyl-gamma-gl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 N515DRAFT_3769 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 305.0 0.0 3.7e-95 3.7e-95 2 340 .. 7 317 .. 6 319 .] 0.95 Alignments for each domain: == domain 1 score: 305.0 bits; conditional E-value: 3.7e-95 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvd.lkleeleeeeil 65 +++ivGa+G+tGaeL+rl+a+Hp++e+ +vssre g++++e+++ + g+++ ++l++ +++ + lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 7 TIGIVGARGHTGAELIRLIATHPALELG-FVSSRElDGQRVAEHVDGYAGELRyANLDPAAVA--A 69 699************************9.9999999***************998899988777..6 PP TIGR01850 66 eeadvvflAlphgvsaelvpellekg..vkvidlSadfRlkdaevYekwYgkkhekeelleeavYG 129 + advv+lAlp+g +a++v+++ +++ + ++dlSad+R+++ +++YG lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 70 QGADVVVLALPNGKAAPYVEAIDAAKpeTLILDLSADYRFNE-------------------RWYYG 116 79******************998855459************4...................478** PP TIGR01850 130 lpElnreeikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfae 195 lpEl+r + ++ ++i+nPGCyaTa++L++aPl + + ++ +++sG+SgAG+++s+k++ ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 117 LPELTRGKWRGERRISNPGCYATAIQLSIAPLKDVLAAP---PVSFGVSGYSGAGTTPSDKNNPEK 179 ********************************8655443...69********************** PP TIGR01850 196 vnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrkl 261 +++nl+pY++t+H H++E +++l+ v+f+ph++p++rG++ t+++ l +++++ee+ + lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 180 LRDNLMPYSLTGHTHEQEASRHLG------LPVEFMPHVAPHFRGLTVTTNLYLVRPMKREEILQR 239 ************************......78********************************** PP TIGR01850 262 yeevYedepfvrvlkegelPstkavlgsnfvdig.vavdeetkrvvvvsaiDNLvKGaagqAvqnl 326 ++++Y++e++v+v++ e+P+++++++++++++g +av + krvv+v+++DNL+KGaa+qA+qn+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 240 FRHAYDGEKLVKVVD--EAPWVSQIAHRHHAEVGgFAVSVDGKRVVIVATLDNLLKGAATQAIQNI 303 **************9..9***************99******************************* PP TIGR01850 327 NlmlgfdetegLek 340 N ++g de+++++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3769 304 NRAIGVDEYTSIPL 317 **********9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (319 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 2.12 // [ok]
This GapMind analysis is from Apr 09 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