Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate Ac3H11_2548 N-formylglutamate deformylase (EC 3.5.1.68)
Query= reanno::acidovorax_3H11:Ac3H11_2548 (270 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2548 Length = 270 Score = 553 bits (1425), Expect = e-162 Identities = 270/270 (100%), Positives = 270/270 (100%) Query: 1 MTTTPPPFTFHQGTAPLLVSMPHAGTYVPPVLAARFTDEARQVPDTDWHMERLYAFAKDM 60 MTTTPPPFTFHQGTAPLLVSMPHAGTYVPPVLAARFTDEARQVPDTDWHMERLYAFAKDM Sbjct: 1 MTTTPPPFTFHQGTAPLLVSMPHAGTYVPPVLAARFTDEARQVPDTDWHMERLYAFAKDM 60 Query: 61 GASILVATHSRYVVDLNRPPDGASLYPGQSVTGLCPVDTFDDTPIYAQGDVPDDAEVAAR 120 GASILVATHSRYVVDLNRPPDGASLYPGQSVTGLCPVDTFDDTPIYAQGDVPDDAEVAAR Sbjct: 61 GASILVATHSRYVVDLNRPPDGASLYPGQSVTGLCPVDTFDDTPIYAQGDVPDDAEVAAR 120 Query: 121 RDAVWAPYHAQLRAELSRIRAQHGVAVLWDAHSIRSVLPRFFEGKLPDLNLGTADGASCD 180 RDAVWAPYHAQLRAELSRIRAQHGVAVLWDAHSIRSVLPRFFEGKLPDLNLGTADGASCD Sbjct: 121 RDAVWAPYHAQLRAELSRIRAQHGVAVLWDAHSIRSVLPRFFEGKLPDLNLGTADGASCD 180 Query: 181 PALAQALLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYMQEALPF 240 PALAQALLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYMQEALPF Sbjct: 181 PALAQALLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYMQEALPF 240 Query: 241 DYLPEVAAEVQPHLERLLEAALAFAAARRK 270 DYLPEVAAEVQPHLERLLEAALAFAAARRK Sbjct: 241 DYLPEVAAEVQPHLERLLEAALAFAAARRK 270 Lambda K H 0.321 0.135 0.416 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: 366 Number of extensions: 5 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: 270 Length of database: 270 Length adjustment: 25 Effective length of query: 245 Effective length of database: 245 Effective search space: 60025 Effective search space used: 60025 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate Ac3H11_2548 (N-formylglutamate deformylase (EC 3.5.1.68))
to HMM TIGR02017 (hutG: N-formylglutamate deformylase (EC 3.5.1.68))
# 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.carbon/TIGR02017.hmm # target sequence database: /tmp/gapView.4596.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02017 [M=263] Accession: TIGR02017 Description: hutG_amidohyd: N-formylglutamate deformylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-116 374.0 0.0 2.3e-116 373.8 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2548 N-formylglutamate deformylase (E Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2548 N-formylglutamate deformylase (EC 3.5.1.68) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.8 0.0 2.3e-116 2.3e-116 4 262 .. 9 266 .. 6 267 .. 0.99 Alignments for each domain: == domain 1 score: 373.8 bits; conditional E-value: 2.3e-116 TIGR02017 4 evqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraais 65 ++++G+aPll+s+Ph+Gt +++ +++r++++a+++ dtdWh+e+ly+fa+d+Ga+++ a+ s lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2548 9 TFHQGTAPLLVSMPHAGTYVPPVLAARFTDEARQVPDTDWHMERLYAFAKDMGASILVATHS 70 799*********************************************************** PP TIGR02017 66 rlvidvnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaal 127 r+v+d+nr+p+gaslypgq+ tgl+P +tfd++p+y +G+ P++ae++ r++ ++ Pyha+l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2548 71 RYVVDLNRPPDGASLYPGQSVTGLCPVDTFDDTPIYAQGDVPDDAEVAARRDAVWAPYHAQL 132 ************************************************************** PP TIGR02017 128 raeierlralhgkivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcaka 189 rae+ r+ra+hg++vl+dahsirsv+Pr+feGklPd+nlGt dg+scdpala+a+ a+++ a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2548 133 RAELSRIRAQHGVAVLWDAHSIRSVLPRFFEGKLPDLNLGTADGASCDPALAQALLAIAQSA 194 ************************************************************** PP TIGR02017 190 kglssvlnGrfkGGyitrhygqPqngvhavqlelaqrgyleeetePvaydeakaealravlk 251 g++ vlnGrfkGG+itrhygqP++++havqle++q +y++ e+ P+ y ++ a++++ +l+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2548 195 PGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYMQ-EALPFDYLPEVAAEVQPHLE 255 *****************************************.******************** PP TIGR02017 252 ellealldfae 262 +llea+l+fa+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2548 256 RLLEAALAFAA 266 *********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (270 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.63 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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