Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate AO353_12285 AO353_12285 N-formylglutamate deformylase
Query= reanno::pseudo3_N2E3:AO353_12285 (266 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12285 Length = 266 Score = 546 bits (1408), Expect = e-160 Identities = 266/266 (100%), Positives = 266/266 (100%) Query: 1 VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPEAKSLPDTDWHIPTLYEFAAELGAS 60 VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPEAKSLPDTDWHIPTLYEFAAELGAS Sbjct: 1 VDKVLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPEAKSLPDTDWHIPTLYEFAAELGAS 60 Query: 61 TLAAEYSRFVIDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERASYLEKV 120 TLAAEYSRFVIDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERASYLEKV Sbjct: 61 TLAAEYSRFVIDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERASYLEKV 120 Query: 121 WTPYHSTLQQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPQLA 180 WTPYHSTLQQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPQLA Sbjct: 121 WTPYHSTLQQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPQLA 180 Query: 181 SQLEAICARHTDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEVEPFRYRP 240 SQLEAICARHTDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEVEPFRYRP Sbjct: 181 SQLEAICARHTDYSHVLNGRFKGGHITRHYGNPAENIHAVQLELGQCTYMEEVEPFRYRP 240 Query: 241 DLAAPTQVVLKELLQGLLAWGQKHYA 266 DLAAPTQVVLKELLQGLLAWGQKHYA Sbjct: 241 DLAAPTQVVLKELLQGLLAWGQKHYA 266 Lambda K H 0.320 0.137 0.420 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: 432 Number of extensions: 7 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: 266 Length of database: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate AO353_12285 AO353_12285 (N-formylglutamate deformylase)
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.8034.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-123 395.6 0.0 5.7e-123 395.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_12285 AO353_12285 N-formylglutamate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_12285 AO353_12285 N-formylglutamate deformylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 395.5 0.0 5.7e-123 5.7e-123 2 262 .. 4 262 .. 3 263 .. 0.99 Alignments for each domain: == domain 1 score: 395.5 bits; conditional E-value: 5.7e-123 TIGR02017 2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisr 66 +l++++G++Pllis+Ph+G++lt+ave++l +ak+l dtdWhi ly+fa +lGa++++a++sr lcl|FitnessBrowser__pseudo3_N2E3:AO353_12285 4 VLNFKQGRVPLLISMPHAGVRLTPAVEAGLIPEAKSLPDTDWHIPTLYEFAAELGASTLAAEYSR 68 799************************************************************** PP TIGR02017 67 lvidvnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraei 131 +vid+nr+ +++++y+g attgl+P+t+fdg pl+++G +Ps++e++++l+k++ Pyh++l++e+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_12285 69 FVIDLNRPSDDKPMYVG-ATTGLYPATLFDGVPLFREGLEPSAEERASYLEKVWTPYHSTLQQEL 132 *****************.*********************************************** PP TIGR02017 132 erlralhgkivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvl 196 +rl+a +g+++l+dahsirsviP+lf+GklPdfnlGt++g+scdp la+++ea+ca+ + +s+vl lcl|FitnessBrowser__pseudo3_N2E3:AO353_12285 133 ARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPQLASQLEAICARHTDYSHVL 197 ***************************************************************** PP TIGR02017 197 nGrfkGGyitrhygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkellealldfa 261 nGrfkGG+itrhyg+P++++havqlel q +y+e e+eP+ y+++ a+++++vlkell+ ll+++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_12285 198 NGRFKGGHITRHYGNPAENIHAVQLELGQCTYME-EVEPFRYRPDLAAPTQVVLKELLQGLLAWG 261 *********************************9.*****************************9 PP TIGR02017 262 e 262 + lcl|FitnessBrowser__pseudo3_N2E3:AO353_12285 262 Q 262 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (266 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: 00:00:00.03 # Mc/sec: 2.19 // [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