Align N-formylglutamate amidohydrolase (EC 3.5.1.68) (characterized)
to candidate AZOBR_RS23510 AZOBR_RS23510 N-formylglutamate amidohydrolase
Query= metacyc::MONOMER-11615 (267 letters) >FitnessBrowser__azobra:AZOBR_RS23510 Length = 266 Score = 293 bits (750), Expect = 3e-84 Identities = 140/263 (53%), Positives = 184/263 (69%), Gaps = 2/263 (0%) Query: 4 VLSFHQGRLPLLISMPHAGLRLSDAVRDGLVEEARSLPDTDWHIPQLYDFARDLGASVVA 63 V F R P+L+S+PH G L D LV EA+ LPDTDWH+P+LYDF DLG V+ Sbjct: 3 VFGFRAARRPVLVSLPHVGTALPDGFIGRLVPEAQGLPDTDWHLPRLYDFLEDLGVGVIQ 62 Query: 64 AEYSRFVIDLNRPDDDKPLYAGATTGLYPATLFEGEPLFKEGLAPSGEERKRYLEQIWRP 123 A +SR+V+DLNRP +D PLY+GATTGL P TLF+G PL++ G P E + + W P Sbjct: 63 ARFSRYVVDLNRPSNDTPLYSGATTGLCPTTLFDGAPLYQPGAEPDPGEVAERVTRYWTP 122 Query: 124 YHGTLRRELDRLREQFGYALLWDAHSIRSHIPHLFDGKLPDFNLGTFNGASCDPVLAERL 183 YH + E+ RLR++FG A+L+DAHSIRS +P LF+G+LPD N+GT +G S DPVL++RL Sbjct: 123 YHDAITAEMTRLRDRFGRAVLFDAHSIRSVVPRLFEGRLPDLNIGTNDGRSADPVLSDRL 182 Query: 184 QGVCAE--ATGYSHVLNGRFKGGHITRHYGDPAKHIHAVQLELAQSTYMEETEPFTYRED 241 V A+ A G++HVLNGRFKGGHITRH+G P++ HAVQLE+AQ TYMEE PF + E Sbjct: 183 VAVGADAGADGFTHVLNGRFKGGHITRHFGRPSEGWHAVQLEMAQVTYMEEDAPFAFDEA 242 Query: 242 LAQPTQVVLKQLLQALLAWGAER 264 A+ + L++ + A+ W ER Sbjct: 243 RAERIRPHLRRFIGAMADWAEER 265 Lambda K H 0.321 0.139 0.430 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: 306 Number of extensions: 20 Number of successful extensions: 2 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: 267 Length of database: 266 Length adjustment: 25 Effective length of query: 242 Effective length of database: 241 Effective search space: 58322 Effective search space used: 58322 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 AZOBR_RS23510 AZOBR_RS23510 (N-formylglutamate amidohydrolase)
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.6440.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-112 359.7 0.0 5.3e-112 359.5 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS23510 AZOBR_RS23510 N-formylglutamate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS23510 AZOBR_RS23510 N-formylglutamate amidohydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 359.5 0.0 5.3e-112 5.3e-112 4 263 .] 5 264 .. 2 264 .. 0.97 Alignments for each domain: == domain 1 score: 359.5 bits; conditional E-value: 5.3e-112 TIGR02017 4 evqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidvn 72 ++ + P+l+slPh Gt l+d rlv +a+ l dtdWh+ +lydf++dlG v++a++sr+v+d+n lcl|FitnessBrowser__azobra:AZOBR_RS23510 5 GFRAARRPVLVSLPHVGTALPDGFIGRLVPEAQGLPDTDWHLPRLYDFLEDLGVGVIQARFSRYVVDLN 73 5778899************************************************************** PP TIGR02017 73 rdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgki 141 r+ ++++ly+g attgl+P+t+fdg ply+ G +P++ e+++r+t+y+ Pyh+a+ ae+ rlr+ +g++ lcl|FitnessBrowser__azobra:AZOBR_RS23510 74 RPSNDTPLYSG-ATTGLCPTTLFDGAPLYQPGAEPDPGEVAERVTRYWTPYHDAITAEMTRLRDRFGRA 141 ***********.********************************************************* PP TIGR02017 142 vlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcak..akglssvlnGrfkGGyitrh 208 vl+dahsirsv+PrlfeG+lPd+n+Gtndg+s+dp+l+d+++av a a g+++vlnGrfkGG+itrh lcl|FitnessBrowser__azobra:AZOBR_RS23510 142 VLFDAHSIRSVVPRLFEGRLPDLNIGTNDGRSADPVLSDRLVAVGADagADGFTHVLNGRFKGGHITRH 210 *******************************************987522689***************** PP TIGR02017 209 ygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkellealldfaee 263 +g+P++g havqle+aq +y+e e P+a+dea+ae +r +l++++ a+ d+aee lcl|FitnessBrowser__azobra:AZOBR_RS23510 211 FGRPSEGWHAVQLEMAQVTYME-EDAPFAFDEARAERIRPHLRRFIGAMADWAEE 264 **********************.889***************************85 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.12 // [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