Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate WP_028310933.1 H566_RS0107350 N-formylglutamate deformylase
Query= reanno::acidovorax_3H11:Ac3H11_2548 (270 letters) >NCBI__GCF_000482785.1:WP_028310933.1 Length = 267 Score = 315 bits (808), Expect = 5e-91 Identities = 153/263 (58%), Positives = 187/263 (71%), Gaps = 2/263 (0%) Query: 1 MTTTPPP-FTFHQGTAPLLVSMPHAGTYVPPVLAARFTDEARQVPDTDWHMERLYAFAKD 59 MTT P ++ +GT PLL+S+PH GT +P + A+ TDE V DTDWH++ LYAFA+ Sbjct: 1 MTTLDTPIYSLKRGTRPLLISIPHLGTRIPDEVRAQLTDEGPIVADTDWHLDTLYAFAEA 60 Query: 60 MGASILVATHSRYVVDLNRPPDGASLYPGQSVTGLCPVDTFDDTPIYAQGDVPDDAEVAA 119 MGASIL A SRY +DLNRP DG SLYPGQ+ TGLCP +TF +Y G PD AE A Sbjct: 61 MGASILGAKVSRYAIDLNRPADGQSLYPGQTTTGLCPTETFKGVHLYPAGKEPDAAETAR 120 Query: 120 RRDAVWAPYHAQLRAELSRIRAQHGVAVLWDAHSIRSVLPRFFEGKLPDLNLGTADGASC 179 R DA W PYH L+ ELSR++A+HG VLW+AHSI S+LPR F+GKLPD N GTADG SC Sbjct: 121 RLDAYWKPYHGALQDELSRLKAEHGQVVLWEAHSIASILPRLFDGKLPDFNFGTADGRSC 180 Query: 180 DPALAQALLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYMQEALP 239 + A+LA P +T V NGRFKGGHITR YG P++ +HA+QLEM QC YM E +P Sbjct: 181 GAGVIGAVLAALDGTP-FTHVHNGRFKGGHITRAYGNPSEGVHAIQLEMCQCIYMDEEVP 239 Query: 240 FDYLPEVAAEVQPHLERLLEAAL 262 F Y P++A +VQP LER+L AAL Sbjct: 240 FGYRPDLAVKVQPWLERMLAAAL 262 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: 259 Number of extensions: 8 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: 270 Length of database: 267 Length adjustment: 25 Effective length of query: 245 Effective length of database: 242 Effective search space: 59290 Effective search space used: 59290 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 WP_028310933.1 H566_RS0107350 (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.14156.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-107 345.3 0.0 1.4e-107 345.0 0.0 1.0 1 lcl|NCBI__GCF_000482785.1:WP_028310933.1 H566_RS0107350 N-formylglutamate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_028310933.1 H566_RS0107350 N-formylglutamate deformylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 345.0 0.0 1.4e-107 1.4e-107 3 258 .. 9 262 .. 7 264 .. 0.98 Alignments for each domain: == domain 1 score: 345.0 bits; conditional E-value: 1.4e-107 TIGR02017 3 levqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidv 71 ++++rG+ Pllis+Ph Gt+++d+v+++l+++ +++dtdWh++ ly+fa+ +Ga+++ a++sr+ id+ lcl|NCBI__GCF_000482785.1:WP_028310933.1 9 YSLKRGTRPLLISIPHLGTRIPDEVRAQLTDEGPIVADTDWHLDTLYAFAEAMGASILGAKVSRYAIDL 77 7899***************************************************************** PP TIGR02017 72 nrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgk 140 nr+ +g+slypgq+ttgl+P++tf g ly +G++P++ae ++rl+ y+kPyh al++e+ rl+a hg+ lcl|NCBI__GCF_000482785.1:WP_028310933.1 78 NRPADGQSLYPGQTTTGLCPTETFKGVHLYPAGKEPDAAETARRLDAYWKPYHGALQDELSRLKAEHGQ 146 ********************************************************************* PP TIGR02017 141 ivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhy 209 +vl++ahsi+s +Prlf+GklPdfn Gt dg+sc ++ av a+++ + +++v nGrfkGG+itr y lcl|NCBI__GCF_000482785.1:WP_028310933.1 147 VVLWEAHSIASILPRLFDGKLPDFNFGTADGRSCGAGVIGAVLAALD-GTPFTHVHNGRFKGGHITRAY 214 ***********************************************.9******************** PP TIGR02017 210 gqPqngvhavqlelaqrgyleeetePvaydeakaealravlkelleall 258 g+P++gvha+qle++q y++ e +P+ y+++ a +++ l+++l a+l lcl|NCBI__GCF_000482785.1:WP_028310933.1 215 GNPSEGVHAIQLEMCQCIYMD-EEVPFGYRPDLAVKVQPWLERMLAAAL 262 *********************.899********************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (267 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.23 // [ok]
This GapMind analysis is from Sep 24 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