Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_029000584.1 H537_RS0128505 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000430725.1:WP_029000584.1 Length = 259 Score = 297 bits (761), Expect = 1e-85 Identities = 150/257 (58%), Positives = 193/257 (75%), Gaps = 8/257 (3%) Query: 3 LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62 L RIIPCLDV GRVVKGVNF +L DAGDPVE A Y+ GADEL FLDI+A+ +GR Sbjct: 2 LAKRIIPCLDVTGGRVVKGVNFVELRDAGDPVEIAARYNDQGADELTFLDITATSDGRDV 61 Query: 63 MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122 +L ++ A F+PLTVGGGVR VED R LL AGADKV+ NSAAVA P+++ + ++++G Sbjct: 62 ILHIIEAVASQVFIPLTVGGGVRTVEDVRRLLNAGADKVSFNSAAVANPQVIRDASEKYG 121 Query: 123 AQCVVAAIDARR--------NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSM 174 AQC+V AIDA+R G W+VYTHGGR+ G++A+ A + GAGEILLTSM Sbjct: 122 AQCIVVAIDAKRRQGDDLAARGPGWDVYTHGGRKNVGLDAVAWAKQMAEHGAGEILLTSM 181 Query: 175 DKDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQY 234 D+DGT+ G+DLELTR V+D+VPVPVIASGGVG L+H+ EG+ G A A+LAASIFH+G++ Sbjct: 182 DRDGTKIGFDLELTRAVSDAVPVPVIASGGVGALEHLSEGIRVGGADAVLAASIFHYGEF 241 Query: 235 SLAEAHEALAKAGLTVR 251 ++A+A LA+ G+ VR Sbjct: 242 TVAQAKALLARDGIPVR 258 Lambda K H 0.320 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: 258 Number of extensions: 13 Number of successful extensions: 3 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: 255 Length of database: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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 WP_029000584.1 H537_RS0128505 (imidazole glycerol phosphate synthase subunit HisF)
to HMM TIGR00735 (hisF: imidazoleglycerol phosphate synthase, cyclase subunit)
# 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/TIGR00735.hmm # target sequence database: /tmp/gapView.1669.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00735 [M=254] Accession: TIGR00735 Description: hisF: imidazoleglycerol phosphate synthase, cyclase subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-116 373.6 1.7 2.4e-116 373.4 1.7 1.0 1 lcl|NCBI__GCF_000430725.1:WP_029000584.1 H537_RS0128505 imidazole glycero Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_029000584.1 H537_RS0128505 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.4 1.7 2.4e-116 2.4e-116 1 254 [] 1 258 [. 1 258 [. 0.99 Alignments for each domain: == domain 1 score: 373.4 bits; conditional E-value: 2.4e-116 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 mlakriipCLdv+ grvvkGv+f +lrdaGdpve+a++y+++Gadel+fldita+s++r+++l+++e v lcl|NCBI__GCF_000430725.1:WP_029000584.1 1 MLAKRIIPCLDVTGGRVVKGVNFVELRDAGDPVEIAARYNDQGADELTFLDITATSDGRDVILHIIEAV 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 a +vfiPltvgGG++++edv++ll+aGadkvs n+aav++p++i+++++++G+q+ivvaidakr++ + lcl|NCBI__GCF_000430725.1:WP_029000584.1 70 ASQVFIPLTVGGGVRTVEDVRRLLNAGADKVSFNSAAVANPQVIRDASEKYGAQCIVVAIDAKRRQGDD 138 ****************************************************************99765 PP TIGR00735 139 e....akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPvi 203 ++v+++gGr++++ld+v+wak+++e GaGeilltsmd+dGtk G+dlel+++v++av +Pvi lcl|NCBI__GCF_000430725.1:WP_029000584.1 139 LaargPGWDVYTHGGRKNVGLDAVAWAKQMAEHGAGEILLTSMDRDGTKIGFDLELTRAVSDAVPVPVI 207 5888899************************************************************** PP TIGR00735 204 asgGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 asgG+G+ ehl e++ g ada+Laas+fh++e+t+ + k+ la g++vr lcl|NCBI__GCF_000430725.1:WP_029000584.1 208 ASGGVGALEHLSEGIRVGGADAVLAASIFHYGEFTVAQAKALLARDGIPVR 258 *************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (259 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: 00:00:00.00 # Mc/sec: 7.69 // [ok]
This GapMind analysis is from Apr 10 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