Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate WP_078429927.1 BK574_RS20715 imidazole glycerol phosphate synthase subunit HisF
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_002019605.1:WP_078429927.1 Length = 252 Score = 281 bits (718), Expect = 1e-80 Identities = 149/251 (59%), Positives = 184/251 (73%), Gaps = 3/251 (1%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 L KRI+PCLDV GRVVKGV FVNLRDAGDPVE A YDE GADELVFLDISA+HE R Sbjct: 2 LTKRIIPCLDVKEGRVVKGVQFVNLRDAGDPVELAAFYDEQGADELVFLDISASHEGRET 61 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 +++VV VA ++ IP TVGGG+ SL D +++L +GADKVS+N+AAV RPELI E AD+FG Sbjct: 62 MVEVVEEVAGKLAIPFTVGGGINSLADMKRVLRAGADKVSLNTAAVNRPELITEGADYFG 121 Query: 123 AQAVVLAIDARWRGDFP--EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDGTK 180 +Q +V+AIDA++ + V+ GGR PT VEWA + V GAGEILLTSMD+DG K Sbjct: 122 SQCIVVAIDAKYDEELSSWRVYTHGGRTPTDWEVVEWAQEAVRRGAGEILLTSMDQDGEK 181 Query: 181 EGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAF-QAGAEAALAASVFHFGEIPIPKLK 239 G+DL LT+ V V VPVIASGGAG E F + F + +AALAAS+FH+ E + ++K Sbjct: 182 TGFDLPLTKAVNAVVTVPVIASGGAGAKECFYDVFTETKCDAALAASIFHYKETSVAEVK 241 Query: 240 RYLAEKGVHVR 250 L EKGV +R Sbjct: 242 SLLKEKGVPMR 252 Lambda K H 0.321 0.138 0.398 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: 239 Number of extensions: 10 Number of successful extensions: 4 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: 252 Length of database: 252 Length adjustment: 24 Effective length of query: 228 Effective length of database: 228 Effective search space: 51984 Effective search space used: 51984 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: 46 (22.3 bits)
Align candidate WP_078429927.1 BK574_RS20715 (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.1325.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-122 394.2 0.4 1.2e-122 394.1 0.4 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078429927.1 BK574_RS20715 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078429927.1 BK574_RS20715 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.1 0.4 1.2e-122 1.2e-122 1 254 [] 1 252 [] 1 252 [] 0.99 Alignments for each domain: == domain 1 score: 394.1 bits; conditional E-value: 1.2e-122 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 ml+kriipCLdvk+grvvkGvqf nlrdaGdpvela+ yde+Gadelvfldi+as+e+retm+evve+v lcl|NCBI__GCF_002019605.1:WP_078429927.1 1 MLTKRIIPCLDVKEGRVVKGVQFVNLRDAGDPVELAAFYDEQGADELVFLDISASHEGRETMVEVVEEV 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 a k++iP+tvgGGi+s++d+k++lraGadkvs+ntaav++peli+e ad fGsq+ivvaidak+++e lcl|NCBI__GCF_002019605.1:WP_078429927.1 70 AGKLAIPFTVGGGINSLADMKRVLRAGADKVSLNTAAVNRPELITEGADYFGSQCIVVAIDAKYDEEL- 137 ****************************************************************9987. PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 ++++v+++gGr+ td++vvewa+e+ ++GaGeilltsmd+dG+k+G+dl l+k+v+ +v++PviasgG lcl|NCBI__GCF_002019605.1:WP_078429927.1 138 -SSWRVYTHGGRTPTDWEVVEWAQEAVRRGAGEILLTSMDQDGEKTGFDLPLTKAVNAVVTVPVIASGG 205 .79****************************************************************** PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 aG++e ++++f+++k daaLaas+fh++e+++ evk+ l+e+gv++r lcl|NCBI__GCF_002019605.1:WP_078429927.1 206 AGAKECFYDVFTETKCDAALAASIFHYKETSVAEVKSLLKEKGVPMR 252 ********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (252 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: 10.45 // [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