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_086508673.1 BZY95_RS03890 imidazole glycerol phosphate synthase subunit HisF
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_002151265.1:WP_086508673.1 Length = 257 Score = 309 bits (791), Expect = 4e-89 Identities = 154/257 (59%), Positives = 200/257 (77%), Gaps = 6/257 (2%) Query: 1 MSLAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEER 60 M LAKRI+PCLDV AGRVVKGVNF+ +RDAGDPVE A+ Y+ GADE+ FLDI+A+HE+R Sbjct: 1 MGLAKRIIPCLDVDAGRVVKGVNFIGIRDAGDPVEIAQRYNLQGADEITFLDITASHEDR 60 Query: 61 AILLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADH 120 +++V R+A VFIPLTVGGG+R+ +D R +L +GADKVS+N+AAV P+ +RE A+ Sbjct: 61 DTTVEMVERIAGEVFIPLTVGGGIRTCDDIRTMLNAGADKVSINTAAVTNPDFVREAAER 120 Query: 121 FGAQAVVLAIDAR---WRGDFP--EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMD 175 FG+Q +V+AIDA+ G+ P E+ GGR PTGL AVEWA K VE GAGE+LLTSMD Sbjct: 121 FGSQCIVVAIDAKRVSTEGETPRWEIFTHGGRRPTGLDAVEWAKKMVEYGAGELLLTSMD 180 Query: 176 RDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLE-AFQAGAEAALAASVFHFGEIP 234 RDGTK G+DL +TR +++AV VPVIASGG G ++H + + GA+A LAAS+FHFGE Sbjct: 181 RDGTKAGFDLGVTRAISDAVTVPVIASGGVGNLDHLVAGVLEGGADAVLAASIFHFGEYT 240 Query: 235 IPKLKRYLAEKGVHVRL 251 IP+ KRY+AE+G+ +RL Sbjct: 241 IPEAKRYMAERGIEMRL 257 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: 255 Number of extensions: 11 Number of successful extensions: 5 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: 257 Length adjustment: 24 Effective length of query: 228 Effective length of database: 233 Effective search space: 53124 Effective search space used: 53124 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_086508673.1 BZY95_RS03890 (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.27027.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-118 380.8 0.7 1.5e-118 380.6 0.7 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508673.1 BZY95_RS03890 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508673.1 BZY95_RS03890 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.6 0.7 1.5e-118 1.5e-118 1 254 [] 2 256 .. 2 256 .. 0.98 Alignments for each domain: == domain 1 score: 380.6 bits; conditional E-value: 1.5e-118 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 +lakriipCLdv++grvvkGv+f +rdaGdpve+a++y+ +Gade++flditas+e+r+t +e+ver+ lcl|NCBI__GCF_002151265.1:WP_086508673.1 2 GLAKRIIPCLDVDAGRVVKGVNFIGIRDAGDPVEIAQRYNLQGADEITFLDITASHEDRDTTVEMVERI 70 59******************************************************************* PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreae.n 137 a +vfiPltvgGGi++ +d++++l+aGadkvsintaav++p++++e+a+rfGsq+ivvaidakr+ + lcl|NCBI__GCF_002151265.1:WP_086508673.1 71 AGEVFIPLTVGGGIRTCDDIRTMLNAGADKVSINTAAVTNPDFVREAAERFGSQCIVVAIDAKRVSTeG 139 ***************************************************************986515 PP TIGR00735 138 eeakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasg 206 e +e+ ++gGr+ t+ld+vewak++ e GaGe+lltsmd+dGtk+G+dl +++++++av++Pviasg lcl|NCBI__GCF_002151265.1:WP_086508673.1 140 ETPRWEIFTHGGRRPTGLDAVEWAKKMVEYGAGELLLTSMDRDGTKAGFDLGVTRAISDAVTVPVIASG 208 679****************************************************************** PP TIGR00735 207 GaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 G+G+ +hl ++l+g ada+Laas+fh++e+ti e k+y+aerg+++r lcl|NCBI__GCF_002151265.1:WP_086508673.1 209 GVGNLDHLVAGVLEGGADAVLAASIFHFGEYTIPEAKRYMAERGIEMR 256 **********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (257 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: 00:00:00.01 # Mc/sec: 6.38 // [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