Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_020561661.1 A3OW_RS0101490 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000372865.1:WP_020561661.1 Length = 258 Score = 308 bits (789), Expect = 7e-89 Identities = 153/256 (59%), Positives = 194/256 (75%), Gaps = 5/256 (1%) Query: 1 MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60 M L RIIPCLDV +GRVVKGV F D+ DAGDPVE A+ YD GADEL FLDI+A+H+ R Sbjct: 1 MGLAKRIIPCLDVDNGRVVKGVKFLDIRDAGDPVEIARRYDREGADELTFLDITATHDDR 60 Query: 61 GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120 TM+ VV + A F+PLTVGGG+R ++D R +L AGADKV +NSAAVA PE V E A R Sbjct: 61 ETMVHVVEQVASEVFIPLTVGGGIRTLDDIRRMLNAGADKVGINSAAVANPEFVYEAAQR 120 Query: 121 FGAQCVVAAIDARR-----NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMD 175 FG+QC+V AIDA++ D WE++THGGR+PT I A+ A + GAGEILLTSMD Sbjct: 121 FGSQCIVVAIDAKKVSAGNEPDRWEIFTHGGRKPTDIEAVGWAQKMVAYGAGEILLTSMD 180 Query: 176 KDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYS 235 +DGTR+G+DL LTR ++++V VPVIASGGVG LDH+ EG+ +G A A+LAASIFHFG+Y+ Sbjct: 181 RDGTREGFDLALTRAISEAVTVPVIASGGVGCLDHLAEGILQGKADAVLAASIFHFGEYT 240 Query: 236 LAEAHEALAKAGLTVR 251 + +A + +A G+ VR Sbjct: 241 IRQAKQHMAARGIEVR 256 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: 241 Number of extensions: 6 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: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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_020561661.1 A3OW_RS0101490 (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.26286.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-120 387.1 1.5 1.8e-120 386.9 1.5 1.0 1 lcl|NCBI__GCF_000372865.1:WP_020561661.1 A3OW_RS0101490 imidazole glycero Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000372865.1:WP_020561661.1 A3OW_RS0101490 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 386.9 1.5 1.8e-120 1.8e-120 1 254 [] 2 256 .. 2 256 .. 0.98 Alignments for each domain: == domain 1 score: 386.9 bits; conditional E-value: 1.8e-120 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 +lakriipCLdv++grvvkGv+f ++rdaGdpve+a++yd+eGadel+fldita++++retm++vve+v lcl|NCBI__GCF_000372865.1:WP_020561661.1 2 GLAKRIIPCLDVDNGRVVKGVKFLDIRDAGDPVEIARRYDREGADELTFLDITATHDDRETMVHVVEQV 70 59******************************************************************* PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 a +vfiPltvgGGi++++d++++l+aGadkv in+aav++pe+++e+a+rfGsq+ivvaidak++ + lcl|NCBI__GCF_000372865.1:WP_020561661.1 71 ASEVFIPLTVGGGIRTLDDIRRMLNAGADKVGINSAAVANPEFVYEAAQRFGSQCIVVAIDAKKVSAGN 139 ***************************************************************998766 PP TIGR00735 139 e.akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasg 206 e +e+ ++gGr+ td+++v wa+++ + GaGeilltsmd+dGt++G+dl+l+++++eav++Pviasg lcl|NCBI__GCF_000372865.1:WP_020561661.1 140 EpDRWEIFTHGGRKPTDIEAVGWAQKMVAYGAGEILLTSMDRDGTREGFDLALTRAISEAVTVPVIASG 208 5489***************************************************************** PP TIGR00735 207 GaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 G+G +hl+e++l+gkada+Laas+fh++e+ti++ k+++a+rg++vr lcl|NCBI__GCF_000372865.1:WP_020561661.1 209 GVGCLDHLAEGILQGKADAVLAASIFHFGEYTIRQAKQHMAARGIEVR 256 ***********************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (258 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: 00:00:00.01 # Mc/sec: 6.20 // [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