Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_051955467.1 DL88_RS01890 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000745425.1:WP_051955467.1 Length = 265 Score = 335 bits (859), Expect = 6e-97 Identities = 166/250 (66%), Positives = 201/250 (80%), Gaps = 1/250 (0%) Query: 3 LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62 L R+IPCLDV DGRVVKGVNF DL DAGDPV+ A YDAAGADELCFLDI+ASHE R Sbjct: 2 LKARVIPCLDVKDGRVVKGVNFVDLRDAGDPVQCAMAYDAAGADELCFLDITASHEDRSI 61 Query: 63 MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122 + DVV RTAE CFMPLTVGGGVR +D R LLLAGADKV++ SAAV + V A++FG Sbjct: 62 LFDVVERTAEACFMPLTVGGGVRTEDDIRKLLLAGADKVSIMSAAVTDRDFVRRAAEKFG 121 Query: 123 AQCVVAAIDARRNG-DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRD 181 +QCVV AIDA+ G WEV+THGGR+PTGI+A+ +A ++ GAGEILLTSMD+DGT+ Sbjct: 122 SQCVVVAIDAKATGPGRWEVFTHGGRKPTGIDAIAYARDVAERGAGEILLTSMDRDGTKA 181 Query: 182 GYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHE 241 G+DL LTR VA+SVP+PVIASGGVG LDH+VEG+ +G A A+LAASIFHFG +++AEA + Sbjct: 182 GFDLALTRAVAESVPIPVIASGGVGTLDHLVEGIAQGGADAVLAASIFHFGTFTIAEAKD 241 Query: 242 ALAKAGLTVR 251 +A+ GL +R Sbjct: 242 YMARHGLPMR 251 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: 273 Number of extensions: 9 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: 255 Length of database: 265 Length adjustment: 24 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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_051955467.1 DL88_RS01890 (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.27346.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-110 352.8 0.9 5.1e-110 352.7 0.9 1.0 1 lcl|NCBI__GCF_000745425.1:WP_051955467.1 DL88_RS01890 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_051955467.1 DL88_RS01890 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 352.7 0.9 5.1e-110 5.1e-110 1 254 [] 1 251 [. 1 251 [. 0.99 Alignments for each domain: == domain 1 score: 352.7 bits; conditional E-value: 5.1e-110 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 ml r+ipCLdvkdgrvvkGv+f +lrdaGdpv+ a +yd+ Gadel flditas+e+r+++ +vver+ lcl|NCBI__GCF_000745425.1:WP_051955467.1 1 MLKARVIPCLDVKDGRVVKGVNFVDLRDAGDPVQCAMAYDAAGADELCFLDITASHEDRSILFDVVERT 69 7899***************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae f+PltvgGG+++ +d++kll aGadkvsi +aav++ ++++++a++fGsq++vvaidak + lcl|NCBI__GCF_000745425.1:WP_051955467.1 70 AEACFMPLTVGGGVRTEDDIRKLLLAGADKVSIMSAAVTDRDFVRRAAEKFGSQCVVVAIDAKATGP-- 136 ***************************************************************9886.. PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 + +ev ++gGr+ t++d++++a++v+e+GaGeilltsmd+dGtk+G+dl+l+++v+e+v iPviasgG lcl|NCBI__GCF_000745425.1:WP_051955467.1 137 -GRWEVFTHGGRKPTGIDAIAYARDVAERGAGEILLTSMDRDGTKAGFDLALTRAVAESVPIPVIASGG 204 .69****************************************************************** PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 +G+ +hl e++++g ada+Laas+fh++ +ti e k+y+a +g+++r lcl|NCBI__GCF_000745425.1:WP_051955467.1 205 VGTLDHLVEGIAQGGADAVLAASIFHFGTFTIAEAKDYMARHGLPMR 251 ********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (265 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: 6.85 // [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