Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate GFF908 PGA1_c09240 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__Phaeo:GFF908 Length = 253 Score = 343 bits (880), Expect = 2e-99 Identities = 171/250 (68%), Positives = 206/250 (82%), Gaps = 1/250 (0%) Query: 3 LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62 L TRIIPCLDVADGRVVKGVNF L DAGDPVE AK YDAAGADE+CFLDI A+HE RGT Sbjct: 2 LKTRIIPCLDVADGRVVKGVNFVGLRDAGDPVEAAKAYDAAGADEICFLDIHATHENRGT 61 Query: 63 MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122 M D+V RTAE CF+PLTVGGGVR ED RALLLAGADKV+ NSAAVA P+++ E AD+FG Sbjct: 62 MFDMVRRTAEQCFVPLTVGGGVRTKEDVRALLLAGADKVSFNSAAVANPDVIREAADQFG 121 Query: 123 AQCVVAAIDARRNG-DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRD 181 +QC V AIDA+ WE++THGGRR TGI+A++ A + GAGEILLTSMD+DGT+ Sbjct: 122 SQCTVCAIDAKTVAPGKWEIFTHGGRRETGIDAVEFARLVVAKGAGEILLTSMDRDGTKS 181 Query: 182 GYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHE 241 G++L LTR ++D+V VPVIASGGVG LDH+VEGVT+G ASA+LAASIFHFG++++ EA + Sbjct: 182 GFNLPLTRAISDAVDVPVIASGGVGTLDHLVEGVTEGGASAVLAASIFHFGEFTVQEAKQ 241 Query: 242 ALAKAGLTVR 251 +A AG+ +R Sbjct: 242 HMAAAGIPMR 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: 294 Number of extensions: 8 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: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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 GFF908 PGA1_c09240 (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.20489.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-108 346.6 1.3 4e-108 346.5 1.3 1.0 1 lcl|FitnessBrowser__Phaeo:GFF908 PGA1_c09240 imidazole glycerol p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF908 PGA1_c09240 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 346.5 1.3 4e-108 4e-108 1 254 [] 1 251 [. 1 251 [. 0.99 Alignments for each domain: == domain 1 score: 346.5 bits; conditional E-value: 4e-108 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPl 77 ml riipCLdv dgrvvkGv+f lrdaGdpve ak+yd+ Gade+ fldi a++e+r tm ++v+r+ae+ f+Pl lcl|FitnessBrowser__Phaeo:GFF908 1 MLKTRIIPCLDVADGRVVKGVNFVGLRDAGDPVEAAKAYDAAGADEICFLDIHATHENRGTMFDMVRRTAEQCFVPL 77 7999************************************************************************* PP TIGR00735 78 tvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtikgGrestd 154 tvgGG+++ edv+ ll aGadkvs n+aav++p++i+e+ad+fGsq+ v aidak++a +k+e+ ++gGr++t+ lcl|FitnessBrowser__Phaeo:GFF908 78 TVGGGVRTKEDVRALLLAGADKVSFNSAAVANPDVIREAADQFGSQCTVCAIDAKTVAP---GKWEIFTHGGRRETG 151 *******************************************************9997...69************* PP TIGR00735 155 ldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasv 231 +d+ve+a+ v ++GaGeilltsmd+dGtksG++l l++++++av++PviasgG+G+ +hl e++++g a a+Laas+ lcl|FitnessBrowser__Phaeo:GFF908 152 IDAVEFARLVVAKGAGEILLTSMDRDGTKSGFNLPLTRAISDAVDVPVIASGGVGTLDHLVEGVTEGGASAVLAASI 228 ***************************************************************************** PP TIGR00735 232 fhkreltieevkeylaergvkvr 254 fh++e+t++e k+++a+ g+++r lcl|FitnessBrowser__Phaeo:GFF908 229 FHFGEFTVQEAKQHMAAAGIPMR 251 ********************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (253 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: 6.01 // [ok]
This GapMind analysis is from Apr 09 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