Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate RR42_RS18885 RR42_RS18885 imidazole glycerol phosphate synthase
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS18885 Length = 256 Score = 298 bits (763), Expect = 7e-86 Identities = 146/254 (57%), Positives = 194/254 (76%), Gaps = 5/254 (1%) Query: 3 LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62 L RIIPCLDV +GRVVKGVNF +L DAGDPVE A+ YD GADE+ FLDI+A+ +GR Sbjct: 2 LAKRIIPCLDVTNGRVVKGVNFVELRDAGDPVEIARRYDEQGADEITFLDITATSDGRDL 61 Query: 63 MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122 +L ++ A F+PLTVGGGVR VED R LL AGADK++VNS+A+A P+LV++ R+G Sbjct: 62 ILHIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISVNSSAIANPQLVSDATARYG 121 Query: 123 AQCVVAAIDARRNG-----DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKD 177 +QC+V AIDA+R+ WEV+THGGR+ TG++A+ A + GAGE+LLTSMD+D Sbjct: 122 SQCIVVAIDAKRSSAPGEPARWEVFTHGGRKATGLDAVAWAREMAARGAGELLLTSMDRD 181 Query: 178 GTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLA 237 GT+ G+DLELTR V+D+V VPVIASGGVG+L + +G+ GHA A+LAASIFH+G++++ Sbjct: 182 GTKSGFDLELTRAVSDAVSVPVIASGGVGSLKDLADGIKLGHADAVLAASIFHYGEHTVG 241 Query: 238 EAHEALAKAGLTVR 251 EA +A+ G+ VR Sbjct: 242 EAKAFMAREGIPVR 255 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: 248 Number of extensions: 10 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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 RR42_RS18885 RR42_RS18885 (imidazole glycerol phosphate synthase)
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.702.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-116 373.0 0.5 3.5e-116 372.9 0.5 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS18885 RR42_RS18885 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS18885 RR42_RS18885 imidazole glycerol phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.9 0.5 3.5e-116 3.5e-116 1 254 [] 1 255 [. 1 255 [. 0.99 Alignments for each domain: == domain 1 score: 372.9 bits; conditional E-value: 3.5e-116 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 mlakriipCLdv++grvvkGv+f +lrdaGdpve+a++yde+Gade++fldita+s++r+ +l+++e v lcl|FitnessBrowser__Cup4G11:RR42_RS18885 1 MLAKRIIPCLDVTNGRVVKGVNFVELRDAGDPVEIARRYDEQGADEITFLDITATSDGRDLILHIIEAV 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 a +vfiPltvgGG++ +edv++ll+aGadk+s+n++a+++p+l+++++ r+Gsq+ivvaidakr+ lcl|FitnessBrowser__Cup4G11:RR42_RS18885 70 ASQVFIPLTVGGGVRAVEDVRRLLNAGADKISVNSSAIANPQLVSDATARYGSQCIVVAIDAKRSSAPG 138 ***************************************************************998754 PP TIGR00735 139 e.akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasg 206 e a +ev ++gGr+ t+ld+v+wa+e++++GaGe+lltsmd+dGtksG+dlel+++v++av++Pviasg lcl|FitnessBrowser__Cup4G11:RR42_RS18885 139 EpARWEVFTHGGRKATGLDAVAWAREMAARGAGELLLTSMDRDGTKSGFDLELTRAVSDAVSVPVIASG 207 449****************************************************************** PP TIGR00735 207 GaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 G+G+ + l++++ g+ada+Laas+fh++e t++e k+++a +g++vr lcl|FitnessBrowser__Cup4G11:RR42_RS18885 208 GVGSLKDLADGIKLGHADAVLAASIFHYGEHTVGEAKAFMAREGIPVR 255 ***********************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (256 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: 00:00:00.00 # Mc/sec: 9.64 // [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