Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate HSERO_RS20315 HSERO_RS20315 imidazole glycerol phosphate synthase
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS20315 Length = 254 Score = 311 bits (796), Expect = 1e-89 Identities = 152/252 (60%), Positives = 197/252 (78%), Gaps = 1/252 (0%) Query: 1 MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60 M L RIIPCLDV GRVVKGVNF +L DAGDPVE A+ YD GADEL FLDI+AS +GR Sbjct: 1 MALAKRIIPCLDVTAGRVVKGVNFLELRDAGDPVEIARRYDEQGADELTFLDITASSDGR 60 Query: 61 GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120 +LD++ A F+PLTVGGGVR VED R LL AGADKV +N++AV P+LVA+ A + Sbjct: 61 DLILDIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKVGINTSAVTNPQLVADAASK 120 Query: 121 FGAQCVVAAIDARRNGD-HWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGT 179 +G+QC+V AIDA+R GD WEVYTHGGR+ TG++A++ A + +LGAGEILLTSMD+DGT Sbjct: 121 YGSQCIVVAIDAKRAGDGKWEVYTHGGRKATGLDAVEWARKMAQLGAGEILLTSMDRDGT 180 Query: 180 RDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEA 239 + G+DL+LTR V+++V +PVIASGGVG L + +G+TKG A A+LAASIFH+GQ+++ EA Sbjct: 181 KSGFDLDLTRAVSEAVSIPVIASGGVGGLQDLADGITKGKADAVLAASIFHYGQHTVQEA 240 Query: 240 HEALAKAGLTVR 251 +A +++R Sbjct: 241 KRFMADQNISMR 252 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: 254 Number of extensions: 13 Number of successful extensions: 4 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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 HSERO_RS20315 HSERO_RS20315 (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.30412.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-117 376.5 2.7 3.1e-117 376.3 2.7 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS20315 HSERO_RS20315 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS20315 HSERO_RS20315 imidazole glycerol phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 376.3 2.7 3.1e-117 3.1e-117 2 254 .] 3 252 .. 2 252 .. 0.99 Alignments for each domain: == domain 1 score: 376.3 bits; conditional E-value: 3.1e-117 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 lakriipCLdv++grvvkGv+f +lrdaGdpve+a++yde+Gadel+flditass++r+ +l+++e v lcl|FitnessBrowser__HerbieS:HSERO_RS20315 3 LAKRIIPCLDVTAGRVVKGVNFLELRDAGDPVEIARRYDEQGADELTFLDITASSDGRDLILDIIEAV 70 9******************************************************************* PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaen 137 a +vfiPltvgGG++ +edv++ll+aGadkv int+av++p+l++++a ++Gsq+ivvaidakr + lcl|FitnessBrowser__HerbieS:HSERO_RS20315 71 ASQVFIPLTVGGGVRAVEDVRRLLNAGADKVGINTSAVTNPQLVADAASKYGSQCIVVAIDAKRAGD- 137 ****************************************************************987. PP TIGR00735 138 eeakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPvias 205 +k+ev+++gGr+ t+ld+vewa+++++lGaGeilltsmd+dGtksG+dl l+++v+eav+iPvias lcl|FitnessBrowser__HerbieS:HSERO_RS20315 138 --GKWEVYTHGGRKATGLDAVEWARKMAQLGAGEILLTSMDRDGTKSGFDLDLTRAVSEAVSIPVIAS 203 ..69**************************************************************** PP TIGR00735 206 gGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 gG+G + l+++++kgkada+Laas+fh+++ t++e k+++a++++++r lcl|FitnessBrowser__HerbieS:HSERO_RS20315 204 GGVGGLQDLADGITKGKADAVLAASIFHYGQHTVQEAKRFMADQNISMR 252 **********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (254 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: 7.61 // [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