Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate PP_0293 PP_0293 Imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__Putida:PP_0293 Length = 256 Score = 308 bits (790), Expect = 5e-89 Identities = 152/256 (59%), Positives = 196/256 (76%), Gaps = 5/256 (1%) Query: 1 MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60 M L RIIPCLDV +GRVVKGV F ++ DAGDPVE A+ YD GADE+ FLDI+AS +GR Sbjct: 1 MALAKRIIPCLDVDNGRVVKGVKFENIRDAGDPVEIARRYDEQGADEITFLDITASVDGR 60 Query: 61 GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120 T L V R A F+PLTVGGGVR V+D R LL AGADKV++N+AAV PE V E ADR Sbjct: 61 DTTLHTVERMASQVFIPLTVGGGVRTVQDIRNLLNAGADKVSINTAAVFNPEFVGEAADR 120 Query: 121 FGAQCVVAAIDARR-----NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMD 175 FG+QC+V AIDA++ WE++THGGR+PTG++A++ A + LGAGEILLTSMD Sbjct: 121 FGSQCIVVAIDAKKVSGPGEAPRWEIFTHGGRKPTGLDAVEWAKKMEGLGAGEILLTSMD 180 Query: 176 KDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYS 235 +DG ++G+DL +TR ++D++ +PVIASGGVGNL H+ +G+ +GHASA+LAASIFHFG+Y+ Sbjct: 181 QDGMKNGFDLGVTRAISDALGIPVIASGGVGNLQHLADGILEGHASAVLAASIFHFGEYT 240 Query: 236 LAEAHEALAKAGLTVR 251 + EA +A G+ VR Sbjct: 241 VPEAKAYMASRGIVVR 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: 238 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: 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 PP_0293 PP_0293 (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.5699.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-118 380.1 0.4 2.6e-118 379.9 0.4 1.0 1 lcl|FitnessBrowser__Putida:PP_0293 PP_0293 Imidazole glycerol phosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_0293 PP_0293 Imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.9 0.4 2.6e-118 2.6e-118 2 254 .] 3 256 .] 2 256 .] 0.98 Alignments for each domain: == domain 1 score: 379.9 bits; conditional E-value: 2.6e-118 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiP 76 lakriipCLdv++grvvkGv+f+n+rdaGdpve+a++yde+Gade++flditas ++r+t l+ ver+a +vfiP lcl|FitnessBrowser__Putida:PP_0293 3 LAKRIIPCLDVDNGRVVKGVKFENIRDAGDPVEIARRYDEQGADEITFLDITASVDGRDTTLHTVERMASQVFIP 77 9************************************************************************** PP TIGR00735 77 ltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreae.neeakyevtikgGr 150 ltvgGG+++++d+++ll+aGadkvsintaav +pe++ e+adrfGsq+ivvaidak++ e+ +e+ ++gGr lcl|FitnessBrowser__Putida:PP_0293 78 LTVGGGVRTVQDIRNLLNAGADKVSINTAAVFNPEFVGEAADRFGSQCIVVAIDAKKVSGpGEAPRWEIFTHGGR 152 *******************************************************9987525779********** PP TIGR00735 151 estdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkada 225 + t+ld+vewak++e lGaGeilltsmd+dG+k+G+dl +++++++a+ iPviasgG+G+ +hl++++l+g+a a lcl|FitnessBrowser__Putida:PP_0293 153 KPTGLDAVEWAKKMEGLGAGEILLTSMDQDGMKNGFDLGVTRAISDALGIPVIASGGVGNLQHLADGILEGHASA 227 *************************************************************************** PP TIGR00735 226 aLaasvfhkreltieevkeylaergvkvr 254 +Laas+fh++e+t+ e k+y+a+rg+ vr lcl|FitnessBrowser__Putida:PP_0293 228 VLAASIFHFGEYTVPEAKAYMASRGIVVR 256 **************************998 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: 6.54 // [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