Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate 8501585 DvMF_2304 imidazole glycerol phosphate synthase subunit HisF (RefSeq)
Query= SwissProt::Q7SIB9 (252 letters) >FitnessBrowser__Miya:8501585 Length = 259 Score = 255 bits (652), Expect = 5e-73 Identities = 132/256 (51%), Positives = 178/256 (69%), Gaps = 7/256 (2%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 L+KRI+PCLDV GR+ KGV F D GDPVE AR Y E GADE+VF DI+A+HE+R I Sbjct: 2 LSKRIIPCLDVRNGRLTKGVKFEGNVDIGDPVETARRYYEQGADEIVFYDITASHEDRGI 61 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 LDVV RVA +FIP +VGGG+ ++ED R +L++GA+KVSVNS AV+ P++I + A FG Sbjct: 62 FLDVVERVASEIFIPFSVGGGINTVEDMRAVLVAGAEKVSVNSGAVKNPDIISQGAAAFG 121 Query: 123 AQAVVLAIDARWRGDFP------EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDR 176 +QA+V+ +D + E+ + GGR G+ A+EWA LGAGE+ + S+D Sbjct: 122 SQAIVVGMDVKQVQKSEAIPSGYEIVIHGGRKFMGMDAIEWAKTCEALGAGELCVNSIDA 181 Query: 177 DGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAF-QAGAEAALAASVFHFGEIPI 235 DGTK+GY+L LTRM+A+AV +PVIASGGAG H +A + GA AAL AS+ H+G+ I Sbjct: 182 DGTKDGYELTLTRMIADAVSIPVIASGGAGSPAHMYDAITRGGATAALIASIVHYGQYTI 241 Query: 236 PKLKRYLAEKGVHVRL 251 P LKR ++ G +R+ Sbjct: 242 PDLKRQISGMGAKLRM 257 Lambda K H 0.321 0.138 0.398 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: 239 Number of extensions: 12 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: 252 Length of database: 259 Length adjustment: 24 Effective length of query: 228 Effective length of database: 235 Effective search space: 53580 Effective search space used: 53580 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate 8501585 DvMF_2304 (imidazole glycerol phosphate synthase subunit HisF (RefSeq))
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.17633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-107 342.9 2.0 5.6e-107 342.7 2.0 1.0 1 lcl|FitnessBrowser__Miya:8501585 DvMF_2304 imidazole glycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501585 DvMF_2304 imidazole glycerol phosphate synthase subunit HisF (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 342.7 2.0 5.6e-107 5.6e-107 1 254 [] 1 256 [. 1 256 [. 0.98 Alignments for each domain: == domain 1 score: 342.7 bits; conditional E-value: 5.6e-107 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPl 77 ml+kriipCLdv++gr++kGv+f+ d+Gdpve a++y+e+Gade+vf+ditas+e+r + l+vverva ++fiP+ lcl|FitnessBrowser__Miya:8501585 1 MLSKRIIPCLDVRNGRLTKGVKFEGNVDIGDPVETARRYYEQGADEIVFYDITASHEDRGIFLDVVERVASEIFIPF 77 89*************************************************************************** PP TIGR00735 78 tvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaenee..akyevtikgGres 152 +vgGGi+++ed++ +l aGa+kvs+n+ avk+p++i++ a fGsqaivv++d k+++++e+ + ye++i+gGr+ lcl|FitnessBrowser__Miya:8501585 78 SVGGGINTVEDMRAVLVAGAEKVSVNSGAVKNPDIISQGAAAFGSQAIVVGMDVKQVQKSEAipSGYEIVIHGGRKF 154 **********************************************************9988889************ PP TIGR00735 153 tdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaa 229 ++d++ewak +e+lGaGe+ ++s+d+dGtk+Gy+l+l++ +++av+iPviasgGaG++ h+++a+++g a aaL a lcl|FitnessBrowser__Miya:8501585 155 MGMDAIEWAKTCEALGAGELCVNSIDADGTKDGYELTLTRMIADAVSIPVIASGGAGSPAHMYDAITRGGATAALIA 231 ***************************************************************************** PP TIGR00735 230 svfhkreltieevkeylaergvkvr 254 s++h++++ti ++k+ + g k+r lcl|FitnessBrowser__Miya:8501585 232 SIVHYGQYTIPDLKRQISGMGAKLR 256 ***************9998887776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (259 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.55 // [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