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 CA265_RS03610 CA265_RS03610 imidazole glycerol phosphate synthase subunit HisF
Query= SwissProt::Q7SIB9 (252 letters) >FitnessBrowser__Pedo557:CA265_RS03610 Length = 379 Score = 278 bits (710), Expect = 2e-79 Identities = 143/250 (57%), Positives = 179/250 (71%), Gaps = 1/250 (0%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 L+KRI+PCLDV GR VKGVNFV+LRDAGDPVE A Y + GADELVFLDI+ATHE R Sbjct: 130 LSKRIIPCLDVKDGRTVKGVNFVDLRDAGDPVELAAQYAQQGADELVFLDITATHERRKT 189 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 ++++V VA ++ IP T+GGG+ + DA LL +GADK+S+NSAAVR P+LI +LA FG Sbjct: 190 MIEMVKSVARQLNIPFTIGGGITEIADAEALLNAGADKISINSAAVRNPKLIEDLAKTFG 249 Query: 123 AQAVVLAIDARWRGDFPEVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDGTKEG 182 Q VVLA+D ++ VH+ GGR+ T L W + +LGAGEILLTSMD DGTK G Sbjct: 250 VQFVVLAVDTKYVDGKNMVHLNGGRLITELETENWIKQAEDLGAGEILLTSMDHDGTKAG 309 Query: 183 YDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQ-AGAEAALAASVFHFGEIPIPKLKRY 241 +D L V + + +P+IASGGAG M HF E FQ A +AALAASVFH+GEI IP LK+ Sbjct: 310 FDCGLLSKVNQMINIPIIASGGAGNMAHFTEVFQKANVDAALAASVFHYGEILIPDLKQE 369 Query: 242 LAEKGVHVRL 251 L + VR+ Sbjct: 370 LKRNNIPVRI 379 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: 268 Number of extensions: 13 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: 252 Length of database: 379 Length adjustment: 27 Effective length of query: 225 Effective length of database: 352 Effective search space: 79200 Effective search space used: 79200 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: 48 (23.1 bits)
Align candidate CA265_RS03610 CA265_RS03610 (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.17424.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-108 348.3 0.7 1.4e-108 348.0 0.7 1.1 1 lcl|FitnessBrowser__Pedo557:CA265_RS03610 CA265_RS03610 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS03610 CA265_RS03610 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 348.0 0.7 1.4e-108 1.4e-108 2 254 .] 130 378 .. 129 378 .. 0.99 Alignments for each domain: == domain 1 score: 348.0 bits; conditional E-value: 1.4e-108 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 l+kriipCLdvkdgr vkGv+f +lrdaGdpvela++y+++Gadelvfldita++e+r+tm+e+v+ v lcl|FitnessBrowser__Pedo557:CA265_RS03610 130 LSKRIIPCLDVKDGRTVKGVNFVDLRDAGDPVELAAQYAQQGADELVFLDITATHERRKTMIEMVKSV 197 89****************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaen 137 a+++ iP+t+gGGi +i+d++ ll+aGadk+sin+aav++p+li++la++fG+q +v+a+d+k++ lcl|FitnessBrowser__Pedo557:CA265_RS03610 198 ARQLNIPFTIGGGITEIADAEALLNAGADKISINSAAVRNPKLIEDLAKTFGVQFVVLAVDTKYVDG- 264 ***************************************************************9875. PP TIGR00735 138 eeakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPvias 205 k v+ +gGr t+l++ +w+k++e+lGaGeilltsmd+dGtk+G+d ll kv++ ++iP+ias lcl|FitnessBrowser__Pedo557:CA265_RS03610 265 ---KNMVHLNGGRLITELETENWIKQAEDLGAGEILLTSMDHDGTKAGFDCGLLSKVNQMINIPIIAS 329 ...5689************************************************************* PP TIGR00735 206 gGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 gGaG++ h++e+f+k+++daaLaasvfh++e+ i ++k+ l+ ++++vr lcl|FitnessBrowser__Pedo557:CA265_RS03610 330 GGAGNMAHFTEVFQKANVDAALAASVFHYGEILIPDLKQELKRNNIPVR 378 ***********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (379 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: 9.97 // [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