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 WP_012676316.1 PERMA_RS04305 imidazole glycerol phosphate synthase cyclase subunit
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_000021565.1:WP_012676316.1 Length = 252 Score = 327 bits (838), Expect = 1e-94 Identities = 172/251 (68%), Positives = 204/251 (81%), Gaps = 2/251 (0%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 LAKRI+PCLDV+ GRVVKGVNFVNL DAGDPVEAA+AYDEAGADELVFLDI+A+ EER I Sbjct: 2 LAKRIIPCLDVNKGRVVKGVNFVNLVDAGDPVEAAKAYDEAGADELVFLDITASAEERDI 61 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 +LDVV + AE VF+PLTVGGGVRSLED RKLL SGADKVS+N+AAV+ P L+ A FG Sbjct: 62 ILDVVKQTAETVFMPLTVGGGVRSLEDVRKLLESGADKVSINTAAVKNPSLVESAAVRFG 121 Query: 123 AQAVVLAIDARWRG-DFPEVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDGTKE 181 + +V+AIDA+ G D EV++ GGR TG+ AVEWA +LGAGEILLTSMDRDGTK Sbjct: 122 SSTIVVAIDAKRTGKDRWEVYINGGRTATGIDAVEWAKAVEDLGAGEILLTSMDRDGTKN 181 Query: 182 GYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIPIPKLKR 240 GYD+ LTR ++EAV +PVIASGGAG+ E F +AF G A+AALAAS+FHF E+ I +LK Sbjct: 182 GYDIALTRAISEAVSIPVIASGGAGKKEDFYDAFTEGKADAALAASLFHFKELTIGELKE 241 Query: 241 YLAEKGVHVRL 251 +L EKG+ VRL Sbjct: 242 FLKEKGIPVRL 252 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: 252 Number of extensions: 11 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: 252 Length adjustment: 24 Effective length of query: 228 Effective length of database: 228 Effective search space: 51984 Effective search space used: 51984 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: 46 (22.3 bits)
Align candidate WP_012676316.1 PERMA_RS04305 (imidazole glycerol phosphate synthase cyclase subunit)
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.3108.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-124 398.0 2.3 8.6e-124 397.8 2.3 1.0 1 lcl|NCBI__GCF_000021565.1:WP_012676316.1 PERMA_RS04305 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021565.1:WP_012676316.1 PERMA_RS04305 imidazole glycerol phosphate synthase cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 397.8 2.3 8.6e-124 8.6e-124 1 254 [] 1 251 [. 1 251 [. 0.99 Alignments for each domain: == domain 1 score: 397.8 bits; conditional E-value: 8.6e-124 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 mlakriipCLdv++grvvkGv+f nl daGdpve ak+yde Gadelvflditas+e+r+++l+vv+++ lcl|NCBI__GCF_000021565.1:WP_012676316.1 1 MLAKRIIPCLDVNKGRVVKGVNFVNLVDAGDPVEAAKAYDEAGADELVFLDITASAEERDIILDVVKQT 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae+vf+PltvgGG++s+edv+kll++Gadkvsintaavk+p l++ +a rfGs +ivvaidakr+ + lcl|NCBI__GCF_000021565.1:WP_012676316.1 70 AETVFMPLTVGGGVRSLEDVRKLLESGADKVSINTAAVKNPSLVESAAVRFGSSTIVVAIDAKRTGKD- 137 ****************************************************************9975. PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 +ev+i+gGr+ t++d+vewak+ve+lGaGeilltsmd+dGtk+Gyd++l+++++eav+iPviasgG lcl|NCBI__GCF_000021565.1:WP_012676316.1 138 --RWEVYINGGRTATGIDAVEWAKAVEDLGAGEILLTSMDRDGTKNGYDIALTRAISEAVSIPVIASGG 204 ..8****************************************************************** PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 aGk+e +++af++gkadaaLaas+fh++elti+e+ke+l+e+g++vr lcl|NCBI__GCF_000021565.1:WP_012676316.1 205 AGKKEDFYDAFTEGKADAALAASLFHFKELTIGELKEFLKEKGIPVR 251 **********************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (252 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.76 // [ok]
This GapMind analysis is from Apr 10 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