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_028950472.1 Q385_RS0104230 imidazole glycerol phosphate synthase subunit HisF
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_000619805.1:WP_028950472.1 Length = 252 Score = 316 bits (810), Expect = 3e-91 Identities = 163/251 (64%), Positives = 203/251 (80%), Gaps = 2/251 (0%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 LAKRI+PCLDV+ GRVVKGVNFVNL DAGDPVE A AYD+ GADE+VFLDI+A+ E+R I Sbjct: 2 LAKRIIPCLDVNKGRVVKGVNFVNLIDAGDPVEIAAAYDKEGADEIVFLDITASAEDRDI 61 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 +LDVV + AE VF+PLTVGGGVRSLED RKLL +GADKVS+N+AAV+ P L+ A FG Sbjct: 62 ILDVVKKTAETVFMPLTVGGGVRSLEDIRKLLENGADKVSINTAAVKNPSLVESAAVRFG 121 Query: 123 AQAVVLAIDARWRGDFP-EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDGTKE 181 + +V+AIDA+ + EV++ GGR PTG+ AV+WA +LGAGEILLTSMD+DGTK Sbjct: 122 SSTIVVAIDAKKIDENKWEVYINGGRTPTGIDAVQWAKAVEDLGAGEILLTSMDKDGTKS 181 Query: 182 GYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIPIPKLKR 240 GYD+ LT+ V+EAV +PVIASGGAG+ EHF E F+ G A+AALAAS+FHF E+ I +LK+ Sbjct: 182 GYDVELTKAVSEAVKIPVIASGGAGKKEHFYEVFEEGKADAALAASLFHFKEVGIKELKQ 241 Query: 241 YLAEKGVHVRL 251 +L EK V+VR+ Sbjct: 242 FLKEKNVNVRI 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: 241 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: 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_028950472.1 Q385_RS0104230 (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.13585.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-123 396.4 4.4 2.5e-123 396.3 4.4 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028950472.1 Q385_RS0104230 imidazole glycero Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028950472.1 Q385_RS0104230 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 396.3 4.4 2.5e-123 2.5e-123 1 254 [] 1 251 [. 1 251 [. 0.99 Alignments for each domain: == domain 1 score: 396.3 bits; conditional E-value: 2.5e-123 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 mlakriipCLdv++grvvkGv+f nl daGdpve+a++yd+eGade+vflditas+e+r+++l+vv+++ lcl|NCBI__GCF_000619805.1:WP_028950472.1 1 MLAKRIIPCLDVNKGRVVKGVNFVNLIDAGDPVEIAAAYDKEGADEIVFLDITASAEDRDIILDVVKKT 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae+vf+PltvgGG++s+ed++kll+ Gadkvsintaavk+p l++ +a rfGs +ivvaidak+ en lcl|NCBI__GCF_000619805.1:WP_028950472.1 70 AETVFMPLTVGGGVRSLEDIRKLLENGADKVSINTAAVKNPSLVESAAVRFGSSTIVVAIDAKKIDEN- 137 ***************************************************************98775. PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 k+ev+i+gGr+ t++d+v+wak+ve+lGaGeilltsmdkdGtksGyd+el+k+v+eavkiPviasgG lcl|NCBI__GCF_000619805.1:WP_028950472.1 138 --KWEVYINGGRTPTGIDAVQWAKAVEDLGAGEILLTSMDKDGTKSGYDVELTKAVSEAVKIPVIASGG 204 ..9****************************************************************** PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 aGk+eh++e+f +gkadaaLaas+fh++e+ i+e+k++l+e++v+vr lcl|NCBI__GCF_000619805.1:WP_028950472.1 205 AGKKEHFYEVFEEGKADAALAASLFHFKEVGIKELKQFLKEKNVNVR 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 8.11 // [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