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_048061292.1 MTH_RS06415 imidazole glycerol phosphate synthase cyclase subunit
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_000008645.1:WP_048061292.1 Length = 274 Score = 263 bits (671), Expect = 4e-75 Identities = 146/273 (53%), Positives = 183/273 (67%), Gaps = 24/273 (8%) Query: 3 LAKRIVPCLD----VHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHE 58 LAKRI+PCLD V GRVVKGV F +R AGDPVE A Y E GADE+VFLDI+A+HE Sbjct: 2 LAKRIIPCLDCDLQVPNGRVVKGVEFKQIRYAGDPVELATRYYEDGADEIVFLDITASHE 61 Query: 59 ERAILLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELA 118 R + V+ E VF+P+ VGGG+R ED K+L +GADK S N+AA++ PELI E + Sbjct: 62 RRETMTHVIEATTENVFVPICVGGGIRKPEDYFKMLKAGADKCSTNTAAIKNPELINEAS 121 Query: 119 DHFGAQAVVLAIDARWR-------GD------------FPEVHVAGGRVPTGLHAVEWAV 159 D G+QA V+AIDA+ R D + E + GGR TG+ AV+WA+ Sbjct: 122 DLVGSQACVVAIDAKRRYIENPRESDERFIIEVDDGYCWYECSIYGGREFTGIDAVKWAM 181 Query: 160 KGVELGAGEILLTSMDRDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG- 218 + + GAGEILLTSMDRDGTK GYD+ LTR ++E + +PVIASGG G EH EAF G Sbjct: 182 ECQDRGAGEILLTSMDRDGTKMGYDIPLTRTMSENLDIPVIASGGVGEPEHIYEAFTDGK 241 Query: 219 AEAALAASVFHFGEIPIPKLKRYLAEKGVHVRL 251 A+AALAAS+FHF E P+P +K YL +GV +RL Sbjct: 242 ADAALAASIFHFNEYPVPAVKEYLRSRGVPIRL 274 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: 232 Number of extensions: 12 Number of successful extensions: 6 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: 274 Length adjustment: 25 Effective length of query: 227 Effective length of database: 249 Effective search space: 56523 Effective search space used: 56523 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 WP_048061292.1 MTH_RS06415 (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.28216.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-126 406.5 0.0 2.2e-126 406.3 0.0 1.0 1 lcl|NCBI__GCF_000008645.1:WP_048061292.1 MTH_RS06415 imidazole glycerol p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008645.1:WP_048061292.1 MTH_RS06415 imidazole glycerol phosphate synthase cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.3 0.0 2.2e-126 2.2e-126 1 254 [] 1 273 [. 1 273 [. 0.99 Alignments for each domain: == domain 1 score: 406.3 bits; conditional E-value: 2.2e-126 TIGR00735 1 mlakriipCLdvkd....grvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlev 65 mlakriipCLd++ grvvkGv+fk++r+aGdpvela++y+e+Gade+vflditas+e+retm++v lcl|NCBI__GCF_000008645.1:WP_048061292.1 1 MLAKRIIPCLDCDLqvpnGRVVKGVEFKQIRYAGDPVELATRYYEDGADEIVFLDITASHERRETMTHV 69 8**********9988899*************************************************** PP TIGR00735 66 vervaekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakre 134 +e ++e+vf+P++vgGGi++ ed+ k+l+aGadk+s+ntaa+k+peli+e++d +Gsqa+vvaidakr+ lcl|NCBI__GCF_000008645.1:WP_048061292.1 70 IEATTENVFVPICVGGGIRKPEDYFKMLKAGADKCSTNTAAIKNPELINEASDLVGSQACVVAIDAKRR 138 ********************************************************************* PP TIGR00735 135 aenee...............akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydl 188 + ++ ++ye++i+gGre t++d+v+wa+e++++GaGeilltsmd+dGtk+Gyd+ lcl|NCBI__GCF_000008645.1:WP_048061292.1 139 YIENPresderfiievddgyCWYECSIYGGREFTGIDAVKWAMECQDRGAGEILLTSMDRDGTKMGYDI 207 *9766999************************************************************* PP TIGR00735 189 ellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 l+++++e+++iPviasgG+G++eh++eaf++gkadaaLaas+fh++e+ + vkeyl++rgv++r lcl|NCBI__GCF_000008645.1:WP_048061292.1 208 PLTRTMSENLDIPVIASGGVGEPEHIYEAFTDGKADAALAASIFHFNEYPVPAVKEYLRSRGVPIR 273 ****************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (274 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: 7.58 // [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