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_084274989.1 B8779_RS02410 imidazole glycerol phosphate synthase subunit HisF
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_900176045.1:WP_084274989.1 Length = 254 Score = 301 bits (771), Expect = 9e-87 Identities = 154/249 (61%), Positives = 189/249 (75%), Gaps = 1/249 (0%) Query: 4 AKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAIL 63 AKRI+PCLDV GRVVKGVNFV L+DAGDPVE A+ Y+E GADE+ FLDI+AT+EER + Sbjct: 6 AKRIIPCLDVDKGRVVKGVNFVGLKDAGDPVEVAKRYNEEGADEITFLDITATYEERDTI 65 Query: 64 LDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFGA 123 + +V VA+ VFIPLTVGGG+R L+D LL G DKVS+NSAAV+ P+ + E A FG+ Sbjct: 66 VHIVEEVAKEVFIPLTVGGGIRELQDIYNLLAVGCDKVSINSAAVKNPDFVNEAAKRFGS 125 Query: 124 QAVVLAIDARWRGDFPEVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDGTKEGY 183 Q +V+AIDA+ GD V AGGR +G A+EWA + + GAGEILLTSMD DGTK GY Sbjct: 126 QCIVVAIDAKRVGDSWHVFTAGGRNDSGKDAIEWAKEVYDRGAGEILLTSMDADGTKAGY 185 Query: 184 DLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIPIPKLKRYL 242 DL LTR +++AV +PVIASGGAG MEH +AF G A+AALAAS+FHF EI I +LK YL Sbjct: 186 DLELTRAISDAVEIPVIASGGAGTMEHIKDAFTKGHADAALAASIFHFKEIDIMELKHYL 245 Query: 243 AEKGVHVRL 251 +G+ VRL Sbjct: 246 QNEGIPVRL 254 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: 231 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 228 Effective length of database: 230 Effective search space: 52440 Effective search space used: 52440 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_084274989.1 B8779_RS02410 (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.15130.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-121 388.4 2.8 7.4e-121 388.2 2.8 1.0 1 lcl|NCBI__GCF_900176045.1:WP_084274989.1 B8779_RS02410 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176045.1:WP_084274989.1 B8779_RS02410 imidazole glycerol phosphate synthase subunit HisF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.2 2.8 7.4e-121 7.4e-121 2 254 .] 5 253 .. 4 253 .. 0.99 Alignments for each domain: == domain 1 score: 388.2 bits; conditional E-value: 7.4e-121 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverva 70 +akriipCLdv++grvvkGv+f l+daGdpve+ak+y+eeGade++fldita+ e+r+t++++ve+va lcl|NCBI__GCF_900176045.1:WP_084274989.1 5 FAKRIIPCLDVDKGRVVKGVNFVGLKDAGDPVEVAKRYNEEGADEITFLDITATYEERDTIVHIVEEVA 73 69******************************************************************* PP TIGR00735 71 ekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaenee 139 ++vfiPltvgGGi++++d+ +ll+ G dkvsin+aavk+p++++e+a+rfGsq+ivvaidakr+ ++ lcl|NCBI__GCF_900176045.1:WP_084274989.1 74 KEVFIPLTVGGGIRELQDIYNLLAVGCDKVSINSAAVKNPDFVNEAAKRFGSQCIVVAIDAKRVGDS-- 140 ***************************************************************9985.. PP TIGR00735 140 akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGa 208 ++v + gGr+ + d++ewakev ++GaGeilltsmd+dGtk+Gydlel++++++av+iPviasgGa lcl|NCBI__GCF_900176045.1:WP_084274989.1 141 --WHVFTAGGRNDSGKDAIEWAKEVYDRGAGEILLTSMDADGTKAGYDLELTRAISDAVEIPVIASGGA 207 ..******************************************************************* PP TIGR00735 209 GkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 G++eh+++af+kg+adaaLaas+fh++e++i e+k+yl+++g++vr lcl|NCBI__GCF_900176045.1:WP_084274989.1 208 GTMEHIKDAFTKGHADAALAASIFHFKEIDIMELKHYLQNEGIPVR 253 *********************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (254 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.51 // [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