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_011611401.1 TERY_RS08255 imidazole glycerol phosphate synthase subunit HisF
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_000014265.1:WP_011611401.1 Length = 256 Score = 298 bits (763), Expect = 7e-86 Identities = 156/253 (61%), Positives = 196/253 (77%), Gaps = 5/253 (1%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 LAKRI+PCLDV+AGRVVKGVNFVNL+DAGDPVE A+ Y+ AGADELVFLDI+ATHE+R Sbjct: 2 LAKRILPCLDVNAGRVVKGVNFVNLQDAGDPVELAQVYNHAGADELVFLDITATHEDRDT 61 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 ++DVV R AE+VFIPLTVGGG++SLE+ + LL +GADKVS+NSAAVR P LI + +D FG Sbjct: 62 IIDVVYRTAEQVFIPLTVGGGIQSLENIKNLLRAGADKVSINSAAVRNPNLINQASDRFG 121 Query: 123 AQAVVLAIDARWRGDFP----EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDG 178 Q +V+AIDA R + +V+V GGR TG A+ WA++ + GAGE+LLTSMD DG Sbjct: 122 NQCIVVAIDACRRCEPDNLGWDVYVRGGRENTGKDAIAWAIEVEKRGAGEVLLTSMDADG 181 Query: 179 TKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIPIPK 237 T+ GYDL LTR +AE+V +PVIASGGAG +H +A G AEAAL AS+ H+G++ I + Sbjct: 182 TQAGYDLELTRTIAESVQIPVIASGGAGNCQHIFQALTEGKAEAALLASLLHYGQLSIAE 241 Query: 238 LKRYLAEKGVHVR 250 +K YLA V VR Sbjct: 242 IKDYLAGHEVPVR 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: 226 Number of extensions: 13 Number of successful extensions: 5 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: 256 Length adjustment: 24 Effective length of query: 228 Effective length of database: 232 Effective search space: 52896 Effective search space used: 52896 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_011611401.1 TERY_RS08255 (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.22045.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-123 396.5 0.6 2.5e-123 396.3 0.6 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011611401.1 TERY_RS08255 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011611401.1 TERY_RS08255 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 0.6 2.5e-123 2.5e-123 1 254 [] 1 254 [. 1 254 [. 1.00 Alignments for each domain: == domain 1 score: 396.3 bits; conditional E-value: 2.5e-123 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverv 69 mlakri+pCLdv++grvvkGv+f nl+daGdpvela++y++ Gadelvfldita++e+r+t+++vv r+ lcl|NCBI__GCF_000014265.1:WP_011611401.1 1 MLAKRILPCLDVNAGRVVKGVNFVNLQDAGDPVELAQVYNHAGADELVFLDITATHEDRDTIIDVVYRT 69 8******************************************************************** PP TIGR00735 70 aekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaene 138 ae+vfiPltvgGGi+s+e++k+llraGadkvsin+aav++p+li++++drfG q+ivvaida r+ e + lcl|NCBI__GCF_000014265.1:WP_011611401.1 70 AEQVFIPLTVGGGIQSLENIKNLLRAGADKVSINSAAVRNPNLINQASDRFGNQCIVVAIDACRRCEPD 138 ********************************************************************* PP TIGR00735 139 eakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgG 207 + ++v+++gGre+t+ d+++wa eve++GaGe+lltsmd+dGt++Gydlel+++++e+v+iPviasgG lcl|NCBI__GCF_000014265.1:WP_011611401.1 139 NLGWDVYVRGGRENTGKDAIAWAIEVEKRGAGEVLLTSMDADGTQAGYDLELTRTIAESVQIPVIASGG 207 ********************************************************************* PP TIGR00735 208 aGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 aG+++h+ +a+++gka+aaL as++h+++l+i e+k+yla ++v+vr lcl|NCBI__GCF_000014265.1:WP_011611401.1 208 AGNCQHIFQALTEGKAEAALLASLLHYGQLSIAEIKDYLAGHEVPVR 254 *********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (256 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: 00:00:00.08 # Mc/sec: 0.73 // [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