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_011780025.1 MVAN_RS14115 imidazole glycerol phosphate synthase cyclase subunit
Query= SwissProt::Q7SIB9 (252 letters) >NCBI__GCF_000015305.1:WP_011780025.1 Length = 261 Score = 299 bits (766), Expect = 3e-86 Identities = 159/255 (62%), Positives = 189/255 (74%), Gaps = 7/255 (2%) Query: 3 LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62 +A R++PCLDV GRVVKGVNF NLRDAGDPVE A AYD GADEL FLD++A+ RA Sbjct: 7 VATRVIPCLDVDGGRVVKGVNFANLRDAGDPVELAAAYDAEGADELTFLDVTASSSGRAT 66 Query: 63 LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122 +LDVV R AE+VFIPLTVGGGVRS+ D LL +GADKVSVN+AA+ RPEL+ EL+ FG Sbjct: 67 MLDVVRRTAEQVFIPLTVGGGVRSVADVDALLRAGADKVSVNTAAIARPELLSELSRQFG 126 Query: 123 AQAVVLAIDARW--RGDFP-----EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMD 175 +Q +VL++DAR G P EV GGR TG+ AVEWAV+G ELG GEILL SMD Sbjct: 127 SQCIVLSVDARTVPEGSQPTPSGWEVTTHGGRRGTGIDAVEWAVQGAELGVGEILLNSMD 186 Query: 176 RDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAGAEAALAASVFHFGEIPI 235 DGTK G+DL + R V AV VPVIASGGAG +EHF A AGA+A LAASVFHFGE+ I Sbjct: 187 ADGTKAGFDLEMLRAVRGAVTVPVIASGGAGAVEHFAPAVAAGADAVLAASVFHFGELTI 246 Query: 236 PKLKRYLAEKGVHVR 250 ++K + +G+ VR Sbjct: 247 GQVKAAMKAEGITVR 261 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: 251 Number of extensions: 13 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: 261 Length adjustment: 24 Effective length of query: 228 Effective length of database: 237 Effective search space: 54036 Effective search space used: 54036 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_011780025.1 MVAN_RS14115 (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.7620.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-118 378.5 1.3 7.6e-118 378.3 1.3 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011780025.1 MVAN_RS14115 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011780025.1 MVAN_RS14115 imidazole glycerol phosphate synthase cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.3 1.3 7.6e-118 7.6e-118 2 254 .] 7 261 .] 6 261 .] 0.99 Alignments for each domain: == domain 1 score: 378.3 bits; conditional E-value: 7.6e-118 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverva 70 +a r+ipCLdv+ grvvkGv+f nlrdaGdpvela++yd+eGadel+fld+tass++r+tml+vv+r+a lcl|NCBI__GCF_000015305.1:WP_011780025.1 7 VATRVIPCLDVDGGRVVKGVNFANLRDAGDPVELAAAYDAEGADELTFLDVTASSSGRATMLDVVRRTA 75 689****************************************************************** PP TIGR00735 71 ekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaenee 139 e+vfiPltvgGG++s++dv+ llraGadkvs+ntaa+++pel++el+++fGsq+iv+++da+++ e ++ lcl|NCBI__GCF_000015305.1:WP_011780025.1 76 EQVFIPLTVGGGVRSVADVDALLRAGADKVSVNTAAIARPELLSELSRQFGSQCIVLSVDARTVPEGSQ 144 *******************************************************************99 PP TIGR00735 140 ...akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPvias 205 + +evt++gGr+ t++d+vewa +++elG+Geill+smd+dGtk+G+dle+l++v+ av++Pvias lcl|NCBI__GCF_000015305.1:WP_011780025.1 145 ptpSGWEVTTHGGRRGTGIDAVEWAVQGAELGVGEILLNSMDADGTKAGFDLEMLRAVRGAVTVPVIAS 213 99999**************************************************************** PP TIGR00735 206 gGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 gGaG++eh++ a+++g ada+Laasvfh++elti++vk+ ++++g++vr lcl|NCBI__GCF_000015305.1:WP_011780025.1 214 GGAGAVEHFAPAVAAG-ADAVLAASVFHFGELTIGQVKAAMKAEGITVR 261 *************999.*******************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (261 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: 7.50 // [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