Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011155881.1 TX73_RS01620 imidazole glycerol phosphate synthase cyclase subunit
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000195775.1:WP_011155881.1 Length = 255 Score = 350 bits (897), Expect = e-101 Identities = 169/251 (67%), Positives = 208/251 (82%), Gaps = 2/251 (0%) Query: 6 RIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGTMLD 65 R+IPCLDV DGRVVKGVNF DL DAGDPVE A YDAAGADELCFLDI+A+HE RG MLD Sbjct: 5 RVIPCLDVKDGRVVKGVNFVDLRDAGDPVEAAIAYDAAGADELCFLDITATHENRGIMLD 64 Query: 66 VVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFGAQC 125 VV RTAE CFMP+TVGGGVR V+D + LL +GADKV++NSAAVAR E V E A++FG QC Sbjct: 65 VVRRTAEACFMPVTVGGGVRTVDDIKTLLRSGADKVSINSAAVARREFVKEAAEKFGDQC 124 Query: 126 VVAAIDARR--NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRDGY 183 +V AIDA+R D WE++THGGR+ TGI+A++ A + LGAGEILLTSMD+DGT+ G+ Sbjct: 125 IVVAIDAKRVPGRDRWEIFTHGGRKGTGIDAIEFAQEVVSLGAGEILLTSMDRDGTKSGF 184 Query: 184 DLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHEAL 243 D+ LTR +ADSV VPVIASGGVGNLDH+V+G+ +GHA+A+LAASIFHFG+Y++ +A + + Sbjct: 185 DIPLTRAIADSVGVPVIASGGVGNLDHLVDGIREGHATAVLAASIFHFGEYTIRQAKDHM 244 Query: 244 AKAGLTVRHPP 254 +AGL +R P Sbjct: 245 VQAGLPMRLDP 255 Lambda K H 0.320 0.136 0.400 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: 292 Number of extensions: 13 Number of successful extensions: 3 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: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_011155881.1 TX73_RS01620 (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.2902.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-109 351.5 2.5 1.3e-109 351.3 2.5 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011155881.1 TX73_RS01620 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011155881.1 TX73_RS01620 imidazole glycerol phosphate synthase cyclase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 351.3 2.5 1.3e-109 1.3e-109 2 254 .] 2 252 .. 1 252 [. 0.99 Alignments for each domain: == domain 1 score: 351.3 bits; conditional E-value: 1.3e-109 TIGR00735 2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevverva 70 + r+ipCLdvkdgrvvkGv+f +lrdaGdpve a +yd+ Gadel fldita++e+r +ml+vv+r+a lcl|NCBI__GCF_000195775.1:WP_011155881.1 2 FKVRVIPCLDVKDGRVVKGVNFVDLRDAGDPVEAAIAYDAAGADELCFLDITATHENRGIMLDVVRRTA 70 678****************************************************************** PP TIGR00735 71 ekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaenee 139 e f+P+tvgGG+++++d+k+llr+Gadkvsin+aav++ e++ke+a++fG q+ivvaidakr+ lcl|NCBI__GCF_000195775.1:WP_011155881.1 71 EACFMPVTVGGGVRTVDDIKTLLRSGADKVSINSAAVARREFVKEAAEKFGDQCIVVAIDAKRVPGR-- 137 ****************************************************************987.. PP TIGR00735 140 akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGa 208 +e+ ++gGr+ t++d++e+a+ev +lGaGeilltsmd+dGtksG+d+ l+++++++v +PviasgG+ lcl|NCBI__GCF_000195775.1:WP_011155881.1 138 DRWEIFTHGGRKGTGIDAIEFAQEVVSLGAGEILLTSMDRDGTKSGFDIPLTRAIADSVGVPVIASGGV 206 59******************************************************************* PP TIGR00735 209 GkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 G+ +hl +++ +g+a a+Laas+fh++e+ti++ k+++++ g+++r lcl|NCBI__GCF_000195775.1:WP_011155881.1 207 GNLDHLVDGIREGHATAVLAASIFHFGEYTIRQAKDHMVQAGLPMR 252 *******************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (255 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: 10.28 // [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