Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_012284027.1 HM1_RS13855 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000019165.1:WP_012284027.1 Length = 261 Score = 317 bits (811), Expect = 2e-91 Identities = 160/256 (62%), Positives = 197/256 (76%), Gaps = 7/256 (2%) Query: 3 LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62 L RIIPCLDV GRVVKG NF +L DAGDPVE A VYD GADE+ FLDI+AS +GR Sbjct: 2 LAKRIIPCLDVHGGRVVKGTNFVNLRDAGDPVELAAVYDKEGADEVVFLDITASSDGRAI 61 Query: 63 MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122 MLDVV RTAE F+P TVGGG+R VED R +L AGADK+++N++AV P+L+++ A +FG Sbjct: 62 MLDVVRRTAEEVFIPFTVGGGLRSVEDIREMLKAGADKISLNTSAVQTPKLISDGAWKFG 121 Query: 123 AQCVVAAIDARRNGD-------HWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMD 175 +QC+V AIDARR D WEVYTHGGR+PTGI+ L+ A + LGAGEILLTSMD Sbjct: 122 SQCIVVAIDARRRRDAEGNPVEGWEVYTHGGRKPTGIDVLEWARRVEELGAGEILLTSMD 181 Query: 176 KDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYS 235 KDGT+DGYD+ LTR V+++V +PVIASGGVGNLDH+VEG+T G A A LAASIFH+ +Y+ Sbjct: 182 KDGTKDGYDIPLTRAVSEAVTIPVIASGGVGNLDHIVEGLTVGKADAALAASIFHYREYT 241 Query: 236 LAEAHEALAKAGLTVR 251 + E E L + G+ VR Sbjct: 242 IGETKEYLRERGVHVR 257 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: 258 Number of extensions: 15 Number of successful extensions: 2 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: 261 Length adjustment: 24 Effective length of query: 231 Effective length of database: 237 Effective search space: 54747 Effective search space used: 54747 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_012284027.1 HM1_RS13855 (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.927196.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-125 402.9 0.3 2.8e-125 402.7 0.3 1.0 1 NCBI__GCF_000019165.1:WP_012284027.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019165.1:WP_012284027.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 402.7 0.3 2.8e-125 2.8e-125 1 254 [] 1 257 [. 1 257 [. 0.99 Alignments for each domain: == domain 1 score: 402.7 bits; conditional E-value: 2.8e-125 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekv 73 mlakriipCLdv+ grvvkG++f nlrdaGdpvela++yd+eGade+vflditass++r++ml+vv+r+ae+v NCBI__GCF_000019165.1:WP_012284027.1 1 MLAKRIIPCLDVHGGRVVKGTNFVNLRDAGDPVELAAVYDKEGADEVVFLDITASSDGRAIMLDVVRRTAEEV 73 8************************************************************************ PP TIGR00735 74 fiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaenee...akye 143 fiP+tvgGG++s+ed++++l+aGadk+s+nt+av++p+li++ a +fGsq+ivvaida+r+ ++e +e NCBI__GCF_000019165.1:WP_012284027.1 74 FIPFTVGGGLRSVEDIREMLKAGADKISLNTSAVQTPKLISDGAWKFGSQCIVVAIDARRRRDAEGnpvEGWE 146 *************************************************************9988778889** PP TIGR00735 144 vtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehlee 216 v+++gGr+ t++dv+ewa++veelGaGeilltsmdkdGtk+Gyd+ l+++v+eav+iPviasgG+G+ +h+ e NCBI__GCF_000019165.1:WP_012284027.1 147 VYTHGGRKPTGIDVLEWARRVEELGAGEILLTSMDKDGTKDGYDIPLTRAVSEAVTIPVIASGGVGNLDHIVE 219 ************************************************************************* PP TIGR00735 217 aflkgkadaaLaasvfhkreltieevkeylaergvkvr 254 +++ gkadaaLaas+fh+re+ti+e keyl+ergv+vr NCBI__GCF_000019165.1:WP_012284027.1 220 GLTVGKADAALAASIFHYREYTIGETKEYLRERGVHVR 257 *************************************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: 00:00:00.04 # Mc/sec: 1.36 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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