Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011840686.1 RSPH17029_RS04670 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q5NMD6 (255 letters) >NCBI__GCF_000015985.1:WP_011840686.1 Length = 253 Score = 353 bits (907), Expect = e-102 Identities = 177/250 (70%), Positives = 208/250 (83%), Gaps = 1/250 (0%) Query: 3 LCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGT 62 L TRIIPCLDVADGRVVKGVNF DL DAGDPVE A+ YDAAGADELCFLDI A+HE RGT Sbjct: 2 LKTRIIPCLDVADGRVVKGVNFVDLRDAGDPVEAARAYDAAGADELCFLDIHATHENRGT 61 Query: 63 MLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFG 122 M D+V RTAE CFMPLTVGGGVR +D RALLLAGADKV+ NSAAVA P +VAE ADRFG Sbjct: 62 MYDLVTRTAEQCFMPLTVGGGVRTHQDVRALLLAGADKVSFNSAAVADPTVVAEAADRFG 121 Query: 123 AQCVVAAIDARRNG-DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRD 181 +QC+V AIDA+ WE++THGGRR TGI+A+ A ++ GAGEILLTSMD+DGTR Sbjct: 122 SQCIVVAIDAKTVAPGRWEIFTHGGRRATGIDAVAFACDVASRGAGEILLTSMDRDGTRA 181 Query: 182 GYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHE 241 G++L LTR ++D+VP+PVIASGGVG LDH+VEGVT+G ASA+LAASIFHFG++++ EA Sbjct: 182 GFNLPLTRAISDAVPIPVIASGGVGTLDHLVEGVTEGGASAVLAASIFHFGEFTIGEAKA 241 Query: 242 ALAKAGLTVR 251 +A AG+ VR Sbjct: 242 HMASAGIPVR 251 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: 309 Number of extensions: 8 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: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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_011840686.1 RSPH17029_RS04670 (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.687390.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-108 347.8 0.6 1.8e-108 347.6 0.6 1.0 1 NCBI__GCF_000015985.1:WP_011840686.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015985.1:WP_011840686.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 347.6 0.6 1.8e-108 1.8e-108 1 254 [] 1 251 [. 1 251 [. 0.99 Alignments for each domain: == domain 1 score: 347.6 bits; conditional E-value: 1.8e-108 TIGR00735 1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekv 73 ml riipCLdv dgrvvkGv+f +lrdaGdpve a++yd+ Gadel fldi a++e+r tm ++v+r+ae+ NCBI__GCF_000015985.1:WP_011840686.1 1 MLKTRIIPCLDVADGRVVKGVNFVDLRDAGDPVEAARAYDAAGADELCFLDIHATHENRGTMYDLVTRTAEQC 73 7999********************************************************************* PP TIGR00735 74 fiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevti 146 f+PltvgGG+++ +dv+ ll aGadkvs n+aav++p++++e+adrfGsq+ivvaidak++a + +e+ + NCBI__GCF_000015985.1:WP_011840686.1 74 FMPLTVGGGVRTHQDVRALLLAGADKVSFNSAAVADPTVVAEAADRFGSQCIVVAIDAKTVAP---GRWEIFT 143 ***********************************************************9997...69***** PP TIGR00735 147 kgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeafl 219 +gGr+ t++d+v++a +v+++GaGeilltsmd+dGt++G++l l++++++av iPviasgG+G+ +hl e+++ NCBI__GCF_000015985.1:WP_011840686.1 144 HGGRRATGIDAVAFACDVASRGAGEILLTSMDRDGTRAGFNLPLTRAISDAVPIPVIASGGVGTLDHLVEGVT 216 ************************************************************************* PP TIGR00735 220 kgkadaaLaasvfhkreltieevkeylaergvkvr 254 +g a a+Laas+fh++e+ti+e k+++a+ g++vr NCBI__GCF_000015985.1:WP_011840686.1 217 EGGASAVLAASIFHFGEFTIGEAKAHMASAGIPVR 251 *********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (254 nodes) Target sequences: 1 (253 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: 13.27 // [ok]
This GapMind analysis is from Aug 31 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