Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_007474890.1 CMTB2_RS06465 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q9X0C8 (201 letters) >NCBI__GCF_000170735.1:WP_007474890.1 Length = 200 Score = 147 bits (370), Expect = 2e-40 Identities = 82/203 (40%), Positives = 120/203 (59%), Gaps = 15/203 (7%) Query: 3 IGIISVGPGNIMNLYRGVKRASENFEDVSIELVESPRNDLYDLLFIPGVGHFGEGMRRLR 62 IGI+ GN+ ++ + + E V+ ++ + YD LF+PGVG FG+ M L+ Sbjct: 2 IGIVYYNMGNLASVKNAFNKLNVKAEVVT----DADKLKNYDKLFLPGVGAFGDAMEHLK 57 Query: 63 ENDLIDFVRKHVEDERYVVGVCLGMQLLFEESEEAPGVKGLSLIEGNVV-----KLRSRR 117 E +L + ++++++ +YV GVCLGMQLLFE+S E GL +IEG VV K+ + Sbjct: 58 EYNLDEAIKEYIKSGKYVFGVCLGMQLLFEKSYEFGEHSGLGIIEGEVVRFDKAKIGEHK 117 Query: 118 LPHMGWNEVIFK-----DTFPNGYYYFVHTYRAVCEEEHVLGTTEYDGEIFPSAVRKGRI 172 +P MGWN+V K + N Y YFVH+Y VC+E++V+G T Y G F SAV K + Sbjct: 118 IPQMGWNKVFNKKSKIFEGLDNPYLYFVHSYHTVCDEKYVIGKTIY-GYEFVSAVNKDNV 176 Query: 173 LGFQFHPEKSSKIGRKLLEKVIE 195 G Q HPEKS G K+LE ++ Sbjct: 177 FGLQPHPEKSHNEGLKILENFVK 199 Lambda K H 0.322 0.143 0.427 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: 144 Number of extensions: 10 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: 201 Length of database: 200 Length adjustment: 21 Effective length of query: 180 Effective length of database: 179 Effective search space: 32220 Effective search space used: 32220 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: 45 (21.9 bits)
Align candidate WP_007474890.1 CMTB2_RS06465 (imidazole glycerol phosphate synthase subunit HisH)
to HMM TIGR01855 (hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-))
# 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/TIGR01855.hmm # target sequence database: /tmp/gapView.19163.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01855 [M=198] Accession: TIGR01855 Description: IMP_synth_hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-73 232.6 0.7 2.1e-73 232.4 0.7 1.0 1 lcl|NCBI__GCF_000170735.1:WP_007474890.1 CMTB2_RS06465 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000170735.1:WP_007474890.1 CMTB2_RS06465 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.4 0.7 2.1e-73 2.1e-73 1 197 [. 2 199 .. 2 200 .] 0.96 Alignments for each domain: == domain 1 score: 232.4 bits; conditional E-value: 2.1e-73 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 i+++ y++gNl+svk+a++++++++evv+d+++l+++dkl+lPGVGaf +am++l+e++l+ +++ k lcl|NCBI__GCF_000170735.1:WP_007474890.1 2 IGIVYYNMGNLASVKNAFNKLNVKAEVVTDADKLKNYDKLFLPGVGAFGDAMEHLKEYNLDEAIKEYIK 70 789********************************************************99999***** PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek....kvPhiGWnevevvkesellkgle 134 ++k+v g+ClGmQllfeks+E +e++glg+i+g+v++++++k k+P++GWn+v k+s++++gl+ lcl|NCBI__GCF_000170735.1:WP_007474890.1 71 SGKYVFGVCLGMQLLFEKSYEFGEHSGLGIIEGEVVRFDKAKigehKIPQMGWNKVFN-KKSKIFEGLD 138 ***************************************9999999********9865.6678*****8 PP TIGR01855 135 eearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 + ++YfvHsY+ ++ e ++v+ k+ yg +fv+av+kdn++g+Q HPEkS++ Glk+l+nf++ lcl|NCBI__GCF_000170735.1:WP_007474890.1 139 N-PYLYFVHSYHTVCDE-KYVIGKTIYGYEFVSAVNKDNVFGLQPHPEKSHNEGLKILENFVK 199 7.56***********98.7******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (200 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.02 // [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