Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_077244046.1 B1A74_RS05750 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >NCBI__GCF_001995255.1:WP_077244046.1 Length = 221 Score = 184 bits (468), Expect = 8e-52 Identities = 94/212 (44%), Positives = 129/212 (60%), Gaps = 4/212 (1%) Query: 1 MNKIVVVDYGMGNLRSVAQALRH-VAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRS 59 M + V+DYGMGNL SV +AL H AP + + + +R ADR+V PGQGA D M++ Sbjct: 1 METVAVIDYGMGNLHSVERALTHEAAPGQRILRTDDPEILREADRLVFPGQGAAGDAMQA 60 Query: 60 LRESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEE-GDTPGLGLLPGKVVRFDLEGMRQD 118 L G+ + E + ++P G+C+G+Q+L + S+E G LG++PG V RF Q Sbjct: 61 LARRGLNRLLPELAGSRPFLGLCLGQQILMEHSDESGGVDLLGVIPGGVARFPERSDAQ- 119 Query: 119 DGSLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFA 178 G KVP MGWN V T HPLW G+ + +FYFVHS+ P ++A V T YG FA Sbjct: 120 -GRRLKVPHMGWNRVQPTGEHPLWHGLPETPWFYFVHSFRVQPRDAASVAAHTDYGETFA 178 Query: 179 CAVARDNIFATQFHPEKSASAGLQLYRNFVHW 210 A+AR ++F Q HPEKSA+ GL+L NF+ W Sbjct: 179 SALARGSLFTMQCHPEKSAACGLRLLNNFLRW 210 Lambda K H 0.322 0.137 0.431 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: 176 Number of extensions: 8 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: 212 Length of database: 221 Length adjustment: 22 Effective length of query: 190 Effective length of database: 199 Effective search space: 37810 Effective search space used: 37810 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_077244046.1 B1A74_RS05750 (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.19364.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-61 193.6 0.0 1.8e-61 193.4 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077244046.1 B1A74_RS05750 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_077244046.1 B1A74_RS05750 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 193.4 0.0 1.8e-61 1.8e-61 1 197 [. 4 209 .. 4 210 .. 0.93 Alignments for each domain: == domain 1 score: 193.4 bits; conditional E-value: 1.8e-61 TIGR01855 1 ivvidygvgNlksvkkalerv...gaesevvkdskelekadklvlPGVGafkeamkklrelelellaek 66 ++vidyg+gNl+sv++al + g++ ++d + l++ad+lv+PG Ga+ +am+ l +++l+ l lcl|NCBI__GCF_001995255.1:WP_077244046.1 4 VAVIDYGMGNLHSVERALTHEaapGQRILRTDDPEILREADRLVFPGQGAAGDAMQALARRGLNRL-LP 71 79****************8761124455567778999*************************7777.57 PP TIGR01855 67 vvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek.......kvPhiGWnevevvkese 128 + + ++p+lg+ClG Q+l+e+s+E++ v+ lg+i+g v ++ ++ kvPh+GWn+v+++ e++ lcl|NCBI__GCF_001995255.1:WP_077244046.1 72 ELAGSRPFLGLCLGQQILMEHSDESGGVDLLGVIPGGVARFPERSdaqgrrlKVPHMGWNRVQPTGEHP 140 888999***********************************99888899999***************** PP TIGR01855 129 llkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 l +gl e +YfvHs++v++++ v a +dyge+f +a++++ ++++Q HPEkS++ Gl+ll+nfl+ lcl|NCBI__GCF_001995255.1:WP_077244046.1 141 LWHGLPETPWFYFVHSFRVQPRDAASVAAHTDYGETFASALARGSLFTMQCHPEKSAACGLRLLNNFLR 209 *******************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (221 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 0.01s 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