Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_075386979.1 BK574_RS20705 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >NCBI__GCF_002019605.1:WP_075386979.1 Length = 213 Score = 151 bits (382), Expect = 8e-42 Identities = 89/209 (42%), Positives = 128/209 (61%), Gaps = 11/209 (5%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63 I V+DYGMGNL SV++AL + D +S +V +++ AD ++LPG G+ D M L+ Sbjct: 2 IGVIDYGMGNLHSVSKALERL--NKDYFVSEKVEELQKADGLILPGVGSFRDAMEILQNE 59 Query: 64 GVQDAVIEASRT-KPLFGVCVGEQMLFDWSEE-GDTPGLGLLPGKVVRFDLEGMRQDDGS 121 G+ D V+E +++ KPL G+C+G Q+LF+ SEE G+T GL LLPG V RF G+ + G Sbjct: 60 GLADFVVEWAKSGKPLLGICLGMQLLFEESEENGETKGLNLLPGVVRRFP--GVSAE-GE 116 Query: 122 LFKVPQMGWNHV--HQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFAC 179 +KVP MGWN + HQ H L + + +N YFVHSY + + V+ + Y + Sbjct: 117 TYKVPHMGWNQLEFHQPD-HSLLKDV-ENGHVYFVHSYVVRTDDQSVVIASSNYDGEVPA 174 Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFV 208 V R NI TQFHPEKS+ G+ + N+V Sbjct: 175 VVGRANIMGTQFHPEKSSFIGMSILANYV 203 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: 161 Number of extensions: 9 Number of successful extensions: 6 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: 213 Length adjustment: 21 Effective length of query: 191 Effective length of database: 192 Effective search space: 36672 Effective search space used: 36672 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_075386979.1 BK574_RS20705 (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.18823.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-72 228.0 0.0 5.4e-72 227.8 0.0 1.0 1 lcl|NCBI__GCF_002019605.1:WP_075386979.1 BK574_RS20705 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_075386979.1 BK574_RS20705 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.8 0.0 5.4e-72 5.4e-72 1 197 [. 2 204 .. 2 205 .. 0.95 Alignments for each domain: == domain 1 score: 227.8 bits; conditional E-value: 5.4e-72 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 i+vidyg+gNl+sv+kaler++ +v+++ +el+kad l+lPGVG+f++am+ l++ +l ++ + +k lcl|NCBI__GCF_002019605.1:WP_075386979.1 2 IGVIDYGMGNLHSVSKALERLNKDYFVSEKVEELQKADGLILPGVGSFRDAMEILQNEGLADFVVEWAK 70 79*********************************************************99999***** PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek......kvPhiGWnevevvk.esellk 131 ++kp+lgiClGmQllfe+seE++e+kgl l++g v+++ kvPh+GWn++e+ + +++llk lcl|NCBI__GCF_002019605.1:WP_075386979.1 71 SGKPLLGICLGMQLLFEESEENGETKGLNLLPGVVRRFPGVSaegetyKVPHMGWNQLEFHQpDHSLLK 139 **************************************8554556788**********98763679*** PP TIGR01855 132 gleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 ++e+++ vYfvHsY+v++ +++ v+a+++y+ + +a+v + ni+g+QFHPEkS+ +G+++l n+++ lcl|NCBI__GCF_002019605.1:WP_075386979.1 140 DVENGH-VYFVHSYVVRTDDQSVVIASSNYDGEVPAVVGRANIMGTQFHPEKSSFIGMSILANYVK 204 **9987.********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (213 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: 9.23 // [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