Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_028950919.1 Q385_RS0106665 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >NCBI__GCF_000619805.1:WP_028950919.1 Length = 205 Score = 172 bits (435), Expect = 5e-48 Identities = 94/206 (45%), Positives = 126/206 (61%), Gaps = 11/206 (5%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63 I +VDYGMGNLRSV +AL V +V + D+ AD VV+PG GA D + +L Sbjct: 2 IALVDYGMGNLRSVEKALEKVG--FNVLRTSNPEDLDKADAVVVPGVGAFGDAIHNLERF 59 Query: 64 GVQDAVIEA-SRTKPLFGVCVGEQMLFDWSEE-GDTPGLGLLPGKVVRFDLEGMRQDDGS 121 G+++ +IE ++ KP G+C+G Q+LF++ E G GLG+L G VVRFD + Sbjct: 60 GLKNKIIEVINQGKPYLGICLGLQILFEYGYEFGQHEGLGILKGSVVRFD-------ERL 112 Query: 122 LFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFACAV 181 K+P MGWN +H+ ++EGI D FFYFVHSYYA P + V T Y DF +V Sbjct: 113 PIKIPHMGWNQIHKKKDSKMFEGIKDGEFFYFVHSYYANPEDKTVVATTTDYAIDFCSSV 172 Query: 182 ARDNIFATQFHPEKSASAGLQLYRNF 207 DN++A QFHPEKS +AGL+L NF Sbjct: 173 EVDNLWAVQFHPEKSQTAGLKLLENF 198 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: 153 Number of extensions: 8 Number of successful extensions: 5 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: 205 Length adjustment: 21 Effective length of query: 191 Effective length of database: 184 Effective search space: 35144 Effective search space used: 35144 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_028950919.1 Q385_RS0106665 (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.3050.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-77 244.1 0.0 6e-77 244.0 0.0 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028950919.1 Q385_RS0106665 imidazole glycero Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028950919.1 Q385_RS0106665 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 244.0 0.0 6e-77 6e-77 1 197 [. 2 200 .. 2 201 .. 0.98 Alignments for each domain: == domain 1 score: 244.0 bits; conditional E-value: 6e-77 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 i+++dyg+gNl+sv+kale+vg+++ +++ ++l+kad++v+PGVGaf +a+++l++++l+ + +v + lcl|NCBI__GCF_000619805.1:WP_028950919.1 2 IALVDYGMGNLRSVEKALEKVGFNVLRTSNPEDLDKADAVVVPGVGAFGDAIHNLERFGLKNKIIEVIN 70 789********************************************************777779**** PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkesellkgleee 136 ++kp lgiClG+Q+lfe ++E ++++glg++kg+v++++++ k+Ph+GWn+++ +k+s++++g++++ lcl|NCBI__GCF_000619805.1:WP_028950919.1 71 QGKPYLGICLGLQILFEYGYEFGQHEGLGILKGSVVRFDERLpiKIPHMGWNQIHKKKDSKMFEGIKDG 139 *****************************************999************************* PP TIGR01855 137 arvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 + +YfvHsY++++e++ v +++dy +f ++ve dn+ +vQFHPEkS+++Glkll+nf++ lcl|NCBI__GCF_000619805.1:WP_028950919.1 140 EFFYFVHSYYANPEDKTVVATTTDYAIDFCSSVEVDNLWAVQFHPEKSQTAGLKLLENFKK 200 ***********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (205 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: 7.04 // [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