Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_012284029.1 HM1_RS13865 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::DvH:209219 (213 letters) >NCBI__GCF_000019165.1:WP_012284029.1 Length = 204 Score = 169 bits (429), Expect = 3e-47 Identities = 92/204 (45%), Positives = 121/204 (59%), Gaps = 10/204 (4%) Query: 1 MLAILDYKAGNQTSVRRALDHLGIPCVITADPEVIQGAAGVIFPGVGAAGQAMNELVTTG 60 M+AI+DY GN SV++ L+ G +T+DPE ++ A GVI PGVGA AM L +G Sbjct: 1 MIAIIDYGMGNLRSVQKGLEKAGYAGFVTSDPEAVRSAPGVILPGVGAFADAMENLRRSG 60 Query: 61 LDEVLRRQVQAGRPLLGICVGCQIMLDYSQEND-TKALGIIPGECRLFNPAWTDEDGAPI 119 + + V AG+P LGIC+G Q+M + S+E + LGI PG R + + Sbjct: 61 MIAPIMETVAAGKPFLGICLGFQLMFEASEEGGYFEGLGIFPGMVRRL--------PSGL 112 Query: 120 RVPHMGWNHIVQRRPCELLKGIEPEAEFYFVHSYYPAPPE-EYVIATCTYGAEFCAIHGG 178 +VPHMGWN + RR +L GI A +YFVHSYY P E + VIAT YG +FCA+ G Sbjct: 113 KVPHMGWNELTLRRESAILAGIPSGAAYYFVHSYYVDPAEPDLVIATVDYGFDFCAVAGR 172 Query: 179 PGLWAVQFHPEKSGRPGLRLLANF 202 + QFHPEKS GLR+L NF Sbjct: 173 GNVSGAQFHPEKSSDLGLRILQNF 196 Lambda K H 0.322 0.141 0.455 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: 196 Number of extensions: 9 Number of successful extensions: 3 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: 213 Length of database: 204 Length adjustment: 21 Effective length of query: 192 Effective length of database: 183 Effective search space: 35136 Effective search space used: 35136 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_012284029.1 HM1_RS13865 (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.3795864.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-74 236.0 0.0 1.9e-74 235.8 0.0 1.0 1 NCBI__GCF_000019165.1:WP_012284029.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019165.1:WP_012284029.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.8 0.0 1.9e-74 1.9e-74 1 195 [. 2 196 .. 2 199 .. 0.98 Alignments for each domain: == domain 1 score: 235.8 bits; conditional E-value: 1.9e-74 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 i++idyg+gNl+sv+k le++g+ +v++d +++++a ++lPGVGaf++am++lr++++ + + ++v+++kp NCBI__GCF_000019165.1:WP_012284029.1 2 IAIIDYGMGNLRSVQKGLEKAGYAGFVTSDPEAVRSAPGVILPGVGAFADAMENLRRSGMIAPIMETVAAGKP 74 79*********************************************************77777999999*** PP TIGR01855 74 vlgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeearvYfvHsYa 146 +lgiClG Ql+fe seEg+ +glg+++g v++l + kvPh+GWne++ +es++l+g+ ++a +YfvHsY+ NCBI__GCF_000019165.1:WP_012284029.1 75 FLGICLGFQLMFEASEEGGYFEGLGIFPGMVRRLPSGLKVPHMGWNELTLRRESAILAGIPSGAAYYFVHSYY 147 ************************************************************************* PP TIGR01855 147 veleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknf 195 v ++e + v+a++dyg +f a+ ++n+ g+QFHPEkS++ Gl++l+nf NCBI__GCF_000019165.1:WP_012284029.1 148 VDPAEPDLVIATVDYGFDFCAVAGRGNVSGAQFHPEKSSDLGLRILQNF 196 ************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (204 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: 00:00:00.01 # Mc/sec: 3.36 // [ok]
This GapMind analysis is from Jul 25 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