Align Imidazole glycerol phosphate synthase subunit HisH; IGP synthase glutaminase subunit; IGP synthase subunit HisH; ImGP synthase subunit HisH; IGPS subunit HisH; EC 4.3.2.10; EC 3.5.1.2 (characterized)
to candidate WP_015798527.1 AFER_RS05675 imidazole glycerol phosphate synthase subunit HisH
Query= SwissProt::Q7SIC0 (200 letters) >NCBI__GCF_000023265.1:WP_015798527.1 Length = 205 Score = 140 bits (354), Expect = 1e-38 Identities = 85/203 (41%), Positives = 111/203 (54%), Gaps = 6/203 (2%) Query: 1 MRMKALLIDYGSGNLRSAAKALEAAGFSVAVAQDPKAHEEADLLVLPGQGHFGQVMRAFQ 60 M ++ D G GN+ +A A A G V D +EA LLV+PG GH G V+ A Sbjct: 1 MSAAIVVADIGIGNIGAAVGAWRALGHPVRRGSDRADFDEARLLVVPGVGHLGSVLDALA 60 Query: 61 ESGFVERVRRHLERGLPFLGICVGMQVLYEGSEEAPGVRGLGLVPGEVRRFR-AGRVPQM 119 +G E + R ERG+ LG+CVGMQ L++G +EAP GLGL+PG V R A R+P+M Sbjct: 61 ATGLDEAMVRRRERGMATLGVCVGMQALFDGGDEAPDRVGLGLLPGWVERMSPAPRLPEM 120 Query: 120 GWNALEF----GGAFAPLTGRHFYFANSYYGPLTPYSLGKGEYEGTPFTALLAKENLLAP 175 WN L G A L G YF +SY TP +L E+ GT + A ++ LL Sbjct: 121 QWNRLRVAEGASGPLAVLEGAWVYFVHSYAVATTPAALAFEEFGGT-WVAAAGRDALLGV 179 Query: 176 QFHPEKSGKAGLAFLALARRYFE 198 QFHPE+SG GL FL R+ + Sbjct: 180 QFHPERSGAKGLRFLDALWRWVQ 202 Lambda K H 0.322 0.141 0.425 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: 140 Number of extensions: 11 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: 200 Length of database: 205 Length adjustment: 21 Effective length of query: 179 Effective length of database: 184 Effective search space: 32936 Effective search space used: 32936 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_015798527.1 AFER_RS05675 (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.18836.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-49 152.8 0.0 5.9e-49 152.6 0.0 1.0 1 lcl|NCBI__GCF_000023265.1:WP_015798527.1 AFER_RS05675 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023265.1:WP_015798527.1 AFER_RS05675 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 152.6 0.0 5.9e-49 5.9e-49 1 197 [. 5 199 .. 5 200 .. 0.97 Alignments for each domain: == domain 1 score: 152.6 bits; conditional E-value: 5.9e-49 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 ivv d+g+gN+ + a +++g ++ +d+ + ++a lv+PGVG+ ++++ l ++l+ + ++++ lcl|NCBI__GCF_000023265.1:WP_015798527.1 5 IVVADIGIGNIGAAVGAWRALGHPVRRGSDRADFDEARLLVVPGVGHLGSVLDALAATGLDEAMVRRRE 73 7999*******************************************************8888899999 PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeear 138 ++ +lg+C+GmQ lf+ ++E+ + glgl++g v++++ + ++P++ Wn++ v++ + + e+a lcl|NCBI__GCF_000023265.1:WP_015798527.1 74 RGMATLGVCVGMQALFDGGDEAPDRVGLGLLPGWVERMSPAPRLPEMQWNRLRVAEGASGPLAVLEGAW 142 999*******************************************************99999****** PP TIGR01855 139 vYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 vYfvHsYav ++ a+la+ ++g ++vaa +d+++gvQFHPE+Sg++Gl++l +++ lcl|NCBI__GCF_000023265.1:WP_015798527.1 143 VYFVHSYAVATTP--AALAFEEFGGTWVAAAGRDALLGVQFHPERSGAKGLRFLDALWR 199 **********998..9**************************************98876 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: 6.47 // [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