Align Imidazole glycerol phosphate synthase subunit HisH 2; EC 4.3.2.10; IGP synthase glutaminase subunit 2; EC 3.5.1.2; IGP synthase subunit HisH 2; ImGP synthase subunit HisH 2; IGPS subunit HisH 2 (uncharacterized)
to candidate WP_066919161.1 ACG33_RS04770 imidazole glycerol phosphate synthase subunit HisH
Query= curated2:P72138 (202 letters) >NCBI__GCF_001579945.1:WP_066919161.1 Length = 205 Score = 202 bits (513), Expect = 4e-57 Identities = 100/202 (49%), Positives = 135/202 (66%), Gaps = 3/202 (1%) Query: 1 MIVVIDYGVGNIASVLNMLKRVGAKAKASDSREDIEQAEKLILPGVGAFDAGMQTLRKSG 60 MI +++ +GN+ S++NML+R+G + SD +DI QAEKLILPGVGAF AGM+ L++ G Sbjct: 1 MITIVNIDIGNVGSIVNMLRRIGVRTLISDIPDDISQAEKLILPGVGAFGAGMEGLKRKG 60 Query: 61 LVDVLTEQVMIKRKPVMGVCLGSQMLGLRSEEGAEPGLGWIDMDSVRFERRDDR--KVPH 118 LV+ LTE VM ++ P++GVCLG Q+L S+E + PGLGWI VR R +DR +VPH Sbjct: 61 LVEALTEAVMQRQVPILGVCLGMQLLAESSKEASCPGLGWIRGKVVRL-RPEDRYLRVPH 119 Query: 119 MGWNQVSPQLEHPILSGINEQSRFYFVHSYYMVPKDPDDILLSCNYGQKFTAAVARDNVF 178 MGWN V P + ++ RFYF HS+YM D D++ YG F AV + NVF Sbjct: 120 MGWNTVKPIPGAALFDPTADEPRFYFAHSFYMDCADRVDVVAEATYGFTFPVAVQKRNVF 179 Query: 179 GFQFHPEKSHKFGMQLFKNFVE 200 G QFHPEKSH+FG ++ + F E Sbjct: 180 GVQFHPEKSHRFGREVLRRFSE 201 Lambda K H 0.322 0.139 0.412 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: 155 Number of extensions: 7 Number of successful extensions: 2 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: 202 Length of database: 205 Length adjustment: 21 Effective length of query: 181 Effective length of database: 184 Effective search space: 33304 Effective search space used: 33304 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_066919161.1 ACG33_RS04770 (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.10009.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-70 221.6 0.0 4.9e-70 221.4 0.0 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066919161.1 ACG33_RS04770 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066919161.1 ACG33_RS04770 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.4 0.0 4.9e-70 4.9e-70 1 197 [. 2 201 .. 2 202 .. 0.98 Alignments for each domain: == domain 1 score: 221.4 bits; conditional E-value: 4.9e-70 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvv 68 i+++++++gN+ s+ ++l+r+g+++ +++ +++++a+kl+lPGVGaf ++m+ l++++ +e+l+e v+ lcl|NCBI__GCF_001579945.1:WP_066919161.1 2 ITIVNIDIGNVGSIVNMLRRIGVRTLISDIPDDISQAEKLILPGVGAFGAGMEGLKRKGlVEALTEAVM 70 789****************************************************************** PP TIGR01855 69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkesellkgle 134 +++ p+lg+ClGmQll+e+s+E+ +++glg+i gkv++l+ e +vPh+GWn+v+++ +l+ lcl|NCBI__GCF_001579945.1:WP_066919161.1 71 QRQVPILGVCLGMQLLAESSKEA-SCPGLGWIRGKVVRLRPEDrylRVPHMGWNTVKPIPGAALFDPTA 138 **********************6.69**************998899*********************** PP TIGR01855 135 eearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 +e r+Yf Hs+++ +++ +v+a a+yg +f+ av+k n++gvQFHPEkS+++G+++l++f e lcl|NCBI__GCF_001579945.1:WP_066919161.1 139 DEPRFYFAHSFYMDCADRVDVVAEATYGFTFPVAVQKRNVFGVQFHPEKSHRFGREVLRRFSE 201 ************************************************************976 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.68 // [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