Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_011611747.1 TERY_RS10170 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000014265.1:WP_011611747.1 Length = 214 Score = 150 bits (378), Expect = 2e-41 Identities = 90/208 (43%), Positives = 122/208 (58%), Gaps = 12/208 (5%) Query: 7 STVALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQAL 66 ST+A+IDY GNL SV L +G + +T + E+ +AD V+LPGVG+F +Q L Sbjct: 2 STIAVIDYDMGNLHSVCKGLEKAGATPK---ITDSSIEIDKADAVILPGVGSFDPAVQHL 58 Query: 67 KAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDPS 126 + +P K V+ G+PFLGIC+G+Q+L + EE G GLG GKV + ++P Sbjct: 59 RTRNLEIPI--KQVIASGKPFLGICLGLQILFESSEE-GQEPGLGIFAGKVCRFK-SEPG 114 Query: 127 CKVPHMGWNQIGLTTDSHPLL-RAGE---AYFLHSYAFVPEDESTLLATTEHGG-LVTAA 181 +P MGWN++ T H L G YF+HSY P D AT HG VTAA Sbjct: 115 LTIPQMGWNKLQFTQPEHLLWSEIGSQPWVYFVHSYYVDPTDSQVTAATVTHGHQTVTAA 174 Query: 182 VGRDNIMGVQFHPEKSQSYGLEFLSRFL 209 VG+DN++ VQFHPEKS + GL+ LS F+ Sbjct: 175 VGKDNLIAVQFHPEKSSTAGLKILSNFV 202 Lambda K H 0.318 0.136 0.409 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: 163 Number of extensions: 16 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: 213 Length of database: 214 Length adjustment: 22 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_011611747.1 TERY_RS10170 (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.3291.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-70 220.5 0.0 1.1e-69 220.3 0.0 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011611747.1 TERY_RS10170 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011611747.1 TERY_RS10170 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 220.3 0.0 1.1e-69 1.1e-69 1 197 [. 4 203 .. 4 204 .. 0.95 Alignments for each domain: == domain 1 score: 220.3 bits; conditional E-value: 1.1e-69 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 i+vidy++gNl+sv k le++ga+++++++s e++kad+++lPGVG+f+ a+++lr ++le+ +++v + lcl|NCBI__GCF_000014265.1:WP_011611747.1 4 IAVIDYDMGNLHSVCKGLEKAGATPKITDSSIEIDKADAVILPGVGSFDPAVQHLRTRNLEIPIKQVIA 72 79*********************************************************99999***** PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkes.ellkglee 135 ++kp+lgiClG+Q+lfe+seEg +++glg++ gkv ++++e ++P++GWn++++++ + l +++ + lcl|NCBI__GCF_000014265.1:WP_011611747.1 73 SGKPFLGICLGLQILFESSEEG-QEPGLGIFAGKVCRFKSEPglTIPQMGWNKLQFTQPEhLLWSEIGS 140 *********************6.68***************9999**********99876516779**** PP TIGR01855 136 earvYfvHsYaveleeeeavlakadyge.kfvaavekdnivgvQFHPEkSgktGlkllknfle 197 + vYfvHsY+v +++++ + a++++g+ + +aav kdn+++vQFHPEkS+++Glk+l+nf++ lcl|NCBI__GCF_000014265.1:WP_011611747.1 141 QPWVYFVHSYYVDPTDSQVTAATVTHGHqTVTAAVGKDNLIAVQFHPEKSSTAGLKILSNFVS 203 ****************99999999**7615799****************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (214 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: 5.95 // [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