Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_012992061.1 THAL_RS05215 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000025605.1:WP_012992061.1 Length = 204 Score = 157 bits (398), Expect = 1e-43 Identities = 94/206 (45%), Positives = 132/206 (64%), Gaps = 17/206 (8%) Query: 9 VALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQALKA 68 VAL+DYG GNL SV AL GL +V T++PD + +AD +VLPGVGAF ++ LKA Sbjct: 3 VALVDYGMGNLLSVRKALQVVGL---EVVQTSDPDFLPEADAIVLPGVGAFRDAVRNLKA 59 Query: 69 --IPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDPS 126 I D + K +E+G+PFLGIC+G+QLL ++ E+G +GLG ++G+V L P+ + Sbjct: 60 SGIWDQL----KKQIEEGKPFLGICLGLQLLFERSYEFGEEEGLGVLRGEVV-LLPH--T 112 Query: 127 CKVPHMGWNQIGLTTDSHPLLRA----GEAYFLHSYAFVPEDESTLLATTEHGGLVTAAV 182 +VPH+GWNQI DS P+L YF+HSY VP+D S +L T++G ++V Sbjct: 113 VRVPHIGWNQIFRKKDS-PVLEGVPDGAYLYFVHSYHVVPKDPSCILTVTDYGIDFVSSV 171 Query: 183 GRDNIMGVQFHPEKSQSYGLEFLSRF 208 +N++ VQFHPEKSQ GL L + Sbjct: 172 EWENVLAVQFHPEKSQKMGLRILKNW 197 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: 165 Number of extensions: 15 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_012992061.1 THAL_RS05215 (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.8616.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-74 235.7 0.0 2.4e-74 235.5 0.0 1.0 1 lcl|NCBI__GCF_000025605.1:WP_012992061.1 THAL_RS05215 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025605.1:WP_012992061.1 THAL_RS05215 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.5 0.0 2.4e-74 2.4e-74 1 197 [. 3 199 .. 3 200 .. 0.97 Alignments for each domain: == domain 1 score: 235.5 bits; conditional E-value: 2.4e-74 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 ++++dyg+gNl sv+kal+ vg e++ ++d + l +ad++vlPGVGaf++a+++l+ +++ +k+ + lcl|NCBI__GCF_000025605.1:WP_012992061.1 3 VALVDYGMGNLLSVRKALQVVGLEVVQTSDPDFLPEADAIVLPGVGAFRDAVRNLKASGIWDQLKKQIE 71 689********************************************************5555588999 PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeear 138 ++kp+lgiClG+Qllfe+s+E +e++glg++ g+v+ l ++++vPhiGWn++ +k+s++l+g+ ++a+ lcl|NCBI__GCF_000025605.1:WP_012992061.1 72 EGKPFLGICLGLQLLFERSYEFGEEEGLGVLRGEVVLLPHTVRVPHIGWNQIFRKKDSPVLEGVPDGAY 140 999****************************************************************** PP TIGR01855 139 vYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 +YfvHsY+v++++ + +l+ +dyg +fv++ve +n+++vQFHPEkS+k+Gl++lkn+++ lcl|NCBI__GCF_000025605.1:WP_012992061.1 141 LYFVHSYHVVPKDPSCILTVTDYGIDFVSSVEWENVLAVQFHPEKSQKMGLRILKNWAK 199 ********************************************************975 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 5.65 // [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