Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_011320708.1 AVA_RS20365 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000204075.1:WP_011320708.1 Length = 211 Score = 145 bits (366), Expect = 5e-40 Identities = 88/206 (42%), Positives = 118/206 (57%), Gaps = 12/206 (5%) Query: 9 VALIDYGAGNLRSVANALLASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQALKA 68 VA+IDY GNL SV L +G ++T + E+ +AD V+LPGVGAF +Q+L++ Sbjct: 4 VAVIDYEMGNLHSVCKGLEKAGATP---IITHSHQELTKADAVILPGVGAFDPAVQSLRS 60 Query: 69 IPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDPSCK 128 P K + G+PFLGIC+G+Q+L + E G GLG IKGKV ++P Sbjct: 61 RDLEQPI--KDTIASGKPFLGICLGLQILFESSAE-GTQPGLGIIKGKVRRFI-SEPGIT 116 Query: 129 VPHMGWNQIGLTTDSHPLLR----AGEAYFLHSYAFVPEDESTLLATTEHGG-LVTAAVG 183 +PHMGWNQ+ LT L YF+HSY P + AT HG VTAA+ Sbjct: 117 IPHMGWNQLELTQPKSILWEHLPPQPWVYFVHSYYVDPVEPQVRAATVTHGTQTVTAAIA 176 Query: 184 RDNIMGVQFHPEKSQSYGLEFLSRFL 209 +N+M VQFHPEKS + GL+ LS F+ Sbjct: 177 HENLMAVQFHPEKSSNIGLQILSNFV 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: 145 Number of extensions: 13 Number of successful extensions: 7 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: 211 Length adjustment: 21 Effective length of query: 192 Effective length of database: 190 Effective search space: 36480 Effective search space used: 36480 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_011320708.1 AVA_RS20365 (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.2802709.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-68 214.0 0.0 1e-67 213.8 0.0 1.0 1 NCBI__GCF_000204075.1:WP_011320708.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011320708.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 213.8 0.0 1e-67 1e-67 1 197 [. 4 203 .. 4 204 .. 0.94 Alignments for each domain: == domain 1 score: 213.8 bits; conditional E-value: 1e-67 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkp 73 ++vidy++gNl+sv k le++ga++ ++++++el+kad+++lPGVGaf+ a+++lr ++le+ ++++ +++kp NCBI__GCF_000204075.1:WP_011320708.1 4 VAVIDYEMGNLHSVCKGLEKAGATPIITHSHQELTKADAVILPGVGAFDPAVQSLRSRDLEQPIKDTIASGKP 76 79*********************************************************888889******** PP TIGR01855 74 vlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvkes.ellkgleeearvYfvH 143 +lgiClG+Q+lfe+s Eg+ ++glg+ikgkv+++ +e ++Ph+GWn++e ++ + l + l + vYfvH NCBI__GCF_000204075.1:WP_011320708.1 77 FLGICLGLQILFESSAEGT-QPGLGIIKGKVRRFISEPgiTIPHMGWNQLELTQPKsILWEHLPPQPWVYFVH 148 *****************75.7*************999999***********98766267789*********** PP TIGR01855 144 sYaveleeeeavlakadyg.ekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 sY+v + e + a++++g ++ +aa++++n+++vQFHPEkS+++Gl++l+nf++ NCBI__GCF_000204075.1:WP_011320708.1 149 SYYVDPVEPQVRAATVTHGtQTVTAAIAHENLMAVQFHPEKSSNIGLQILSNFVS 203 ********9999999999725689*****************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (211 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: 17.81 // [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