Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_012173019.1 AZC_RS23070 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000010525.1:WP_012173019.1 Length = 215 Score = 236 bits (601), Expect = 3e-67 Identities = 121/215 (56%), Positives = 150/215 (69%), Gaps = 10/215 (4%) Query: 8 TVALIDYGAGNLRSVANALLASGL--ARENLVVTANPDEVLQADRVVLPGVGAFASCMQA 65 TVA++DYG+GNL S A A+ + L E +VVT++PD V ADRVVLPGVGAFA C + Sbjct: 2 TVAIVDYGSGNLHSAAKAIERAALDTGGERIVVTSDPDVVRAADRVVLPGVGAFADCRRG 61 Query: 66 LKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDP 125 L A+P MV ALE+AV +GRPFLGICVG+QLLA++G E+GV GLGWIKG+V + P+DP Sbjct: 62 LDAVPGMVAALEEAVHGRGRPFLGICVGLQLLAERGLEHGVTAGLGWIKGEVDRITPSDP 121 Query: 126 SCKVPHMGWNQIGLTTDSHPLLR-------AGEAYFLHSYAFVPEDESTLLATTEHGGLV 178 K+PHMGWN + +H LL AYF+HSYAF D + LLATT++ G + Sbjct: 122 DLKIPHMGWNTL-QPARAHALLEGIPLGPDGLHAYFVHSYAFKLADPADLLATTDYAGTI 180 Query: 179 TAAVGRDNIMGVQFHPEKSQSYGLEFLSRFLDWNP 213 TAAV RDN+ G QFHPEKSQ GL L+ FL W P Sbjct: 181 TAAVARDNVAGTQFHPEKSQKLGLALLANFLKWRP 215 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: 205 Number of extensions: 8 Number of successful extensions: 3 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: 215 Length adjustment: 22 Effective length of query: 191 Effective length of database: 193 Effective search space: 36863 Effective search space used: 36863 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_012173019.1 AZC_RS23070 (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.967036.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-65 206.5 0.0 2e-65 206.4 0.0 1.0 1 NCBI__GCF_000010525.1:WP_012173019.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000010525.1:WP_012173019.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.4 0.0 2e-65 2e-65 1 197 [. 3 212 .. 3 213 .. 0.92 Alignments for each domain: == domain 1 score: 206.4 bits; conditional E-value: 2e-65 TIGR01855 1 ivvidygvgNlksvkkalerv.....gaesevvkdskelekadklvlPGVGafkeamkklrele..lellaek 66 ++++dyg+gNl+s +ka+er+ g + +v++d + ++ ad++vlPGVGaf+++ + l + +l+e NCBI__GCF_000010525.1:WP_012173019.1 3 VAIVDYGSGNLHSAAKAIERAaldtgGERIVVTSDPDVVRAADRVVLPGVGAFADCRRGLDAVPgmVAALEEA 75 79***********99988876333336677899999*************************997777888889 PP TIGR01855 67 vvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkesellkgle.. 134 v +++p+lgiC+G+Qll+e++ E++ + glg+ikg+v++++ + k+Ph+GWn+++++++++ll+g+ NCBI__GCF_000010525.1:WP_012173019.1 76 VHGRGRPFLGICVGLQLLAERGLEHGVTAGLGWIKGEVDRITPSDpdlKIPHMGWNTLQPARAHALLEGIPlg 148 9999**************************************988899**********************733 PP TIGR01855 135 .eearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 ++ ++YfvHsYa +l++ ++la++dy +++aav++dn++g+QFHPEkS+k Gl+ll nfl+ NCBI__GCF_000010525.1:WP_012173019.1 149 pDGLHAYFVHSYAFKLADPADLLATTDYAGTITAAVARDNVAGTQFHPEKSQKLGLALLANFLK 212 356789********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (215 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 13.92 // [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