Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_072906780.1 BUB13_RS06005 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >NCBI__GCF_900142125.1:WP_072906780.1 Length = 207 Score = 184 bits (466), Expect = 1e-51 Identities = 101/207 (48%), Positives = 129/207 (62%), Gaps = 7/207 (3%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63 I ++DY MGNLRSV +A + D R+S + DI AD+VVLPG GA DC+ +LRE Sbjct: 2 INIIDYEMGNLRSVEKAFEKLG--FDARVSDKPEDIATADKVVLPGVGAFRDCINNLREG 59 Query: 64 G-VQDAVIEASRTKPLFGVCVGEQMLFDWSEE-GDTPGLGLLPGKVVRFDLEGMRQDDGS 121 G V+ + KPL G+CVG QM+FD SEE G GLGL+PGKVVRF GM + G Sbjct: 60 GFVEPLLAHVEAGKPLLGICVGMQMMFDESEEFGRHAGLGLIPGKVVRFP-SGM-VEGGE 117 Query: 122 LFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGR-DFACA 180 KVP MGWN++ P++ G+ D++F YFVHSYY V YG +F + Sbjct: 118 RLKVPHMGWNNISLKKDSPIFSGVKDDSFVYFVHSYYCAAENVEDVAATCTYGDVEFCAS 177 Query: 181 VARDNIFATQFHPEKSASAGLQLYRNF 207 + RDNI ATQFHPEKS GLQ+++NF Sbjct: 178 LWRDNIMATQFHPEKSQDIGLQIFKNF 204 Lambda K H 0.322 0.137 0.431 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: 173 Number of extensions: 9 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: 212 Length of database: 207 Length adjustment: 21 Effective length of query: 191 Effective length of database: 186 Effective search space: 35526 Effective search space used: 35526 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_072906780.1 BUB13_RS06005 (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.23680.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-73 233.2 0.0 1.3e-73 233.0 0.0 1.0 1 lcl|NCBI__GCF_900142125.1:WP_072906780.1 BUB13_RS06005 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900142125.1:WP_072906780.1 BUB13_RS06005 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 233.0 0.0 1.3e-73 1.3e-73 1 197 [. 2 206 .. 2 207 .] 0.96 Alignments for each domain: == domain 1 score: 233.0 bits; conditional E-value: 1.3e-73 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvv 68 i +idy++gNl+sv+ka+e++g+ ++v+++ +++ +adk+vlPGVGaf++++++lre + +e l +v lcl|NCBI__GCF_900142125.1:WP_072906780.1 2 INIIDYEMGNLRSVEKAFEKLGFDARVSDKPEDIATADKVVLPGVGAFRDCINNLREGGfVEPL-LAHV 69 689********************************************************77777.7888 PP TIGR01855 69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek.......kvPhiGWnevevvkesell 130 +++kp+lgiC+GmQ++f++seE +++ glgli+gkv+++ + + kvPh+GWn+++ +k+s+++ lcl|NCBI__GCF_900142125.1:WP_072906780.1 70 EAGKPLLGICVGMQMMFDESEEFGRHAGLGLIPGKVVRFPSGMveggerlKVPHMGWNNISLKKDSPIF 138 9999***********************************98877888899******************* PP TIGR01855 131 kgleeearvYfvHsYaveleeeeavlakadyge.kfvaavekdnivgvQFHPEkSgktGlkllknfle 197 +g+++++ vYfvHsY+ e+ e+v a+++yg +f a++ +dni+++QFHPEkS+++Gl+++knf e lcl|NCBI__GCF_900142125.1:WP_072906780.1 139 SGVKDDSFVYFVHSYYCAAENVEDVAATCTYGDvEFCASLWRDNIMATQFHPEKSQDIGLQIFKNFGE 206 *******************************6439******************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (207 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: 6.51 // [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