Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_014027255.1 PYRFU_RS08460 imidazoleglycerol-phosphate dehydratase
Query= SwissProt::Q9S5G5 (355 letters) >NCBI__GCF_000223395.1:WP_014027255.1 Length = 189 Score = 137 bits (344), Expect = 3e-37 Identities = 74/173 (42%), Positives = 111/173 (64%), Gaps = 4/173 (2%) Query: 173 RNTKETQIDVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTV 232 R T ET++ V V + G + TG+ FFDHML+ + + G +E++V+ +DDHH V Sbjct: 6 RETGETRVHVCVETGK-GELRGATGIPFFDHMLETFSRYSGLSIEVSVQELKRVDDHHVV 64 Query: 233 EDTGLALGEALKIALGDKRGICRFGFVL-PMDECLARCALDISGRPHLEYKA-EFTYQRV 290 ED + LG AL LGD++GI RFG+ L PMD+ LA A+D++ RP+ + +++ + Sbjct: 65 EDVAIVLGRALDKMLGDRKGIRRFGYALIPMDDALAYAAVDLARRPYFVSRGLQWSRDSI 124 Query: 291 GDLSTEMIEHFFRSLSYTMGVTLHLK-TKGKNDHHRVESLFKAFGRTLRQAIR 342 G L+ E +EHF RSL++ TLH+ G NDHH+VE+LFKA G LR+A++ Sbjct: 125 GGLALENVEHFLRSLAFEARFTLHVGIVYGSNDHHKVEALFKAVGIALREAMK 177 Lambda K H 0.322 0.140 0.420 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: 189 Number of extensions: 11 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: 355 Length of database: 189 Length adjustment: 24 Effective length of query: 331 Effective length of database: 165 Effective search space: 54615 Effective search space used: 54615 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: 47 (22.7 bits)
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