Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_075386978.1 BK574_RS20700 imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::Q9S5G5 (355 letters) >NCBI__GCF_002019605.1:WP_075386978.1 Length = 195 Score = 171 bits (434), Expect = 1e-47 Identities = 90/194 (46%), Positives = 124/194 (63%), Gaps = 4/194 (2%) Query: 166 DRYAHVVRNTKETQIDVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLY 225 +R + R T ETQI +Q +D EG S +NT V F HMLD HG F + ++ KGD+ Sbjct: 2 ERTGSIERITGETQIKLQFGIDGEGKSDLNTNVPFMTHMLDLFTKHGHFDLTLDAKGDVD 61 Query: 226 IDDHHTVEDTGLALGEALKIALGDKRGICRFG-FVLPMDECLARCALDISGRPHLEYKAE 284 +DDHHT ED G+ LG ALK ALGDKRGI R+G +PMDE LA+ +D+S RPHLE++AE Sbjct: 62 VDDHHTTEDIGICLGIALKDALGDKRGIKRYGNAFVPMDETLAQVVVDLSNRPHLEFRAE 121 Query: 285 FTYQRVGDLSTEMIEHFFRSLSYTMGVTLHLKTK-GKNDHHRVESLFKAFGRTLRQAIRV 343 F ++VG TE++ F L+ + LH+ G N HH +E++FKA GR L A ++ Sbjct: 122 FPSEKVGTFDTELVHEFLWKLALEARMNLHVIVHYGHNTHHMIEAVFKALGRALDDATQI 181 Query: 344 EGDT--LPSSKGVL 355 + +PS+KG+L Sbjct: 182 DERVKGVPSTKGML 195 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: 224 Number of extensions: 9 Number of successful extensions: 4 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: 195 Length adjustment: 25 Effective length of query: 330 Effective length of database: 170 Effective search space: 56100 Effective search space used: 56100 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