Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_011306320.1 MBAR_RS07030 imidazoleglycerol-phosphate dehydratase
Query= SwissProt::Q9S5G5 (355 letters) >NCBI__GCF_000195895.1:WP_011306320.1 Length = 191 Score = 193 bits (491), Expect = 3e-54 Identities = 91/190 (47%), Positives = 128/190 (67%), Gaps = 1/190 (0%) Query: 167 RYAHVVRNTKETQIDVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYI 226 R + R TKET I +++ LD G + +NTG+GFFDHML A H F +++ +GDLY+ Sbjct: 2 RTGRMSRKTKETDIQLELNLDGTGIADVNTGIGFFDHMLTSFARHAEFDLKVRAEGDLYV 61 Query: 227 DDHHTVEDTGLALGEALKIALGDKRGICRFGFV-LPMDECLARCALDISGRPHLEYKAEF 285 D+HH VEDTG+ LG+ L ALGD G RFG +PMDE LA ALDI GR +L KAEF Sbjct: 62 DEHHLVEDTGIVLGKVLAEALGDMAGTARFGEARIPMDEALADVALDIGGRSYLVLKAEF 121 Query: 286 TYQRVGDLSTEMIEHFFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEG 345 +VG ST++++HFF +L+ +T+H G NDHH++E+LFKAF +++A+++EG Sbjct: 122 ASPQVGQFSTQLVKHFFETLASNAKITIHASVYGDNDHHKIEALFKAFAYAMKRAVKIEG 181 Query: 346 DTLPSSKGVL 355 + S+KG L Sbjct: 182 KEVKSTKGTL 191 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: 206 Number of extensions: 10 Number of successful extensions: 2 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: 191 Length adjustment: 24 Effective length of query: 331 Effective length of database: 167 Effective search space: 55277 Effective search space used: 55277 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