Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_013258247.1 DEBA_RS07130 imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::Q9S5G5 (355 letters) >NCBI__GCF_000143965.1:WP_013258247.1 Length = 195 Score = 169 bits (428), Expect = 5e-47 Identities = 90/193 (46%), Positives = 126/193 (65%), Gaps = 4/193 (2%) Query: 167 RYAHVVRNTKETQIDVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYI 226 R A + R T+ET I +++ LD G ++I+TGVGFFDHML IA HG F +E+ KGDL++ Sbjct: 3 RTATIKRETRETAISLRLDLDGRGEARIDTGVGFFDHMLTHIAFHGRFDLEVTAKGDLHV 62 Query: 227 DDHHTVEDTGLALGEALKIALGDKRGICRF-GFVLPMDECLARCALDISGRPHLEYKAEF 285 D HHTVED G+ LG+AL+ ALGDK G+ R+ G +PMDE LA+ +D+S RP + +A Sbjct: 63 DAHHTVEDVGICLGQALRQALGDKLGVARYGGAFVPMDEALAQVVVDLSNRPFMRLEAAR 122 Query: 286 TYQRVGDLSTEMIEHFFRSLSYTMGVTLH-LKTKGKNDHHRVESLFKAFGRTLRQAIRVE 344 VG ++ E F R+L+ G+TLH + G NDHH +E+ FKA GR L QA ++ Sbjct: 123 LPGAVGAFDGQLAEEFLRALANAAGLTLHVILHYGSNDHHMLEAAFKALGRALDQATAMD 182 Query: 345 --GDTLPSSKGVL 355 + S+KG+L Sbjct: 183 PRQGGVASTKGML 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: 215 Number of extensions: 9 Number of successful extensions: 5 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 09 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