Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_011372710.1 SUDEN_RS05675 imidazoleglycerol-phosphate dehydratase
Query= SwissProt::Q9S5G5 (355 letters) >NCBI__GCF_000012965.1:WP_011372710.1 Length = 190 Score = 141 bits (355), Expect = 2e-38 Identities = 80/186 (43%), Positives = 110/186 (59%), Gaps = 4/186 (2%) Query: 173 RNTKETQIDVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTV 232 R TKET I V + ++ G SKI+TGVGF DHMLD + H +EI KGD +IDDHH+V Sbjct: 6 RKTKETDITVSLDINGNGKSKIDTGVGFLDHMLDSFSKHSLIDLEITCKGDTHIDDHHSV 65 Query: 233 EDTGLALGEALKIALGDKRGICRFGFV-LPMDECLARCALDISGRPHLEYKAEFTYQRVG 291 ED G+ LG AL + RFG + MDE C LD+S RP+L Y+ +VG Sbjct: 66 EDIGIVLGALFAEALYPVSNMERFGSANIVMDEACVSCDLDLSNRPYLVYEVNLA-GKVG 124 Query: 292 DLSTEMIEHFFRSLSYTMGVTLHL-KTKGKNDHHRVESLFKAFGRTLRQAI-RVEGDTLP 349 TE++E FFR+ ++ H+ +GKN HH +E+ FKA LR+A+ + E +P Sbjct: 125 QFDTELVEEFFRAFVLNARISTHIVLQRGKNRHHIIEAAFKAVAVALRRAMQKNERVGIP 184 Query: 350 SSKGVL 355 S+K +L Sbjct: 185 STKDML 190 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: 170 Number of extensions: 13 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: 190 Length adjustment: 24 Effective length of query: 331 Effective length of database: 166 Effective search space: 54946 Effective search space used: 54946 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