Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_093428503.1 BM272_RS09245 imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::D2QPE6 (382 letters) >NCBI__GCF_900112605.1:WP_093428503.1 Length = 196 Score = 186 bits (473), Expect = 4e-52 Identities = 96/195 (49%), Positives = 127/195 (65%), Gaps = 2/195 (1%) Query: 190 ARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVNGDLH 249 +R A V R T ET IRV L+LDG GRA + TG+ F DHML+QVA+H DL + GDL Sbjct: 2 SRQAEVRRQTLETDIRVALDLDGSGRATLDTGVPFLDHMLEQVARHGQVDLEVGAVGDLD 61 Query: 250 IDEHHTIEDTALALGEAYRRALGDKRGISRYGFL-LPMDEALAQVGIDFSGRPWLVWDAE 308 ID HHT+ED + LG+A RALGDK GI RYG + +P+DEAL++V +DFSGRP LVW+ Sbjct: 62 IDAHHTVEDVGITLGQALARALGDKAGIQRYGHVYVPLDEALSRVVLDFSGRPGLVWNVA 121 Query: 309 FKREKIGDMPTEMFYHFFKSFSDTALCNLNI-KVEGDNEHHKIEAIFKAFAKAIKMAVRR 367 F R+ +G+ T++F+ FF+ + A L++ + GDN HH E FKAF +A++ A Sbjct: 122 FPRQWVGEFDTDLFHEFFQGLVNHAWMTLHVDNLRGDNSHHVAETAFKAFGRALRAAAEP 181 Query: 368 DINELDNLPSTKGVL 382 D STKG L Sbjct: 182 DPRLGGAAASTKGSL 196 Lambda K H 0.320 0.136 0.403 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: 196 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: 382 Length of database: 196 Length adjustment: 25 Effective length of query: 357 Effective length of database: 171 Effective search space: 61047 Effective search space used: 61047 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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