Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_025273931.1 HALAL_RS0110285 imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::D2QPE6 (382 letters) >NCBI__GCF_000527155.1:WP_025273931.1 Length = 202 Score = 166 bits (419), Expect = 7e-46 Identities = 93/204 (45%), Positives = 127/204 (62%), Gaps = 14/204 (6%) Query: 190 ARTALVERNTKETQIRVELNLD-GRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVNGDL 248 +RTA V R T ET + V L+LD D+ TG+GF+DHML Q+ KH G L++ GDL Sbjct: 2 SRTAHVNRTTGETSVDVHLDLDPDTVTVDVSTGVGFYDHMLHQLGKHGGFGLSVRTEGDL 61 Query: 249 HIDEHHTIEDTALALGEAYRRALGDKRGISRYG-FLLPMDEALAQVGIDFSGRPWLVWDA 307 HID HHT+EDTA+ALG A+ ALGDKRG+ R+ +P+DEAL++ +D SGRP+ V D Sbjct: 62 HIDAHHTLEDTAIALGSAFAEALGDKRGVVRFADATVPLDEALSRAVVDLSGRPYCVHDE 121 Query: 308 EFKREKI--GDMPTEMFYHFFKSFSDTALCNLNIKV-------EGDNEHHKIEAIFKAFA 358 + GD PT M H +SF+ A L++ V + + HH +E+ FKA A Sbjct: 122 PLEMADTIGGDYPTSMTRHVLESFAHHARICLHVSVLRASNPGQKPDAHHIVESQFKALA 181 Query: 359 KAIKMAVRRDINELDNLPSTKGVL 382 +A++ A RR E D +PSTKGV+ Sbjct: 182 RALRAATRR---EGDEIPSTKGVI 202 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: 242 Number of extensions: 13 Number of successful extensions: 6 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: 202 Length adjustment: 25 Effective length of query: 357 Effective length of database: 177 Effective search space: 63189 Effective search space used: 63189 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 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