Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate YP_004139704.1 Mesci_0482 imidazoleglycerol-phosphate dehydratase
Query= SwissProt::D2QPE6 (382 letters) >NCBI__GCF_000185905.1:YP_004139704.1 Length = 199 Score = 196 bits (498), Expect = 5e-55 Identities = 96/197 (48%), Positives = 133/197 (67%), Gaps = 2/197 (1%) Query: 188 LPARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVNGD 247 +P R+A R TKET I V +++DG G++D+ TG+GFFDHMLDQ+++HS D+ + GD Sbjct: 1 MPPRSAEASRKTKETDISVSIHVDGSGKSDIATGVGFFDHMLDQLSRHSLIDMTVRAKGD 60 Query: 248 LHIDEHHTIEDTALALGEAYRRALGDKRGISRYGFL-LPMDEALAQVGIDFSGRPWLVWD 306 LHID+HHT+EDT +ALG+A +ALG++RGI RY + L MDE L + ID SGRP+LVW+ Sbjct: 61 LHIDDHHTVEDTGIALGQALTKALGERRGIIRYASIDLAMDETLTRAAIDVSGRPFLVWN 120 Query: 307 AEFKREKIGDMPTEMFYHFFKSFSDTALCNLNIKVE-GDNEHHKIEAIFKAFAKAIKMAV 365 F KIG TE+ FF++ + A L++ G N HH E FKA A+A++ A+ Sbjct: 121 VSFSSPKIGTFDTELVREFFQALAQNAGITLHVTNHYGANNHHIAETCFKAVARALRAAL 180 Query: 366 RRDINELDNLPSTKGVL 382 RD + D +PSTKG L Sbjct: 181 ERDPRQPDAVPSTKGSL 197 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: 217 Number of extensions: 12 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: 199 Length adjustment: 25 Effective length of query: 357 Effective length of database: 174 Effective search space: 62118 Effective search space used: 62118 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