Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_014450185.1 LFE_RS10415 imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::D2QPE6 (382 letters) >NCBI__GCF_000284315.1:WP_014450185.1 Length = 204 Score = 187 bits (474), Expect = 3e-52 Identities = 96/195 (49%), Positives = 133/195 (68%), Gaps = 4/195 (2%) Query: 191 RTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVNGDLHI 250 RT VER T+ETQI LNLDG GR+ + TG+ F DHM+DQ+A+H D+ + V GDL + Sbjct: 11 RTFSVERKTRETQIVASLNLDGTGRSRVDTGIPFLDHMIDQIARHGHMDIELSVKGDLEV 70 Query: 251 DEHHTIEDTALALGEAYRRALGDKRGISRYG-FLLPMDEALAQVGIDFSGRPWLVWDAEF 309 D HHT+ED L GE R LGD+ GI+R+G F P+DE+LA V ID SGRP+LVWD F Sbjct: 71 DFHHTVEDAGLVFGELVDRCLGDRVGIARFGHFFAPLDESLAHVVIDLSGRPYLVWDLPF 130 Query: 310 KR-EKIGDMPTEMFYHFFKSFSDTALCNLNIKV-EGDNEHHKIEAIFKAFAKAIKMAVRR 367 +R E++G+M ++ FF++ + + ++ ++ G N HHKIEAIFKAFA+ + MA Sbjct: 131 ERGERVGNMDPDLIMDFFQAVAVASRSTIHGRILYGRNLHHKIEAIFKAFARCLMMAAEI 190 Query: 368 DINELDNLPSTKGVL 382 D + ++PSTKG+L Sbjct: 191 DPRQ-KSVPSTKGIL 204 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: 223 Number of extensions: 18 Number of successful extensions: 2 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: 204 Length adjustment: 25 Effective length of query: 357 Effective length of database: 179 Effective search space: 63903 Effective search space used: 63903 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