Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate NP_347574.1 CA_C0938 imidazoleglycerol-phosphate dehydratase
Query= SwissProt::Q8ABA7 (374 letters) >NCBI__GCF_000008765.1:NP_347574.1 Length = 197 Score = 191 bits (485), Expect = 1e-53 Identities = 97/192 (50%), Positives = 132/192 (68%), Gaps = 2/192 (1%) Query: 183 ERKAEVRRTTKETDIYVSLNLDGNGGCDISTGLGFFDHMLEQIGKHSGMDLTIRVKGDLE 242 +R A + R T ET I V +NLDG G DI TG+GFFDHMLE + KH +DL ++V GDL+ Sbjct: 4 KRTAFIERKTTETSIEVDINLDGEGKYDIDTGIGFFDHMLELMSKHGLIDLKVKVIGDLK 63 Query: 243 VDEHHTIEDTAIALGECIYQALGSKRGIERYGYA-LPMDDCLCQVCLDFGGRPWLVWDAE 301 VD HHT+EDT I +GECI +ALG+K+ I RYG + +PMD+ LCQV +D GR +LV+D E Sbjct: 64 VDSHHTVEDTGIVIGECINKALGNKKSINRYGTSFVPMDESLCQVSMDISGRAFLVFDGE 123 Query: 302 FNREKIGEMPTEMFLHFFKSLSDAAKMNLNIKA-EGQNEHHKIEGIFKALARALKMALKR 360 F EK+G+ TEM FF++L+ A + L+ + G+N HH IEG+FKA RAL A+ + Sbjct: 124 FTCEKLGDFQTEMVEEFFRALAFNAGITLHARVIYGKNNHHMIEGLFKAFGRALSEAVSK 183 Query: 361 DIYHFELPSSKG 372 + + S+KG Sbjct: 184 NTRIKGVMSTKG 195 Lambda K H 0.321 0.140 0.422 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: 210 Number of extensions: 8 Number of successful extensions: 3 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: 374 Length of database: 197 Length adjustment: 25 Effective length of query: 349 Effective length of database: 172 Effective search space: 60028 Effective search space used: 60028 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