Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate BPHYT_RS27000 BPHYT_RS27000 aspartate aminotransferase
Query= curated2:Q0C348 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS27000 Length = 392 Score = 85.1 bits (209), Expect = 3e-21 Identities = 65/208 (31%), Positives = 98/208 (47%), Gaps = 14/208 (6%) Query: 45 PSP---KAVEAAKAAAANVHVYPDPDYGPLRAAIAAAKG-----IADASRVVTSAGSDEI 96 P+P +A+EA + + H P+RAAIAA A A+ V+ +AG+ Sbjct: 47 PAPIVERAIEALRGG--DTHYSAVSGREPVRAAIAAEHTRMTGCAASAANVILTAGAQNG 104 Query: 97 IHLLTQCYAGPGDEVLFTEHAFSMYRVSAGAHGATSVTVPETDMTA---GVNAILGAVSP 153 + + C GDEV+ E + Y A GAT VTVP A +A+ AV+ Sbjct: 105 VFAASLCLLEAGDEVIVPEPMYLTYEACVRAAGATLVTVPVDAARAFHVDCDALEAAVTS 164 Query: 154 RTKILFLANPNNPTGTMLSVDELKALQDALPPHVLFVV-DGAYSEYLGPDYEAQLRDLVD 212 RTK +F A P NPTG ++ +L+ + H L+V+ D Y+E + L Sbjct: 165 RTKAIFFATPCNPTGVVMQRADLERIARLACRHDLWVLSDEVYAELTFEREHVSIAALPG 224 Query: 213 RRDNTVMMRTFSKIYGLAAMRLGWAYMP 240 + TV + + SK + +A R+GWA P Sbjct: 225 MAERTVTLGSLSKSHAMAGWRVGWAIGP 252 Lambda K H 0.318 0.133 0.390 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: 270 Number of extensions: 13 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: 367 Length of database: 392 Length adjustment: 30 Effective length of query: 337 Effective length of database: 362 Effective search space: 121994 Effective search space used: 121994 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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