Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_041643952.1 AZO_RS16855 pyridoxal phosphate-dependent aminotransferase
Query= curated2:Q2RL44 (386 letters) >NCBI__GCF_000061505.1:WP_041643952.1 Length = 385 Score = 99.4 bits (246), Expect = 2e-25 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 15/219 (6%) Query: 94 LKEALAAKLG--------VKQENLIIGNGTDEILKMLAETYINPGDEIVVADPTFSEYEF 145 L+EA+A K+ V+ E I T + +A ++PGDE++V +P + Y Sbjct: 72 LREAVAGKVAALYGSTYDVEHEVTITAGATQALFTAVA-ALVHPGDEVIVFEPVYDSYGP 130 Query: 146 AAQVMGGRAIKVPTR--NFRHDLAAMAAAITPRTRLVFVCNPNNPTGTIVGQAALDGFLK 203 A ++ GGR +++ ++R D AA+AAAITPRTR++ + +P+NPT T+ A D Sbjct: 131 AVELAGGRVVRMQLAAPDYRPDWAAVAAAITPRTRMIMINSPHNPTATVWTAADYDRLAA 190 Query: 204 QV-PPSVLVVLDEAYSDYVTAEHYPNSLAYVRAGRANVIILRTFSKIYGLAGLRVGYGVA 262 + ++VV DE Y V S A A I++ +F K Y + G +VGY VA Sbjct: 191 LLRDTGIIVVSDEVYEHIVFDGLQHRSCAAHPELAARSIVVSSFGKTYHITGWKVGYVVA 250 Query: 263 VPEIIRDLNRVRE--PFNVNLLAQVAAVAALKDEA-HVG 298 E++ + +V + F VN Q A + + + H+G Sbjct: 251 PRELMAEFRKVHQFNVFTVNTPVQYALADYMAEASRHLG 289 Lambda K H 0.319 0.137 0.389 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: 310 Number of extensions: 17 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: 386 Length of database: 385 Length adjustment: 30 Effective length of query: 356 Effective length of database: 355 Effective search space: 126380 Effective search space used: 126380 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: 50 (23.9 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