Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_086509706.1 BZY95_RS09530 aminotransferase
Query= curated2:A7HCR6 (364 letters) >NCBI__GCF_002151265.1:WP_086509706.1 Length = 369 Score = 143 bits (360), Expect = 8e-39 Identities = 115/354 (32%), Positives = 168/354 (47%), Gaps = 17/354 (4%) Query: 1 MPLVPPHVASLTPYVPGKPIEEVEREYGVSNVAKLASNENALGPSPLALAAAREACAK-V 59 MP P H+ P P I+ +ER G +L SNE P +A + V Sbjct: 1 MPRFPDHLKGSGPSNPFPGIKVLERRIGREIPHRLGSNEGLDMPHRALRERFGDAMTEHV 60 Query: 60 HLYPDGSAYLLRNAIAAKLGVPPEEVMVGNGSNELIELLVRTFVLDGEEVLTSAQSFVAY 119 + Y D A +R +A+ G+P E +V G++ LI L +RT G V++++ ++ + Sbjct: 61 YCYGDAEALGVRQRLASLYGLPLEHTLVDAGADSLIALALRTVAEPGCTVVSASGTYPTF 120 Query: 120 KLAAHEHGRTLVEAPMK---GRFHYDLDALRKLLSR-RTKLVFLANPDNPTGTWFTEAEL 175 A LVE P + G DL+AL R +LV++ANPDNP+G + E+ Sbjct: 121 GYFARGQNCHLVERPYREAPGLLTPDLEALLAAAQEHRARLVYVANPDNPSGHLHGDDEI 180 Query: 176 TPFLDAVPKDTLVVLDEAYVEYVDAPGFQDGLALRRKYPNVVVLRTFSKIYGLAGMRLGY 235 +P+D ++LDEAY ++ D D R P V+ LRT SK +GLAGMR+GY Sbjct: 181 RRLRAELPEDCWLLLDEAYHDFRDDA---DSPFSREALPGVIRLRTLSKAHGLAGMRIGY 237 Query: 236 GLARPEVVEYVDRVRPPFNTNLVAQAAGAAALGDSAHVAKSRALVLEERPFLAKGLAALG 295 +A PE + + +VR + + + Q L V V R LA+ LG Sbjct: 238 AIAEPETLAMMMKVRIHYAVSSLTQIIAETVLDRHTEVEAHIRAVKARRERLARHFRELG 297 Query: 296 AIVVPSQGNFVL-----ADFPGRTGKDLFEALLREGVIARPVAGYGFPSALRIT 344 A V+PS NF+ A+ GR ++L EA +IARP A LRIT Sbjct: 298 AEVLPSATNFIALRFSSAELAGRLNQELLEA---GRLIARP-AHPDLGHVLRIT 347 Lambda K H 0.320 0.138 0.399 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: 369 Number of extensions: 17 Number of successful extensions: 5 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: 364 Length of database: 369 Length adjustment: 30 Effective length of query: 334 Effective length of database: 339 Effective search space: 113226 Effective search space used: 113226 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: 49 (23.5 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