Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011840543.1 RSPH17029_RS03545 pyridoxal phosphate-dependent aminotransferase
Query= curated2:A7HCR6 (364 letters) >NCBI__GCF_000015985.1:WP_011840543.1 Length = 367 Score = 174 bits (442), Expect = 3e-48 Identities = 127/334 (38%), Positives = 177/334 (52%), Gaps = 12/334 (3%) Query: 2 PLVPPHVASLTPYVPGKPIEEVEREYGVSNVAKLASNENALGPSPLALAAAREACAKVHL 61 P P V SL VP E ER G A+L +NE+ GPSP A+AA A A+V L Sbjct: 4 PRYTPLVESLPSTVPFVGPETQERARGRPFRARLGANESLFGPSPRAVAAMAAAAAEVSL 63 Query: 62 YPDGSAYLLRNAIAAKLGVPPEEVMVGNGSNELIELLVRTFVLDGEEVLTSAQSFVAYKL 121 Y D + LR A+AA GV P +V VG G + L+ LVR V +G V+TS ++ + Sbjct: 64 YGDPEIHALRTALAAHHGVAPAQVTVGEGVDGLLGNLVRLLVDEGAPVVTSEGAYPTFAF 123 Query: 122 AAHEHGRTLVEAPMKGRFHYDLDALRKLLSR-RTKLVFLANPDNPTGTWFTEAELTPFLD 180 G L + P +G H D +AL R ++V+ ANPDNP G+ A + ++ Sbjct: 124 HVAGFGGRLHKVPYQGD-HEDPEALAAEARRVGARIVYFANPDNPMGSHHPAASVRALIE 182 Query: 181 AVPKDTLVVLDEAYVEYVDAPGFQDGLA--LRRKYPNVVVLRTFSKIYGLAGMRLGYGLA 238 A+P+ TL+ LDEAYVE AP +G A + + P V+ RTFSK YG+AG+R+GY + Sbjct: 183 ALPEGTLLALDEAYVEL--AP---EGTAPEIDPEDPRVIRFRTFSKAYGMAGLRVGYAIG 237 Query: 239 RPEVVEYVDRVRPPFNTNLVAQAAGAAALGDSAHVAKSRALVLEERPFLAKGLAALGAIV 298 +++ D+VR F +AQA AAL D A +A +A V R + + G Sbjct: 238 ARDLIRAFDKVRNHFGVGRIAQAGALAALEDRAWLAHVQAEVQAARAEIGRIAEGCGLTP 297 Query: 299 VPSQGNFVLADFPGRTGKDLFEALLREGVIARPV 332 +PS NFV D GR G A+L E ++AR + Sbjct: 298 LPSATNFVTIDC-GRDGA-FARAVLTE-LVARDI 328 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: 335 Number of extensions: 18 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: 364 Length of database: 367 Length adjustment: 30 Effective length of query: 334 Effective length of database: 337 Effective search space: 112558 Effective search space used: 112558 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 16 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