Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate GFF2362 PGA1_c23930 putative histidinol-phosphate aminotransferase
Query= curated2:A7HCR6 (364 letters) >FitnessBrowser__Phaeo:GFF2362 Length = 369 Score = 178 bits (452), Expect = 2e-49 Identities = 120/333 (36%), Positives = 169/333 (50%), Gaps = 9/333 (2%) Query: 2 PLVPPHVASLTPYVPGKPIEEVEREYGVSNVAKLASNENALGPSPLALAAAREACAKVHL 61 P P SL VP E ER+ G A+L +NEN GPSP A+AA + + ++ Sbjct: 4 PRYTPLAQSLPASVPFVGPETQERQRGAPFAARLGANENIFGPSPKAIAAMQGSLGEIWK 63 Query: 62 YPDGSAYLLRNAIAAKLGVPPEEVMVGNGSNELIELLVRTFVLDGEEVLTSAQSFVAYKL 121 Y D ++ LR A+AA V PE +M+G G + L+ LVR + +G+ V+TS ++ + Sbjct: 64 YGDAESHDLRAALAAHHSVAPENIMIGEGIDGLLGYLVRLLIGEGDAVVTSLGAYPTFNY 123 Query: 122 AAHEHGRTLVEAPMKGRFHYDLDALRKLLSRRTKLVFLANPDNPTGTWFTEAELTPFLDA 181 G L P + K KLV+LANPDNP G+W + A L +DA Sbjct: 124 HVAGFGGVLHTVPYQDDHEDPAALFAKAAEVDAKLVYLANPDNPMGSWHSGAGLLAAMDA 183 Query: 182 VPKDTLVVLDEAYVEYVDAPGFQDGLALRRKY--PNVVVLRTFSKIYGLAGMRLGYGLAR 239 +P+ L++LDEAY++ AP DG AL P V+ RTFSK YG+AG R+GY LA Sbjct: 184 LPEGCLLLLDEAYIDC--AP---DGTALPIDINDPRVIRTRTFSKAYGMAGARVGYVLAE 238 Query: 240 PEVVEYVDRVRPPFNTNLVAQAAGAAALGDSAHVAKSRALVLEERPFLAKGLAALGAIVV 299 ++ ++VR F N AQ AAL D A +A+ + R +A+ G + Sbjct: 239 AGLISAFNKVRNHFGMNRTAQIGALAALRDQAWLAEVLGRIATARNRIAQIARDNGLTPL 298 Query: 300 PSQGNFVLAD--FPGRTGKDLFEALLREGVIAR 330 PS NFV D G K + E L+ +GV R Sbjct: 299 PSATNFVAIDCGADGAFAKSVLEGLVDQGVFVR 331 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: 332 Number of extensions: 13 Number of successful extensions: 2 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 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