Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate 3608695 Dshi_2088 aminotransferase class I and II (RefSeq)
Query= curated2:A7HCR6 (364 letters) >FitnessBrowser__Dino:3608695 Length = 372 Score = 187 bits (475), Expect = 4e-52 Identities = 132/334 (39%), Positives = 175/334 (52%), Gaps = 11/334 (3%) Query: 2 PLVPPHVASLTPYVPGKPIEEVEREYGVSNVAKLASNENALGPSPLALAAAREACAKVHL 61 P P SL VP E ER G A+L +NE+A GPSP A+AA EA + Sbjct: 7 PRFTPLAQSLPATVPFVGPETQERARGRPFAARLGANESAFGPSPRAVAAMAEAATGAWM 66 Query: 62 YPDGSAYLLRNAIAAKLGVPPEEVMVGNGSNELIELLVRTFVLDGEEVLTSAQSFVAYKL 121 Y D ++ LR A+AA V E V+VG G + L+ LVR V G+ V+TSA ++ + Sbjct: 67 YGDPESHDLRAALAAHHRVGMENVIVGEGIDGLLGYLVRLLVAPGDTVVTSAGAYPTFNY 126 Query: 122 AAHEHGRTLVEAPMKGRFHYDLDALRKLLSR-RTKLVFLANPDNPTGTWFTEAELTPFLD 180 G TL P + H D AL + K ++LANPDNP G+W +T +D Sbjct: 127 HVAGFGGTLHAVPYRDD-HEDPQALLDMARAVDAKAIYLANPDNPMGSWHAAGVITDMID 185 Query: 181 AVPKDTLVVLDEAYVEYVDAPGFQDGLA--LRRKYPNVVVLRTFSKIYGLAGMRLGYGLA 238 A+P L++LDEAY+E AP DG A + P V+ LRTFSK GLAG R+GYG+A Sbjct: 186 ALPPGCLLLLDEAYIEL--AP---DGTAPEIAPDDPRVIRLRTFSKARGLAGARVGYGIA 240 Query: 239 RPEVVEYVDRVRPPFNTNLVAQAAGAAALGDSAHVAKSRALVLEERPFLAKGLAALGAIV 298 P ++ +VR F + V+QAA AAL DS H+AK A R +A+ AA G Sbjct: 241 APGLISAFGKVRNHFGMSRVSQAAALAALQDSDHLAKVVAKTAAARTRIAEIGAAHGLRA 300 Query: 299 VPSQGNFVLADF--PGRTGKDLFEALLREGVIAR 330 +PS NFV D G K + EAL+ + R Sbjct: 301 LPSATNFVTLDCGGDGARAKAILEALIARDIFVR 334 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: 346 Number of extensions: 15 Number of successful extensions: 4 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: 372 Length adjustment: 30 Effective length of query: 334 Effective length of database: 342 Effective search space: 114228 Effective search space used: 114228 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