Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_068464880.1 APY04_RS16090 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_001541235.1:WP_068464880.1 Length = 367 Score = 238 bits (608), Expect = 1e-67 Identities = 130/335 (38%), Positives = 196/335 (58%), Gaps = 1/335 (0%) Query: 37 VKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSN 96 +KL+SNE P G A A A + L RYPD A +L+ A++ RYG+ + G GS+ Sbjct: 32 IKLSSNETPFGPSPKAVEAYRAADAALERYPDGAATKLREAIARRYGLNPARIICGAGSD 91 Query: 97 DILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDD 156 ++L + AHA++ +G +Y Q+ F +Y + GA +V P D+DA+L V++ Sbjct: 92 ELLTMLAHAYLGEGDEAIYTQHGFLLYRIIILANGATPVVAPETGLRTDIDAILNRVTER 151 Query: 157 TRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRY 216 T+++F+ANPNNPTGT++ ++ + ++P HV++VLD AY EY+ + I V Sbjct: 152 TKMVFLANPNNPTGTYVSFDEIRSLRAQLPPHVLLVLDAAYAEYVRRNDYEAGIELVATT 211 Query: 217 PNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFL 276 N +++RTFSK GLAGLR+G+A + D+LNR+R PFN++ + A AA+ D A Sbjct: 212 HNTVMTRTFSKIHGLAGLRIGWAYCPEAVADVLNRIRGPFNLSVPSLLAGAAAIEDSAHE 271 Query: 277 EKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDA-AGNRVNLELLKQGVIVR 335 E S A N + L+ LGL+ PS NF+LV N+ A N + L ++G+IVR Sbjct: 272 EMSVAHNEKWLAWLSGEIAALGLKVTPSVANFILVHFPNEGARTANEADRYLKQRGIIVR 331 Query: 336 PVGNYGLPQWLRITIGLPEENEAFIAALERTLAAA 370 V +YG P LRITIG ++N A AAL +A + Sbjct: 332 KVASYGFPDCLRITIGSVDDNRAVAAALTDFMAGS 366 Lambda K H 0.318 0.135 0.385 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: 385 Number of extensions: 16 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: 370 Length of database: 367 Length adjustment: 30 Effective length of query: 340 Effective length of database: 337 Effective search space: 114580 Effective search space used: 114580 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 (21.7 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