Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011736874.1 PPRO_RS15090 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000015045.1:WP_011736874.1 Length = 350 Score = 159 bits (402), Expect = 1e-43 Identities = 105/340 (30%), Positives = 176/340 (51%), Gaps = 23/340 (6%) Query: 32 DEATIVKLASNENPLGMPESAQRA----MAQAASELGRYPDANAFELKAALSERYGVPAD 87 D ++ +KL +NENP + A M + L YP A++ L+ A SE YG Sbjct: 22 DISSWIKLNTNENPYPPSPKVREAILAEMGDDGASLRTYPSASSQRLREAASELYGFDPS 81 Query: 88 WVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLD 147 W+ + NGS+++L A +G + Y S++ YA ++ GA+ +G D Sbjct: 82 WIIMANGSDELLNNLIRACASEGDEVGYVHPSYSYYATLSEIQGAKVRT-----FGLTED 136 Query: 148 AMLAAVSD--DTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV--VVVLDEAYTEYLPQ 203 +A D R+ F+ PN P G ++++++ R ++V+DEAY ++ Sbjct: 137 FRIAGFPDRYQGRVFFLTTPNAPLGFSFP----LSYVEEIARSCQGLLVIDEAYADFADT 192 Query: 204 EKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQ 263 +++ VR+Y N++V+RTFSK++ LAG+R+G AIA+PE+ L+++R +N++ LAQ Sbjct: 193 ----NALELVRKYENVVVTRTFSKSYALAGMRLGLAIARPEIVAALDKIRDHYNLDRLAQ 248 Query: 264 AAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRV 323 A+ IA+L D+ + +S A + + +G +PS NFV D G RV Sbjct: 249 ASCIASLGDQEYFRQSCARIRETREWFSAGLRSIGFSLIPSQTNFVF--ASPPDRNGRRV 306 Query: 324 NLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAAL 363 L + ++VR + L LRI+IG +E E +AAL Sbjct: 307 YDALYSRKILVRHFSDPILAHGLRISIGTRQEMELTLAAL 346 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: 343 Number of extensions: 20 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: 370 Length of database: 350 Length adjustment: 29 Effective length of query: 341 Effective length of database: 321 Effective search space: 109461 Effective search space used: 109461 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