Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF2362 PGA1_c23930 putative histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Phaeo:GFF2362 Length = 369 Score = 159 bits (401), Expect = 1e-43 Identities = 103/334 (30%), Positives = 170/334 (50%), Gaps = 4/334 (1%) Query: 38 KLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSND 97 +L +NEN G A AM + E+ +Y DA + +L+AAL+ + V + + +G G + Sbjct: 36 RLGANENIFGPSPKAIAAMQGSLGEIWKYGDAESHDLRAALAAHHSVAPENIMIGEGIDG 95 Query: 98 ILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSD-D 156 +L + +G ++V + ++ + G G VP D A+ A ++ D Sbjct: 96 LLGYLVRLLIGEGDAVVTSLGAYPTFNYHVAGFGGVLHTVPYQDDHEDPAALFAKAAEVD 155 Query: 157 TRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRY 216 +L+++ANP+NP G++ G L A +D +P +++LDEAY + P ++ Sbjct: 156 AKLVYLANPDNPMGSWHSGAGLLAAMDALPEGCLLLLDEAYIDCAPDGT---ALPIDIND 212 Query: 217 PNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFL 276 P ++ +RTFSKA+G+AG RVG+ +A+ L N+VR F +N AQ A+AAL D+A+L Sbjct: 213 PRVIRTRTFSKAYGMAGARVGYVLAEAGLISAFNKVRNHFGMNRTAQIGALAALRDQAWL 272 Query: 277 EKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRP 336 + A R+ + GL +PS NFV + G D A V L+ QGV VR Sbjct: 273 AEVLGRIATARNRIAQIARDNGLTPLPSATNFVAIDCGADGAFAKSVLEGLVDQGVFVRM 332 Query: 337 VGNYGLPQWLRITIGLPEENEAFIAALERTLAAA 370 + +R++ G ++ +F AL L A Sbjct: 333 PFAAPQNRCIRVSCGPEDQLNSFARALPLALERA 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: 337 Number of extensions: 13 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: 369 Length adjustment: 30 Effective length of query: 340 Effective length of database: 339 Effective search space: 115260 Effective search space used: 115260 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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