Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_017599139.1 D471_RS0113730 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000341125.1:WP_017599139.1 Length = 360 Score = 233 bits (594), Expect = 6e-66 Identities = 141/355 (39%), Positives = 198/355 (55%), Gaps = 14/355 (3%) Query: 9 YVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPD 68 Y+R++ I P + R+ + +KL+SNE+P G S + A+AQA++EL RYPD Sbjct: 9 YLRSVLESI---PAYKPGRKVVGPDGRSIKLSSNESPFGPLPSVREAVAQASAELNRYPD 65 Query: 69 ANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQ 128 A L L+ GVP + V LG GS +L+ A E G +VYA SF Y L + Sbjct: 66 PGATALVTELARHLGVPEEHVALGAGSVGLLQQLLEAVGEPGAEVVYAWRSFEAYPLLAE 125 Query: 129 GLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188 G ++ VP HDLDA+ A+++ TR++ V NPNNPTGT + +L AFLD+VP H Sbjct: 126 LAGVTSVRVPLRDETHDLDAIADAITESTRMVLVCNPNNPTGTTVPKGELLAFLDRVPEH 185 Query: 189 VVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDL 248 V+V+LDEAY EY+ + D + R PN+ V RTFSKA+GLA +R+G+ +A P + Sbjct: 186 VLVILDEAYHEYVRDPRVPDGVELYRDRPNVAVLRTFSKAYGLAAVRLGYLVAHPHVAAA 245 Query: 249 LNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNF 308 + PF VN LAQAA IA+L + L + R+ +A G P++ NF Sbjct: 246 ARKTLVPFAVNHLAQAAGIASLAARDELMERVEATVGERTRVRDALIASGWTVPPTEANF 305 Query: 309 VLVRVGND--DAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIA 361 V +RVG D D A E K GV VRP G R+++G PEEN+ F++ Sbjct: 306 VWLRVGEDTLDFAA-----ECAKVGVSVRPFEGEG----ARVSLGTPEENDVFLS 351 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: 349 Number of extensions: 15 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: 360 Length adjustment: 30 Effective length of query: 340 Effective length of database: 330 Effective search space: 112200 Effective search space used: 112200 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