Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_058929814.1 AU252_RS05230 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_001484605.1:WP_058929814.1 Length = 365 Score = 211 bits (538), Expect = 2e-59 Identities = 133/356 (37%), Positives = 193/356 (54%), Gaps = 16/356 (4%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V + PY+ G+ R G D A LASNE+ +A A+A AA + RYPD+ Sbjct: 21 VAGLPPYVPGR------RSAGTDMAA---LASNESHYEPLPAAAAAVAAAAGTMNRYPDS 71 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 A EL+ ++ GV A V G GS +L+ + G +++A SF Y + + Sbjct: 72 AAVELRERIARHLGVTAAEVAAGPGSVGVLQQIITGLCDAGDEVIFAWRSFEAYPILVEL 131 Query: 130 LGARAIVVPAV-KYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188 GA + +P + GHDLDAM AAV+ T++I + PNNPTG I ++EAFL V Sbjct: 132 AGALPVRIPLDDREGHDLDAMAAAVTARTKVILLCTPNNPTGVPISHERIEAFLQSVRSD 191 Query: 189 VVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDL 248 ++VV+DEAY EY DS+A R+YPN+ + RTFSKA+GLAGLRVG+A+A P + + Sbjct: 192 ILVVIDEAYVEYAEAGSGPDSLALYRQYPNVCILRTFSKAYGLAGLRVGYAVAAPAIAEG 251 Query: 249 LNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNF 308 L R PF+V+ LAQ AA+A+L+ +E A Q R+ + G + S GNF Sbjct: 252 LRRTALPFSVSALAQKAAVASLDAGEEIEARVAAVRQERARMAAQLEAQGWKLQASQGNF 311 Query: 309 VLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364 + +R +D A R+ + G++VR G +RIT+ P N+ + LE Sbjct: 312 LWIRADDDLCA--RLVDAFDRAGILVRAYQGDG----VRITVASPASNDRVLRLLE 361 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: 359 Number of extensions: 17 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: 365 Length adjustment: 30 Effective length of query: 340 Effective length of database: 335 Effective search space: 113900 Effective search space used: 113900 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 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