Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate Ga0059261_2299 Ga0059261_2299 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Korea:Ga0059261_2299 Length = 376 Score = 266 bits (680), Expect = 7e-76 Identities = 151/363 (41%), Positives = 216/363 (59%), Gaps = 11/363 (3%) Query: 9 YVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPD 68 ++ IAPY+ GK ++ R+ +KL+SNENPLG + A+ A A AA+ L RYPD Sbjct: 13 WIMDIAPYVPGKSKTDDGRK-------AIKLSSNENPLGTSDKARAAFATAANSLERYPD 65 Query: 69 ANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQ 128 A+A EL+ AL+E +G+ A + GNGS+++L +AA AF G I+Y Y F VY +AT+ Sbjct: 66 ASAVELREALAELHGLDAARIIYGNGSDEVLHLAAGAFAGPGDEIIYVNYGFTVYPIATK 125 Query: 129 GLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188 +GA +V Y D+DA+LA+V+D TR++FVANPNNPTGT+ ++ + Sbjct: 126 RVGATPVVAADADYATDVDAILASVTDRTRIVFVANPNNPTGTYASREEIARLHAGLRPD 185 Query: 189 VVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDL 248 +++VLD AY EY+ E + + PN+LV+RTFSK +GLA R+G+ E+ + Sbjct: 186 ILLVLDHAYAEYIEGEIDDGGMELAKTQPNVLVTRTFSKLYGLAAERIGWGYGSAEVIEA 245 Query: 249 LNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKL---GLEYVPSD 305 ++R+R PF++ AAAIAAL+D AF+E + + NAQ R + KL GL VPS Sbjct: 246 MHRIRLPFSITIAGTAAAIAALHDSAFVEHTRSHNAQWRRWFADEIAKLGNAGLRAVPSQ 305 Query: 306 GNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALER 365 NFVLV + L+ +G IVR + GLP LRITIG EE A A L + Sbjct: 306 ANFVLV-LFEGALTAEAAYKGLMDEGYIVRWLPGQGLPHGLRITIGTEEETRAVAAILNK 364 Query: 366 TLA 368 +A Sbjct: 365 LVA 367 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: 380 Number of extensions: 16 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: 376 Length adjustment: 30 Effective length of query: 340 Effective length of database: 346 Effective search space: 117640 Effective search space used: 117640 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: 50 (23.9 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