Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate AO353_02065 AO353_02065 aspartate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__pseudo3_N2E3:AO353_02065 Length = 370 Score = 370 bits (950), Expect = e-107 Identities = 191/359 (53%), Positives = 249/359 (69%), Gaps = 3/359 (0%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V+ ++PY+ GKP+ E+ARE +D A IVKLASNENPLG A A+ + +EL RYPD Sbjct: 13 VQQLSPYVPGKPVDELARELDIDPAKIVKLASNENPLGASPKALAAIREELAELTRYPDG 72 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 N F LK L+E+ V + VTLGNGSNDILE+ A A++ G + V+++++FAVY + TQ Sbjct: 73 NGFALKTLLAEQCRVELNQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIVTQA 132 Query: 130 LGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV 189 +GA A V+PA +GHDL AML A+ +TR++F+ANPNNPTGT+ + L+ FL VP V Sbjct: 133 VGAEARVIPAKDWGHDLSAMLEAIDSNTRVVFIANPNNPTGTWFDAEALDEFLQDVPERV 192 Query: 190 VVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLL 249 +VVLDEAY EY D + ++ YPNLLVSRTFSKA+GLA LRVG+ ++ + D+L Sbjct: 193 LVVLDEAYIEYAEGSDLPDGLDFLAAYPNLLVSRTFSKAYGLAALRVGYGLSTAVVADVL 252 Query: 250 NRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFV 309 NRVRQPFNVN+LA AAA AAL D +L +S LN G ++L F +LGL ++PS GNF+ Sbjct: 253 NRVRQPFNVNSLALAAACAALQDDEYLAESRRLNESGMQQLEAGFRELGLSWIPSKGNFI 312 Query: 310 LVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTLA 368 V +G A V LL +GVIVRPV NYG+P LRITIGLP EN F+ AL + LA Sbjct: 313 CVDLGRVAAP---VFQGLLHEGVIVRPVANYGMPNHLRITIGLPAENSRFLEALAKVLA 368 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: 424 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: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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