Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate N515DRAFT_3488 N515DRAFT_3488 aromatic-amino-acid transaminase
Query= BRENDA::W0PFQ7 (399 letters) >FitnessBrowser__Dyella79:N515DRAFT_3488 Length = 400 Score = 452 bits (1164), Expect = e-132 Identities = 221/395 (55%), Positives = 288/395 (72%), Gaps = 2/395 (0%) Query: 5 FNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEAHA 64 F +VE+ P DPILGL E Y AD R KVNLGVG+YYD+ G+IPLL+AV E E++ + Sbjct: 4 FASVEMTPGDPILGLTEAYLADARPGKVNLGVGIYYDEQGRIPLLRAVHEVEQRLAQEAK 63 Query: 65 ARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQPDS 124 RGYLPI+G+ Y +G Q+L+FG +S ++ GR T Q +GG+GAL++GAD LK+ P + Sbjct: 64 PRGYLPIDGLPAYTQGTQKLVFGAESPLLAAGRVATSQTIGGSGALRVGADVLKKALPKA 123 Query: 125 TVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHACC 184 + IS+PSWENHR +F AGF+V Y+YYD THGL+F G A + + G++++LHACC Sbjct: 124 KIAISNPSWENHRVVFIAAGFEVVEYTYYDPQTHGLDFAGMLADLGKLEPGTVVLLHACC 183 Query: 185 HNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF-I 243 HNPTGVD + QWQQ+ +VKER L+PF+D+AYQGF G+ DA VRLFA G+ F + Sbjct: 184 HNPTGVDLNAAQWQQVVEVVKERQLLPFIDMAYQGFDQGIDADATAVRLFAASGIESFVV 243 Query: 244 SSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQILNT 303 +SS++KSFSLYGER GALT V + DEA RV S +KR IR+ YS+P THGG +VA +LN+ Sbjct: 244 TSSYAKSFSLYGERAGALTFVAADRDEALRVQSLVKRTIRSIYSSPSTHGGALVAGVLNS 303 Query: 304 PELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQVER 363 PEL A WE EL +MR+RI MR + +KL A G Q F F+ Q GMFSYSGL+K QV+R Sbjct: 304 PELRAMWEQELGEMRERIHAMRAGMVEKLAAHGAPQ-FAFIQQQAGMFSYSGLSKAQVDR 362 Query: 364 LRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAV 398 LR E+ IYA+ +GRICVAALN N+D+V A+AAV Sbjct: 363 LRDEYAIYAIGTGRICVAALNRSNLDTVAAAVAAV 397 Lambda K H 0.318 0.134 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: 449 Number of extensions: 11 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: 399 Length of database: 400 Length adjustment: 31 Effective length of query: 368 Effective length of database: 369 Effective search space: 135792 Effective search space used: 135792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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