Align aspartate aminotransferase (EC 2.6.1.1) (characterized)
to candidate Ga0059261_1688 Ga0059261_1688 Aspartate/tyrosine/aromatic aminotransferase
Query= metacyc::MONOMER-13012 (397 letters) >FitnessBrowser__Korea:Ga0059261_1688 Length = 395 Score = 340 bits (871), Expect = 5e-98 Identities = 171/392 (43%), Positives = 247/392 (63%), Gaps = 2/392 (0%) Query: 1 MFSVLKPLPTDPILGLMAAYKQDTNPNKIDLGVGVYKDELGNTPVLKAVKKAEAFRLENE 60 MF+ L P DPILGL QD +P+K+DLG+G+Y++E G PVL VK AE + E + Sbjct: 1 MFADLAEPPLDPILGLAQLLAQDKSPDKVDLGIGIYQNEHGEAPVLDCVKTAERWLAETQ 60 Query: 61 TSKSYIGLAGNLDYCQKMESLLLGEHKTLLANRVRTAQAPGGTGALRVAAEFIMRCNPKA 120 SK Y+ AGN DY + LL G+ A R RT QAPGGTGALR+A++ + + P+ Sbjct: 61 PSKRYLSSAGNADYNTQTRGLLFGKGSDGFA-RSRTIQAPGGTGALRLASDLLRKLRPEG 119 Query: 121 TVWVTTPTWANHISLFEAAGLTVKEYPYYDYENKDLLFDEMINTLKQVPKGDVVLLHACC 180 V++ PTW NH + +A+G V YPYYD L FDEM+ L + D +LLH CC Sbjct: 120 RVFIPGPTWPNHPGILKASGHEVVVYPYYDMAAGALRFDEMMAALADLGPRDTLLLHGCC 179 Query: 181 HNPSGMDLNEAQWKVVAELAKEVGFTPLVDIAYQGFGSSLEEDARGLRILADAVEELIIC 240 HNP+G DL+ QW+ VA L + G LVD+AY G G L EDA G+R+LA+ + E I+ Sbjct: 180 HNPTGADLDREQWRAVAGLVAKSGAAVLVDLAYLGLGDGLAEDAAGIRLLAEQIPEFIVA 239 Query: 241 SSCSKNFGLYRERIGACSLIAKDSATADISNSVLLSVVRSIYSMPPAHGADIVNTILSST 300 SS SKNF LYRER+GA +++ A ++++ L V R+++SMPP HGA +V +L Sbjct: 240 SSYSKNFALYRERVGALTVVGGSEKDAVLAHAHALPVARTLWSMPPDHGAAVVAKVLGDA 299 Query: 301 ELTQMWHQELDEMRSRINGLRTQIKETLATKDIAQDFSFIERQHGMFSFLGINKEQITRL 360 EL ++W EL MR RIN +R ++ LA + +D+ FI +Q GMF+ LGI + + L Sbjct: 300 ELRRVWEGELTLMRGRINAMRERLATRLAAQG-TRDYGFIAKQRGMFTMLGIAPDAVETL 358 Query: 361 QKEYGIYIVGSSRVNVAGVSDANIEYFANAVA 392 ++++ +++ S R+NVAG++ N++ A+A+A Sbjct: 359 RRDHHVHLTSSGRINVAGLNANNVDRVADAIA 390 Lambda K H 0.318 0.134 0.388 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: 401 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: 397 Length of database: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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 Jul 25 2024. The underlying query database was built on Jul 25 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