Align aspartate aminotransferase (EC 2.6.1.1) (characterized)
to candidate 6937578 Sama_1733 aromatic amino acid aminotransferase (RefSeq)
Query= metacyc::MONOMER-13012 (397 letters) >FitnessBrowser__SB2B:6937578 Length = 396 Score = 484 bits (1247), Expect = e-141 Identities = 235/395 (59%), Positives = 289/395 (73%), Gaps = 1/395 (0%) Query: 1 MFSVLKPLPTDPILGLMAAYKQDTNPNKIDLGVGVYKDELGNTPVLKAVKKAEAFRLENE 60 MF L LP DPILGL+ Y++D++P+K+DLGVGVYKD GNTP+L VK AE R E Sbjct: 1 MFEHLSALPADPILGLLTKYREDSHPHKVDLGVGVYKDPAGNTPILNCVKTAETLRTSTE 60 Query: 61 TSKSYIGLAGNLDYCQKMESLLLG-EHKTLLANRVRTAQAPGGTGALRVAAEFIMRCNPK 119 T+K YIG G+ + + M L G +H + A R+RT PGGTGALRVAAEFI +C P Sbjct: 61 TTKVYIGPTGSAPFNELMNELAFGADHAVVQARRIRTVSTPGGTGALRVAAEFIAKCKPG 120 Query: 120 ATVWVTTPTWANHISLFEAAGLTVKEYPYYDYENKDLLFDEMINTLKQVPKGDVVLLHAC 179 AT+WV+ PTWANH LF+AAGLTVK YPYYDY+NK L F+EM+ LKQV D VLLHAC Sbjct: 121 ATIWVSDPTWANHTGLFQAAGLTVKTYPYYDYDNKCLKFNEMLAALKQVGAEDAVLLHAC 180 Query: 180 CHNPSGMDLNEAQWKVVAELAKEVGFTPLVDIAYQGFGSSLEEDARGLRILADAVEELII 239 CHNPSG DL+ AQW V E+AK+ GF P +D+AYQGFG ++EDA G+R +A AV+ +++ Sbjct: 181 CHNPSGQDLSTAQWDAVVEVAKDKGFLPFIDMAYQGFGDGVDEDAYGVRAMAAAVDNMVL 240 Query: 240 CSSCSKNFGLYRERIGACSLIAKDSATADISNSVLLSVVRSIYSMPPAHGADIVNTILSS 299 SSCSKNFGLYRERIGACS+I KDSA AD+S SVLL VVR IYSMPPAHGA IV TIL S Sbjct: 241 ASSCSKNFGLYRERIGACSIIGKDSAQADVSLSVLLYVVRCIYSMPPAHGAAIVETILGS 300 Query: 300 TELTQMWHQELDEMRSRINGLRTQIKETLATKDIAQDFSFIERQHGMFSFLGINKEQITR 359 EL W EL MR RING R + + L +DFSFI RQ GMFSFLGI++ Q+ Sbjct: 301 NELKAQWLDELKVMRDRINGNRAMLVDKLHALGTNRDFSFIARQKGMFSFLGISEAQVNT 360 Query: 360 LQKEYGIYIVGSSRVNVAGVSDANIEYFANAVADV 394 L K+Y IY+VGSSR+++AG+S+ N++Y A ++ V Sbjct: 361 LMKDYSIYMVGSSRISIAGISEENVDYLAKSIIAV 395 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: 457 Number of extensions: 12 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: 397 Length of database: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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