Align aspartate aminotransferase (EC 2.6.1.1) (characterized)
to candidate 201550 SO2406 aspartate aminotransferase (NCBI ptt file)
Query= metacyc::MONOMER-13012 (397 letters) >FitnessBrowser__MR1:201550 Length = 396 Score = 510 bits (1314), Expect = e-149 Identities = 246/395 (62%), Positives = 300/395 (75%), Gaps = 1/395 (0%) Query: 1 MFSVLKPLPTDPILGLMAAYKQDTNPNKIDLGVGVYKDELGNTPVLKAVKKAEAFRLENE 60 MF+ L +P DPILGL+ Y++DT+P K+DLGVGVYKD GNTP+L VKKAE FRLE E Sbjct: 1 MFNSLIAMPADPILGLLTQYREDTHPQKVDLGVGVYKDPAGNTPILNCVKKAEKFRLETE 60 Query: 61 TSKSYIGLAGNLDYCQKMESLLLG-EHKTLLANRVRTAQAPGGTGALRVAAEFIMRCNPK 119 T+K YIG G+ + M L G +H ++ANR+RT PGGTGALRVA +FI RCNP Sbjct: 61 TTKVYIGPTGSPQFNTLMTELAFGSDHSAIIANRIRTVSTPGGTGALRVAGDFIKRCNPN 120 Query: 120 ATVWVTTPTWANHISLFEAAGLTVKEYPYYDYENKDLLFDEMINTLKQVPKGDVVLLHAC 179 A +WV+ PTWANH LFEAAG+TVK YPYYDY++K L FDEM+ L QV DVVLLHAC Sbjct: 121 AVLWVSDPTWANHTGLFEAAGITVKTYPYYDYDSKSLKFDEMLAALSQVSPDDVVLLHAC 180 Query: 180 CHNPSGMDLNEAQWKVVAELAKEVGFTPLVDIAYQGFGSSLEEDARGLRILADAVEELII 239 CHNPSGMDL QW V L KE GFTPL+D+AYQGFG ++ DA G+R +A AV+ +I+ Sbjct: 181 CHNPSGMDLTTDQWDKVVTLTKEQGFTPLIDMAYQGFGDGVDIDAYGVRKMAAAVDNMIL 240 Query: 240 CSSCSKNFGLYRERIGACSLIAKDSATADISNSVLLSVVRSIYSMPPAHGADIVNTILSS 299 CSSCSKNFGLYRERIG+CS++AKD+ TA+I+ SVLL VVR +YSMPPAHGA IV TIL S Sbjct: 241 CSSCSKNFGLYRERIGSCSVVAKDANTANIAQSVLLYVVRCLYSMPPAHGAAIVETILGS 300 Query: 300 TELTQMWHQELDEMRSRINGLRTQIKETLATKDIAQDFSFIERQHGMFSFLGINKEQITR 359 ELTQ W EL MR RING R + E L +A+DFSFI RQ GMFSFLG+N EQ+ R Sbjct: 301 KELTQEWLDELKVMRDRINGNRAILVEKLKANGVARDFSFIARQKGMFSFLGVNPEQVAR 360 Query: 360 LQKEYGIYIVGSSRVNVAGVSDANIEYFANAVADV 394 LQKE+ IY+VGSSR+++AG+S+ N++Y A ++A V Sbjct: 361 LQKEFSIYMVGSSRISIAGISEDNVDYLAQSIAKV 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: 469 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