Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate GFF4291 PS417_21975 glutamate-pyruvate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__WCS417:GFF4291 Length = 403 Score = 357 bits (916), Expect = e-103 Identities = 176/380 (46%), Positives = 248/380 (65%), Gaps = 3/380 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI +LPPYVF ELK AR +G D+IDL MGNPDG TP +V+ +Q Q HGY Sbjct: 12 RIDRLPPYVFNITAELKMAARRRGEDIIDLSMGNPDGPTPPHIVEKLVQVAQREDTHGYS 71 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G RRAI+ WY RY V +DP+SEA+ +GSKEGL+HL +A ++ GD VLVP+P+ Sbjct: 72 TSKGIPRLRRAISRWYKDRYEVDIDPESEAIVTIGSKEGLAHLMLATLDQGDTVLVPNPS 131 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G VIAG V S+ L P D+ +L K K++ +PSNPT + Sbjct: 132 YPIHIYGAVIAGAQVRSVPLVPGVDFFAELERAIRGSIPKPKMMILGFPSNPTAQCVELD 191 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE ++A A++Y++L++HDL YA++ +DG++ S++++PGAKDI VEF TLSK+YNMAGW Sbjct: 192 FFERVIALAKQYDVLVIHDLAYADIVYDGWKAPSIMQVPGAKDIAVEFFTLSKSYNMAGW 251 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 R+GF+VGN ++ L +K+ DYG F LQ AA AL+ + ++ ++YR RR+ L+ Sbjct: 252 RIGFMVGNPELVNALARIKSYHDYGTFTPLQVAAIAALEGDQQCVKDIAEQYRQRRNVLV 311 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 +GL ELGW V KA+MY+W K P +GS +FA LL + V V+PG FG G+ + Sbjct: 312 KGLHELGWMVENPKASMYVWAKIPEQYAALGSLEFAKKLLLEAKVCVSPGIGFGEYGDDH 371 Query: 368 VRISLIADCDRLGEALDRIK 387 VR +LI + DR+ +A+ I+ Sbjct: 372 VRFALIENQDRIRQAVRGIR 391 Lambda K H 0.321 0.140 0.427 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: 488 Number of extensions: 28 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: 403 Length of database: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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 (21.8 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