Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Ac3H11_3720 Uncharacterized PLP-dependent aminotransferase YfdZ
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3720 Length = 408 Score = 352 bits (903), Expect = e-101 Identities = 178/395 (45%), Positives = 250/395 (63%), Gaps = 6/395 (1%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI +LPPYVF ELK AR +G D+ID+ MGNPDGATP +V + Q P HGY Sbjct: 12 RIDRLPPYVFNITAELKLAARRRGEDIIDMSMGNPDGATPPHIVAKLTEVAQRPDTHGYS 71 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G RRAI++WY RY V + PD+EA+ +GSKEGL+HL +A ++ GD VLVP P+ Sbjct: 72 ASKGIPRLRRAISHWYKDRYAVDIHPDTEAIVTIGSKEGLAHLMLATLDRGDTVLVPDPS 131 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G VIAG + S+ + P+ D+ +L K K++ F +PSNPT Sbjct: 132 YPIHIYGAVIAGADIRSVPVAPDVDFFAELEKAIRGSYPKPKMMIFGFPSNPTAQCVELS 191 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE ++A A+K++IL+VHDL YA++ +DGY+ S++E+PGAKD+ VEF TLSK+YNMAGW Sbjct: 192 FFERVIALAKKHDILVVHDLAYADIVYDGYRAPSIMEVPGAKDVAVEFFTLSKSYNMAGW 251 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVGF+VGN ++ L +K+ DYG F LQ AA AL+ + ++ +Y+ RRD L Sbjct: 252 RVGFMVGNPDLVAALARIKSYHDYGTFTPLQVAAIAALEGDQQCVKDIAAQYQRRRDVLY 311 Query: 311 QGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 +GL E GW V KA+MY+W + P +GS +FA LL + V V+PG FG G+ Y Sbjct: 312 KGLTEAGWAVDCPKASMYIWARIPEPYRALGSLEFARQLLDKAKVCVSPGIGFGDQGDEY 371 Query: 368 VRISLIADCDRLGEALDRIKQAGIRYRPEALVSAP 402 VR +LI + R+ +A+ I+ ++ + L+ P Sbjct: 372 VRFALIENEARIRQAVRGIR---AMFKADGLLKVP 403 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: 473 Number of extensions: 22 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: 408 Length adjustment: 31 Effective length of query: 372 Effective length of database: 377 Effective search space: 140244 Effective search space used: 140244 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