Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Dsui_2909 Dsui_2909 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__PS:Dsui_2909 Length = 395 Score = 355 bits (910), Expect = e-102 Identities = 177/380 (46%), Positives = 246/380 (64%), Gaps = 3/380 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYVF ELK AR +G D+ID+ MGNPDGATP+ +VD + A Q HGY Sbjct: 6 RIKRLPPYVFNITGELKMAARRRGEDIIDMSMGNPDGATPKHIVDKMVDATQRGDTHGYS 65 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G R+AI +WY RRY V DPDSEA+ +GSKEGL+HL +A ++ GD VLVP+P+ Sbjct: 66 VSKGIPRLRKAICDWYLRRYNVEFDPDSEAVVTIGSKEGLAHLMLATLDRGDTVLVPNPS 125 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G +IAG S+ + + D+ +L E K K++ +PSNPT + Sbjct: 126 YPIHIYGAIIAGANTRSVRMTDDVDFFEELQRAIRECTPKPKMMILGFPSNPTARCVELD 185 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 FFE +VA A++++IL+VHDL YA++ FDGY+ S++E+PGA+D+ VEF T+SK+YNMAGW Sbjct: 186 FFERVVALAKEHDILVVHDLAYADIVFDGYRAPSIMEVPGARDVAVEFFTMSKSYNMAGW 245 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 RVG++VGN+ + L +K+ DYG F +Q A+ AL P + EV+Q Y RR+ L Sbjct: 246 RVGYMVGNKELCAALARIKSYHDYGTFTPIQVASVIALDGPQDCVEEVRQTYELRRNVLA 305 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 +GL E GW V KA+MY+W K P +GS +FA LL + V V+PG FG G+ + Sbjct: 306 KGLHEAGWMVEVPKASMYIWAKIPEPYAHLGSLEFAKKLLAEAKVAVSPGIGFGDYGDDH 365 Query: 368 VRISLIADCDRLGEALDRIK 387 VR +LI + R +A+ IK Sbjct: 366 VRFALIENEARTRQAIRGIK 385 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: 469 Number of extensions: 19 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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