Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_012116528.1 XAUT_RS23075 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000017645.1:WP_012116528.1 Length = 398 Score = 283 bits (725), Expect = 5e-81 Identities = 164/380 (43%), Positives = 215/380 (56%), Gaps = 12/380 (3%) Query: 11 TTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAI 70 TT+F MS LA AVNLGQGFPD+ GP + + A DA+ G NQYPP G LR A Sbjct: 24 TTIFEVMSQLARTHEAVNLGQGFPDDPGPEDVRRKAADAVVNGWNQYPPMMGLPELRAAA 83 Query: 71 AAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAG 130 AA R ++ DP+ EV+VT GATEA+A A+L L+EPG EV+L +P YD+Y P+V AG Sbjct: 84 AAHYRHWQELELDPDAEVMVTSGATEALAGALLALIEPGDEVVLFQPLYDAYLPLVKRAG 143 Query: 131 AHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVA 190 V L P +++ +AL A + RT+ ++ N+P NPTG V S +LA +AE VA Sbjct: 144 GIPRLVRLEPPS--WSITREALTAAFSERTKLVLFNNPQNPTGVVYSRADLALLAEFCVA 201 Query: 191 ANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAEL 250 + + DEV+EH++FD L GM ERT+ ISSA K+F TGWK+G L Sbjct: 202 FDAYAVCDEVWEHVIFDGVAFTSLMALPGMRERTVKISSAGKIFGMTGWKVGLVFAAPPL 261 Query: 251 IAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIGFAVH 310 + + A Q+L++ Q AVA L D + +R L+ RDRLA GL +GF+V Sbjct: 262 MKVLSKAHQFLTFTTPPNLQVAVAYGLGKADDYFTGMRADLQRSRDRLAQGLAGLGFSVL 321 Query: 311 DSYGTYFLCAD-PRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQADVWNHL 369 S GTYFL D D FC L GVA IP+SAF D + Sbjct: 322 PSAGTYFLSIDLAAHTNAADDEAFCLDLVRTHGVATIPVSAF---------YAQDAVKSV 372 Query: 370 VRFTFCKRDDTLDEAIRRLS 389 VRF F KRD+T+D A+ RL+ Sbjct: 373 VRFCFAKRDETIDRALERLA 392 Lambda K H 0.321 0.135 0.405 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: 432 Number of extensions: 20 Number of successful extensions: 4 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: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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