Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate CCNA_00775 CCNA_00775 aspartate aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__Caulo:CCNA_00775 Length = 385 Score = 293 bits (749), Expect = 7e-84 Identities = 168/380 (44%), Positives = 218/380 (57%), Gaps = 12/380 (3%) Query: 11 TTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAI 70 TT+F MS LA + GA+NLGQGFPD+ GP + +AA A+ G NQYPP G LR A+ Sbjct: 11 TTIFERMSGLARQYGAINLGQGFPDDQGPLPVREAAARALIEGSNQYPPMRGLPELRAAV 70 Query: 71 AAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAG 130 A R + DP+TE++VT GATEA+AAA L+ PG EV+L +P YD+Y P+V AG Sbjct: 71 AGHYGRTQDLTLDPDTEIVVTSGATEALAAAFTSLISPGDEVVLFQPLYDAYLPLVRRAG 130 Query: 131 AHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVA 190 V L P F + L A + RTR +++NSP NP G V +LA +AE+ V Sbjct: 131 GVPRLVKLSPPHWRF--ERAMLEAAFSNRTRMVVLNSPLNPAGVVAPDEDLALLAEVCVR 188 Query: 191 ANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAEL 250 ++V + DEV+E +VFD RH PL F GM ERT+ I SA K+F TGWK+G+ C L Sbjct: 189 HDVVAVCDEVWEAVVFDGRRHRPLMSFPGMRERTVKIGSAGKLFGMTGWKVGFLCAAPPL 248 Query: 251 IAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIGFAVH 310 + AA Q+L++ Q VA LD AW + +L+ RDRL AGL + G+ V Sbjct: 249 ARALAAAHQFLTFTTPPNLQAGVAWGLDNHRAWFDDMPANLQRSRDRLTAGLRDAGYVVL 308 Query: 311 DSYGTYFLCADPRPLGYD-DSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQADVWNHL 369 +S GTYFL D G D FC + GVAAIP+SAF D + Sbjct: 309 ESQGTYFLNVDLAASGIALDDVTFCERCVTEHGVAAIPVSAFF---------AEDPVTTV 359 Query: 370 VRFTFCKRDDTLDEAIRRLS 389 VR F K D TLDEA+RRL+ Sbjct: 360 VRLCFAKADATLDEAVRRLA 379 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: 428 Number of extensions: 19 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: 385 Length adjustment: 31 Effective length of query: 366 Effective length of database: 354 Effective search space: 129564 Effective search space used: 129564 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 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