Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_011157568.1 TX73_RS10265 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000195775.1:WP_011157568.1 Length = 385 Score = 289 bits (740), Expect = 8e-83 Identities = 162/379 (42%), Positives = 217/379 (57%), Gaps = 12/379 (3%) Query: 12 TVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAIA 71 TVF MS LA A+NLGQGFPD+ GP + +AA DA+ G NQYP G LR+AI+ Sbjct: 12 TVFEAMSQLARDNDAINLGQGFPDDPGPEDIRRAAADAVLNGYNQYPSMIGLPELRQAIS 71 Query: 72 AQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAGA 131 GV DP TEV+VT GATEA+A+A+L +VEPG EV++ +P YDSY P++ AG Sbjct: 72 THYAHWHGVQLDPMTEVMVTSGATEALASAILSVVEPGDEVIVFQPVYDSYLPIIRQAGG 131 Query: 132 HRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVAA 191 V L P + + ++LRR +T+A++ N+P NP V +L +A Sbjct: 132 IPRLVRLEPPH--WRITEESLRRVFNAKTKAIVFNNPLNPAAVVYPREDLELLARFCQEF 189 Query: 192 NLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAELI 251 + V I DEV+EH+ FD H+PL GM +RTI I SA K+F+ TGWK+G+ C +L+ Sbjct: 190 DAVAICDEVWEHVTFDGLSHIPLITIPGMRDRTIKIGSAGKIFSLTGWKVGFVCAAPKLL 249 Query: 252 AGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIGFAVHD 311 Q+L++ Q AVA L D + +R L RDRLA GL+ IGF V Sbjct: 250 RVAAKVHQFLAFTTAPNLQAAVAYGLGKSDDYFLQMRKDLARSRDRLAQGLSSIGFPVIR 309 Query: 312 SYGTYFLCADPRPLGYDDSTE-FCAALPEKVGVAAIPMSAFCDPAAGQASQQADVWNHLV 370 S GTYFL D PLG +++ E FC + VAAIP+SAF + + +V Sbjct: 310 SQGTYFLTVDLSPLGLNETDEAFCKRIVTDYKVAAIPVSAF---------YEEEPVTSVV 360 Query: 371 RFTFCKRDDTLDEAIRRLS 389 RF F K+D TLD A+ RLS Sbjct: 361 RFCFAKKDQTLDTALERLS 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: 418 Number of extensions: 15 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 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