Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_026127539.1 D471_RS0108560 putative succinyldiaminopimelate transaminase DapC
Query= BRENDA::P9WPZ5 (397 letters) >NCBI__GCF_000341125.1:WP_026127539.1 Length = 393 Score = 388 bits (997), Expect = e-112 Identities = 198/389 (50%), Positives = 253/389 (65%), Gaps = 10/389 (2%) Query: 3 VSRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPG 62 + R+R Y TVFAEM+ LA +VNLGQGFPD DGP +L+AA I GVNQYPPG G Sbjct: 6 IDRMRSYGETVFAEMTRLAVETESVNLGQGFPDTDGPRSLLEAATGHILDGVNQYPPGSG 65 Query: 63 SAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSY 122 LRRA++ R RH+G++ DP++EV VTVGAT IAA++L LVE G EV++ EP YDSY Sbjct: 66 RPELRRAVSRYRARHYGIELDPDSEVYVTVGATAGIAASLLALVERGDEVVVFEPMYDSY 125 Query: 123 SPVVAMAGAHRVTVPLVPDGR--GFALDADALRRAVTPRTRALIINSPHNPTGAVLSATE 180 + ++++AG R V L PD F D D LR AV PRTR +I+N+PHNPTG V +A E Sbjct: 126 AAMISLAGGVRRPVALRPDPERGAFTFDPDELRAAVGPRTRVIIVNTPHNPTGTVFTAEE 185 Query: 181 LAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWK 240 L IA++ +L+ +TDEVYE L FD H+PLA GM ERT+++SS KMF T WK Sbjct: 186 LETIAQVCREHDLLALTDEVYEFLTFDGLPHVPLATLPGMRERTLSVSSVGKMFAVTAWK 245 Query: 241 IGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAA 300 GW GP L+ VR Q+L++ Q A+A A+D E AW+ + R SL+A+RDRLAA Sbjct: 246 TGWVMGPEPLVRAVRTVNQFLTFSANGALQLAIADAIDHEGAWIESQRASLQAKRDRLAA 305 Query: 301 GLTEIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQAS 360 GL GF V+ GTYFL AD RPLG+ D ALP + GVAA+P F D Sbjct: 306 GLVRAGFDVYPCEGTYFLMADIRPLGHGDGLTVARALPREAGVAAVPAQVFYD------- 358 Query: 361 QQADVWNHLVRFTFCKRDDTLDEAIRRLS 389 + +HL+RF FCKRD+ LDEA+ RL+ Sbjct: 359 -HEEEGSHLLRFAFCKRDEVLDEAVDRLT 386 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: 452 Number of extensions: 20 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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