Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate Dsui_3376 Dsui_3376 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P9WPZ5 (397 letters) >FitnessBrowser__PS:Dsui_3376 Length = 388 Score = 239 bits (611), Expect = 8e-68 Identities = 151/390 (38%), Positives = 206/390 (52%), Gaps = 19/390 (4%) Query: 4 SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63 S+L TT+F MS LA GA+NL QGFPD + A A+ G NQY P G Sbjct: 10 SKLPWVGTTIFTVMSKLAAECGAINLSQGFPDFQADRSLFDAVHQAMLDGRNQYAPMTGL 69 Query: 64 APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123 LR+AIAA+ + +G YD E+E+ VT GAT+A+ A+ PG EV++ P YDSY Sbjct: 70 PELRQAIAAKVQALYGTAYDAESEITVTAGATQALFTAIAAFAGPGDEVIVFAPVYDSYV 129 Query: 124 PVVAMAGAHRVTVPL-VPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELA 182 P + GA V L PD + D + +R +TPRTR +I+N+PHNPTG++L A +L Sbjct: 130 PAIETVGAKAVYANLRYPD---YKPDWNEVRALITPRTRMIIVNTPHNPTGSLLDAADLE 186 Query: 183 AIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIG 242 A+AE+ N+VV+ DEVYEH+ F+ H LA +A R++ +SS K ++ TGWKIG Sbjct: 187 ALAELTRDTNIVVLGDEVYEHICFE-GEHQSLARHPELAARSLIVSSFGKTYHITGWKIG 245 Query: 243 WACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGL 302 + G A L+A R Q+ + AP Q +A A + + L R +RD L Sbjct: 246 YCYGAAALMAEFRKVHQFNVFTVHAPSQVGLA-AFMADHSRHLQLAEFYRQKRDFFRQQL 304 Query: 303 TEIGFAVHDSYGTYFLCAD----PRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQ 358 F + S GTYF A P P TEF L +VGVA IP+S F Sbjct: 305 AGTKFELLPSRGTYFQLARYDALPGPAADLPDTEFAQWLTREVGVAVIPVSVFYPDGRD- 363 Query: 359 ASQQADVWNHLVRFTFCKRDDTLDEAIRRL 388 + +VRF F K++ TL A +L Sbjct: 364 --------DKVVRFCFAKQESTLAAAGEKL 385 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: 381 Number of extensions: 28 Number of successful extensions: 6 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: 388 Length adjustment: 31 Effective length of query: 366 Effective length of database: 357 Effective search space: 130662 Effective search space used: 130662 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