Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ac3H11_2295 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2295 Length = 401 Score = 147 bits (372), Expect = 4e-40 Identities = 128/395 (32%), Positives = 187/395 (47%), Gaps = 38/395 (9%) Query: 1 MSAVSDRLPTFPWDKLEPYKAR----AAAHPDGIVDLSVGTPVDPVPELIQKALVAAADS 56 M+ + L +P+++L A AA P + L +G P P P+ I+ AL + Sbjct: 1 MNPLLSHLQPYPFERLRQLFAGVTPPAAYSP---ISLGMGEPRHPTPQFIKDALSNNLEG 57 Query: 57 -PGYPTVWGTPELRDALTGWVERRLGARGVTHHHVLPIVGSKE-LVAWLPTQLGLGPGDK 114 YP G P LR+A T W+ +R VLP+ GS+E L A+ T + G Sbjct: 58 LASYPATAGEPRLREAFTRWLNQRYALTLDPGTQVLPVNGSREALFAFAQTIIDPSKGQP 117 Query: 115 -VAHPRLAYPTYEVGARLARADH------------VVYDDPTELDPTGLKLLWLNSPSNP 161 V P Y YE A LA A V +D E +LL++ SP NP Sbjct: 118 LVVCPNPFYQIYEGAALLAGAQPYYAPSDPARNFAVNWDTVPESVWERTQLLFVCSPGNP 177 Query: 162 TGKVLSKAELTRIVAWAREHGILVFSDECYLELGWEADPV--SVLHPDVCGG-SYEGIVS 218 TG V+ E ++ A + +G ++ SDECY E+ + +P + + G ++ ++S Sbjct: 178 TGAVMPLCEWQKLFALSDRYGFVIASDECYSEIYFRDEPPLGGLQAAEKLGRRDFKNLIS 237 Query: 219 VHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQ 278 SLSKRSN+ G R+ F+AGD A++ L R + G S QAA +AA GD+ HV E Sbjct: 238 FTSLSKRSNVPGLRSGFVAGDAALIKSFLLYRTYHGSAMSPIVQAASIAAWGDEQHVVEN 297 Query: 279 RERYAARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAH-----LADLGILVAP 333 R RY ++ A LL+ + +A YLWA ++ T A LA + V P Sbjct: 298 RTRY-RKKFAQVTPLLAGVMEVALPDAGFYLWAKVPDALGMTDAEFARALLAQYNVTVLP 356 Query: 334 GDFY------GSAGEQFVRVALTA-TDERVAAAVR 361 G + + G Q VR+AL A T+E V AA+R Sbjct: 357 GSYLAREAQGSNPGAQRVRMALVAETEECVEAALR 391 Lambda K H 0.319 0.135 0.420 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: 416 Number of extensions: 22 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: 364 Length of database: 401 Length adjustment: 30 Effective length of query: 334 Effective length of database: 371 Effective search space: 123914 Effective search space used: 123914 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 (21.7 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