Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 3606628 Dshi_0060 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__Dino:3606628 Length = 393 Score = 137 bits (346), Expect = 4e-37 Identities = 117/378 (30%), Positives = 161/378 (42%), Gaps = 34/378 (8%) Query: 8 LPTFPWDKLEPYKARAAAHPDG--IVDLSVGTPVDPVPELIQKALVAAADSPG-YPTVWG 64 LP + + +L +A HP G + +S+G P P P++ AL A YP G Sbjct: 10 LPEYAFPRL---RALLDGHPPGGSTLAMSIGEPQHPFPQIATDALAEALPLFNKYPPNDG 66 Query: 65 TPELRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDK------VAHP 118 PEL A+ WV+ R G + VL + G++E L L P K VA P Sbjct: 67 APELCAAIADWVQGRYGVKLDPARQVLALNGTRE--GLFAACLALCPDTKAGGQPLVAMP 124 Query: 119 RLAYPTYEVGARLARADHVVYDDPTE---------LDPTGLK---LLWLNSPSNPTGKVL 166 Y Y VGA+ A A + + E L P L + ++ SPSNP G V Sbjct: 125 NPFYQVYAVGAQAAGARPLFVNATAETGFLPNLTTLPPETLDRIAIAYVCSPSNPQGAVA 184 Query: 167 SKAELTRIVAWAREHGILVFSDECYLELGWEADPVSVLH-PDVCGGSYEGIVSVHSLSKR 225 ++ A +H VF+DECY E+ E P L G E +V HSLSKR Sbjct: 185 DAGYWRALIGLAEKHDFYVFADECYAEIYRETPPCGALEIATAMGADPERVVIFHSLSKR 244 Query: 226 SNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERYAAR 285 SNL G R+ F AG P + + ++R + G P A D+AHV E R YAA+ Sbjct: 245 SNLPGLRSGFAAGGPRAMAEMKKLRAYAGAPLPGPLHPVATAVWRDEAHVVENRALYAAK 304 Query: 286 RTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADLGILVAPGDFY------GS 339 D +L A +LW + + + G+ V PG + G+ Sbjct: 305 FDT-ADTILGAVPGYTSPAAGFFLWLPVEDGEAAALKLWTETGVRVLPGAYLSRDTETGN 363 Query: 340 AGEQFVRVALTATDERVA 357 G F+RVAL A VA Sbjct: 364 PGAGFIRVALVADAPDVA 381 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: 411 Number of extensions: 28 Number of successful extensions: 5 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: 393 Length adjustment: 30 Effective length of query: 334 Effective length of database: 363 Effective search space: 121242 Effective search space used: 121242 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