Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ga0059261_1288 Ga0059261_1288 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__Korea:Ga0059261_1288 Length = 401 Score = 147 bits (371), Expect = 5e-40 Identities = 119/384 (30%), Positives = 179/384 (46%), Gaps = 35/384 (9%) Query: 7 RLPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSP---GYPTVW 63 RLP + ++ +A A A + I+DL +G P P P+ + L A P GY Sbjct: 10 RLPPYVIAEVNGMRAAARAAGEDIIDLGMGNPDLPPPQHVIDKLCEVAQKPSAHGYSQSK 69 Query: 64 GTPELRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDKVAHPRLAYP 123 G P LR A + RR G V+ +GSKE +A L T + PGD + P +YP Sbjct: 70 GIPGLRRAQANYYGRRFGVDVDPESEVVVTMGSKEGLASLATAI-TAPGDVILAPNPSYP 128 Query: 124 TYEVGARLARAD-HVVYDDPTELDPTGLK-----------LLWLNSPSNPTGKVLSKAEL 171 + G +A A V P E L+ +L +N PSNPT + + A Sbjct: 129 IHTFGFIIAGATIRAVPTTPDEHYFESLERAMNFTVPRPSILVVNYPSNPTAETVDLAFY 188 Query: 172 TRIVAWAREHGILVFSDECYLELGWEADP-VSVLHPDVCGGSYEGIVSVHSLSKRSNLAG 230 R+VAWA+E+ + + SD Y EL ++ P VS+L G+ + + SLSK ++AG Sbjct: 189 ERLVAWAKENKVWIISDLAYSELYYDGKPTVSILQ---VKGAKDVAIEFTSLSKTYSMAG 245 Query: 231 YRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAAL-GDDAHVREQRERYAARRTAL 289 +R F G+ ++ + +++ + P QAA AAL G V R+ Y RR L Sbjct: 246 WRIGFAVGNKQLIAAMTRVKSYLDYGAFTPVQAAACAALNGPQDIVEANRQLYHKRRDVL 305 Query: 290 RDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADL----------GILVAPGDFYGS 339 ++ G+ I AS++ WA + +AHL L + VAPG YG Sbjct: 306 VESFGRAGWDIPAPPASMFAWAPLPPA----LAHLGSLEFSKQLLSHAKVAVAPGVGYGE 361 Query: 340 AGEQFVRVALTATDERVAAAVRRL 363 GE FVR+A+ ++R+ A R + Sbjct: 362 NGEGFVRIAMVENEQRLRQAARNV 385 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: 405 Number of extensions: 20 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: 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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