Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Ga0059261_2226 Ga0059261_2226 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q3MDN5 (390 letters) >FitnessBrowser__Korea:Ga0059261_2226 Length = 399 Score = 158 bits (400), Expect = 2e-43 Identities = 117/399 (29%), Positives = 188/399 (47%), Gaps = 19/399 (4%) Query: 1 MQFAKRLEKIPPYLFAEINRKREALIAQGVDIINIGVGDPDKPTPAHILQAMREAIDEAS 60 MQ + L +I P + + L QG+D+I +G G+PD TP + +A EAI + Sbjct: 1 MQTSAALNRIQPSATLAMTSRVFELKRQGIDVIGLGAGEPDFDTPDFVKEAAIEAIRKGI 60 Query: 61 NHNYPPYEGTQEFREAAVKWMERRFGVVDLNPNTEVVSSIGSKEAIHNTFLAFVEAGDYT 120 Y +GT E + A V R G+ V S G K + N F A ++AGD Sbjct: 61 T-KYTNVDGTPELKAAIVGKFARDNGLTYAENQISVNS--GGKHTLFNAFCATIDAGDEV 117 Query: 121 LIPDPGYPVYRTSTIFAGGEPFTMPLKAENKFLPDLDLIPEEVARKAKMLWVNYPNNPTG 180 +IP P + Y FAGG+P + AE + + + + + K + +N P+NPTG Sbjct: 118 VIPAPYWVSYPDVVEFAGGKPVFIAAGAEANYKIKPEQLEAAITARTKWVVLNSPSNPTG 177 Query: 181 ALATLEFFEELVAFCQQH-SILLCHDHAYSEMAYDGYKPPSVLQI-PGAKDIAIEFHSLS 238 A + + L ++H ++L+ D Y + YDG++ ++ Q+ P + + + +S Sbjct: 178 AAYSAAELKALGEVLERHPNVLIYADDMYEHILYDGFEFATIAQVCPSLYERTLTANGVS 237 Query: 239 KSYNMTGWRIGFAVGNAYAIQGLSQVKTNVDSGVFKAIQKAAIAAYNTDEVELQAVMSVY 298 K+Y MTGWRIG+A G + I+ + ++++ S Q A++AA N D+ L+ + + Sbjct: 238 KAYAMTGWRIGYAGGPQWLIKAMGKLQSQSTSNPCSVSQAASVAALNGDQSFLKDRAAAF 297 Query: 299 QNRRDIIVKGL-QSLGWPIEPPKATLYVW--------VPVPPGY---TSTEFTTLLLDKC 346 Q RRD++V L Q G P+ YV+ P G T LLD Sbjct: 298 QKRRDLVVSMLGQINGMNCPRPEGAFYVYPEFSQLIGKTTPKGLVIDTDETMVGYLLDDA 357 Query: 347 GIVVPPGVGYGVSGEGYFRIALTICEERLHEAIQRMQDA 385 + G +G S RI+ E+ L EA R+Q+A Sbjct: 358 KVAAVHGGAFGFSPA--LRISYATSEDVLAEACGRIQEA 394 Lambda K H 0.319 0.137 0.414 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: 366 Number of extensions: 19 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: 390 Length of database: 399 Length adjustment: 31 Effective length of query: 359 Effective length of database: 368 Effective search space: 132112 Effective search space used: 132112 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