Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate AZOBR_RS20195 AZOBR_RS20195 aminotransferase
Query= BRENDA::Q8TQ40 (389 letters) >FitnessBrowser__azobra:AZOBR_RS20195 Length = 369 Score = 156 bits (395), Expect = 8e-43 Identities = 108/355 (30%), Positives = 171/355 (48%), Gaps = 7/355 (1%) Query: 36 IDLGVGDPDLPTHPHIVEAMREAVCDPKTHQYPSYAGMPEFREAAAEWCKKYKGIELDPA 95 I+LG G PD +++ +A+ + +QYP G P+ R+A A +++ G+++D Sbjct: 11 INLGQGFPDERGPADVLDVAAKAILEG-WNQYPPMMGTPDLRQALAAHGRRFYGLDIDWK 69 Query: 96 TEVLSLIGSKEAVAHIPLAFVNPGDVVLYTDPGYPVYKIGTLFAGGEPYSLPLKAENSFL 155 TEVL G+ EA+ L + PGD V+ P Y Y AGG P + LKA + Sbjct: 70 TEVLVTSGATEALTASLLGLIEPGDEVVLFQPMYDSYLPIVRLAGGVPRFVSLKAPDWSF 129 Query: 156 PDLDSIPADILKRAKLFFFNYPNNPTSATADMKFFEKVVEFCKKNDIIAVHDNAYSQMVY 215 D + A + KL N P NP + E + EF ++ D AV D Y +V+ Sbjct: 130 TRAD-LEAAFSPKTKLVLINDPLNPAAKVFSRAELELLAEFVQRFDAFAVCDEVYEHIVF 188 Query: 216 DGYDAPSFLAAEGAMDIGIELYSHSKTYNMTGWRLGFAVGSKALIKGLGKVKSNVDSGVF 275 DG + G D +++ S KT+++TGW++G+ G+ L++ + K + Sbjct: 189 DGRQHIPLMTLPGMRDRCLKIGSAGKTFSLTGWKVGYVTGAPHLLQPVAKAHQYITFTTP 248 Query: 276 DAIQIAGIAALSSSQACVDDTNKIYEERRNVLIEGLTAMGLEVKPPKATFYVWAPV-PTG 334 +Q A L A + + +R+ L +GL A+G EV P T++V A V P G Sbjct: 249 PNLQTAVAYGLGKDDAYFAGLSSGLQAKRDRLADGLRAVGFEVLPSAGTYFVVADVSPFG 308 Query: 335 FTSIE--FAKLLLEEAGIVATPGVGF--GDAGEGYVRFALTKPVERIKEAVERMK 385 F + F + L EAG+ A P F DA ++RF +K E + AVER++ Sbjct: 309 FDGNDEAFCRRLTAEAGVTAIPVGAFFVQDAPRSFIRFCFSKRDEILDGAVERLR 363 Lambda K H 0.319 0.137 0.409 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: 359 Number of extensions: 15 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: 389 Length of database: 369 Length adjustment: 30 Effective length of query: 359 Effective length of database: 339 Effective search space: 121701 Effective search space used: 121701 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