Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 3607347 Dshi_0762 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q8TQ40 (389 letters) >FitnessBrowser__Dino:3607347 Length = 400 Score = 165 bits (418), Expect = 2e-45 Identities = 120/381 (31%), Positives = 186/381 (48%), Gaps = 25/381 (6%) Query: 20 AIDEAKDEMIAKGVDVIDLGVGDPDLPTHPHIVEAMREAVCDPKTHQYPSYAGMPEFREA 79 A+ +E+ A G DVI LG G+PD T +I +A + A+ KT +Y + G+PE ++A Sbjct: 18 AVTNMANELKAAGRDVIGLGAGEPDFDTPQNIKDAGKAAIDAGKT-KYTAVDGIPELKKA 76 Query: 80 AAEWCKKYKGIELDPATEVLSLIGSKEAVAHIPLAFVNPGDVVLYTDPGYPVYKIGTLFA 139 K+ G++ D T+V G K+ + + +A +NPGD V+ P + Y L A Sbjct: 77 IVAKFKRDNGLDYD-TTQVTVANGGKQILINALMATMNPGDEVIIPAPYWVSYPDMVLLA 135 Query: 140 GGEPYSLPLKAENSFLPDLDSIPADILKRAKLFFFNYPNNPTSA---TADMKFFEKVVEF 196 GGEP + F D + A I R K F FN P+NPT A A++K V+ Sbjct: 136 GGEPVIAEASIQTGFKLTADQLEAAITPRTKWFIFNSPSNPTGAGYTAAELKELTDVL-- 193 Query: 197 CKKNDIIAVHDNAYSQMVYDGYDAPSFLAAEGAM-DIGIELYSHSKTYNMTGWRLGFAVG 255 + + + D+ Y +VYD ++ + E + + + SK Y MTGWR+G+A G Sbjct: 194 LRHPHVWVMTDDMYEHLVYDDFEFATPAQVEPKLYNRTLTCNGVSKAYAMTGWRIGYAAG 253 Query: 256 SKALIKGLGKVKSNVDSGVFDAIQIAGIAALSSSQACVDDTNKIYEERRNVLIEGLT-AM 314 K LI + K++S S Q A + AL +Q + + NK ++ RR++++ L A Sbjct: 254 PKELIGAMRKIQSQSTSNPCSISQWAAVEALDGTQDYIPENNKTFKRRRDLVVGMLNDAQ 313 Query: 315 GLEVKPPKATFYVWAPV-------PTGFTSI----EFAKLLLEEAGIVATPGVGFGDAGE 363 G+ P+ FYV+ + G T I FAK LLEE G+ G FG + Sbjct: 314 GISCPKPEGAFYVYPSIAGCIGKTSAGGTKITDDEAFAKALLEEKGVAVVFGAAFGLSPN 373 Query: 364 GYVRF-----ALTKPVERIKE 379 V + ALT+ RI++ Sbjct: 374 FRVSYATSDDALTEACTRIQD 394 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: 391 Number of extensions: 17 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: 400 Length adjustment: 31 Effective length of query: 358 Effective length of database: 369 Effective search space: 132102 Effective search space used: 132102 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