Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Ac3H11_2295 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)
Query= BRENDA::O66630 (387 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2295 Length = 401 Score = 184 bits (467), Expect = 4e-51 Identities = 124/365 (33%), Positives = 183/365 (50%), Gaps = 20/365 (5%) Query: 34 IDLGVGDPDMPTPKPIVEAAKKALENPENHKYPSYVGKYEFRKAVADWYKRRFDVDLDPN 93 I LG+G+P PTP+ I +A LE + YP+ G+ R+A W +R+ + LDP Sbjct: 32 ISLGMGEPRHPTPQFIKDALSNNLEGLAS--YPATAGEPRLREAFTRWLNQRYALTLDPG 89 Query: 94 TEVITLIGSKEGIAHFPLAFVNPGD---IVLCPDPAYPVYRIGAIFAGGTPYTVPLKEEN 150 T+V+ + GS+E + F ++P +V+CP+P Y +Y A+ AG PY P Sbjct: 90 TQVLPVNGSREALFAFAQTIIDPSKGQPLVVCPNPFYQIYEGAALLAGAQPYYAPSDPAR 149 Query: 151 NFLPDLDSIPEDVAKKAKIIWINYPNNPTSAPPTLEFYKKLVDWAKEYNVIIASDNAYSE 210 NF + D++PE V ++ +++++ P NPT A L ++KL + Y +IASD YSE Sbjct: 150 NFAVNWDTVPESVWERTQLLFVCSPGNPTGAVMPLCEWQKLFALSDRYGFVIASDECYSE 209 Query: 211 IYTGQEKPPSILQVP---GAKDV--AIEFHSLSKTYNMTGWRIGMAVGNKELVAGLGKVK 265 IY E P LQ G +D I F SLSK N+ G R G G+ L+ + Sbjct: 210 IYFRDEPPLGGLQAAEKLGRRDFKNLISFTSLSKRSNVPGLRSGFVAGDAALIKSFLLYR 269 Query: 266 TNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRERKKIMTEALEKIGLEIYRSDYTFYL 325 T S VQ A I A E+ V + R YR++ +T L + +E+ D FYL Sbjct: 270 TYHGSAMSPIVQAASIAAWG-DEQHVVENRTRYRKKFAQVTPLLAGV-MEVALPDAGFYL 327 Query: 326 WIKVPE--GYTSAEFVGRLIDEAGIVCTPGNGFGEYGEG------YFRISLTVPTERLLE 377 W KVP+ G T AEF L+ + + PG+ +G R++L TE +E Sbjct: 328 WAKVPDALGMTDAEFARALLAQYNVTVLPGSYLAREAQGSNPGAQRVRMALVAETEECVE 387 Query: 378 AAERI 382 AA RI Sbjct: 388 AALRI 392 Lambda K H 0.317 0.139 0.413 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: 415 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 387 Length of database: 401 Length adjustment: 31 Effective length of query: 356 Effective length of database: 370 Effective search space: 131720 Effective search space used: 131720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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