Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate HSERO_RS10805 HSERO_RS10805 succinyldiaminopimelate aminotransferase
Query= BRENDA::O66630 (387 letters) >FitnessBrowser__HerbieS:HSERO_RS10805 Length = 403 Score = 179 bits (454), Expect = 1e-49 Identities = 128/397 (32%), Positives = 194/397 (48%), Gaps = 31/397 (7%) Query: 8 LKVLPPYLFAELDRKKQEKIEQGVDV------IDLGVGDPDMPTPKPIVEAAKKALENPE 61 L L PY F +L +K+ G+ I LG+G+P PTP I +A L Sbjct: 5 LDQLQPYPFEKL-----KKLFAGITPDPAYRPISLGIGEPKHPTPAFIQQALIDNLAGLA 59 Query: 62 NHKYPSYVGKYEFRKAVADWYKRRFDVDL-DPNTEVITLIGSKEGIAHFPLAFVNP---G 117 + YP+ +G R A+ADW ++R+D+ DP TE++ + GS+E + V+P G Sbjct: 60 S--YPATLGSDALRGAIADWLQKRYDIPRPDPATEILPVNGSREALFSLTQTVVDPTRPG 117 Query: 118 DIVLCPDPAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNN 177 +V+CP+P Y +Y A AG PY V + NF PD +P+DV ++ +++++ P N Sbjct: 118 ALVMCPNPFYQIYEGSAYLAGAQPYFVNSDPKRNFAPDFSQVPQDVWERVQLLFVCSPGN 177 Query: 178 PTSAPPTLEFYKKLVDWAKEYNVIIASDNAYSEIYTGQEKPPSILQVPG--AKDV--AIE 233 PT A TLE +K+L + Y +IASD YSEIY ++ P +Q +D I Sbjct: 178 PTGAVLTLEDWKELFALSDRYGFVIASDECYSEIYFNEDPPLGGMQAARLLGRDYRRLIS 237 Query: 234 FHSLSKTYNMTGWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEK 293 F SLSK N+ G R G G+ ++ +T + +Q A ++A E V+ Sbjct: 238 FSSLSKRSNVPGMRSGFVAGDAAILKKFLLYRTYHGAAMSPVIQAASVLAWQ-DETHVQG 296 Query: 294 IRDVYRERKKIMTEALEKIGLEIYRSDYTFYLWIKVPE--GYTSAEFVGRLIDEAGIVCT 351 Y + +T L+++ LE+ D FYLW KV + + EF RL E + Sbjct: 297 NIAKYVTKFSQVTPLLQEV-LEVALPDAAFYLWAKVDKLVNISDTEFAQRLYAEYNVTVL 355 Query: 352 PGNGFGEY------GEGYFRISLTVPTERLLEAAERI 382 PG+ G G R++L E LEAA+RI Sbjct: 356 PGSYLAREAHGVNPGAGRIRMALVAEVEECLEAAQRI 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: 457 Number of extensions: 22 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: 387 Length of database: 403 Length adjustment: 31 Effective length of query: 356 Effective length of database: 372 Effective search space: 132432 Effective search space used: 132432 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