Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_089323728.1 CHB58_RS08740 succinyldiaminopimelate transaminase
Query= BRENDA::O66630 (387 letters) >NCBI__GCF_900188395.1:WP_089323728.1 Length = 387 Score = 266 bits (680), Expect = 7e-76 Identities = 148/374 (39%), Positives = 217/374 (58%), Gaps = 10/374 (2%) Query: 8 LKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPENHKYPS 67 L+ + PY EL + K+ + G + D G GDP PT I EA K A+ PE +YP+ Sbjct: 5 LRNMKPYPMDELVKAKELLKKDGKKIYDFGTGDPKEPTAPFIREAVKTAI--PEVSQYPT 62 Query: 68 YVGKYEFRKAVADWYKRRFDVDLDPNTEVITLIGSKEGIAHFPLAFVNPGDI---VLCPD 124 G+ + R+A++ W+KRRFDV+LD E+I GSKE I HFPL F++ V+ Sbjct: 63 VKGRKDLREAISSWFKRRFDVELDSEKEIIPSAGSKEAIFHFPLVFIDADSDKKRVIFGT 122 Query: 125 PAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNNPTSAPPT 184 PAYPVY G +FA G P + LK E FL LD +PE++ K+ KI+W+NYP+NPT A Sbjct: 123 PAYPVYERGTLFAQGIPTSYTLKYEEGFLLRLDKMPEEILKETKIVWLNYPHNPTGATAP 182 Query: 185 LEFYKKLVDWAKEYNVIIASDNAYSEIYTGQEKPPSILQVPGAKDVAIEFHSLSKTYNMT 244 L +++ + +EY++I+ SD Y+EIY +EKPPS LQV K+ + FHSLSK MT Sbjct: 183 LSYFEDMYQICREYDIIMCSDECYTEIYF-EEKPPSALQV--GKENVVVFHSLSKRSGMT 239 Query: 245 GWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRERKKI 304 G+R G G+ ++ + +++ G +Q G E VE+ R ++R++K+I Sbjct: 240 GYRSGFVAGDSRIIQEYLRFRSSFGVGSPDFIQ-VGAREAWKDESHVEERRLIFRKKKEI 298 Query: 305 MTEALEKIGLEIYRSDYTFYLWIKVPEGYTSAEFVGRLIDEAGIVCTPGNGFGEYGEGYF 364 + ++ G E +FY W+KVP G TS ++ L+ + GIV +PG FG GEG+F Sbjct: 299 FEKFFKEEGFEFLDVKASFYFWVKVPFGLTSKDYAFHLL-KYGIVVSPGEFFGSGGEGFF 357 Query: 365 RISLTVPTERLLEA 378 RI+L + EA Sbjct: 358 RIALVPSVDECEEA 371 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: 449 Number of extensions: 38 Number of successful extensions: 7 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: 387 Length adjustment: 30 Effective length of query: 357 Effective length of database: 357 Effective search space: 127449 Effective search space used: 127449 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 10 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