Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_019895362.1 A377_RS0106195 diaminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_000384235.1:WP_019895362.1 Length = 417 Score = 156 bits (395), Expect = 9e-43 Identities = 124/410 (30%), Positives = 190/410 (46%), Gaps = 47/410 (11%) Query: 23 PAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQ--GETLWHISNV 80 PA F VKGQ ++ WD+ GKEY+DF G V GH +P L A+ + + H ++ Sbjct: 19 PAVF--VKGQNAKQWDETGKEYIDFYAGAGVLNFGHNNPKLKAAMMDYLAEDGVLHSLDM 76 Query: 81 FTNEPALRLGRKLIEATFAERVV----------FMN-SGTEANETAFKLARHYACVRHSP 129 T R I+ F E ++ FM +GT A E A KLAR Sbjct: 77 MTAAK-----RDFIQG-FVETILQPRKMDYKLQFMGPTGTNAVEAALKLARKVTG----- 125 Query: 130 FKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFND--------LHAVKA 181 + +IAF FHG +L ++ + G + H PF L ++A Sbjct: 126 -RQNVIAFAQGFHGMTLGALACTANGYFRQAAGVPLNHVSHCPFETNVGGGLAMLDTLRA 184 Query: 182 VMDDHT------CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRT 235 + D+ + A++VEPIQ EGGV A+ E+LQGL +L ALL+ D++Q G GRT Sbjct: 185 LYDNTSGGAEKPAAILVEPIQAEGGVNVASAEWLQGLDKLAKDLGALLIVDDIQAGCGRT 244 Query: 236 GDLFAYMHYGVTPDILTSAKALGG-GFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAV 294 G F++ G+ PDI+T AK LGG G PI+ L E + PG H T+ G L+ Sbjct: 245 GQYFSFDEAGIDPDIITLAKGLGGLGTPIAMNLVKPEHDQHWQPGEHTGTFRGQNLSFVA 304 Query: 295 AGAAFDIINTPEVLEGIQAKRQRFVDHLQKIDQQY-DVFSDIRGMGLLIGAEL--KPQYK 351 A +++ + K + V L+++ Q Y D +RG G++ ++ K Sbjct: 305 GREALRYFEDDQLMNAVHDKGEIMVGALEQMAQTYPDAGFSVRGKGMMQALDVGDGALAK 364 Query: 352 GRARDFLYAGAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVA 401 AR+ G G G V++ P L + + ++ G++ + A+A Sbjct: 365 AVARECFERGMLFG--PCGVGGSVIKLIPPLTIPEDELVAGLEILSEALA 412 Lambda K H 0.322 0.138 0.415 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: 440 Number of extensions: 24 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: 406 Length of database: 417 Length adjustment: 31 Effective length of query: 375 Effective length of database: 386 Effective search space: 144750 Effective search space used: 144750 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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