Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_019894837.1 A377_RS0103865 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:P59317 (406 letters) >NCBI__GCF_000384235.1:WP_019894837.1 Length = 433 Score = 166 bits (420), Expect = 1e-45 Identities = 110/341 (32%), Positives = 178/341 (52%), Gaps = 29/341 (8%) Query: 32 QGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALRLG 90 QGSRI G+E +D G+ HP +V A+ Q +T+ HI T+EPA++L Sbjct: 35 QGSRITLANGRELIDGMSSWWAAIHGYNHPDIVRAMHAQIDTMPHIMFGGLTHEPAIQLA 94 Query: 91 RKLIEAT--FAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFT 148 ++L++ + E+V F++SG+ A E A K+A Y R P K+++++ +HG + T Sbjct: 95 QQLVKLSPEGLEKVFFVDSGSVAMEVAIKMALQYQISRGKPSKSRLLSIKGGYHGDTFAT 154 Query: 149 VSVGGQ------------PKYSDGFGPKP-ADIIHVPFNDLHAVKAVMDDH---TCAVVV 192 +++ P++ F P+P + + +D+ A++ ++ H A+ + Sbjct: 155 MALCDPDNGMHTTFGPLLPRHF--FAPRPNPGMDNTDNSDIEALETMLAKHHDQIAAITL 212 Query: 193 EPI-QGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDIL 251 EPI QG GG+ P +L+ +R LCD+ LL+ DE+ G GRTG+LF G+TPDI+ Sbjct: 213 EPIIQGAGGMRPYRPAYLKQVRALCDRFDVLLIADEIATGFGRTGELFGCDWAGITPDIM 272 Query: 252 TSAKAL-GGGFPVSAMLTTAEIASAFHPGS-----HGSTYGGNPLACAVAGAAFDIINTP 305 K L GG ++A L T ++ G HG TY NPLACA A A D + Sbjct: 273 ALGKTLTGGHITLAATLATEAVSDTISQGEPGLLMHGPTYMANPLACAAASANIDTLLAS 332 Query: 306 EVLEGIQAKRQHFVDHLQKIDQQYDVFSDIRGMGLLIGAEL 346 + I ++HF HL+ +++Q D D+R +G + EL Sbjct: 333 PWRDNIARIQRHFETHLRPLNEQ-DSVKDVRILGAIAAVEL 372 Lambda K H 0.322 0.138 0.416 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: 20 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: 433 Length adjustment: 32 Effective length of query: 374 Effective length of database: 401 Effective search space: 149974 Effective search space used: 149974 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 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