Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 218 bits (556), Expect = 2e-61 Identities = 136/394 (34%), Positives = 202/394 (51%), Gaps = 41/394 (10%) Query: 30 KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALR 88 + + + +WD +G+E++DFAGGIAV GH HP + A+ Q E H V E ++ Sbjct: 30 RAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGYESYIQ 89 Query: 89 LGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145 + KL + FA++ SG+EA E A K+AR Y + +IAF + +HGR+ Sbjct: 90 VCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTK------RAGVIAFTSGYHGRT 143 Query: 146 LFTVSVGGQ-PKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHT----------------- 187 + +++ G+ YS G G A++ F A+ V DD Sbjct: 144 MAALALTGKVAPYSKGMGLMSANVFRAEFPC--ALHGVSDDDAMASIERIFKNDAEPSDI 201 Query: 188 CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVT 247 A+++EP+QGEGG A +P F+Q LR LCD+ +L+ DEVQ G GRTG FA GV+ Sbjct: 202 AAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAMEQMGVS 261 Query: 248 PDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEV 307 DI T AK++ GGFP+S + A++ A PG G TYGGNPLACA A A ++ ++ Sbjct: 262 ADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEKL 321 Query: 308 LEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL------KPQYKGRARDFLYAG 361 LE A R L + ++ +D+RG+G + EL PQY L Sbjct: 322 LERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDGKPAPQY---CAQILAEA 378 Query: 362 AEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGM 393 G+++L+ G +V+R L V D +D G+ Sbjct: 379 RNRGLILLSCGTYGNVLRILVPLTVSDTQLDAGL 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: 460 Number of extensions: 18 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: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 Effective search space: 147750 Effective search space used: 147750 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 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