Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= curated2:P59317 (406 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 227 bits (578), Expect = 5e-64 Identities = 135/385 (35%), Positives = 206/385 (53%), Gaps = 23/385 (5%) Query: 17 ILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWH 76 + +Y + VKGQG ++WD+ G EY+D GG AV ++GH HP V + Q TL Sbjct: 3 LFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGF 62 Query: 77 ISNVFTNEPALRLGRKLIEATFAE--RVVFMNSGTEANETAFKLARHYACVRHSPFKTKI 134 SN N+ ++ +L + + E + +NSG EANE A KLA Y +TK+ Sbjct: 63 YSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNG------RTKV 116 Query: 135 IAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVM-DDHTCAVVVE 193 I+F AFHGR+ V P + ++P ND+ A+K + CAV++E Sbjct: 117 ISFSKAFHGRTSLAVEATNNPTIIAPINNN-GHVTYLPLNDIEAMKQELAKGDVCAVIIE 175 Query: 194 PIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTS 253 IQG GG+ T EF+Q LR++C + +L+ DE+Q G GR+G FA+ + + PDI+T Sbjct: 176 GIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITV 235 Query: 254 AKALGGGFPVSAMLTTAEIASAFHP--GSHGSTYGGNPLACAVAGAAFDIINTPEVLEGI 311 AK +G GFP++ +L I+ F P G G+T+GGN LAC+ A A D+I ++E Sbjct: 236 AKGIGNGFPMAGVL----ISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENA 291 Query: 312 QAKRQHFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEEGVMVLNA 371 +A + ++ L+K Q ++RG GL+IG E + K +Y +E V + Sbjct: 292 KAVGDYLLEELKKFPQ----IKEVRGRGLMIGLEFEEPIKELRSRLIY---DEHVFTGAS 344 Query: 372 GPDVMRFAPSLVVEDADIDEGMHRF 396 G +V+R P L + + DE + RF Sbjct: 345 GTNVLRLLPPLCLSMEEADEFLARF 369 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: 419 Number of extensions: 19 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: 406 Length of database: 373 Length adjustment: 30 Effective length of query: 376 Effective length of database: 343 Effective search space: 128968 Effective search space used: 128968 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