Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate 7025360 Shewana3_2520 aminotransferase (RefSeq)
Query= SwissProt::P40732 (405 letters) >FitnessBrowser__ANA3:7025360 Length = 452 Score = 149 bits (375), Expect = 2e-40 Identities = 122/352 (34%), Positives = 173/352 (49%), Gaps = 42/352 (11%) Query: 6 TAITRATFDEVILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVE 65 T++TRA LPVY +G + G++ ID G+ HPA++ Sbjct: 19 TSMTRA------LPVYGVHS-----AQGCELELVDGRKLIDGTSSWWACVHGYGHPAILT 67 Query: 66 ALKSQGETLWHTS-NVFTNEPALRLGRKLIDATFAE--RVLFMNSGTEANETAFKLARHY 122 A++ Q L H T+EPA+ L +KL+ T +V +SG+ A E A K+A Y Sbjct: 68 AMERQLHQLSHVMFGGITHEPAITLCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMALQY 127 Query: 123 ACVRHSPF-----KTKIIAFHNAFHGRSLFTVSV----GGQPKYSDGFGPKPA--DIIHV 171 + P K +I+ +HG + +SV GG K D Sbjct: 128 WQGQDLPLAQKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVTKQCFVDAPQT 187 Query: 172 PF------NDLHAVKAVMDDH---TCAVVVEPI-QGEGGVQAATPEFLKGLRDLCDEHQA 221 PF +DL ++ ++ + AV++EPI QG GG++ + E+L+GLR LCDE+ Sbjct: 188 PFGEPLRQDDLAPMQRILREQHPEIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNV 247 Query: 222 LLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGF-PVSAMLTTQEIA-----SA 275 LL+ DE+ G GRTG LFAY H +TPDIL KAL GG+ ++A L T +A S Sbjct: 248 LLILDEIATGFGRTGKLFAYEHADITPDILCLGKALTGGYISLAATLCTDNVAQGISQSP 307 Query: 276 FHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHL-QAID 326 V HG T+ GNPLACA A A+ D+IN E + QQ + L AID Sbjct: 308 AGVFMHGPTFMGNPLACAAACASLDLINQQEWPAQVAAIEQQMQRELADAID 359 Lambda K H 0.322 0.137 0.412 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: 445 Number of extensions: 23 Number of successful extensions: 2 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: 405 Length of database: 452 Length adjustment: 32 Effective length of query: 373 Effective length of database: 420 Effective search space: 156660 Effective search space used: 156660 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: 51 (24.3 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