Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_086508150.1 BZY95_RS01045 aspartate aminotransferase family protein
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_002151265.1:WP_086508150.1 Length = 404 Score = 506 bits (1302), Expect = e-148 Identities = 241/398 (60%), Positives = 309/398 (77%) Query: 9 TRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALK 68 TRA FD+ ++P Y+P + IPV+G+GSR+WDQ+G+EY+DFAGGIAV +LGHCHP LV AL Sbjct: 6 TRADFDQYMVPNYSPQKVIPVRGEGSRLWDQEGREYIDFAGGIAVNSLGHCHPVLVKALT 65 Query: 69 TQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLARHYACVRHS 128 QG LWH+SNV+TNEP+L+L + L+E TFA++ F +SG EANE A KLAR +A Sbjct: 66 EQGNKLWHLSNVYTNEPSLKLAKTLVERTFADKAYFCSSGGEANEAALKLARRWAHDNFG 125 Query: 129 PFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTC 188 K +I++F+ +FHGR+ FTVSVGGQPKYS GFGP P I+H FN+L +V+ +++D TC Sbjct: 126 EHKHRIVSFYQSFHGRTFFTVSVGGQPKYSQGFGPVPGGIVHGEFNNLDSVRDLINDDTC 185 Query: 189 AVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTP 248 AV+VEP+QGEGG+T AT EFLQGLR+LCD H ALL+FDEVQ G+GRTG L+AYM YG+ P Sbjct: 186 AVMVEPMQGEGGITPATQEFLQGLRDLCDAHDALLIFDEVQTGVGRTGSLYAYMEYGIEP 245 Query: 249 DILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVL 308 DILTSAKALGGGFPI AMLTT +A A G+HGSTYGGN LA AVA AA + I+TPEVL Sbjct: 246 DILTSAKALGGGFPIGAMLTTDRVAPALAIGTHGSTYGGNALASAVALAAVEHIDTPEVL 305 Query: 309 EGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVMV 368 G++ + F +HL+ I++++ VF +IRGMGLLIGAE+ P+YK RA+D L E G+M Sbjct: 306 GGVKQRHDLFREHLEAINRKHGVFREIRGMGLLIGAEMTPEYKDRAKDILPLAIEEGLMA 365 Query: 369 LNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406 L AGP+V+R APSLV+ +ADI EGM R A+ ++V A Sbjct: 366 LIAGPNVLRMAPSLVIPEADIAEGMARLERAIERLVAA 403 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: 547 Number of extensions: 21 Number of successful extensions: 1 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: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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