Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_106717846.1 CU100_RS17540 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_003010935.1:WP_106717846.1 Length = 427 Score = 238 bits (606), Expect = 3e-67 Identities = 136/400 (34%), Positives = 211/400 (52%), Gaps = 32/400 (8%) Query: 30 KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALR 88 K +G+ +WD +G+ Y+DF GGI V +GH HP +V+A+K Q ETL H V EP + Sbjct: 33 KAKGTELWDVEGRRYLDFVGGIGVLNVGHNHPRVVDAVKRQIETLSHACFQVLGYEPYVA 92 Query: 89 LGRKLIEATFAE-RVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLF 147 L KL + + F SG EA E + K+AR Y + +IAF FHGR+L Sbjct: 93 LAEKLNTLIGKDYKSAFFTSGAEAVENSVKIARGYTN------RPAVIAFRGGFHGRTLL 146 Query: 148 TVSVGGQPK-YSDGFGPKPADIIHVPFNDLHAVKAVMD---------------DHTCAVV 191 VS+ G + Y FGP +I H+P+ + + D + A++ Sbjct: 147 GVSLTGMSQPYKQNFGPFAPEIFHIPYPNAYRGVTTADALAALAEVFATDVAPERVAAII 206 Query: 192 VEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDIL 251 +EP+QG+GG A F+ LRE+ ++H +L+ DE+Q G GRTG++F + H G+ PD++ Sbjct: 207 IEPVQGDGGFHPAPVNFVAALREITNKHGIVLILDEIQTGFGRTGEMFGFQHSGIEPDLV 266 Query: 252 TSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGI 311 T AK+L GG P+SA++ AEI A PG G TYGGN LACA A A + ++L Sbjct: 267 TIAKSLAGGLPLSAVVGKAEIMDAPTPGGLGGTYGGNALACAAALAVIETFERDDILRNG 326 Query: 312 QAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL------KPQYKGRARDFLYAGAEAG 365 + + + L + Q++ D+RG+G ++ E+ K R + L + G Sbjct: 327 RQRAAQLRKGLIALQQRHAFIGDVRGLGFMLAIEIVSDRATKAPDADRTQHVLDEARKGG 386 Query: 366 VMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVAKV 403 ++++ G + +RF LV +A+IDE + A+ +V Sbjct: 387 LLLIKCGIHRNTVRFLAPLVATEAEIDEALAALGEALERV 426 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: 491 Number of extensions: 31 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: 427 Length adjustment: 31 Effective length of query: 375 Effective length of database: 396 Effective search space: 148500 Effective search space used: 148500 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 Jul 26 2024. The underlying query database was built on Jul 25 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