Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_012050389.1 SWIT_RS21305 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_000016765.1:WP_012050389.1 Length = 425 Score = 238 bits (606), Expect = 3e-67 Identities = 151/413 (36%), Positives = 220/413 (53%), Gaps = 42/413 (10%) Query: 19 PIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS 78 PI+A + + IWD G+ YVDFAGGIAV GH HP ++ A++ Q H++ Sbjct: 24 PIFA------ARADNAEIWDVDGQHYVDFAGGIAVLNTGHRHPKVIAAVQEQLALYTHMA 77 Query: 79 -NVFTNEPALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKI 134 V EP + L +L T + + +G EA E A KLAR + ++ + Sbjct: 78 FQVAAYEPYVALAERLNALAPFTGEAKTILFTTGAEATENAVKLARA------ATGRSAV 131 Query: 135 IAFHNAFHGRSLFTVSVGGQ-PKYSDGFGPKPADIIHVPF----------NDLHAVK--- 180 IAF FHGR+L +++ G+ Y FGP P +I HVPF L A++ Sbjct: 132 IAFGGGFHGRTLLAMAMTGKVAPYKQQFGPMPGEIFHVPFPVAAHGGSVEETLRAIEMVF 191 Query: 181 --AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDL 238 AV A+++EPI GEGG A E L+ LR LCD+H +L+ DEVQ G GRTG + Sbjct: 192 RVAVEPGRVAALIIEPILGEGGFYEAPVELLRALRALCDRHGIILIADEVQTGFGRTGRM 251 Query: 239 FAYMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAA 298 FA H GV PD++T AK+L GGFP+S ++ + I A PG G TYGGNP+ACA A A Sbjct: 252 FAIEHSGVEPDLVTVAKSLAGGFPLSGVIGRSAIMEASEPGGMGGTYGGNPVACAAALAV 311 Query: 299 FDIINTPEVLEGIQAKRQRFVDHLQKIDQQYDV--FSDIRGMGLLIGAELKPQYKG---- 352 D+I ++L+ A R + L+ + ++ D+ ++IRG G +IG ++ G Sbjct: 312 LDVIAEEQLLDRAVAIGARIKERLRLLARRNDLVPITEIRGPGAMIGFDIVTSRTGYEPD 371 Query: 353 --RARDFLYAGAEAGVMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVA 401 R + A EAG+++L+ G +V+R L V D +D G+ + A+A Sbjct: 372 PETTRRVVEAAREAGLILLSCGIHGNVIRILVPLTVPDDILDAGLAKLEQALA 424 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: 467 Number of extensions: 22 Number of successful extensions: 5 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 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