Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__azobra:AZOBR_RS19630 Length = 428 Score = 238 bits (607), Expect = 3e-67 Identities = 143/419 (34%), Positives = 220/419 (52%), Gaps = 42/419 (10%) Query: 18 LPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHI 77 +P+Y + + + +WD +G ++DFAGGIAV GH HP ++ A+K Q + H Sbjct: 22 MPVYVD------RAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHT 75 Query: 78 SNVFTN-EPALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTK 133 + T E + L +L + + ++ F +G EA E A K+AR + + Sbjct: 76 CAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIARAHTG------RPG 129 Query: 134 IIAFHNAFHGRSLFTVSVGGQP-KYSDGFGPKPADIIHVPFNDLHAVKAVMDD------- 185 +IAF AFHGR+L +++ G+ Y GFGP PA++ H PF + + +V D Sbjct: 130 VIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDSLKALEQL 189 Query: 186 --------HTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGD 237 A++VEP+QGEGG A PEFLQ LR++CD++ LL+ DE+Q G RTG Sbjct: 190 FKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGK 249 Query: 238 LFAYMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGA 297 +FA H GV PD++T AK+L GGFP+SA+ AEI A PG G TY G+PLA A A Sbjct: 250 MFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAALA 309 Query: 298 AFDIINTPEVLEGIQAKRQRFVDHLQKIDQQ--YDVFSDIRGMGLLIGAEL------KPQ 349 D+I ++++ +R + + Q+ V D+R +G +I EL K Sbjct: 310 VLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEP 369 Query: 350 YKGRARDFLYAGAEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406 + + AE G+++L+ G +V+R L DA +DEG+ ++ ++V A Sbjct: 370 AAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSLEELVSA 428 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: 437 Number of extensions: 20 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: 428 Length adjustment: 31 Effective length of query: 375 Effective length of database: 397 Effective search space: 148875 Effective search space used: 148875 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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