Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_009547763.1 CCE_RS14630 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000017845.1:WP_009547763.1 Length = 422 Score = 664 bits (1712), Expect = 0.0 Identities = 316/405 (78%), Positives = 362/405 (89%) Query: 21 SPAAEFKTADFDTYVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPA 80 +PA F FD YVM+TYGRFPIAI RG+G LWDT+GK YLDFVAGIATCTLGH HPA Sbjct: 9 NPAKSFDPQHFDNYVMHTYGRFPIAIDRGEGCRLWDTKGKEYLDFVAGIATCTLGHGHPA 68 Query: 81 LVRAVSDQIQKLHHVSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKY 140 LV+ VS+QIQ LHHVSNLYYIP+QGELA+W++EHSCAD+VFFCNSGAEANEAAIKL+RKY Sbjct: 69 LVKTVSEQIQSLHHVSNLYYIPQQGELAQWMIEHSCADKVFFCNSGAEANEAAIKLIRKY 128 Query: 141 AHTVLDFLEQPVILTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLEN 200 +HTVLDFLEQPVILTAKASFHGRTLATITATGQPKYQQ F+PL+PGF YVPYNDI+++E+ Sbjct: 129 SHTVLDFLEQPVILTAKASFHGRTLATITATGQPKYQQDFEPLMPGFAYVPYNDIKAIEH 188 Query: 201 KVADLDEGNSRVAAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRT 260 +AD+DEGN RVAAI LEPLQGEGGVRPG++ YF R+R+ICD+N+ILLVFDEVQVGVGR+ Sbjct: 189 AIADIDEGNRRVAAIMLEPLQGEGGVRPGEIEYFLRLRKICDENNILLVFDEVQVGVGRS 248 Query: 261 GKLWGYEHLGVEPDIFTSAKGLAGGVPIGAMMCKKFCDVFEPGNHASTFGGNPLACAAGL 320 GKLWGYE+LGVEPD+ TSAKGLAGG+PIGAMMCK+FC+V PG HASTFGGNPLACAA L Sbjct: 249 GKLWGYENLGVEPDVLTSAKGLAGGIPIGAMMCKEFCNVLTPGTHASTFGGNPLACAAAL 308 Query: 321 AVLKTIEGDRLLDNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSV 380 VLKTIE + +L NVQARGEQLR+ L I + PTLFT+VRGWGLINGLEI+ E S+TS+ Sbjct: 309 TVLKTIEEENILQNVQARGEQLRTRLRAIAQKDPTLFTDVRGWGLINGLEINEEMSITSI 368 Query: 381 EIVKAAMEQGLLLAPAGPKVLRFVPPLVVTEAEIAQAVEILRQAI 425 +IVKAAME+GLLLAPAGPKVLRFVPPL+VTE EI QA ++L AI Sbjct: 369 DIVKAAMEEGLLLAPAGPKVLRFVPPLIVTEEEINQAADLLETAI 413 Lambda K H 0.320 0.137 0.405 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: 613 Number of extensions: 18 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: 429 Length of database: 422 Length adjustment: 32 Effective length of query: 397 Effective length of database: 390 Effective search space: 154830 Effective search space used: 154830 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 (21.8 bits) S2: 51 (24.3 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