Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_015943022.1 DHAF_RS03890 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000021925.1:WP_015943022.1 Length = 399 Score = 410 bits (1053), Expect = e-119 Identities = 213/396 (53%), Positives = 276/396 (69%), Gaps = 16/396 (4%) Query: 22 QYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKL 81 + VM+TYGR P+AI KG+G +WD EGK YLDFV G+A +LGH+HPA+++A+ Q +++ Sbjct: 14 EVVMNTYGRLPMAIVKGKGTTVWDIEGKQYLDFVTGLAVSSLGHSHPAVVEAIQKQAEEI 73 Query: 82 HHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYA--HTVSDFLEQ 139 H SNLY+IP Q ALA+ +VEHS AD+VFFCNSGAEANEAAIK+ RKYA H D E Sbjct: 74 LHTSNLYWIPNQIALAEKLVEHSFADQVFFCNSGAEANEAAIKIARKYAKEHYSEDKYE- 132 Query: 140 PVILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNR 199 IL+ +SFHGRTLAT+TATGQ KYQK + PLP+GF YVP ND+ LEE + N Sbjct: 133 --ILTLVNSFHGRTLATLTATGQTKYQKGYAPLPEGFTYVPINDLAQLEEKM------NP 184 Query: 200 RVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLG 259 +VAA+MLE +QGEGGV P +VE+ R++CD+ G LL+ DE+QVG+GRTGK + YE Sbjct: 185 KVAAVMLEPIQGEGGVFPLEVEFLAKARKLCDDYGALLIFDEIQVGLGRTGKLFAYEWSN 244 Query: 260 IEPDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQE 318 + PDI T AK L GG+PIG M+ K+ A F PG+HASTFGGNP + A AV++ L +E Sbjct: 245 VVPDIMTLAKALGGGVPIGVMLAKEKVASTFKPGDHASTFGGNPLATAVGCAVMDVLTEE 304 Query: 319 NLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKG 378 LE+V R + + L+ LA+KY +++RG G I G L+ E+V+ A EKG Sbjct: 305 GFLEDVQKRAQYFKQELQKLADKYQTGTEIRGQGFILGW----PLDRLGAEIVEGAREKG 360 Query: 379 LLLAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLA 414 LL+ G K LRF+PPL VS EI+EAI +LDQ A Sbjct: 361 LLINFVGGKALRFLPPLNVSYQEIDEAITILDQIFA 396 Lambda K H 0.319 0.136 0.406 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: 488 Number of extensions: 19 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: 418 Length of database: 399 Length adjustment: 31 Effective length of query: 387 Effective length of database: 368 Effective search space: 142416 Effective search space used: 142416 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: 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