Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_009562813.1 AFE_RS01930 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000021485.1:WP_009562813.1 Length = 388 Score = 335 bits (860), Expect = 1e-96 Identities = 179/392 (45%), Positives = 249/392 (63%), Gaps = 12/392 (3%) Query: 24 VMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHH 83 +M TY R PVA A+GEG L+DTEG+ YLD +AGIA C LGH+HPA+ +A+ Q +L H Sbjct: 3 LMSTYARLPVAFARGEGVWLYDTEGRRYLDALAGIAVCGLGHSHPAVTRALQTQAGQLLH 62 Query: 84 ISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVIL 143 SNLY IP Q L+ + S D FFCNSGAEANEAAIK+ R + H + +P IL Sbjct: 63 TSNLYRIPAQEKLSDTLCAVSGMDAAFFCNSGAEANEAAIKIARLHGH--GKGIAEPQIL 120 Query: 144 SAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVAA 203 ++FHGRTLAT+TATG + Q+ F PL GF PY D+ + + + N + A Sbjct: 121 VFSNAFHGRTLATLTATGNFRIQEGFSPLLPGFVRAPYGDLSTVRALV----QANPGICA 176 Query: 204 IMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENL-GIEP 262 I+ E LQGEGGVRP + +R +CD +G+LL+LDEVQ G+GRTG ++ Y+ + G+ P Sbjct: 177 ILAEPLQGEGGVRPAPEGFLTGLREVCDAHGLLLMLDEVQTGIGRTGAFFAYQQIPGLRP 236 Query: 263 DIFTSAKGLAGGIPIGAMMC-KDSCAVFNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 D+ + AKGL G+PIGAM+ + + A+F PG+H +TFGG P CAAA AV++T++QE+L Sbjct: 237 DVLSLAKGLGNGVPIGAMLAGQSTAALFGPGKHGTTFGGGPLVCAAAQAVLDTMQQEDLP 296 Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381 + G LR L+ +P ++RG GL+ G+E+ E +V+ A+E GLL+ Sbjct: 297 AHAGRMGALLRQRLQKRLGGHPEVLEIRGMGLMVGIELAHKPE----RLVERALEAGLLI 352 Query: 382 APAGPKVLRFVPPLIVSAAEINEAIALLDQTL 413 KV+R +PPLI+ AEI+ +A L L Sbjct: 353 NVTAEKVIRLLPPLILQEAEIDLLVAGLASLL 384 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: 442 Number of extensions: 19 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: 418 Length of database: 388 Length adjustment: 31 Effective length of query: 387 Effective length of database: 357 Effective search space: 138159 Effective search space used: 138159 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