Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_006748314.1 THITH_RS09650 aspartate aminotransferase family protein
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000227685.2:WP_006748314.1 Length = 398 Score = 318 bits (816), Expect = 1e-91 Identities = 166/396 (41%), Positives = 250/396 (63%), Gaps = 13/396 (3%) Query: 35 VMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKLHH 94 + TY R P+A G+G+ LWDTEG+ YLD ++GIA C LGHAHP + A+++Q L H Sbjct: 5 LQTTYNRLPVAFEHGEGAWLWDTEGRRYLDALSGIAVCGLGHAHPKIAAAIAEQAHTLIH 64 Query: 95 VSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVIL 154 SNLY +P Q +LA+ + + D+ FFCNSGAEANEAAIKL R + H + +P I+ Sbjct: 65 TSNLYRVPLQEQLARRLCALAGMDQAFFCNSGAEANEAAIKLARLHGHR--RGIARPKIV 122 Query: 155 TAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRVAA 214 + SFHGRTLAT++ATG + Q F+PLV GF VPY D + VA+L G+ +AA Sbjct: 123 VMEGSFHGRTLATLSATGNARIQNGFEPLVEGFIRVPYGDSAA----VAELG-GDPEIAA 177 Query: 215 IFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVEPD 274 I +EP+ GEGG+R Y + +R + ++ LL+ DE+Q G+GRTG+ + ++H + PD Sbjct: 178 ILVEPITGEGGIRLPPSGYLRELRTLATRHHWLLMLDEIQSGIGRTGQWFAFQHEDIVPD 237 Query: 275 IFTSAKGLAGGVPIGA-MMCKKFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRLLD 333 + + AKGL GVPIGA ++ D+F PG+H +TFGGNPL C A LAVL ++ + L + Sbjct: 238 VLSLAKGLGNGVPIGASLVSGAATDLFTPGSHGTTFGGNPLVCRAALAVLDVMQEEALGE 297 Query: 334 NVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAMEQGLLL 393 G+ L L E +P + E+RG GL+ G+E+ ++ E+V+ A+++GLL+ Sbjct: 298 QAARHGDMLLRLLQERLGSHPEVI-EIRGKGLMLGIELDRPAT----ELVRQALDRGLLI 352 Query: 394 APAGPKVLRFVPPLVVTEAEIAQAVEILRQAIATLV 429 +V+R +PPL+ + +IA+ + + ++ L+ Sbjct: 353 NVTAERVVRLLPPLITDDDQIAEIADTVADLVSRLI 388 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: 456 Number of extensions: 21 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: 429 Length of database: 398 Length adjustment: 31 Effective length of query: 398 Effective length of database: 367 Effective search space: 146066 Effective search space used: 146066 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