Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_012991318.1 THAL_RS01365 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000025605.1:WP_012991318.1 Length = 379 Score = 323 bits (827), Expect = 7e-93 Identities = 177/393 (45%), Positives = 257/393 (65%), Gaps = 21/393 (5%) Query: 23 YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82 ++M TY R PV KG+G L+D +GK YLD V+GIA LG+ ++A+ Q +KL Sbjct: 2 WLMETYQRLPVRFVKGKGVYLYDEKGKRYLDLVSGIAVNALGYGDRDQVKAICHQAKKLI 61 Query: 83 HISNLYYIPEQGALAQWIVEHSCAD-KVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPV 141 H+SNL+ P Q LA+ +VE +VFFCNSG EANEAAIKLVR+Y + ++ Sbjct: 62 HVSNLFENPWQEKLAKLLVERFWTKGRVFFCNSGTEANEAAIKLVRRYFRLRGE--DRYR 119 Query: 142 ILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRV 201 I++ ++SFHGRT +++AT Q K Q F+PL +GF Y +NDI ++E+ ITD + Sbjct: 120 IITFQNSFHGRTFGSMSATAQKKIQTGFEPLLEGFDYAIFNDISSVEKLITD------KT 173 Query: 202 AAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIE 261 AA+MLE +QGEGGVR D ++ + ++++C E G+LL+LDEVQ G+GRTGK++ Y++ +E Sbjct: 174 AAVMLEIVQGEGGVRVADRQFLEDLQKLCRERGLLLLLDEVQTGIGRTGKFYAYQHFQLE 233 Query: 262 PDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENL 320 PDI T AKGL GG+PIGA++ ++ A F+ G H STFGGNP +CA+AL VVE + + L Sbjct: 234 PDIITLAKGLGGGVPIGALLAREEVAKAFDAGSHGSTFGGNPLACASALVVVEKVSE--L 291 Query: 321 LENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLL 380 L++V GE L L +VRG GL+ +E++++ + EVV A+EKGL+ Sbjct: 292 LDHVREVGEYFMERLAALGR-----GEVRGMGLMLALELESNCK----EVVLKALEKGLV 342 Query: 381 LAPAGPKVLRFVPPLIVSAAEINEAIALLDQTL 413 + KVLRFVPPLI+ ++ A+ +L + L Sbjct: 343 INCTAKKVLRFVPPLILQKRHVDIAVRILRRVL 375 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: 415 Number of extensions: 21 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: 379 Length adjustment: 31 Effective length of query: 387 Effective length of database: 348 Effective search space: 134676 Effective search space used: 134676 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 Jul 25 2024. The underlying query database was built on Jul 25 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