Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_013429890.1 CALKRO_RS04390 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000166775.1:WP_013429890.1 Length = 401 Score = 349 bits (895), Expect = e-100 Identities = 183/398 (45%), Positives = 258/398 (64%), Gaps = 15/398 (3%) Query: 22 QYVMHTYG-RFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQK 80 QY ++ +G R P+A +GEGC L+D++ K YLDF++GI+ C LGH+HP + A+ QI+K Sbjct: 12 QYYVNVFGSRIPLAFVRGEGCILYDSQNKEYLDFISGISVCNLGHSHPKFVAALKEQIEK 71 Query: 81 LHHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQP 140 L H S+L+YI Q LA+ + E S DKVFFCNSGAEANEAAIKLVR Y + L + Sbjct: 72 LIHTSSLFYIEPQALLAKKLAEVSKFDKVFFCNSGAEANEAAIKLVRNYFYKKG--LSKY 129 Query: 141 VILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRR 200 I++ ++SFHGRTLAT ATGQ KYQK F+P+P+GF V DI ++ AI D + Sbjct: 130 KIITLENSFHGRTLATTAATGQKKYQKPFEPMPEGFINVEA-DIEKIKNAIDD------K 182 Query: 201 VAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGI 260 AA+M+E +Q EGG++ E+ + + +C E+G+L V+DE+Q G+GR G +G+E I Sbjct: 183 TAAVMIELVQAEGGIKVLSKEFVQKLYSLCKEHGLLFVIDEIQTGIGRCGSLFGFEQYDI 242 Query: 261 EPDIFTSAKGLAGGIPIGAMMCKDSCAVFNPGEHASTFGGNPFSCAAALAVVETLEQENL 320 PDI T AKGL G+PIGAM+CK A F PGEH STFGGN + AAL V++ +E+EN+ Sbjct: 243 TPDIITLAKGLGNGVPIGAMLCKKEVATFEPGEHGSTFGGNLLATRAALEVLKIIEEENI 302 Query: 321 LENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLL 380 +ENVN L+ L L +++ + +DVRG GL+ G+E ++ ++VK GLL Sbjct: 303 IENVNKMSTYLKQKLLELKKEFDFITDVRGLGLLIGVEFSFPVK----DLVKELALAGLL 358 Query: 381 LAP-AGPKVLRFVPPLIVSAAEINEAIALLDQTLAAMA 417 + G V+RF PPLIV I++A+ + + A Sbjct: 359 TSSCGGGNVIRFAPPLIVQKTHIDKALEIFKDVVKRYA 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: 441 Number of extensions: 16 Number of successful extensions: 4 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: 401 Length adjustment: 31 Effective length of query: 387 Effective length of database: 370 Effective search space: 143190 Effective search space used: 143190 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 26 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