Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_011973356.1 MAEO_RS03185 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000017185.1:WP_011973356.1 Length = 403 Score = 336 bits (862), Expect = 7e-97 Identities = 183/394 (46%), Positives = 245/394 (62%), Gaps = 15/394 (3%) Query: 22 QYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKL 81 +Y++ TYGR+ + KG G + D GK Y DF+AGI +GH HP +++ + Q + L Sbjct: 22 KYIIGTYGRYGIVPVKGYGMIVEDINGKKYKDFLAGIGVNNVGHCHPEVVKTLQKQAELL 81 Query: 82 HHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPV 141 H SNLY+I Q L + +VE + DK FF NSGAEANEAAIKL RK H ++ + + Sbjct: 82 IHTSNLYHIIPQVQLGKKLVELTGMDKAFFSNSGAEANEAAIKLARK--HGKNNNIGEGE 139 Query: 142 ILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRV 201 I++ + SFHGRTL TITAT +P YQ+ ++PLP GF YV +NDI AL+E I++ + Sbjct: 140 IITMEHSFHGRTLTTITATAKPAYQEGYEPLPKGFKYVKFNDIEALKEGISN------KT 193 Query: 202 AAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIE 261 AIMLE +QGEGG+ D EY K VR IC++ I+L+ DEVQ G+GRTGK + YE+ I+ Sbjct: 194 TAIMLEPIQGEGGIHIADKEYLKGVRDICNDKNIVLIFDEVQCGMGRTGKMFAYEHYNIK 253 Query: 262 PDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENL 320 PDI T AK L GG PIGA + + A F PG H +TFGGNP +C+A+ A V L E L Sbjct: 254 PDILTLAKALGGGAPIGATIATEEVATAFTPGSHGTTFGGNPLACSASYASVRVL--EGL 311 Query: 321 LENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLL 380 LEN GE L L KY + +VRG GL+ G+E L ++VK +EKG L Sbjct: 312 LENTQNMGEYFITELNKLKNKYGFIKEVRGIGLMIGIE----LSFNGGDIVKKMLEKGYL 367 Query: 381 LAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLA 414 + VLRF+PPLIV +I+ I LD+ + Sbjct: 368 INCTSDVVLRFLPPLIVEKTDIDGLINALDEVFS 401 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: 443 Number of extensions: 22 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: 403 Length adjustment: 31 Effective length of query: 387 Effective length of database: 372 Effective search space: 143964 Effective search space used: 143964 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