Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_013460342.1 SULKU_RS07470 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YMS6 (388 letters) >NCBI__GCF_000183725.1:WP_013460342.1 Length = 388 Score = 373 bits (958), Expect = e-108 Identities = 187/387 (48%), Positives = 261/387 (67%), Gaps = 3/387 (0%) Query: 3 LAARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGKTK 62 L RV+ ++ SIT+AI+ A+ +KA+G ++ SFSAGEPDFDTP IK AA KA+++G TK Sbjct: 2 LTDRVNILSESITIAISTLAQELKAQGKNILSFSAGEPDFDTPQVIKDAAIKAINDGFTK 61 Query: 63 YGAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIPAP 122 Y A G P+L+ AIA KL++DN LDYKP +I NG KHSLYNL I GDEVIIPAP Sbjct: 62 YTAVDGIPELKAAIALKLKRDNGLDYKPNQIIANNGAKHSLYNLFACTIQAGDEVIIPAP 121 Query: 123 YWLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVYTP 182 YW++YPE+V GG V + TD +G+KITPEQL+ A+TPKTK+ +L SPSNPTG VY+ Sbjct: 122 YWVTYPELVMYCGGSVVEIMTDDESGFKITPEQLKAALTPKTKMLILTSPSNPTGAVYSR 181 Query: 183 EEIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYSMT 242 EE+ AL +V+ ++ V SDE+YEK++YDG + S ++ +++ RT+ NG +K+ +MT Sbjct: 182 EELTALGKVLEGTNVIVASDEMYEKLIYDG-EFTSAAAVSDDMYQRTITINGLSKSVAMT 240 Query: 243 GWRLGYLAGP-VDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDC-VEEMRQAFAKRR 300 GWR GY+A +II+A +Q STSN+ + Q AI L D +E MR F RR Sbjct: 241 GWRFGYMAAANTEIIQATKKLQSQSTSNINSITQKAAIVGLNGEADADIEAMRVQFKARR 300 Query: 301 QVMLDRLNAIPGLSTAKPDGAFYLFPDISKTGLKSLEFCDALIEEHKVAVIPGIAFGADD 360 + N I GLS P GAFYLF +I + S++FC L+E+ +AV+PG+ FG++ Sbjct: 301 DEAVKLFNEIDGLSVLSPAGAFYLFVNIKEVSNDSMQFCKELLEDQGIAVVPGVGFGSEG 360 Query: 361 NIRLSYATDLATIEKGLDRLEKFVRSR 387 R S+ATD+ +I +G+ R+ FV ++ Sbjct: 361 YFRFSFATDIDSIREGIKRIAAFVATK 387 Lambda K H 0.317 0.134 0.381 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: 366 Number of extensions: 13 Number of successful extensions: 3 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: 388 Length of database: 388 Length adjustment: 30 Effective length of query: 358 Effective length of database: 358 Effective search space: 128164 Effective search space used: 128164 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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