Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_072908594.1 BUB13_RS10290 pyridoxal phosphate-dependent aminotransferase
Query= CharProtDB::CH_017144 (393 letters) >NCBI__GCF_900142125.1:WP_072908594.1 Length = 386 Score = 234 bits (598), Expect = 2e-66 Identities = 139/394 (35%), Positives = 216/394 (54%), Gaps = 16/394 (4%) Query: 1 MKLAKRVASLTPSATLAITEKAKELKAAGHDVIGLGAGEPDFNTPQHILDAAIKAMNEGH 60 +KL++R +TP + + E+AKEL+AAG D+I L GEPDF TP IL A +A+ EG Sbjct: 3 IKLSQRSQLVTPFLAMEVMERAKELEAAGRDIIYLCLGEPDFPTPPAILAATGQALAEGA 62 Query: 61 TKYTPSGGLPALKEEIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVIIP 120 T YT S GL L++EI + + + EP +VIV G + LF +L+EGDE I+P Sbjct: 63 TSYTHSLGLIELRQEICRFYRDQYAVVIEPEQVIVSSGTSPLMLLLFTAMLEEGDEFILP 122 Query: 121 TPYWVSYPEQVKLAGGVPVYVEGLEQNHFKITPEQLKQAITPRTKAVIINSPSNPTGMIY 180 P + YP VK +GGVP V+ ++ F+ PEQ++ I +T+ ++INSPSNP G + Sbjct: 123 DPGYACYPGFVKFSGGVPALVKTSAEDGFQPQPEQVQALINDKTRGLLINSPSNPAGSVL 182 Query: 181 TAEELKALGEVCLAHGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVSKSHS 240 + +++AL E+ + IVSDEIY LTY G + + E ++ G SK+++ Sbjct: 183 SGAQMQALAEL----PIPIVSDEIYHGLTYQGEERCIL-----EFTDDAFVLGGFSKAYA 233 Query: 241 MTGWRIGYAAGPKDIIKAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEQRL 300 MTGWR+GY PK ++ + L + Q IAA + V MR+ +++R Sbjct: 234 MTGWRLGYLIAPKPCVRTLQTLHQNFLICANHFVQRGGIAALQQCADDVADMREVYDKRR 293 Query: 301 NIIYDKLVQIPGFTCVKPQGAFYLFPNAREAAAMAGCRTVDEFVAALLEEAKVALVPGSG 360 + +L ++ +P+GAFY+ +AR + ++D +L++ VA+ PG Sbjct: 294 QELVKRLRELGFGVHFEPKGAFYVLADARHIDTNSQRLSLD-----ILQKTGVAVTPGID 348 Query: 361 F--GAPDNVRLSYATSLDALETAVERIHRFMEAR 392 F GA +R SY D + A+ERI ++ R Sbjct: 349 FGEGAEGFLRFSYTRPFDEIVVALERIEGYLRQR 382 Lambda K H 0.316 0.133 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: 378 Number of extensions: 15 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: 393 Length of database: 386 Length adjustment: 30 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 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 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