Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_013010833.1 DACET_RS07770 aspartate aminotransferase
Query= CharProtDB::CH_017144 (393 letters) >NCBI__GCF_000025725.1:WP_013010833.1 Length = 430 Score = 193 bits (490), Expect = 9e-54 Identities = 136/401 (33%), Positives = 213/401 (53%), Gaps = 32/401 (7%) Query: 1 MKLAKRVASLTPSATLAITEKAKELKAAGHDVIGLGAGEPDFNTPQHILDAAIKAMNEGH 60 + L V L SATLAI E + L+ G V LG G+ F PQ +++ + N + Sbjct: 9 INLNLNVRGLPLSATLAINELSNSLRQQGKKVYKLGLGQSPFPVPQSVVN---ELKNNAY 65 Query: 61 TK-YTPSGGLPALKEEIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVII 119 K Y P GLP L+ + + + + QGL ++ +++ G+K ++ + L+ GD ++I Sbjct: 66 QKDYLPVRGLPVLQTAVAEYYQKTQGLTFKANNILIGPGSKELMFLI--QLVYYGD-LVI 122 Query: 120 PTPYWVSYPEQVKLAGGVPVYVEGLEQNHFKITPEQLKQAITP---RTKAVIINSPSNPT 176 PTP WVSY Q + G ++ LE+N + + PE+L+ + + VI+N P+NPT Sbjct: 123 PTPSWVSYAPQAHIVGHQVHWLNTLEENEWLLMPEELEALCKEDPNKPRLVILNYPNNPT 182 Query: 177 GMIYTAEELKALGEVCLAHGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVS 236 G YT E+L+ L EV + V+++SDEIY + + G HVSIA+ PE TVI +G+S Sbjct: 183 GGTYTLEQLQELAEVARRYKVVMLSDEIYGETNHEG-NHVSIAKFYPE---GTVISSGLS 238 Query: 237 KSHSMTGWRIGYAAGPKD---IIKAMTDLASHSTSNPTSIAQYAAIAAYS---GPQEPVE 290 K GWR+G A P ++ +M +AS + ++ ++ QYAA+ A+ + + Sbjct: 239 KWCGAGGWRLGTFAFPDSLEWLLNSMASVASETFTSTSAPIQYAAVRAFKFGIDIERYLW 298 Query: 291 QMRQAFEQRLNIIYDKLVQIPGFTCVKPQGAFYLFP---NAREAAAMAGCRTVDEFVAAL 347 R+ Q ++++ L G C P+G FY+FP N RE+ T D+F L Sbjct: 299 NSRKILRQLGRLMHEILTD-AGVRCAYPKGGFYMFPNFENYRESLKAKQITTSDQFCQRL 357 Query: 348 LEEAKVALVPGSGFGAPD---NVRLSY-----ATSLDALET 380 L + VA++PG+ FG P RLSY A +L ALET Sbjct: 358 LNDVGVAVLPGTAFGRPAGELTARLSYVDFDGARALSALET 398 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: 391 Number of extensions: 20 Number of successful extensions: 7 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: 430 Length adjustment: 31 Effective length of query: 362 Effective length of database: 399 Effective search space: 144438 Effective search space used: 144438 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