Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_022671381.1 G415_RS0109140 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::A0A6F8T0V6 (393 letters) >NCBI__GCF_000420385.1:WP_022671381.1 Length = 420 Score = 186 bits (473), Expect = 8e-52 Identities = 127/376 (33%), Positives = 197/376 (52%), Gaps = 24/376 (6%) Query: 3 LAKRVASLTPSATLAITAKAKELKAAGYDVIGLGAGEPDFNTPQHIIAAAIKTMNEGHTK 62 L V L SATL I K+ EL G+ V LG G+ FN P ++ + H K Sbjct: 4 LNMNVKDLPLSATLEINEKSNELLENGFKVYKLGLGQSPFNVPDPVVE---ELKRYAHVK 60 Query: 63 -YTPSGGLPALKEEIIKKFARDQGLSYEPAEIIVCVGAKHALYTLFQVLLDEGDEVIIPT 121 Y P GL L+E + + + + QG+ + P I++ G+K ++ V+ E +++ + Sbjct: 61 DYLPVKGLKRLREAVSEYYLKSQGVRFNPDNILIGPGSKELMFIAQLVMYGE---LLLAS 117 Query: 122 PYWVSYPEQVKLAGGVPVYVEGLEENDFKMTPDQLKQAITPKT---KAVIINSPSNPTGM 178 P WVSY Q K+ G V++E EE+D+ + PD + K +I+N P+NPTG Sbjct: 118 PSWVSYAPQSKILGRNLVWLETKEEDDWLLMPDVVDNYCKNNKYSQKIIILNYPNNPTGK 177 Query: 179 IYTAEELKALGEVCLAHGVLIVSDEIYEKLIYGGAKHVSIAELSPELKEQTIIINGVSKS 238 Y E L+ L EV HGV+++SDEIY +L + G KH+SIA+ P E TII +G+SK Sbjct: 178 TYPLELLRDLAEVFRKHGVIVISDEIYGELHHEG-KHISIAKFYP---EGTIISSGLSKW 233 Query: 239 HSMTGWRIGYAAGP---KDIIQAMTDLASHSTSNPTSIAQYAAIAAYS---GPQEPVEQM 292 GWR+G A P K + M +AS + ++ ++ QYAA+ A++ Q+ +++ Sbjct: 234 AGAGGWRLGTFAIPDELKILADKMASVASETFTSVSAPIQYAAVRAFNIDEALQDYLKRS 293 Query: 293 RQAFEERLNIIYDKLVQIPGFTCIKPQGAFYLFPN---ARKAADMAGCRTVDEFVAALLE 349 R + I+DK ++ G + GAFY PN +K + G +T E LE Sbjct: 294 RAILKALAKYIFDKFNKV-GISVSLADGAFYYLPNFSKFKKQFNKIGIKTSRELCKRALE 352 Query: 350 EAKVALVPGSGFGAPD 365 + +VA +PG FG P+ Sbjct: 353 DIQVAFLPGDDFGRPE 368 Lambda K H 0.316 0.133 0.380 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: 375 Number of extensions: 20 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: 393 Length of database: 420 Length adjustment: 31 Effective length of query: 362 Effective length of database: 389 Effective search space: 140818 Effective search space used: 140818 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