Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_011320397.1 AVA_RS18735 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YY14 (398 letters) >NCBI__GCF_000204075.1:WP_011320397.1 Length = 391 Score = 735 bits (1897), Expect = 0.0 Identities = 373/394 (94%), Positives = 379/394 (96%), Gaps = 7/394 (1%) Query: 1 MTNFTSRMQAVQSPIIPVVGELIQNSPGTISLGQGVVSYSPPPEAIELLPRFLADPANNL 60 MTNFTSRMQAVQSPIIPVVGELIQNSPGTISLGQGVVSYSPPPEAIELLP+FLADPANNL Sbjct: 1 MTNFTSRMQAVQSPIIPVVGELIQNSPGTISLGQGVVSYSPPPEAIELLPKFLADPANNL 60 Query: 61 YKAVEGIPPLLNALTEKLSTFNNIEITTDNCIVVTAGSNMAFMNAILAITSPGDEIILNT 120 YKAVEGIPPLLNALT+KLSTFN +EITTDNCIVVTAGSNMAFMNAILAITSPGDEIILNT Sbjct: 61 YKAVEGIPPLLNALTDKLSTFNKMEITTDNCIVVTAGSNMAFMNAILAITSPGDEIILNT 120 Query: 121 PYYFNHEMAITMAGCRAVLVETDENYQLCPEAIAQAITPKTRAVVTISPNNPTGVVYCED 180 PYYFNHEMAI MAGCRAVLVETDENYQL PEAIAQAITPKTRAVVTISPNNPTGVVYCED Sbjct: 121 PYYFNHEMAIAMAGCRAVLVETDENYQLRPEAIAQAITPKTRAVVTISPNNPTGVVYCED 180 Query: 181 LLRNVNQICANYGIYHISDEAYEYFTYDGVKHVSPASFAGSSEYTISLYSLSKAYGFASW 240 LLRNVNQICAN GIYHISDEAYEYFTYDGVKHVSPASFAGSSEYTISLYSLSKAYGFASW Sbjct: 181 LLRNVNQICANCGIYHISDEAYEYFTYDGVKHVSPASFAGSSEYTISLYSLSKAYGFASW 240 Query: 241 RIGYMVIPKHLLVAIKKVQDTILICPPVVSQYAALGALQAKPEYLQDHIGALAQPAVGIA 300 RIGYMVIPKHLLVAIKKVQDTILICPPVVSQYAALGALQAKPEYLQDHI A IA Sbjct: 241 RIGYMVIPKHLLVAIKKVQDTILICPPVVSQYAALGALQAKPEYLQDHIQA-------IA 293 Query: 301 QVRQIVFDYLKQLQGLCNITPADGAFYVFLKVHTQIDAFALVKQLIQEYKVAVIPGTTFG 360 QVR+IVFDYL QLQGLC ITPADGAFYVFLKVHTQIDAF LVKQLIQEYKVAVIPGTTFG Sbjct: 294 QVRKIVFDYLNQLQGLCTITPADGAFYVFLKVHTQIDAFTLVKQLIQEYKVAVIPGTTFG 353 Query: 361 MENGCYLRVAYGALQKDTVKEGIERLVQGLKTIL 394 ME+GCYLRVAYGALQKDTV+EGIERLVQGLKTIL Sbjct: 354 MESGCYLRVAYGALQKDTVQEGIERLVQGLKTIL 387 Lambda K H 0.320 0.136 0.398 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: 720 Number of extensions: 23 Number of successful extensions: 2 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: 398 Length of database: 391 Length adjustment: 31 Effective length of query: 367 Effective length of database: 360 Effective search space: 132120 Effective search space used: 132120 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 09 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