Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_012411382.1 NPUN_RS25750 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000020025.1:WP_012411382.1 Length = 403 Score = 763 bits (1971), Expect = 0.0 Identities = 368/401 (91%), Positives = 388/401 (96%) Query: 1 MSFDWITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQA 60 MS +WI PA+RIQ+LPPYVFARLDELKAKAREQG+DLIDLGMGNPDGATP PVV+AAI A Sbjct: 1 MSLNWIVPAERIQKLPPYVFARLDELKAKAREQGLDLIDLGMGNPDGATPAPVVEAAIAA 60 Query: 61 LQDPKNHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNP 120 L+DP NHGYPPFEGTASFRRAITNWY+RRYGVVLDPDSEALPLLGSKEGL+HLAIAYVNP Sbjct: 61 LKDPANHGYPPFEGTASFRRAITNWYHRRYGVVLDPDSEALPLLGSKEGLTHLAIAYVNP 120 Query: 121 GDVVLVPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPS 180 GD+VLVPSPAYPAHFRGP IAGG +HSLILKPENDWLIDL AIP+EVAR+AKILYFNYPS Sbjct: 121 GDLVLVPSPAYPAHFRGPAIAGGKIHSLILKPENDWLIDLAAIPDEVARQAKILYFNYPS 180 Query: 181 NPTGATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHT 240 NPT ATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHT Sbjct: 181 NPTAATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHT 240 Query: 241 LSKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQ 300 LSKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIF+ALQ AAETALQLPD+YLHEVQQ Sbjct: 241 LSKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFSALQKAAETALQLPDVYLHEVQQ 300 Query: 301 RYRTRRDFLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAF 360 RYRTRRDFLI GLGELGWD+P+TKATMYLWVKCPVGMGSTDFALN+LQQTGVV+TPGNAF Sbjct: 301 RYRTRRDFLIDGLGELGWDIPRTKATMYLWVKCPVGMGSTDFALNVLQQTGVVLTPGNAF 360 Query: 361 GVAGEGYVRISLIADCDRLGEALDRIKQAGIRYRPEALVSA 401 GVAGEGYVRISLIADCDRLGEAL R KQAGIRY+PEA+VSA Sbjct: 361 GVAGEGYVRISLIADCDRLGEALHRFKQAGIRYQPEAVVSA 401 Lambda K H 0.321 0.140 0.427 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: 701 Number of extensions: 17 Number of successful extensions: 1 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: 403 Length of database: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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 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