Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_024750127.1 CCE_RS17620 aspartate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000017845.1:WP_024750127.1 Length = 394 Score = 630 bits (1626), Expect = 0.0 Identities = 299/393 (76%), Positives = 341/393 (86%) Query: 1 MSFDWITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQA 60 MS W+ ADR++ LPPYVFARLDELKA+AREQG+DLIDLGMGNPDG PQPV++ AI A Sbjct: 1 MSLSWMRRADRLKALPPYVFARLDELKARAREQGLDLIDLGMGNPDGMAPQPVIEGAIAA 60 Query: 61 LQDPKNHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNP 120 LQ P+ HGYPPFEGTASFR AIT WY+R Y V LD SEALPL+GSKEGL HLA+AY+NP Sbjct: 61 LQQPQTHGYPPFEGTASFREAITAWYHRCYRVDLDSSSEALPLIGSKEGLGHLALAYINP 120 Query: 121 GDVVLVPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPS 180 GDVVLVPSP+YPAHFRGP+IAG ++ +IL E DWLIDL +IP+ +A+ AKILYFNYP+ Sbjct: 121 GDVVLVPSPSYPAHFRGPLIAGAQLYPIILSAEKDWLIDLHSIPDNIAKAAKILYFNYPN 180 Query: 181 NPTGATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHT 240 NPT ATAP+ FFEEIV +A YEI+LVHDLCYAELAFDGYQPTSLLEIPG KDIGVEFHT Sbjct: 181 NPTTATAPKAFFEEIVKWATHYEIMLVHDLCYAELAFDGYQPTSLLEIPGGKDIGVEFHT 240 Query: 241 LSKTYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQ 300 LSKTYNMAGWRVGFVVGN +IQGLRTLKTNLDYGIFAA+Q AAETAL LPD Y+ +VQ+ Sbjct: 241 LSKTYNMAGWRVGFVVGNAEIIQGLRTLKTNLDYGIFAAVQAAAETALNLPDSYIKQVQE 300 Query: 301 RYRTRRDFLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAF 360 RY+ RRDFLIQGLGELGW++ ++ATMYLWVKCP STDFAL++L++TG+V TPGNAF Sbjct: 301 RYQNRRDFLIQGLGELGWNIKPSQATMYLWVKCPTHTNSTDFALDVLEKTGIVFTPGNAF 360 Query: 361 GVAGEGYVRISLIADCDRLGEALDRIKQAGIRY 393 G GEGYVRISLIA+CDRLGEAL R+KQAGI Y Sbjct: 361 GEGGEGYVRISLIAECDRLGEALSRLKQAGIGY 393 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: 622 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: 394 Length adjustment: 31 Effective length of query: 372 Effective length of database: 363 Effective search space: 135036 Effective search space used: 135036 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 Sep 17 2021.
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