Align N-succinylcitrulline desuccinylase (EC 3.5.1.-) (characterized)
to candidate 353076 BT3549 acetylornithine deacetylase (NCBI ptt file)
Query= reanno::Btheta:353076 (355 letters) >FitnessBrowser__Btheta:353076 Length = 355 Score = 706 bits (1823), Expect = 0.0 Identities = 355/355 (100%), Positives = 355/355 (100%) Query: 1 MKYDIPTMTAEAVSLLKSLISIPSISREETQAADFLQNYIEAEGMQTGRKGNNVWCLSPM 60 MKYDIPTMTAEAVSLLKSLISIPSISREETQAADFLQNYIEAEGMQTGRKGNNVWCLSPM Sbjct: 1 MKYDIPTMTAEAVSLLKSLISIPSISREETQAADFLQNYIEAEGMQTGRKGNNVWCLSPM 60 Query: 61 FDLKKPTILLNSHIDTVKPVNGWRKDPFTPREENGKLYGLGSNDAGASVVSLLQVFLQLC 120 FDLKKPTILLNSHIDTVKPVNGWRKDPFTPREENGKLYGLGSNDAGASVVSLLQVFLQLC Sbjct: 61 FDLKKPTILLNSHIDTVKPVNGWRKDPFTPREENGKLYGLGSNDAGASVVSLLQVFLQLC 120 Query: 121 RTSQNYNLIYLASCEEEVSGKEGIESVLPGLPPVSFAIVGEPTEMQPAIAEKGLMVLDVT 180 RTSQNYNLIYLASCEEEVSGKEGIESVLPGLPPVSFAIVGEPTEMQPAIAEKGLMVLDVT Sbjct: 121 RTSQNYNLIYLASCEEEVSGKEGIESVLPGLPPVSFAIVGEPTEMQPAIAEKGLMVLDVT 180 Query: 181 ATGKAGHAARDEGDNAIYKVLNDIAWFRDYRFEKESPLLGPVKMSVTVINAGTQHNVVPD 240 ATGKAGHAARDEGDNAIYKVLNDIAWFRDYRFEKESPLLGPVKMSVTVINAGTQHNVVPD Sbjct: 181 ATGKAGHAARDEGDNAIYKVLNDIAWFRDYRFEKESPLLGPVKMSVTVINAGTQHNVVPD 240 Query: 241 KCTFVVDIRSNELYSNEDLFAEIRKHIACDAKARSFRLNSSRIDEKHPFVQKAVKMGRIP 300 KCTFVVDIRSNELYSNEDLFAEIRKHIACDAKARSFRLNSSRIDEKHPFVQKAVKMGRIP Sbjct: 241 KCTFVVDIRSNELYSNEDLFAEIRKHIACDAKARSFRLNSSRIDEKHPFVQKAVKMGRIP 300 Query: 301 FGSPTLSDQALMSFASVKIGPGRSSRSHTAEEYIMLKEIEEAIGIYLDLLDGLKL 355 FGSPTLSDQALMSFASVKIGPGRSSRSHTAEEYIMLKEIEEAIGIYLDLLDGLKL Sbjct: 301 FGSPTLSDQALMSFASVKIGPGRSSRSHTAEEYIMLKEIEEAIGIYLDLLDGLKL 355 Lambda K H 0.317 0.134 0.387 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: 500 Number of extensions: 7 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: 355 Length of database: 355 Length adjustment: 29 Effective length of query: 326 Effective length of database: 326 Effective search space: 106276 Effective search space used: 106276 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: 49 (23.5 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