Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate H281DRAFT_02594 H281DRAFT_02594 3-carboxy-cis,cis-muconate cycloisomerase
Query= curated2:A9FJ48 (430 letters) >FitnessBrowser__Burk376:H281DRAFT_02594 Length = 456 Score = 87.8 bits (216), Expect = 6e-22 Identities = 93/291 (31%), Positives = 137/291 (47%), Gaps = 28/291 (9%) Query: 24 DWQLDQRLLAYDLRATIAHVRGLARIGVLSEAERDALVRELEVLSAQNEAGELRLTEDDE 83 D+ L QR + + +A + AR+GV+ D + RE ++ + + +R E D Sbjct: 33 DYALVQRYIDVE----VALAKAEARVGVIPTDAADVIARESQI--ERIDFDHMR-EETDI 85 Query: 84 DGHSAIEAA--LVARIGDAGKKVHTGRSRNDQVLVATRLYERDALDELAENAAAGARALL 141 G+ + LV G+AG+ VH G + D + A L RDALD + + L+ Sbjct: 86 VGYPILPLVHQLVGMCGEAGRYVHWGATTQDIMDTAVALQVRDALDSIDADIRELRGILV 145 Query: 142 DLARREAETPMPGYTHLQRAVPSSVGY----WAASFVEGLADAIDVVRATRALVDRCPLG 197 DL+++ +TPM G THLQ+A+P + GY W A F + I +R A+V+ Sbjct: 146 DLSKKHRDTPMAGRTHLQQALPVTFGYKTAIWLAMF-DRHQQRIAQLRPRVAVVE---FA 201 Query: 198 GAAGFGVNLPLDRVGVARELGFAGVALNPLASQ---TSRGIIEAQILAAAWQVMAVSRRL 254 GAAG +L V + L A + L A+ G EA L A V ++ Sbjct: 202 GAAGTLASLGDKGFDVQKALA-AELQLGVPATTWHVARDGFAEAVNLLAL--VTGSLGKI 258 Query: 255 AWDLSLFAMSELAFIRLPEAFTTG---SSIMPQKRNPDVVELMRAACSVVQ 302 A D+ + A +E F + E F G SS MPQKRNP ELM AA V+ Sbjct: 259 ATDIMIMASNE--FGEVYEPFVKGRGASSTMPQKRNPISSELMLAAAKAVR 307 Lambda K H 0.320 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: 388 Number of extensions: 16 Number of successful extensions: 3 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: 430 Length of database: 456 Length adjustment: 32 Effective length of query: 398 Effective length of database: 424 Effective search space: 168752 Effective search space used: 168752 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: 51 (24.3 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