Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate BPHYT_RS21425 BPHYT_RS21425 3-carboxy-cis,cis-muconate cycloisomerase
Query= curated2:A9FJ48 (430 letters) >FitnessBrowser__BFirm:BPHYT_RS21425 Length = 459 Score = 74.3 bits (181), Expect = 7e-18 Identities = 74/228 (32%), Positives = 108/228 (47%), Gaps = 15/228 (6%) Query: 89 IEAALVARIGDAGKKVHTGRSRNDQVLVATRLYERDALDELAENAAAGARALLDLARREA 148 + A + A +A K VH G + D + AT L RD D L + + A+ LA Sbjct: 88 LTARVKAADAEASKYVHWGATSQDIIDTATVLQLRDTFDLLDSSLQSTCDAVAKLAATHR 147 Query: 149 ETPMPGYTHLQRAVPSSVGYWAASFVEGL---ADAIDVVRATRALVDRCPLGGAAGFGVN 205 TPM G T LQ+A+P ++G A +++ L + +D +RA RALV GGAAG + Sbjct: 148 TTPMIGRTWLQQALPITLGLKFAQWLDALLRHRERLDALRA-RALV--LQFGGAAGTLAS 204 Query: 206 L----PLDRVGVARELGFAGVALNPLASQTSRGIIEAQILAAAWQVMAVSRRLAWDLSLF 261 L P +A+ELG V P +Q R A+ A ++ ++A D+SL Sbjct: 205 LRDAAPQVTQSLAKELGLT-VPTLPWHTQRDR---IAETAALFGMLIGTLGKIARDISLQ 260 Query: 262 AMSELAFIRLPEAF-TTGSSIMPQKRNPDVVELMRAACSVVQGALAEV 308 +E+ + P A GSS MP KRNP + A + G +A V Sbjct: 261 MQTEIDELAEPAAAGKGGSSTMPHKRNPVGCAAVLTAATRAPGLVATV 308 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: 348 Number of extensions: 25 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: 430 Length of database: 459 Length adjustment: 32 Effective length of query: 398 Effective length of database: 427 Effective search space: 169946 Effective search space used: 169946 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