Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate GFF2282 PS417_11635 3-carboxy-cis,cis-muconate cycloisomerase
Query= curated2:Q2J867 (464 letters) >FitnessBrowser__WCS417:GFF2282 Length = 451 Score = 74.7 bits (182), Expect = 6e-18 Identities = 81/261 (31%), Positives = 121/261 (46%), Gaps = 21/261 (8%) Query: 41 ARVLHRAGLL--DADELAAMLAALDELSDAVAQGRFRPTVEDEDVHTALERGLLERLGTL 98 AR R G++ DA E A L+ + L A+ Q + + +E+ L + G Sbjct: 41 ARAEARCGVIPTDAAEQIATLSQYEALDLALMQ--HETEIVGYPILPLVEQ-LSKICGEA 97 Query: 99 GGKLRAGRSRNDQVATDLRLYLRDSAREVAARLTELSHALVVLAEQHVDTPAPGMTHLQH 158 G + G + D + T + L +R + V + + L LAE++ DTP G THLQH Sbjct: 98 GRYVHWGATTQDIMDTAVVLQVRAALAIVERDIQTVRGLLAGLAERYRDTPMAGRTHLQH 157 Query: 159 AQPISFGHQLLAHVQAFVRDIDRLRDWDVRASVSALGAGALAGSSLPLDPQG------VA 212 A PI+FG++ + F R +RL + R + AGA AG+ L +G + Sbjct: 158 ALPITFGYKCAVWLSMFDRHAERLVELRPRVEIGQF-AGA-AGTLASLGDKGLEVQEALM 215 Query: 213 AELGFDRAFANSLDAVSDRDFAAEFLFVAALIGVHLSRLGEEIVLWTTREFGWVELDDAF 272 +ELG A A RD AE L L+ L ++ +I++ T E G E+ + F Sbjct: 216 SELGLGVPQATWHVA---RDGLAETLNFLGLVTGSLGKIALDIMMMMTSELG--EVYEPF 270 Query: 273 ATG---SSIMPQKKNPDVAEL 290 G SS MPQK+NP EL Sbjct: 271 VKGRGASSTMPQKRNPISCEL 291 Lambda K H 0.321 0.137 0.400 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: 408 Number of extensions: 18 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: 464 Length of database: 451 Length adjustment: 33 Effective length of query: 431 Effective length of database: 418 Effective search space: 180158 Effective search space used: 180158 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 (21.9 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