Align Arginase; EC 3.5.3.1 (uncharacterized)
to candidate Echvi_2468 Echvi_2468 Arginase/agmatinase/formimionoglutamate hydrolase, arginase family
Query= curated2:Q7M0Z3 (298 letters) >FitnessBrowser__Cola:Echvi_2468 Length = 316 Score = 167 bits (424), Expect = 2e-46 Identities = 105/319 (32%), Positives = 173/319 (54%), Gaps = 43/319 (13%) Query: 3 KNMSIVGVPMDLGADRRGVDMGPSAIRYAGVVARLEKMGFNIEDRGDIFVTL-PHHFTET 61 +N+ +V V +L A RG +G A++ A ++ + D F P + + Sbjct: 2 RNIKLVEVRSELAAGTRGASLGIDALKVA-----------SLGKKSDFFTRFDPINVPDA 50 Query: 62 ENH----------KYLDEVVEANEKLANVVSDIMTAGRFPLVLGGDHSIALGTIAGV--A 109 N+ KY+D V E + + + + +FP+VL GDHS A GTI G+ A Sbjct: 51 NNYLWKNNPYPHAKYIDGVHEVLGNVHDTIKALREEKKFPIVLAGDHSTAAGTIMGIKAA 110 Query: 110 KHVKNLGVICLDAHGDLNTGATSPSGNIHGMPLAASLGYGH----------------ERL 153 K LGVI +DAH D+++ TSPSGN+HGMPL L + E++ Sbjct: 111 NPEKRLGVIWIDAHADIHSPYTSPSGNMHGMPLGMCLQEDNLENRQQDPSAEEIEYWEKI 170 Query: 154 TNIGGYTPKVKAENVVIIGARDLDQGERELIKRIGMKVFTMHEIDKLGMARVMDEAIAHV 213 IGG PK+KA ++V I RD ++ E +LI++ G++ FT E+ + G+ ++ +EA+A + Sbjct: 171 KKIGGDFPKIKASDIVYIAVRDTEEPENKLIEKHGIRNFTTQEVRQKGITQISEEALA-I 229 Query: 214 SKNTDGVHLSLDLDGLDPHDAPGVGTPVIGGISYREG-HVSLEMLADADILCSAEFVEVN 272 K+ + +++S D+D +D + G GTPV G++ +E +++E++ D + C E VEVN Sbjct: 230 LKDCEQIYISFDVDSMDSSISVGTGTPVPDGLTVQEALKLNMELIKDKRV-CCWEIVEVN 288 Query: 273 PILDRENMTARVAVALMSS 291 P LD EN+ A+ A ++ S Sbjct: 289 PTLDSENIMAQNAFEVLES 307 Lambda K H 0.319 0.138 0.398 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: 250 Number of extensions: 15 Number of successful extensions: 5 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: 298 Length of database: 316 Length adjustment: 27 Effective length of query: 271 Effective length of database: 289 Effective search space: 78319 Effective search space used: 78319 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. 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