Align Arginase 1, mitochondrial; Arginine amidohydrolase 1; EC 3.5.3.1 (characterized)
to candidate SMc01802 SMc01802 agmatinase
Query= SwissProt::B8AU84 (340 letters) >FitnessBrowser__Smeli:SMc01802 Length = 318 Score = 94.7 bits (234), Expect = 3e-24 Identities = 85/286 (29%), Positives = 130/286 (45%), Gaps = 18/286 (6%) Query: 48 LKAELLRALGGVKASACLLGVPLGHNSSFLQGPAFAPPRIREAIWCGSTNSSTEEGKELN 107 ++ + + L GV+A + G+P +S G F P IR A + ++L Sbjct: 31 MRRKYTKELKGVEA--VVWGIPFDAATSNRPGARFGPQAIRRASAIFDNDPQYPFQRDLF 88 Query: 108 DPRVLTDVGDVPIQEIRDCGVEDDRLMNVVSESVKTVMEEDPLRPLVLGGDHSISYPVVR 167 D GD + D G + E+ K + L L LGGDH ++YP++R Sbjct: 89 ADMATIDYGDC----LLDYGNHARTPQTIEREASKILKSGAYL--LTLGGDHFVTYPILR 142 Query: 168 AVSEKLGGPVDILHLDAHPDIYDAFEGNIYSHASSFARIMEGGY--ARRLLQVGIRSITK 225 A + L GP+ ++ DAH D + +G I H + R G R +Q+GIR+ Sbjct: 143 AHAA-LHGPLALVQFDAHQDTWPDEKGRI-DHGAFVGRAAREGLIDVERSIQIGIRTHAP 200 Query: 226 EGREQGKRFGVEQYEMRTFSKDREKLESLKLGEGVKGVYISVDVDCLDPAFAPGVSHIEP 285 E +G E EMR E +++ + Y++ D+DCLDPAFAPG Sbjct: 201 EDCGIRIVYGYELEEMRA----EEIADTIIRHVDNRPAYLTFDIDCLDPAFAPGTGTPVA 256 Query: 286 GGLSFRDVLNILHNLQGDVVAG-DVVEFNPQRDTVDGMTAMVAAKL 330 GG S +L++L L +AG DVVE P D D +TA+ + + Sbjct: 257 GGPSSAKILSVLRKLGALHIAGSDVVEVAPAYDHAD-LTAIAGSTI 301 Lambda K H 0.318 0.137 0.394 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: 283 Number of extensions: 12 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: 340 Length of database: 318 Length adjustment: 28 Effective length of query: 312 Effective length of database: 290 Effective search space: 90480 Effective search space used: 90480 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 (21.7 bits) S2: 49 (23.5 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