Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate AO353_28745 AO353_28745 peptidyl-arginine deiminase
Query= BRENDA::O86509 (339 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28745 Length = 350 Score = 249 bits (635), Expect = 1e-70 Identities = 139/345 (40%), Positives = 190/345 (55%), Gaps = 25/345 (7%) Query: 5 MPPEWAPHERTWMAWPGPNATFTDA--EELAGARAAWASVARAVRRFEPVTMVHGPGQAA 62 MP EW H TWM WP A + LA + +A VA A+ RFEPV MV P A Sbjct: 13 MPAEWVRHAATWMVWPHNQALWESGWGVTLARVQEDFARVANAIGRFEPVKMVVDPSAVA 72 Query: 63 TARELLGPDVDLVERELDDAWMRDIGPTFVTDGRGGLAAVDWVFNGWGAQDWARWEHDAE 122 +A+ L GP+++L+E ++D+W RD GP+FV + GLA V W FN WG + + + D Sbjct: 73 SAKALCGPNIELIELAVNDSWCRDSGPSFVCHPQQGLAGVSWRFNAWGGK--SAHDLDES 130 Query: 123 IARHVADLAAAPVLSSPLVNEGGAIHVDGEGTVLLTDTVQLGSGRNPGWSREEVEAEIHA 182 +AR + +PL NEGGAIHVDGEGT++ T++V L RNPG S+ E+E Sbjct: 131 LARRALNHLGVACFGTPLSNEGGAIHVDGEGTLITTESVLLNPNRNPGMSKAEMEEIFTR 190 Query: 183 KLGTTTAIWLPHG---LAGDYGRYGTQGHVDIVAAFARPGTVVVHSQRDPRHPDHERSQL 239 LG +WLP + GD T GHVD V AFARPG ++V + H++S + Sbjct: 191 LLGVKKTVWLPGDPDYVTGDM----TDGHVDGVCAFARPGVLLVDA-------THDKSSI 239 Query: 240 YLEILRGR-------TDARGRRLEVVEVPAPTVLKDEEGEWADYSYINHYVCNGGVVLCA 292 Y E++R TDA GR E++++ T D E E SY N Y+ N +++ A Sbjct: 240 YAEVVRENRRALALATDAHGRPFELIDLYEATDAVDTEAEVFCASYTNFYIANNAIIMPA 299 Query: 293 FGDPNDELAAGIFRRLFPERTVTLVDARTIFAGGGGIHCITQQQP 337 +G D +AA + + FP R V V + GGGG+HCITQQQP Sbjct: 300 YGIDADNVAAEVLAQAFPGREVVPVRINHLAHGGGGVHCITQQQP 344 Lambda K H 0.319 0.137 0.443 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: 436 Number of extensions: 27 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: 339 Length of database: 350 Length adjustment: 29 Effective length of query: 310 Effective length of database: 321 Effective search space: 99510 Effective search space used: 99510 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: 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