Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate 5209143 Shew_1621 agmatinase (RefSeq)
Query= curated2:Q8KZT5 (353 letters) >FitnessBrowser__PV4:5209143 Length = 307 Score = 212 bits (539), Expect = 1e-59 Identities = 126/301 (41%), Positives = 178/301 (59%), Gaps = 16/301 (5%) Query: 23 YAGAATYARLPRLD---QVSKADVTVVGVPFDSGVSYRPGARFGANHVREASRLL--RPY 77 Y+ A Y R P LD S ADV V+G+PFD + R G R G +R+AS L Sbjct: 13 YSNAFGYLRQP-LDFKPLESDADVVVIGLPFDMATTGRSGGRMGPGAIRQASVNLAWEEC 71 Query: 78 NPAWDVSPFENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTIALP 137 WD +++++ DAGD+ + + + + ++ A + +G L++ GGDH + LP Sbjct: 72 RWPWDFKLSDHLKMVDAGDLVFDCGDAADFTQRVEDFATAVLDSGKALMSFGGDHFVTLP 131 Query: 138 LLRAAAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVGTRG 197 LLRA ++ G+ +A+LHFDAH DT+ G++Y HGT F A EGI+D VG R Sbjct: 132 LLRAHYKKHGK-MALLHFDAHTDTYSQ--GSKYDHGTMFFHAPNEGIIDASHSVQVGIRT 188 Query: 198 PLYGKKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPAHAP 257 L F ++ +A E VA+I+DR+G+ PLY++ DID LDPA AP Sbjct: 189 EYDKPSHL-------FKVIDAAAANEMTADEIVAQIKDRVGDMPLYVTFDIDCLDPAFAP 241 Query: 258 GTGTPEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELVTLM 317 GTGTP GG+TS + ++IIRG RGMN+VG DVVEVAPAYD AEIT +AG+ + E++ + Sbjct: 242 GTGTPVCGGLTSDKAMKIIRGLRGMNVVGMDVVEVAPAYDSAEITALAGATLGLEMLHVW 301 Query: 318 A 318 A Sbjct: 302 A 302 Lambda K H 0.318 0.137 0.402 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: 322 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: 353 Length of database: 307 Length adjustment: 28 Effective length of query: 325 Effective length of database: 279 Effective search space: 90675 Effective search space used: 90675 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