Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate SMc01802 SMc01802 agmatinase
Query= curated2:Q8KZT5 (353 letters) >FitnessBrowser__Smeli:SMc01802 Length = 318 Score = 192 bits (488), Expect = 1e-53 Identities = 114/301 (37%), Positives = 167/301 (55%), Gaps = 13/301 (4%) Query: 21 PRYAGAATYARLPRLDQVSKADVTVVGVPFDSGVSYRPGARFGANHVREASRLLR--PYN 78 P +AG ++ R ++ + V G+PFD+ S RPGARFG +R AS + P Sbjct: 22 PTHAGILSFMRRKYTKELKGVEAVVWGIPFDAATSNRPGARFGPQAIRRASAIFDNDPQY 81 Query: 79 PAWDVSPFENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTIALPL 138 P + F ++ D GD ++ N +TI++ A + +G+ L+TLGGDH + P+ Sbjct: 82 P-FQRDLFADMATIDYGDCLLDYGNHARTPQTIEREASKILKSGAYLLTLGGDHFVTYPI 140 Query: 139 LRAAAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVGTRGP 198 LRA A G P+A++ FDAH DTW G HG RA EG++D E +G R Sbjct: 141 LRAHAALHG-PLALVQFDAHQDTWPDEKG-RIDHGAFVGRAAREGLIDVERSIQIGIR-- 196 Query: 199 LYGKKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPAHAPG 258 + +D G IV ++ E I + NRP Y++ DID LDPA APG Sbjct: 197 THAPEDC------GIRIVYGYELEEMRAEEIADTIIRHVDNRPAYLTFDIDCLDPAFAPG 250 Query: 259 TGTPEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELVTLMA 318 TGTP AGG +S ++L ++R +++ G+DVVEVAPAYDHA++T +AGS +A ++ L A Sbjct: 251 TGTPVAGGPSSAKILSVLRKLGALHIAGSDVVEVAPAYDHADLTAIAGSTIAMYMLGLRA 310 Query: 319 D 319 + Sbjct: 311 E 311 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: 352 Number of extensions: 25 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: 318 Length adjustment: 28 Effective length of query: 325 Effective length of database: 290 Effective search space: 94250 Effective search space used: 94250 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