Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate 3608333 Dshi_1735 putative agmatinase (RefSeq)
Query= curated2:Q8KZT5 (353 letters) >FitnessBrowser__Dino:3608333 Length = 324 Score = 202 bits (514), Expect = 1e-56 Identities = 114/298 (38%), Positives = 166/298 (55%), Gaps = 12/298 (4%) Query: 23 YAGAATYARLPRLDQVSKADVTVVGVPFDSGVSYRPGARFGANHVREASRLLRPYNP--A 80 Y GA ++ R ++S DV V GVPFD V+ RPG R G +REAS L +P++P Sbjct: 28 YGGALSFLRRRYTKELSGVDVAVSGVPFDLSVTNRPGCRLGPRAIREASSL-QPFDPPYG 86 Query: 81 WDVSPFENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTIALPLLR 140 W P V D GD+A + ++ + + A G+ +T+GGDH I+ P+LR Sbjct: 87 WGFDPLSEFTVVDYGDLAFDYGRAAGFPAALEAHIRTILAAGAAPLTMGGDHYISYPILR 146 Query: 141 AAAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVGTRGPLY 200 A AE G P+++L FDAH DTW HGT F +AV++G++D VG R Sbjct: 147 ALAEVHG-PLSLLQFDAHSDTWPDEDRDRLDHGTMFYKAVKDGLIDPARSVQVGIR---- 201 Query: 201 GKKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPAHAPGTG 260 +D GF ++ + +V+ G AK+R +G+ Y++ DID LDP APGTG Sbjct: 202 ----TTNDTDLGFHVIDAREVHEAGAAAVAAKVRGILGDHKTYLTFDIDCLDPGTAPGTG 257 Query: 261 TPEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELVTLMA 318 TP GG+++ + ++R G+ +VG DVVEV+P YD + T VAG+HV E++ L A Sbjct: 258 TPVWGGLSAGQAAILLRDLAGITVVGGDVVEVSPPYDPSGATAVAGAHVMTEILCLWA 315 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: 373 Number of extensions: 23 Number of successful extensions: 4 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: 324 Length adjustment: 28 Effective length of query: 325 Effective length of database: 296 Effective search space: 96200 Effective search space used: 96200 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