Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate PP_2196 PP_2196 agmatinase
Query= curated2:Q8KZT5 (353 letters) >FitnessBrowser__Putida:PP_2196 Length = 311 Score = 237 bits (605), Expect = 3e-67 Identities = 132/311 (42%), Positives = 182/311 (58%), Gaps = 16/311 (5%) Query: 23 YAGAATYARLPRLDQVSKADVTVVGVPFDSGVSYRPGARFGANHVREAS-RLLRPYNPAW 81 YAG +++R + DV V GVPFD+ S RPGARFG +R AS + + W Sbjct: 15 YAGVVSFSRRRYSRDLRGVDVVVSGVPFDTATSNRPGARFGPRAIRAASVQQAWARHWPW 74 Query: 82 DVSPFENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTIALPLLRA 141 PF+++ V D GD + ++I+ +A + G ++TLGGDH I+ PLL+A Sbjct: 75 AFDPFDHLAVIDYGDCPFDSGTPQSVPDSIEAHAEHILQAGCAMLTLGGDHFISYPLLKA 134 Query: 142 AAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVGTRGPLYG 201 A R G P+A++HFDAH DTW G HGT F A EG++D +G R Sbjct: 135 HARRHG-PLALIHFDAHSDTWPDEAGKRIDHGTMFWHAAREGLVDPAHSVQIGLR----- 188 Query: 202 KKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPAHAPGTGT 261 +D GF I+ + V+ QG +A IR R+G RP+Y++ DID LDPA+APGTGT Sbjct: 189 ---TTNDDSQGFAILDARQVHRQGTEAVIAAIRQRVGERPVYLTFDIDCLDPAYAPGTGT 245 Query: 262 PEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELVTLMADNA 321 P GG+++ + LEI+ G RG+NLVG D+VEVAPAYDHA+IT +AG+ +A E++ L A Sbjct: 246 PVCGGLSTVQALEILGGLRGINLVGMDLVEVAPAYDHADITALAGATLAMEMLCLYA--- 302 Query: 322 VEGDRHGAPNG 332 RH NG Sbjct: 303 ---ARHKVDNG 310 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: 387 Number of extensions: 29 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: 311 Length adjustment: 28 Effective length of query: 325 Effective length of database: 283 Effective search space: 91975 Effective search space used: 91975 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