Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate 17016 b2937 agmatinase (NCBI)
Query= curated2:Q8KZT5 (353 letters) >FitnessBrowser__Keio:17016 Length = 306 Score = 202 bits (514), Expect = 9e-57 Identities = 118/304 (38%), Positives = 177/304 (58%), Gaps = 25/304 (8%) Query: 24 AGAATYARLPRLDQV--SKADVTVVGVPFDSGVSYRPGARFGANHVREASRLLRPYNPAW 81 + A + RLP Q S AD + GVPFD S R G R G +R+ S N AW Sbjct: 14 SNAFGFLRLPMNFQPYDSDADWVITGVPFDMATSGRAGGRHGPAAIRQVST-----NLAW 68 Query: 82 DVSPF-------ENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTI 134 + + F E + V D GD+ + E E +Q +A L A G ++++ GGDH + Sbjct: 69 EHNRFPWNFDMRERLNVVDCGDLVYAFGDAREMSEKLQAHAEKLLAAGKRMLSFGGDHFV 128 Query: 135 ALPLLRAAAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVG 194 LPLLRA A+ G+ +A++HFDAH DT+ G E+ HGT F A +EG++D +G Sbjct: 129 TLPLLRAHAKHFGK-MALVHFDAHTDTYAN--GCEFDHGTMFYTAPKEGLIDPNHSVQIG 185 Query: 195 TRGPLYGKKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPA 254 R + D D+ GF ++ + V + V + +A+++ +G+ P+Y++ DID LDPA Sbjct: 186 IR------TEFDKDN--GFTVLDACQVNDRSVDDVIAQVKQIVGDMPVYLTFDIDCLDPA 237 Query: 255 HAPGTGTPEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELV 314 APGTGTP GG+TS ++++RG + +N+VG DVVEVAPAYD +EIT +A + +A E++ Sbjct: 238 FAPGTGTPVIGGLTSDRAIKLVRGLKDLNIVGMDVVEVAPAYDQSEITALAAATLALEML 297 Query: 315 TLMA 318 + A Sbjct: 298 YIQA 301 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: 332 Number of extensions: 13 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: 306 Length adjustment: 28 Effective length of query: 325 Effective length of database: 278 Effective search space: 90350 Effective search space used: 90350 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