Align Guanidinobutyrase; GBase; EC 3.5.3.7; D-arginase; EC 3.5.3.10 (uncharacterized)
to candidate GFF1960 PGA1_c19930 agmatinase SpeB
Query= curated2:Q8KZT5 (353 letters) >FitnessBrowser__Phaeo:GFF1960 Length = 322 Score = 214 bits (546), Expect = 2e-60 Identities = 117/304 (38%), Positives = 171/304 (56%), Gaps = 10/304 (3%) Query: 23 YAGAATYARLPRLDQVSKADVTVVGVPFDSGVSYRPGARFGANHVREASRLLRPYNP-AW 81 + GA ++ R ++ D+ V GVPFD V+ RPG R G +REAS L P P W Sbjct: 28 FGGATSFLRRKYTKDLTGVDIAVTGVPFDQAVTNRPGTRLGPRAIREASCLQSPDEPYGW 87 Query: 82 DVSPFENIQVADAGDMAVNPFNINEAIETIQQNALDLTANGSKLVTLGGDHTIALPLLRA 141 P + +AD GD+A + ++ + + + A + V LGGDH I+ P+L+A Sbjct: 88 PHKPLSTLAIADYGDLAFDHADVPAFPAALTDHIRGILATETASVVLGGDHYISFPILKA 147 Query: 142 AAERAGEPIAMLHFDAHLDTWDTYFGAEYTHGTPFRRAVEEGILDTEAISHVGTRGPLYG 201 AE+ G PI++L FDAH DTW HGT F +AV+ G++D + VG R Sbjct: 148 YAEKHG-PISLLQFDAHTDTWPDDNMDRIDHGTMFYKAVKMGLVDPKTSVQVGIR----- 201 Query: 202 KKDLDDDHRFGFGIVTSADVYYQGVLETVAKIRDRIGNRPLYISVDIDVLDPAHAPGTGT 261 +D G I+ + V+ G +ET +I+ +G+RP Y++ DID LDPA+APGTGT Sbjct: 202 ---TTNDDTLGVNIIDAPTVHDIGPVETAKRIKAILGDRPTYLTFDIDCLDPAYAPGTGT 258 Query: 262 PEAGGITSRELLEIIRGFRGMNLVGADVVEVAPAYDHAEITGVAGSHVAYELVTLMADNA 321 P GG+TS + I+R G+N+ G DVVEV+P +D T +AG+HVA E++ L+ N Sbjct: 259 PVWGGLTSAQASRILREIAGINIKGGDVVEVSPPFDTTGATAIAGAHVATEIICLLGWNM 318 Query: 322 VEGD 325 + D Sbjct: 319 RDND 322 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: 364 Number of extensions: 21 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: 322 Length adjustment: 28 Effective length of query: 325 Effective length of database: 294 Effective search space: 95550 Effective search space used: 95550 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