Align 2-pyrone-4,6-dicarboxylate lactonase (characterized)
to candidate 3607454 Dshi_0867 amidohydrolase 2 (RefSeq)
Query= CharProtDB::CH_107296 (305 letters) >FitnessBrowser__Dino:3607454 Length = 290 Score = 139 bits (349), Expect = 1e-37 Identities = 102/292 (34%), Positives = 138/292 (47%), Gaps = 21/292 (7%) Query: 15 ANPSKPQFKLPAGAVDAHCHVFGPGNEFPFAPERKYTPCDASKAQ----LYALRDHLGFA 70 A+P+ P+ +P GA DAH H+ ++ P R P + AQ L D LG A Sbjct: 12 AHPTPPRAPVPEGACDAHVHMVA--DDMPLWDGRVEDPAPGTLAQWTARLETHLDALGMA 69 Query: 71 RNVVVQATCHGADNRAMVDACKSSGGKARGVATVKRSISDAELSALHDAGVRGVRFNFVK 130 R V+V + HG DNR A + G +ARG+ V+ SDAEL+AL AGV GVR N+V Sbjct: 70 RVVIVHSILHGGDNRVTTAAVAALGDRARGIGLVRDGASDAELAALAQAGVVGVRLNYVH 129 Query: 131 RLVDFTPKDELMEIAGRIAKLGWHVVIYFEA-VDLPELWDFFTALPTTVVVDHMGRPDVT 189 + E+A R+A G HV + A + EL LP VV DH+G PD+ Sbjct: 130 G--GILSWAGVREMAPRLAAHGMHVQMLMNAHRHMAELAADVRTLPVPVVFDHIGWPDLA 187 Query: 190 KGVDSEEFALFLKFMREHQNVWSKVSCPERLSVTGPKALHGEQNAYQDVVPFARRVVEEF 249 G D FA L+ + K+S P RL Y +V Sbjct: 188 AGPDEPGFAA-LRALVADGAAHVKLSAPYRLC----------DAPYDRAAEAIAALVAAN 236 Query: 250 PDRVLWGTDWPHPNLKDHMPDD-GLLVDFIPHIAPTAQLQQKLLVDNPMRLY 300 PDR LWG+DWPH L + P D G L++ P+ ++++LVD P LY Sbjct: 237 PDRCLWGSDWPHLMLAEAQPPDAGALLNAFFDAVPSEDARRRILVDTPAALY 288 Lambda K H 0.322 0.138 0.444 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: 289 Number of extensions: 21 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: 305 Length of database: 290 Length adjustment: 26 Effective length of query: 279 Effective length of database: 264 Effective search space: 73656 Effective search space used: 73656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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