Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate Ac3H11_3400 Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3400 Length = 375 Score = 351 bits (900), Expect = e-101 Identities = 197/373 (52%), Positives = 255/373 (68%), Gaps = 18/373 (4%) Query: 11 TLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELVITAR 70 +L + +R A +TPLR+RGGG+KDF+G G +LDTR GIV Y+P ELV+T R Sbjct: 4 SLAPIAERVRAAAADQTPLRIRGGGTKDFHGLALHGEVLDTRGLRGIVSYEPSELVVTVR 63 Query: 71 CGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDF 130 GTPLA++EA LAE+ Q L FEPPHF+ SD AT+GG VAAGLSGP R +VGA+RD+ Sbjct: 64 AGTPLAELEALLAEKGQCLPFEPPHFAKTP--SDAATVGGMVAAGLSGPARASVGAVRDY 121 Query: 131 VLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATL 190 +LG V++G+G++L+FGGQVMKNVAGYDVSRLM+G+ GTLGL+ EVSLKVLPV +ATL Sbjct: 122 LLGVTVLNGKGELLTFGGQVMKNVAGYDVSRLMAGAWGTLGLLTEVSLKVLPVAPGEATL 181 Query: 191 RF-ALDEAAALDRLNDWGGQPLPIAASAWHD----GVLHLRLSGAAAALRAARARLGGEA 245 RF + +A AL +L+ WGGQPLP+ AS W G L++RL GA AA+ AA +GG Sbjct: 182 RFDDITQANALRQLHAWGGQPLPLNASCWVQDGGVGTLYVRLRGAVAAVEAACKTMGGTR 241 Query: 246 VDAAQADALWRALREHSHAFFA--PVQAGRALWRIAVPTTAAPLALPGG--QLIEWGGGQ 301 +D A A W A RE + +FA + ALWR++VP TA LALPGG L+EW G Sbjct: 242 MDNATVAADWTACREQTLPWFADRAQRPDHALWRLSVPATAPVLALPGGAEPLVEWHGAL 301 Query: 302 RWWLGGSDSAADSAIVRAAAKAAGGHATLF----RNGDKAVGVFTPLSAPVAAIHQRLKA 357 R W+ +SA ++ +R AA+A GG+A++F G A G+F S + IH RLK Sbjct: 302 R-WVQAPESAGEA--LREAAQAVGGNASVFVAASAGGTGAKGLFDLKSTALEQIHTRLKH 358 Query: 358 TFDPAGIFNPQRM 370 +FDPAGIFNP R+ Sbjct: 359 SFDPAGIFNPGRV 371 Lambda K H 0.321 0.136 0.414 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: 446 Number of extensions: 22 Number of successful extensions: 6 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: 374 Length of database: 375 Length adjustment: 30 Effective length of query: 344 Effective length of database: 345 Effective search space: 118680 Effective search space used: 118680 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 (21.8 bits) S2: 50 (23.9 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