Align glycolate oxidase subunit glcD (characterized)
to candidate CA265_RS09620 CA265_RS09620 FAD-binding oxidoreductase
Query= CharProtDB::CH_024646 (499 letters) >FitnessBrowser__Pedo557:CA265_RS09620 Length = 467 Score = 265 bits (676), Expect = 3e-75 Identities = 161/449 (35%), Positives = 241/449 (53%), Gaps = 7/449 (1%) Query: 31 GLEILHTDEEIIP-YECDGLSAYRTRPLLVVLPKQMEQVTAILAVCHRLRVPVVTRGAGT 89 G E + TD + + Y D R +P +VV P E+V+A+L +C+ VPV RG GT Sbjct: 19 GAEKVFTDADSLENYSHDETEDLRYQPEVVVKPTTPEEVSALLKICNAHHVPVTPRGGGT 78 Query: 90 GLSGGALPLEKGVLLVMARFKEILDINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPS 149 GLSG ALP+ G+ L M +FK ILDI+ +A V+PGV AVA L Y DPS Sbjct: 79 GLSGAALPIYGGISLSMEKFKAILDIDTENLQATVEPGVITEEFINAVAEKGLLYPVDPS 138 Query: 150 SQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALTLGSDALD-SPGFDLLA 208 S+ +C IGGNVA +GG +KYG +L +EV +G+ + G++ L + G++L Sbjct: 139 SKGSCFIGGNVAHGSGGPRVVKYGTIREYILNLEVVLPNGDIIWTGANTLKYASGYNLTQ 198 Query: 209 LFTGSEGMLGVTTEVTVKLLPKPPVARVLLASFDSVEKAGLAVGDIIANGIIPGGLEMMD 268 L GSEG L V T++ KLLPKP + +++ SF + E A AV I G+ P LE M+ Sbjct: 199 LMIGSEGTLAVVTKIVTKLLPKPSQSVLMMGSFSTNEDACAAVSAIFRAGVTPSALEFME 258 Query: 269 NLSIRAAEDFIHAGYPV--DAEAILLCELDGVE-SDVQEDCERVNDILLKAGATDVRLAQ 325 + F + + D A+L+ E DG + D+ ++CE+ N +L + T+V A Sbjct: 259 RKGVEWVIKFDDIKFDLKDDVAALLMIEFDGDDLDDIFKNCEKTNIVLEEHNCTEVLFAD 318 Query: 326 DEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRALPGVLEGIARLSQQYDLRVANVF 385 A++ W R+ +V + + Y D +PR ALP ++ GI + +Y Sbjct: 319 TAAQKEELWRMRRTMAESV-KSNSVYKEEDTVVPRAALPKLVNGIKEIGAKYGFESVCYG 377 Query: 386 HAGDGNMHPLILFDANEPGEFARAEELG-GKILELCVEVGGSISGEHGIGREKINQMCAQ 444 HAGDGN+H I+ ++ + G +I EL +GG++SGEHGIG + M + Sbjct: 378 HAGDGNLHVNIIKAGMSDEDWKNKLKFGIAEIFELTTALGGTLSGEHGIGLVQKEFMPIK 437 Query: 445 FNSDEITTFHAVKAAFDPDGLLNPGKNIP 473 ++ + +K FDP G+LNPGK +P Sbjct: 438 YSEIHLNLMRGIKNIFDPKGILNPGKIMP 466 Lambda K H 0.320 0.140 0.415 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: 583 Number of extensions: 23 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: 499 Length of database: 467 Length adjustment: 34 Effective length of query: 465 Effective length of database: 433 Effective search space: 201345 Effective search space used: 201345 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: 52 (24.6 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