Align glycolate oxidase subunit glcD (characterized)
to candidate BPHYT_RS32905 BPHYT_RS32905 FAD-linked oxidase
Query= CharProtDB::CH_024646 (499 letters) >FitnessBrowser__BFirm:BPHYT_RS32905 Length = 463 Score = 157 bits (397), Expect = 8e-43 Identities = 134/434 (30%), Positives = 198/434 (45%), Gaps = 18/434 (4%) Query: 47 DGLSAYRTRPLLVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGALPLEKGVLLVM 106 D A R RP + +LP+ E V L V R VV +G TGL+GGA P V L + Sbjct: 35 DWSDAPRMRPRMTLLPRNPEDVARALRVLGEHRQAVVVQGGLTGLAGGATPQAGEVALSL 94 Query: 107 ARFKEILDINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGG 166 AR I + +G VQ GV + V ++ D ++ C IGGN A NAGG Sbjct: 95 ARVNAIESFDRIGGTLTVQAGVPLEQLQTFVEAEGWFFPLDLGARGTCQIGGNAATNAGG 154 Query: 167 VHCLKYGLTVHNLLKIEVQTLDGEALTLGSDAL-DSPGFDLLALFTGSEGMLGVTTEVTV 225 +++G +L +EV DG L++ + ++ G DL LF GSEG LGV T + + Sbjct: 155 NRVIRFGTMRDLILGLEVALPDGTMLSMMNRVTKNTTGIDLKQLFIGSEGTLGVITRIVL 214 Query: 226 KLLPKPPVARVLLASFDSVEKAGLAVGDIIANGIIPGGLEMMDNLSIRAAEDFIHA---- 281 KL PKP L + S + A + + A E+M + AA D H Sbjct: 215 KLEPKPSAVNTALCAVASFDDATRLLKYLRARLANLSSFELMWQDFMSAAMDIAHLKAPF 274 Query: 282 --GYPVDAEAILLCELDGVESDVQEDCERVNDILLKAG-ATDVRLAQDEAERVRFWAGRK 338 YPV +L+ L + D + E + +L G DV +AQ + WA R+ Sbjct: 275 GDTYPV---YVLIETLGESDDDDRRALEHSLERMLDDGIVQDVIIAQSIEHAKQLWAYRE 331 Query: 339 NAFPAVGRISPDYYCMDGTIPRRALPGVLEGI-ARLSQQYDLRVANVF-HAGDGNMHPLI 396 + ++ P + D IP + G +E A L++++ + F H GDGN+H L+ Sbjct: 332 TVGELLSKLKP-HAAFDIGIPMDRMNGFVEDARAALNERFSQQAHLFFGHLGDGNLH-LL 389 Query: 397 LFDANEPGEFARAEELGGKILELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAV 456 + + + EEL I +V G IS EHGIG K + ++ E+ + Sbjct: 390 SGPYADAADLLKVEEL---IYAAVNDVQGCISAEHGIGVIKQPFLHYSRSAPELDLMGKL 446 Query: 457 KAAFDPDGLLNPGK 470 KA DP G+LN G+ Sbjct: 447 KALLDPAGILNVGR 460 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: 525 Number of extensions: 26 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: 499 Length of database: 463 Length adjustment: 34 Effective length of query: 465 Effective length of database: 429 Effective search space: 199485 Effective search space used: 199485 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: 51 (24.3 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