Align glycolate oxidase subunit glcD (characterized)
to candidate 3608683 Dshi_2076 FAD linked oxidase domain protein (RefSeq)
Query= CharProtDB::CH_024646 (499 letters) >FitnessBrowser__Dino:3608683 Length = 472 Score = 141 bits (355), Expect = 6e-38 Identities = 133/436 (30%), Positives = 199/436 (45%), Gaps = 37/436 (8%) Query: 58 LVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGAL----PLEKGVLLVMARFKEIL 113 L+V P E+V ++ + +VP++ G GTGL GG + P+ V+L + R + I Sbjct: 43 LLVAPGATEEVATLVRLAQAHKVPIIPYGGGTGLVGGQIAPAGPVP--VILSLRRMRSIR 100 Query: 114 DINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYG 173 + P G + QA + +S+ + +IGG +A NAGGV+ L+YG Sbjct: 101 AVYPEENVLVADAGAVLAEVQQAARDVGRLFPLSLASEGSATIGGVLATNAGGVNVLRYG 160 Query: 174 LTVHNLLKIEVQTLDGEALTLGSDAL--DSPGFDLLALFTGSEGMLGVTTEVTVKLLPKP 231 L +E DG A+ G L ++ G+DL L G+EG LG+ T ++L P P Sbjct: 161 NARDLCLGLEAVMPDG-AIWHGLTRLRKNNMGYDLRHLLIGAEGTLGIITGAALRLSPLP 219 Query: 232 PVARVLL-------ASFDSVEKAGLAVGDII-ANGIIPG-GLEMMDNL--SIRAAEDFIH 280 V L A+ D + AG GD I A +I G G E +RA D Sbjct: 220 QRHGVGLLVVDSPAAALDLLALAGEVAGDTISAFELISGRGFEFFAETMPEMRAPLD--- 276 Query: 281 AGYPVDAEAILLCELDGVESDVQEDCERVNDILLKAG-ATDVRLAQDEAERVRFWAGRKN 339 PV A ++L+ D + E + +AG +D +AQ EA+ WA R+N Sbjct: 277 ---PVPAWSVLIDLAGASGFDPEGALETLFARAAEAGLVSDGVIAQSEAQADALWALREN 333 Query: 340 AFPAVGRISPDYYCMDGTIPRRALPGVLE-GIARLSQQYDLRVANVFHAGDGNMHPLILF 398 P R D ++P +P +E ARL+ D R+ H GDGN+H + Sbjct: 334 -IPEANRRIGSVSSHDISVPLSEIPNFIETATARLAGIGDYRINCFGHVGDGNLHYNVF- 391 Query: 399 DANEPGEFARAEELGGKILELCV-----EVGGSISGEHGIGREKINQMCAQFNSDEITTF 453 +PG E ++ CV E+GGS+S EHG+GR K+ + + + Sbjct: 392 --PQPGRSRADHEDERPAIKTCVHDLVHELGGSVSAEHGVGRLKVEDLERYGDPVKQAAM 449 Query: 454 HAVKAAFDPDGLLNPG 469 A+K A DP GL+NPG Sbjct: 450 RAIKDALDPHGLMNPG 465 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: 659 Number of extensions: 39 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: 499 Length of database: 472 Length adjustment: 34 Effective length of query: 465 Effective length of database: 438 Effective search space: 203670 Effective search space used: 203670 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