Align glycolate oxidase subunit glcD (characterized)
to candidate 3607953 Dshi_1361 D-lactate dehydrogenase (cytochrome) (RefSeq)
Query= CharProtDB::CH_024646 (499 letters) >FitnessBrowser__Dino:3607953 Length = 468 Score = 213 bits (543), Expect = 9e-60 Identities = 134/418 (32%), Positives = 203/418 (48%), Gaps = 7/418 (1%) Query: 56 PLLVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGALPLEKGVLLVMARFKEILDI 115 P V LP++ +V +L +C +P+V G GT L G G+ L A ++L I Sbjct: 51 PDAVFLPRETAEVQDVLRICTAYGMPLVPFGTGTSLEGHVNAPLGGLSLDFAEMNQVLAI 110 Query: 116 NPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLT 175 +P VQPG+ A+++ + L++ DP + S+GG A A G + ++YG Sbjct: 111 HPEDMDCVVQPGITRKALNEELRATGLFFPVDPGAD--ASLGGMAATRASGTNAVRYGTM 168 Query: 176 VHNLLKIEVQTLDGEALTLGSDALD-SPGFDLLALFTGSEGMLGVTTEVTVKLLPKPPVA 234 +L +E T DG + A S G+DL L GSEG LGV TE+T+KL P Sbjct: 169 RDVVLALEAVTADGRVIRTAKRARKTSAGYDLTRLLVGSEGTLGVITELTLKLSGIPEAV 228 Query: 235 RVLLASFDSVEKAGLAVGDIIANGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCE 294 SF SVE A AV I G+ +E +D LS+R+ + P +LL E Sbjct: 229 AGATCSFASVEAACAAVIATIQYGVPVARIEFLDALSVRSINAYSKLSLP--EAPLLLLE 286 Query: 295 LDGVESDVQEDCERVNDILLKAGATDVRLAQDEAERVRFWAGRKNAFPAVGRISP--DYY 352 G E+ V E E +I GA D R + W R +A+ A+ + P D + Sbjct: 287 FHGSEAGVAEQSETFGEIAADHGALAFDWTSDAEARAKMWQARHDAYWAMRALRPGFDAF 346 Query: 353 CMDGTIPRRALPGVLEGIARLSQQYDLRVANVFHAGDGNMHPLILFDANEPGEFARAEEL 412 D +P L + A ++ + + H GDGN H +L D ++PG ARAE Sbjct: 347 VTDVCVPVSRLAEAVSAAAERAEADGIIAPTLGHVGDGNFHVALLIDPDDPGGRARAESY 406 Query: 413 GGKILELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAVKAAFDPDGLLNPGK 470 G + +L + + G+ +GEHGIG+ K+ + + ++ + A+K+A DPD +LNPGK Sbjct: 407 IGWLNDLAISLDGTCTGEHGIGQGKVKYLARELGANTVDVMAALKSAMDPDNILNPGK 464 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: 598 Number of extensions: 35 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: 468 Length adjustment: 34 Effective length of query: 465 Effective length of database: 434 Effective search space: 201810 Effective search space used: 201810 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