Align glycolate oxidase subunit glcD (characterized)
to candidate Pf1N1B4_2274 D-2-hydroxyglutarate dehydrogenase
Query= CharProtDB::CH_024646 (499 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2274 Length = 464 Score = 172 bits (436), Expect = 2e-47 Identities = 136/452 (30%), Positives = 211/452 (46%), Gaps = 18/452 (3%) Query: 30 PGLEILHTDEEIIPYECDGLSAYRTRPLLVVLPKQMEQVTAILAVCHRLRVPVVTRGAGT 89 PG ++L + + Y D + P +V PK EQV AI+ + +V +V G T Sbjct: 16 PG-KVLTDADSLNAYGKDWTKHFAPAPTAIVFPKTTEQVQAIVRWANEHKVALVPSGGRT 74 Query: 90 GLSGGALPLEKGVLLVMARFKEILDINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPS 149 GLS A+ V++ +ILD+N R A QPGV + H LYY D + Sbjct: 75 GLSAAAVAANGEVVVSFDYMNQILDVNLTDRTAVCQPGVVTEQLQNKAEEHGLYYPVDFA 134 Query: 150 SQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALTLGSDAL-DSPGFDLLA 208 S + IGGN+ NAGG+ ++YG+T + + ++V T G+ L L D + ++ G+DL Sbjct: 135 SAGSSQIGGNIGTNAGGIKVIRYGMTRNWVAGMKVVTGKGDLLELNKDLIKNATGYDLRQ 194 Query: 209 LFTGSEGMLGVTTEVTVKL--LPKPPVARVL-LASFDSVEKAGLAVGDIIANGIIPGGLE 265 LF G+EG LG E T++L PK A VL A FDS+ + V + + E Sbjct: 195 LFIGAEGTLGFVVEATMRLDRAPKNLTAMVLGTADFDSI----MPVLHAFQSKLDLTAFE 250 Query: 266 MMDNLSIR--AAEDFIHAGYPVDAEAILLCELDGVESDVQEDCERVNDILLKAG-ATDVR 322 + ++ A + A + D L E + +V + ++ G D Sbjct: 251 FFSDKALAKVMARGDVPAPFESDCPFYALLEFEATTEEVANHALETFEHCVEQGWVLDGV 310 Query: 323 LAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRALPGVLEGI-ARLSQQY-DLR 380 ++Q E + W R+ + +P Y D ++ +P L+ I A + + Y D Sbjct: 311 MSQSETQLQNLWKLREYISETISHWTP--YKNDISVTVSKVPAFLKEIDAIVGEHYPDFE 368 Query: 381 VANVFHAGDGNMHPLILFDANEPGE--FARAEELGGKILELCVEVGGSISGEHGIGREKI 438 + H GDGN+H IL N + FA+ + + E + GSIS EHG+G K Sbjct: 369 IVWFGHIGDGNLHLNILKPDNLSKDEFFAKCATVNKWVFETVEKYNGSISAEHGVGMTKR 428 Query: 439 NQMCAQFNSDEITTFHAVKAAFDPDGLLNPGK 470 + + + EI AVKA FDP+G++NPGK Sbjct: 429 DYLTYSRSPVEIEYMKAVKAVFDPNGIMNPGK 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: 536 Number of extensions: 17 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: 464 Length adjustment: 34 Effective length of query: 465 Effective length of database: 430 Effective search space: 199950 Effective search space used: 199950 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