Align L-2-hydroxyglutarate dehydrogenase; L2HG dehydrogenase; L2HG:quinone oxidoreductase; EC 1.1.5.- (characterized)
to candidate WP_012470588.1 GLOV_RS12590 L-2-hydroxyglutarate oxidase
Query= SwissProt::P37339 (422 letters) >NCBI__GCF_000020385.1:WP_012470588.1 Length = 403 Score = 193 bits (491), Expect = 7e-54 Identities = 130/394 (32%), Positives = 204/394 (51%), Gaps = 11/394 (2%) Query: 3 DFVIIGGGIIGMSTAMQLIDVYPDARIALLEKESAPACHQTGHNSGVIHAGVYYTPGSLK 62 D++IIG GIIG++ A +L + +P A I +++KE+ A H +G NSGV+HAG YY+ SLK Sbjct: 8 DYLIIGAGIIGLALARELKNRFPAADILVIDKEADVAFHGSGRNSGVLHAGFYYSADSLK 67 Query: 63 AQFCLAGNRATKAFCDQNGIRYDNCGKMLVATSDLEMERMRALWERTAANGIEREWLNAD 122 A+F GNR + G+ + C K++VA+ E+E ++ L R NG++ ++ Sbjct: 68 ARFTREGNRMMTDYVTGRGLAINRCHKVVVASDLNEIEGVQELQRRGERNGVDVRIIDEQ 127 Query: 123 ELREREPNITGLG-GIFVPSSGIVSYRDVTAAMAKIFQSRGGEIIYNAEVSGLNEHKNGV 181 EL E +PN G ++ P++ V V A+ ++ G ++ G + + Sbjct: 128 ELAEIDPNAKTTGIALYSPTTATVDPGQVCHALKDDLEAAGVRFLFG---QGYLKRQGDA 184 Query: 182 VIRTRQGGEYEASTLISCSGLMADRLVKMLGLEPGFIICPFRGEYFRLAPEHNQIVNHLI 241 I T G EA I+ +GL AD + + G + I PF+G Y + I + I Sbjct: 185 AILTTGGLVLEAGLTINAAGLYADTVARDYGFSQHYTIIPFKGIYLKYTGTDKPIRTN-I 243 Query: 242 YPIPDPAMPFLGVHLTRMIDGSVTVGPNAVLAFKREGYRKRD-FSFSDTLEILGSSGIRR 300 YP+P+ PFLGVH T +DG++ +GP A+ AF R+ Y + F + LEILG Sbjct: 244 YPVPNLKNPFLGVHYTVTVDGTIKIGPTAIPAFWRQNYAGLEHFRLGELLEILGWESRLF 303 Query: 301 VLQNH-LRS-GLGEMKNSLCKSGYLRLVQKYCPRLSLSDLQPW-PAGVRAQAVSPDGK-L 356 + N RS L E+K +S + L K +++ + W G+RAQ ++ K L Sbjct: 304 LGDNFGFRSLALSELK-KYDRSYFTGLATKMVKQINTAGFNQWSKPGIRAQLLNTATKEL 362 Query: 357 IDDFLFVTTPRTIHTCNAPSPAATSAIPIGAHIV 390 + DF+ +IH NA SPA T + P A +V Sbjct: 363 VQDFVVEGDRHSIHVLNAVSPAFTCSFPFAAWVV 396 Lambda K H 0.321 0.137 0.411 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: 426 Number of extensions: 16 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: 422 Length of database: 403 Length adjustment: 31 Effective length of query: 391 Effective length of database: 372 Effective search space: 145452 Effective search space used: 145452 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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