Align L-2-hydroxyglutarate dehydrogenase (EC 1.1.99.2) (characterized)
to candidate WP_007154818.1 MDG893_RS15820 NAD(P)/FAD-dependent oxidoreductase
Query= BRENDA::Q9H9P8 (463 letters) >NCBI__GCF_000170835.1:WP_007154818.1 Length = 371 Score = 143 bits (361), Expect = 8e-39 Identities = 127/411 (30%), Positives = 194/411 (47%), Gaps = 54/411 (13%) Query: 50 DIVIVGGGIVGLASARALILRHPSLSIGVLEKEKDLAVHQTGHNSGVIHSGIYYKPESLK 109 D V++G GIVGLA ARAL ++ + VLE + NS VIH+GIYY +SLK Sbjct: 10 DTVVIGAGIVGLAVARALAMQ--GREVLVLESGAHFGEGVSSRNSEVIHAGIYYPEDSLK 67 Query: 110 AKLCVQGAALLYEYCQQKGISYKQCGKLIVAVEQEEIPRLQALYEKGLQNGVPGLRLIQQ 169 A+LCV+G +LYEYCQ +GI++++ GK IVA ++ RL + + L+NGVP L+ + + Sbjct: 68 ARLCVRGRRMLYEYCQTRGINHRRSGKWIVANGVSQVERLDTIASQALRNGVP-LQRVTR 126 Query: 170 EDIKKKEPYCRGLMAIDCPHTGIVDYRQVALSFAQDFQEAGGSVLTNFEVKGIEMAKESP 229 ++ P A+ P TGIVD V LS DF+ GG ++ V+ + + Sbjct: 127 RALQVSLPDVTAQEALYSPETGIVDSHGVMLSLLGDFEGHGGQLVCQAPVE-LAVTGHGE 185 Query: 230 SRSIDGMQYPIVIKNTKGEEIRCQYVVTCAGLYSDRI-SELSGCTPD--PRIVPFRGDYL 286 R G Q P E+R Q VV AGL + + + G D PR RG Y Sbjct: 186 HRLWIGGQAPC--------ELRAQRVVNAAGLGAVPLATSWEGVPADIVPRQWLARGVYF 237 Query: 287 LLKPEKCYLVKGNIYPVPDSRFPFLGVHFTPRMDGSIWLGPNAVLAFKREGYRPFDFSAT 346 + K +YP+P+S LGVH T + G GP+ V +RE DFS Sbjct: 238 SYSGHHPF--KSLVYPIPES--GGLGVHLTLDLAGQARFGPD-VEWIERE-----DFS-- 285 Query: 347 DVMDIIINSGLIKLASQNFSYGVTEMYKACFLGATVKYLQKFIPEITISDILRGPAGVRA 406 ++ G K + + ++++ P + S + AG+R Sbjct: 286 ------VDPGRAKSFANS--------------------IRRWWPALDESRLKPAYAGIRP 319 Query: 407 QALDRDGNLVEDFVFDAGVGDIGNRILHVRNAPSPAATSSIAISGMIADEV 457 + L DG DF ++H+ SP T+++AI+ +A+++ Sbjct: 320 KLLGPDGGF-SDFRIAGECRHGVPGLVHLFGIESPGLTAALAIADEVAEQL 369 Lambda K H 0.321 0.140 0.420 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: 414 Number of extensions: 23 Number of successful extensions: 2 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: 463 Length of database: 371 Length adjustment: 31 Effective length of query: 432 Effective length of database: 340 Effective search space: 146880 Effective search space used: 146880 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: 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