Align L-2-hydroxyglutarate dehydrogenase (EC 1.1.99.2) (characterized)
to candidate Echvi_3348 Echvi_3348 Predicted dehydrogenase
Query= BRENDA::Q9H9P8 (463 letters) >FitnessBrowser__Cola:Echvi_3348 Length = 400 Score = 363 bits (932), Expect = e-105 Identities = 189/415 (45%), Positives = 273/415 (65%), Gaps = 18/415 (4%) Query: 48 SFDIVIVGGGIVGLASARALILRHPSLSIGVLEKEKDLAVHQTGHNSGVIHSGIYYKPES 107 ++DI IVGGGIVGLA+ +I + P L + +LEKE +LA HQTG+NSGVIHSG+YYKP S Sbjct: 2 TYDIAIVGGGIVGLATGLKIIQQRPELKVVILEKEHELAKHQTGNNSGVIHSGLYYKPGS 61 Query: 108 LKAKLCVQGAALLYEYCQQKGISYKQCGKLIVAVEQEEIPRLQALYEKGLQNGVPGLRLI 167 LKA C+ G L ++C+++ I ++ GK++VA + E++P LQ L ++GLQNG+ G R I Sbjct: 62 LKATNCISGYHELIQFCEEENIPFEITGKVVVATKDEQLPLLQNLLKRGLQNGLKGTRQI 121 Query: 168 QQEDIKKKEPYCRGLMAIDCPHTGIVDYRQVALSFAQDFQEAGGSVLTNFEVKGIEMAKE 227 +++K+ EPYC+G+ A+ P TGIVDY++VAL++ + F+ GG +L + +VK I K Sbjct: 122 TLDELKEYEPYCKGVAALHVPQTGIVDYKKVALAYGEKFKSLGGEILLDHQVKKIN-HKA 180 Query: 228 SPSRSIDGMQYPIVIKNTKGEEIRCQYVVTCAGLYSDRISELSG-CTPDPRIVPFRGDYL 286 + + I T G+ I + ++ CAGLYSD++++++G D +I+PFRG+Y Sbjct: 181 NQTELI-----------TTGKTILSRLMINCAGLYSDKVADMNGELDLDVKIIPFRGEYY 229 Query: 287 LLKPEKCYLVKGNIYPVPDSRFPFLGVHFTPRMDGSIWLGPNAVLAFKREGYRPFDFSAT 346 LK E+ YLVK IYPVPD FPFLGVHFT M G + GPNAV+AFKREGY+ DF+ Sbjct: 230 KLKKEREYLVKNLIYPVPDPNFPFLGVHFTRMMKGGVEAGPNAVMAFKREGYKRTDFNLK 289 Query: 347 DVMDIIINSGLIKLASQNFSYGVTEMYKACFLGATVKYLQKFIPEITISDILRGPAGVRA 406 + + I GL K+A++ + G+ E Y++ A LQ+ IP+I D++ G AGVRA Sbjct: 290 EFRESITWPGLQKVAAKYWKTGIGEYYRSFSKAAFTTALQELIPDIKEDDLVDGGAGVRA 349 Query: 407 QALDRDGNLVEDFVFDAGVGDIGNRILHVRNAPSPAATSSIAISGMIADEVQQRF 461 QA DR G L++DF ++V NAPSPAATSS++I G ++ +RF Sbjct: 350 QACDRTGGLLDDFAITE-----NTHAINVLNAPSPAATSSLSIGGTVSARALKRF 399 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: 479 Number of extensions: 14 Number of successful extensions: 3 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: 400 Length adjustment: 32 Effective length of query: 431 Effective length of database: 368 Effective search space: 158608 Effective search space used: 158608 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 Apr 09 2024. 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