Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate 206254 DVU0827 glycolate oxidase, subunit GlcD, putative
Query= BRENDA::Q8N465 (521 letters) >MicrobesOnline__882:206254 Length = 471 Score = 169 bits (427), Expect = 3e-46 Identities = 133/434 (30%), Positives = 199/434 (45%), Gaps = 32/434 (7%) Query: 98 GCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARMNRVL 157 G ++RP T +V +LR L V P+ T +VGG VP I+LST RM R++ Sbjct: 52 GTPLAVVRPTTEAQVVELLRWADAERLPVYPRARATNVVGGCVPQRPGIVLSTLRMARII 111 Query: 158 SFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYG 217 + V Q G + +L R VE R P D ++ IGGNVAT AGG+R +RYG Sbjct: 112 DIDEHDFVAVVQPGVITADLQRAVEARGLFYPPDPASQNISSIGGNVATCAGGMRAVRYG 171 Query: 218 SLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPR 277 VLGL VL G VL + K+ G DL +L +GSEGTLG +T V++ P P Sbjct: 172 VTRDYVLGLRAVLPGGEVLATGSRCHKNVVGLDLVRLLVGSEGTLGCLTEVTLKLLPLPE 231 Query: 278 AVNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEF-MDAVCMQLVGRH-LHLASPVQESP 335 A A +L FS + + + F + V ++ +G L A+ + + P Sbjct: 232 AT----------ASLLAGFSDLGAAMDAVRNVFAAGILPVALEFMGPEVLDCAALLNDVP 281 Query: 336 F------YVLIETSGSNAGHDAEKLGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERI 389 + +L GS A E L A+ + + + + LW +R I Sbjct: 282 WPKTVRAALLFRLDGSRAALPLEV--DRLAAAVRDAAPVWSAVGVGRDEEEPLWTIRRSI 339 Query: 390 TEALSRDGYVYK-----YDLSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNV 444 A ++ K D+++P RL + + +RA + ++ +GH+GDGN+H+N+ Sbjct: 340 NPA----SFLVKPDKMSDDVTVPRGRLREALEGIRAIAEARSLTILTFGHVGDGNIHVNI 395 Query: 445 TAEAF---SPSLLAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQL 501 +A A + V + G++S EHGVG K + LM Q+ Sbjct: 396 MHDASVTEEREHALAAKGEVTDLILSLGGTLSGEHGVGLTKAPYVHRQLSKLERGLMAQV 455 Query: 502 KALLDPKGILNPYK 515 KA DP GI+NP K Sbjct: 456 KAAFDPHGIMNPGK 469 Lambda K H 0.321 0.139 0.426 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: 631 Number of extensions: 32 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: 521 Length of database: 471 Length adjustment: 34 Effective length of query: 487 Effective length of database: 437 Effective search space: 212819 Effective search space used: 212819 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