Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate WP_043745229.1 AMB_RS18795 FAD-binding oxidoreductase
Query= BRENDA::Q8N465 (521 letters) >NCBI__GCF_000009985.1:WP_043745229.1 Length = 469 Score = 283 bits (724), Expect = 1e-80 Identities = 178/467 (38%), Positives = 250/467 (53%), Gaps = 20/467 (4%) Query: 67 LAAFERIV-PGGVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLA 125 L A IV PG V+T+ L V+ +G + ++RP ++ EV+ ++R C + Sbjct: 4 LHALSAIVGPGNVITEASDLAPYLVEERGLYQGAALGVVRPGSTAEVAEVVRLCAAAGIP 63 Query: 126 VNPQGGNTGMVGGSVPVFD--EIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEE 183 + PQGGNTG+ GG VP D +++ST R+ R+ + V L +AGCVL L + EE Sbjct: 64 MVPQGGNTGLCGGGVPSEDGQSVVISTERLTRIRAVDPVDFTLTAEAGCVLANLQQAAEE 123 Query: 184 RDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLR 243 + PL LGA+GSC IGGN++TNAGG LRYG+ VLGLEVVL DG V + L LR Sbjct: 124 AGCLFPLSLGAEGSCRIGGNISTNAGGTNVLRYGNTRDLVLGLEVVLPDGRVWNGLKRLR 183 Query: 244 KDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGML 303 KDNTGY L+ LFIG+EGTLGI+T + P+PR + AF+ L FS + Sbjct: 184 KDNTGYALQHLFIGAEGTLGIVTACVLKLFPRPREIATAFVALADLEAALPLFSRARTAS 243 Query: 304 GEILSAFEFMDAVCMQLVGRHLHLASPVQESPF------YVLIETSGSNAGHDAEKLGHF 357 G+ ++A E + ++L RH+ P +PF +L+E S S G E L Sbjct: 244 GDSVTACELVPRRGLELGMRHV----PGVRAPFAAFHDWMLLLELSSSRPGGLREALEEM 299 Query: 358 LEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYDLSLPVERLYDIV-- 415 L A GL D +A + W +RE I EA ++G K+D+++ R+ +++ Sbjct: 300 LGQAFEDGLAVDAVIAESDAQRADFWRIREAIPEAQKKEGGSIKHDVAVATSRVPEMIRR 359 Query: 416 TDLRARLGPHAKHVVGYGHLGDGNLHLNVTAE--AFSPSLLAALEPH---VYEWTAGQQG 470 VV +GHLGDGN H N+T A + LA E V++ +G Sbjct: 360 CTRAVEAAMPGVRVVPFGHLGDGNTHFNLTQPEGADKAAFLARWEEMNRIVHDIVVEMEG 419 Query: 471 SVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTL 517 S+SAEHG+G K D L + KP L LM ++K LDP G +NP K L Sbjct: 420 SISAEHGIGRLKVDELAHYKPGVDLDLMARIKGALDPLGQMNPGKIL 466 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: 698 Number of extensions: 39 Number of successful extensions: 5 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: 469 Length adjustment: 34 Effective length of query: 487 Effective length of database: 435 Effective search space: 211845 Effective search space used: 211845 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