Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate WP_086509740.1 BZY95_RS09535 FAD-binding oxidoreductase
Query= BRENDA::Q8N465 (521 letters) >NCBI__GCF_002151265.1:WP_086509740.1 Length = 463 Score = 295 bits (755), Expect = 2e-84 Identities = 174/459 (37%), Positives = 250/459 (54%), Gaps = 11/459 (2%) Query: 71 ERIVP----GGVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLAV 126 ERIV G V+T + Q VDW+ + ++RP ++E++ ++R CH V Sbjct: 6 ERIVAIVGEGNVLTGDDVAQR-RVDWMSGASCRAGAIVRPADTDELARVMRLCHAVAQPV 64 Query: 127 NPQGGNTGMVGGSVPVFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERDF 186 GG TG+V G DE+ +S RM + + + G + QAG L+ + E D Sbjct: 65 VTHGGLTGLVHGGEASPDELAISLERMTAIEAIDPIGGSMTVQAGIALQTVQEAAAEHDL 124 Query: 187 IMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDN 246 LDLGA+GSC IGGN+ATNAGG+R +RYG + VLGLE VLADG+V+ + + K+N Sbjct: 125 QFALDLGARGSCTIGGNIATNAGGVRVIRYGMMRQQVLGLEAVLADGSVVSSMNRMLKNN 184 Query: 247 TGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGEI 306 GYDLKQLFIGSEGTLGI+T + P+ + A + CP F V LG Sbjct: 185 AGYDLKQLFIGSEGTLGIVTRAVLRLQPRMTSERTALVACPDFDGVTGLLRHLGRTLGGS 244 Query: 307 LSAFEFMDAVCMQLVGRHLHLASPVQES--PFYVLIETSGSNAGHDAEKLGHFLEHALGS 364 L FE M L+ +P + PFY ++E+ GS+ + + LE AL + Sbjct: 245 LGTFEVMWRNHYALLTEESGRNTPPLPARWPFYAIVESLGSDDAANVAQFSAALESALEA 304 Query: 365 GLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYDLSLPVERLYDIVTDLRARLG- 423 GL+ D +A + + +W +RE I + ++ +D+SLP+ + D L R+G Sbjct: 305 GLIEDAVLAQSDAQRQGIWDIREDIEGLIDNLSPLFTFDVSLPIPDMADYADALERRIGE 364 Query: 424 --PHAKHVVGYGHLGDGNLHLNVTAEAFSPSLLAALEPHVYEWTAGQQGSVSAEHGVGFR 481 P + V+ +GHLGDGNLH++V + P +E VY A GS+SAEHG+G Sbjct: 365 RWPEGRMVI-FGHLGDGNLHVSVGVGSGDPQTRRDVEQIVYGPLAELGGSISAEHGIGLE 423 Query: 482 KRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTLPSQ 520 KRD L S+ PG + LM+ LK LDPKG+LN +K L ++ Sbjct: 424 KRDYLPLSRTPGEIALMRTLKQALDPKGLLNRHKILAAE 462 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: 617 Number of extensions: 28 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: 521 Length of database: 463 Length adjustment: 34 Effective length of query: 487 Effective length of database: 429 Effective search space: 208923 Effective search space used: 208923 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 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