Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate 3607953 Dshi_1361 D-lactate dehydrogenase (cytochrome) (RefSeq)
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__Dino:3607953 Length = 468 Score = 163 bits (413), Expect = 1e-44 Identities = 131/421 (31%), Positives = 196/421 (46%), Gaps = 24/421 (5%) Query: 106 PRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARMNRVLSFHSVSGI 165 PR + EV +LR C + + P G T + G + L A MN+VL+ H Sbjct: 57 PRETAEVQDVLRICTAYGMPLVPFGTGTSLEGHVNAPLGGLSLDFAEMNQVLAIHPEDMD 116 Query: 166 LVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLG 225 V Q G + L+ + P+D GA S +GG AT A G +RYG++ VL Sbjct: 117 CVVQPGITRKALNEELRATGLFFPVDPGADAS--LGGMAATRASGTNAVRYGTMRDVVLA 174 Query: 226 LEVVLADGTVLDCLTSLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLG 285 LE V ADG V+ RK + GYDL +L +GSEGTLG+IT +++ P AV A Sbjct: 175 LEAVTADGRVIRTAKRARKTSAGYDLTRLLVGSEGTLGVITELTLKLSGIPEAVAGATC- 233 Query: 286 CPGFAEVLQTFSTCKGMLGEI-----LSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLI 340 FA V + C ++ I ++ EF+DA+ ++ + + L+ P E+P +L+ Sbjct: 234 --SFASV---EAACAAVIATIQYGVPVARIEFLDALSVRSINAYSKLSLP--EAPL-LLL 285 Query: 341 ETSGSNAGHDAEKLGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALS--RDGY 398 E GS AG AE+ F E A G + + + + KM W R A+ R G+ Sbjct: 286 EFHGSEAG-VAEQSETFGEIAADHGALAFDWTSDAEARAKM-WQARHDAYWAMRALRPGF 343 Query: 399 -VYKYDLSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSLLAAL 457 + D+ +PV RL + V+ R GH+GDGN H+ + + P A Sbjct: 344 DAFVTDVCVPVSRLAEAVSAAAERAEADGIIAPTLGHVGDGNFHVALLIDPDDPGGRARA 403 Query: 458 EPHV---YEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLDPKGILNPY 514 E ++ + G+ + EHG+G K L + +M LK+ +DP ILNP Sbjct: 404 ESYIGWLNDLAISLDGTCTGEHGIGQGKVKYLARELGANTVDVMAALKSAMDPDNILNPG 463 Query: 515 K 515 K Sbjct: 464 K 464 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: 604 Number of extensions: 30 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: 468 Length adjustment: 34 Effective length of query: 487 Effective length of database: 434 Effective search space: 211358 Effective search space used: 211358 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