Align D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized)
to candidate N515DRAFT_3582 N515DRAFT_3582 FAD/FMN-containing dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Dyella79:N515DRAFT_3582 Length = 467 Score = 281 bits (720), Expect = 3e-80 Identities = 162/450 (36%), Positives = 248/450 (55%), Gaps = 22/450 (4%) Query: 86 DLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIF 145 DL Y DW R++ + P +VE+ +L + N+ +AVVP GG TGL GG+V Sbjct: 31 DLEHYGRDWTRRWTPAPLAIALPATVEEAQAVLRWANEHGVAVVPSGGRTGLSGGAVAAQ 90 Query: 146 DELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGV 205 EL+LSL +N++ FDP+ L AG+ L+ ++ ++P+D A+GSC +GG Sbjct: 91 GELVLSLERMNRVLGFDPIDRTLTVQAGIALQAVHDAARSHGLIYPVDFAARGSCSIGGN 150 Query: 206 VATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIG 265 +ATNAGG+R++RYG+ + GL+V+ NG+++ + K+++GYDL+ L IGSEGT+G Sbjct: 151 IATNAGGIRVIRYGNTREWIAGLKVIAGNGELLELNRGLIKNSSGYDLRHLTIGSEGTLG 210 Query: 266 IITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMD--AKSQVLA 323 I+ ++ P V L++ + +VF R L L AFEF A VLA Sbjct: 211 IVVEATLRLAEPPPPSQVMLLALPDMAALMQVFALFRARLK--LQAFEFFTDIALRHVLA 268 Query: 324 KSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETEL 383 A L+ EHPFY++ E +++ D+ L F E+ + EG + DG +AQ E + Sbjct: 269 HG----AQRALDGEHPFYVVTEFDAADEAAQDAALAAF-EHGVNEGWIADGAIAQSEAQA 323 Query: 384 QNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAI 443 LW+ RE I E S A YK D+SL + L + ++ A L +A P + Sbjct: 324 AALWRLREGITE-SLAPHKPYKNDISLRIGALPAFLDEIQALLGDA-------YPHFEVV 375 Query: 444 GYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGLGFQKKNY 498 +GH+GDGNLH+NV E + E + + + + GS+SAEHG+G KK Y Sbjct: 376 WFGHIGDGNLHINVLKPEGLADAEFIAQCEQVTKLLAAALQRHGGSISAEHGIGLVKKPY 435 Query: 499 IGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528 + ++S E+ +M+ +K +DPNGILNP K Sbjct: 436 LESTRSAAEIALMRGVKQVFDPNGILNPGK 465 Lambda K H 0.316 0.135 0.385 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: 523 Number of extensions: 22 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: 530 Length of database: 467 Length adjustment: 34 Effective length of query: 496 Effective length of database: 433 Effective search space: 214768 Effective search space used: 214768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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