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 Pf1N1B4_4424 D-2-hydroxyglutarate dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4424 Length = 474 Score = 278 bits (711), Expect = 3e-79 Identities = 167/468 (35%), Positives = 253/468 (54%), Gaps = 21/468 (4%) Query: 76 QEILRA---SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQG 132 Q++L A +E+ + Y D +Y GQ + P S E+V+ ++ C VV QG Sbjct: 10 QQLLGARHVQSNEEAAAYLTDKQGRYVGQVIAAVHPASTEEVAAVVRACVACDTPVVVQG 69 Query: 133 GNTGLVGGSVPIFD--ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMF 190 GNTGL+GG+ P ++L L +N++R D + L +AG IL+ + + +F Sbjct: 70 GNTGLMGGATPDASGRAVLLLLDRMNRVRAVDTDNDTLTVEAGCILQTIQDVARDAGRLF 129 Query: 191 PLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTG 250 PL LGA+GSC +GG + TNAGG +LRYG+ +LGLEVV G+I N + +RKDNTG Sbjct: 130 PLSLGAEGSCTIGGNLGTNAGGTAVLRYGNTRELILGLEVVTAQGEIWNGLRGLRKDNTG 189 Query: 251 YDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILS 310 YDL+ LFIGSEGT+GIIT ++ P PKA + L+ +S AR L+ Sbjct: 190 YDLRDLFIGSEGTLGIITAATLKLFPLPKAQATALLAFDSLAQAVTFLSHARAGFGASLT 249 Query: 311 AFEFMDAKSQVLAKSQLKDAAFP-LEDEHPFYILIETSGSNKD-HDDSKLETFLENVMEE 368 AFE ++A+ L + Q + P L P++ L+E S ++ + H E L E+ Sbjct: 250 AFELLNAECLALLREQFPEGPQPFLGARQPWFALLELSDNHSESHAREAFEQVLGEAFEQ 309 Query: 369 GIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSE 428 ++ D ++A+ + Q LW RE + EA + G K+D+S+P+ + + V T+A L Sbjct: 310 RLLADALIAESLAQSQALWLLRENMSEAQKRAGRNMKHDISVPISQVVAFVADTDALL-- 367 Query: 429 AELVGDSPKPVVGAIGYGHVGDGNLHLNVAVREYNKNIE------KTLEPFVYEFVSSKH 482 P V +GH+GDGNLH NVA + +E L V++ + Sbjct: 368 -----QCHFPGVRHYTFGHLGDGNLHYNVA-HPQDSTVEAHMVHYAALSQLVHDSAHAHG 421 Query: 483 GSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 GS+SAEHG+G K++ +G KSP E+ +M+ +K DP +LNP K + Sbjct: 422 GSISAEHGIGQHKRDMLGRYKSPVELDLMRRIKQALDPKNLLNPGKVL 469 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: 535 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: 474 Length adjustment: 34 Effective length of query: 496 Effective length of database: 440 Effective search space: 218240 Effective search space used: 218240 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