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 CA265_RS09620 CA265_RS09620 FAD-binding oxidoreductase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Pedo557:CA265_RS09620 Length = 467 Score = 223 bits (569), Expect = 9e-63 Identities = 147/475 (30%), Positives = 242/475 (50%), Gaps = 18/475 (3%) Query: 58 FKKLTSDDLNYFKSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLI 117 F K+ + L K+ + +++ ++++ L Y+ D + Q ++V++P + E+VS + Sbjct: 3 FTKINPEILAEIKAAVGAEKVF--TDADSLENYSHDETEDLRYQPEVVVKPTTPEEVSAL 60 Query: 118 LNYCNDEKIAVVPQGGNTGLVGGSVPIFDELILSLANLNKIRDFDPVSGILKCDAGVILE 177 L CN + V P+GG TGL G ++PI+ + LS+ I D D + + GVI E Sbjct: 61 LKICNAHHVPVTPRGGGTGLSGAALPIYGGISLSMEKFKAILDIDTENLQATVEPGVITE 120 Query: 178 NANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQI 237 N V E+ ++P+D +KGSC +GG VA +GG R+++YG++ +L LEVV+PNG I Sbjct: 121 EFINAVAEKGLLYPVDPSSKGSCFIGGNVAHGSGGPRVVKYGTIREYILNLEVVLPNGDI 180 Query: 238 VNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKV 297 + + + K +GY+L QL IGSEGT+ ++T + +PKP + S + ED Sbjct: 181 IWTGANTLKYASGYNLTQLMIGSEGTLAVVTKIVTKLLPKPSQSVLMMGSFSTNEDACAA 240 Query: 298 FVRARQELSEILSAFEFMDAKSQVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSK 357 V A SA EFM+ K V + D F L+D+ ++IE G + D Sbjct: 241 -VSAIFRAGVTPSALEFMERKG-VEWVIKFDDIKFDLKDDVAALLMIEFDGDDLDDIFKN 298 Query: 358 LETFLENVMEEGIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYS 417 E V+EE T+ + A + + LW+ R + E+ ++N + D +P L Sbjct: 299 CEK-TNIVLEEHNCTEVLFADTAAQKEELWRMRRTMAESVKSNSVYKEEDTVVPRAALPK 357 Query: 418 LVEATNARLSEAELVGDSPKPVVGAIGYGHVGDGNLHLNVAVREYNKNIEKTLEPF---- 473 LV +G K ++ YGH GDGNLH+N+ + K F Sbjct: 358 LVNGIKE-------IG--AKYGFESVCYGHAGDGNLHVNIIKAGMSDEDWKNKLKFGIAE 408 Query: 474 VYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528 ++E ++ G++S EHG+G +K ++ S + +M+ +K +DP GILNP K Sbjct: 409 IFELTTALGGTLSGEHGIGLVQKEFMPIKYSEIHLNLMRGIKNIFDPKGILNPGK 463 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: 610 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: 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