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 AO353_21310 AO353_21310 glycolate oxidase subunit GlcD
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21310 Length = 499 Score = 175 bits (443), Expect = 4e-48 Identities = 143/475 (30%), Positives = 229/475 (48%), Gaps = 34/475 (7%) Query: 66 LNYFKSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEK 125 LN + L E +IL E+L Y D + Y+ LVL P+ VE+V +L C+ + Sbjct: 22 LNALREQLPELDILY--REEELKPYECDGLSAYRTTPMLVLLPRYVEQVQAVLKLCHAHR 79 Query: 126 IAVVPQGGNTGLVGGSVPIFDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVME 185 + VV +G TGL GG++P+ ++L +A N+I DP + + GV + V Sbjct: 80 VPVVARGAGTGLSGGALPLEKGVLLVMARFNQILHIDPAARTARVQPGVRNLAISQAVAP 139 Query: 186 QNYMFPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMR 245 + D ++ +C +GG VA NAGG+ L+YG +VL LEV+ G+ + ++ S Sbjct: 140 LGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNVLKLEVLTIEGEHL-TLGSDA 198 Query: 246 KDNTGYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQEL 305 D+ G DL LF GSEG +GIIT V++ +PKP+A V S +S E +A + Sbjct: 199 LDSAGLDLLALFNGSEGLLGIITEVTVKLLPKPQAAKVLLASFDSVE-------KAGGAV 251 Query: 306 SEILSA------FEFMDAKSQVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLE 359 +EI++A E MD + A A +P++ E +L E G D D L Sbjct: 252 AEIIAAGIIPAGLEMMD-NLALRAAEDFVHAGYPVDAE--AILLCELDGVEADVRDDCLR 308 Query: 360 TFLENVMEEGIVTDGVVAQDETELQNLWKWRE-MIPEASQANGGVYKYDVSLPLKDLYSL 418 + V+E ++ A+DE E W R+ P + + Y D ++P ++L + Sbjct: 309 --VRAVLERAGASEVRQARDEAERVKFWAGRKAAFPAIGRLSPDYYCMDGTIPRRELPRV 366 Query: 419 VEATNARLSEAELVGDSPKPVVGAIGYGHVGDGNLH-LNVAVREYNKNIEKT--LEPFVY 475 ++ AEL + V H GDGN+H L + +E+T L + Sbjct: 367 LKGI------AELASEYGLRVANVF---HAGDGNMHPLILFDANQPGELERTEALGGKIL 417 Query: 476 EFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 E GS++ EHG+G +K N + + +E+ + +K+ +D G+LNP K I Sbjct: 418 ELCVKVGGSITGEHGVGREKINQMCAQFNSDELTVFHAIKIAFDAKGLLNPGKNI 472 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: 583 Number of extensions: 25 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: 499 Length adjustment: 35 Effective length of query: 495 Effective length of database: 464 Effective search space: 229680 Effective search space used: 229680 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 Apr 09 2024. 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