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 GFF3803 Psest_3872 FAD/FMN-containing dehydrogenases
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__psRCH2:GFF3803 Length = 472 Score = 288 bits (736), Expect = 4e-82 Identities = 159/470 (33%), Positives = 264/470 (56%), Gaps = 23/470 (4%) Query: 66 LNYFKSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEK 125 ++ K+++ ++L ++++ L+ Y +DW + + ++ PKS+E+V I+ + N+ K Sbjct: 15 IDELKTLVEPGKVL--TDADSLNAYGKDWTKHFAPAPSAIVFPKSIEQVQAIVRWANERK 72 Query: 126 IAVVPQGGNTGLVGGSVPIFDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVME 185 +A+VP GG TGL +V E+++S +N+I +F+ + C GV+ + + Sbjct: 73 VALVPSGGRTGLSAAAVAANGEVVVSFDYMNQILEFNEMDRTAVCQPGVVTAQLQQFAED 132 Query: 186 QNYMFPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMR 245 + +P+D + GS +GG + TNAGG++++RYG V G++VV G ++ + Sbjct: 133 KGLYYPVDFASAGSSQIGGNIGTNAGGIKVIRYGMTRNWVAGMKVVTGKGDVLELNKDLI 192 Query: 246 KDNTGYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQEL 305 K+ TGYDL+QLFIG+EGT+G + ++ +P L F+ + V + +L Sbjct: 193 KNATGYDLRQLFIGAEGTLGFVVEATMRLERQPTNLTALVLGTPDFDSIMPVLHAFQDKL 252 Query: 306 SEILSAFEFMDAK--SQVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLE 363 L+AFEF K ++VL + D P E + PFY L+E + ++ D L TF E Sbjct: 253 D--LTAFEFFSDKALAKVLGRG---DVPAPFETDCPFYALLEFEATTEERADQALATF-E 306 Query: 364 NVMEEGIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATN 423 + +E+G V DGV++Q E +LQNLWK RE I E + ++ YK D+S+ V Sbjct: 307 HCVEQGWVLDGVMSQSEQQLQNLWKLREYISE-TISHWTPYKNDISV-------TVAKVP 358 Query: 424 ARLSEAELVGDSPKPVVGAIGYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFV 478 A L E + + P + +GH+GDGNLHLN+ + E T+ +V+E V Sbjct: 359 AFLKEIDTIVGEHYPDFEIVWFGHIGDGNLHLNILKPDAMDKDEFFGKCATVNKWVFETV 418 Query: 479 SSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528 +GS+SAEHG+G K++Y+ YS+SP E++ MK +K +DPNGI+NP K Sbjct: 419 QKYNGSISAEHGVGMTKRDYLEYSRSPAEIEYMKAVKAVFDPNGIMNPGK 468 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: 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: 472 Length adjustment: 34 Effective length of query: 496 Effective length of database: 438 Effective search space: 217248 Effective search space used: 217248 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