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 RR42_RS06435 RR42_RS06435 2-hydroxyacid dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Cup4G11:RR42_RS06435 Length = 473 Score = 315 bits (806), Expect = 3e-90 Identities = 174/469 (37%), Positives = 271/469 (57%), Gaps = 17/469 (3%) Query: 70 KSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVV 129 ++ L EQ +L +++ D + Y DW ++Y G++ VLRP S E+V+ ++ C+ K+AVV Sbjct: 14 RAALGEQHVL--TDAADQAPYLTDWRKRYTGEAVAVLRPGSAEEVAAAVHACHAHKLAVV 71 Query: 130 PQGGNTGLVGGSVPIFDE--LILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQN 187 PQGGNTGL GG+ P D+ +++SL LN++R DP++ + +AGVIL+ + E Sbjct: 72 PQGGNTGLCGGATPQADQASVVISLQRLNRVRQVDPLNNTITVEAGVILQQLQDTAREHG 131 Query: 188 YMFPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKD 247 +FPL L A+GSC +GG ++TNAGG +LRYG+ LGLEVV P G+I + + +RKD Sbjct: 132 RLFPLSLAAEGSCTIGGNLSTNAGGTAVLRYGNTRELCLGLEVVTPAGEIWDGLRGLRKD 191 Query: 248 NTGYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSE 307 NTGYDL+ LFIG+EGT+GIIT + P P+A + +V + + A+Q Sbjct: 192 NTGYDLRDLFIGAEGTLGIITAAVMKLYPLPRARVTALAAVANPRAALALLAIAQQRAGA 251 Query: 308 ILSAFEFMDAKSQVLAKSQLKDAAFPLEDEHPFYILIETS-GSNKDHDDSKLETFLENVM 366 +L+ FE M + L + +P + HP +L+E S ++DH + E +E Sbjct: 252 MLTGFELMSERCLSLVTTHYPQLRYPFDRPHPQVVLLELSDNESEDHARAIFEALMETAF 311 Query: 367 EEGIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARL 426 E G+V D VVA+ + ++ W RE IP A +G K+D+++P+ + ++ T+A + Sbjct: 312 EAGVVQDAVVAESVQQSRDFWNLREHIPLAQVDDGKNIKHDIAVPISRIADFIDTTDALI 371 Query: 427 SEAELVGDSPKPVVGAIGYGHVGDGNLHLNVA--VREYNKNI---EKTLEPFVYEFVSSK 481 +A P + +GH+GDGNLH NV+ V E + + + V++ V + Sbjct: 372 QQA-------FPGARMVTFGHLGDGNLHYNVSPPVDESHDTFLGNSEAINLIVHDSVHAH 424 Query: 482 HGSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 GS+SAEHGLG K+ KS E+ MM+ +K DP G++NP K I Sbjct: 425 RGSISAEHGLGQLKREENRRYKSGVELAMMRAIKQALDPQGLMNPGKVI 473 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: 17 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: 473 Length adjustment: 34 Effective length of query: 496 Effective length of database: 439 Effective search space: 217744 Effective search space used: 217744 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