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 SMa0244 SMa0244 Dehydrogenase, FAD-dependent
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Smeli:SMa0244 Length = 481 Score = 325 bits (834), Expect = 2e-93 Identities = 183/464 (39%), Positives = 268/464 (57%), Gaps = 16/464 (3%) Query: 70 KSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVV 129 + +L E +L SE+E++ + DW + V+RP+S ++V+ + C + +++V Sbjct: 21 RQMLGEDIVL--SETEEMLRFCRDWHGDVTTGTVAVIRPRSTQQVAAAVKACRELGLSIV 78 Query: 130 PQGGNTGLVGGSVPIFDE--LILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQN 187 PQGGNTGLV G++P E ++LSL+ +N+IR DP ++G IL + + + Sbjct: 79 PQGGNTGLVLGAIPDAPERQVVLSLSRMNRIRKIDPADFSAVVESGCILSELKDAIAKMG 138 Query: 188 YMFPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKD 247 FPL LGA+GSC +GG V+TNAGG+ +LRYG VLGLEVV+P+G I+ + ++RKD Sbjct: 139 MFFPLALGAQGSCQIGGNVSTNAGGVNVLRYGMTRELVLGLEVVLPDGSILEGLSTLRKD 198 Query: 248 NTGYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSE 307 N G DLKQLFIG+EGT+GIIT VSI P P + L + S ED +++ RAR++ + Sbjct: 199 NRGIDLKQLFIGAEGTLGIITAVSITLTPYPDHVATALLGLASLEDAIRLYRRARRDCCD 258 Query: 308 ILSAFEFMDAKSQVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVME 367 ++SAFEFM + LA+ + D P+ E+P Y+L+E SGS D ++ FLE ME Sbjct: 259 LMSAFEFMPPLAFTLAQEAMPDLPIPISAEYPAYVLMEISGSGLVDVDDLMQRFLEGAME 318 Query: 368 EGIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLS 427 EG+V DG +A +T+ +NLW RE + E G + D+S+PL L S VE +S Sbjct: 319 EGLVLDGTIAASQTQARNLWLIREGMNEGQAKRGTHMRTDISVPLSQLASFVEEAEKAVS 378 Query: 428 EAELVGDSPKPVVGAIGYGHVGDGNLHLNV-----AVREYNKNIEKTLEPFVYEFVSSKH 482 EA P ++ YGHVGDGN+HLNV + E + + V E + Sbjct: 379 EA-------LPGAVSVSYGHVGDGNVHLNVLPPAGSTPEERIQLIYKAKTVVNEVLDRYT 431 Query: 483 GSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNP 526 GS+SAEHG+G K+ K++ LK DP I+NP Sbjct: 432 GSISAEHGIGRLKRPDFDARLPATRRKLLTALKHAVDPEMIMNP 475 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: 555 Number of extensions: 20 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: 481 Length adjustment: 34 Effective length of query: 496 Effective length of database: 447 Effective search space: 221712 Effective search space used: 221712 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