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 CCNA_03500 CCNA_03500 FAD/FMN-containing dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Caulo:CCNA_03500 Length = 469 Score = 281 bits (719), Expect = 4e-80 Identities = 155/446 (34%), Positives = 242/446 (54%), Gaps = 27/446 (6%) Query: 93 DWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFDELILSL 152 +W +++G++ L++ P+S +V+ ++ C E +A+ PQGGNTGLV G +P E++LS Sbjct: 35 EWRGRWQGETPLLVTPRSTAEVAAVVGICAAEGVAITPQGGNTGLVAGQIPR-GEILLST 93 Query: 153 ANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAGG 212 L IRD DP+ + +AGV L A+ + F + + ++GSC +GG+++TNAGG Sbjct: 94 QKLTAIRDVDPIDDAMVLEAGVTLYEAHQQAAKVGRRFTVGVASEGSCTIGGLISTNAGG 153 Query: 213 LRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVSI 272 +LRYG + VLG+E V+PNG+I N + +RKDNTGYDLKQL IG+EGT+GI+T S+ Sbjct: 154 TAVLRYGMMREQVLGIEAVLPNGEIWNGLKRLRKDNTGYDLKQLLIGAEGTLGIVTAASL 213 Query: 273 LTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAKSQLKDAAF 332 + V+ + + S + ++ RA+ E + AFE M L + Sbjct: 214 KLQALLASRAVAIVGLASPANAIQLLARAKDETGGAVEAFELMGRLGFELTVRNVPGLRD 273 Query: 333 PLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQNLWKWREM 392 PL + HP+Y+LIE + ++ LE L +E G++ D VAQ ET+++ W RE Sbjct: 274 PLPEAHPWYVLIEIASGEPGAAEAALERLLAGALERGLIADAAVAQTETQMKAFWHIREG 333 Query: 393 IPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVGDGN 452 + G V+K+DVS+P+ + + NA + ++ P + +GHVGDGN Sbjct: 334 HSAGQKPEGAVWKHDVSVPVSKIPDFIGQANAAIEKS-------FPGTRIVAFGHVGDGN 386 Query: 453 LHLNV------------AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIG 500 +H +V A RE I V++ + GS+SAEHGLG K Sbjct: 387 VHYDVLQPVGGDGDAHGAQREAGAKI-------VHDITAGFGGSISAEHGLGAMKTAEAL 439 Query: 501 YSKSPEEVKMMKDLKVHYDPNGILNP 526 K P EV ++ ++ DP I+NP Sbjct: 440 TYKDPIEVAALRAIRGALDPQRIMNP 465 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: 527 Number of extensions: 24 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: 469 Length adjustment: 34 Effective length of query: 496 Effective length of database: 435 Effective search space: 215760 Effective search space used: 215760 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