Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate RR42_RS14190 RR42_RS14190 2-hydroxyacid dehydrogenase
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__Cup4G11:RR42_RS14190 Length = 332 Score = 132 bits (331), Expect = 2e-35 Identities = 85/253 (33%), Positives = 129/253 (50%), Gaps = 19/253 (7%) Query: 70 RLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTRE 129 R V + GYN++D+ A A G+ + P A+ L++ RR+ + + R Sbjct: 70 RAVCNMAVGYNNLDVPALTAAGIVATNTPDVLTETTADFGWALLMATARRVTESEHWLRA 129 Query: 130 GDF---SLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDP--YPNPRIQAL 184 G + S G DL+ +G++G G+IG+ AR AGFG +L ++ P + L Sbjct: 130 GKWERWSYDMFLGMDLYRSTLGILGMGRIGQALARRAAGFGMSVLYHNRSRLPEDTERVL 189 Query: 185 GGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALI 244 RY++ LLA+SD + L P +A + H I A LA MKP A L+N RG +V+ AAL Sbjct: 190 NARYVSKAELLAQSDHLLLVLPYSAQSHHSIGAAELAQMKPSATLVNLARGGVVDDAALA 249 Query: 245 EALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREAL 304 AL+ G++ GLDV+E E + + LL+ PNVV+T H A + + Sbjct: 250 RALREGRIFAAGLDVFEAEPQVHPD--------------LLTVPNVVLTPHIASASEKTR 295 Query: 305 AAIADTTLDNIAA 317 A+AD DN+ A Sbjct: 296 RAMADLAADNLIA 308 Lambda K H 0.323 0.137 0.402 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: 255 Number of extensions: 23 Number of successful extensions: 3 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: 329 Length of database: 332 Length adjustment: 28 Effective length of query: 301 Effective length of database: 304 Effective search space: 91504 Effective search space used: 91504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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