Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 206855 DVU1412 D-isomer specific 2-hydroxyacid dehydrogenase family protein
Query= BRENDA::Q9I530 (329 letters) >MicrobesOnline__882:206855 Length = 326 Score = 173 bits (438), Expect = 6e-48 Identities = 108/271 (39%), Positives = 151/271 (55%), Gaps = 19/271 (7%) Query: 65 AAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRR--LH- 121 A G R V++ + GY+ VD+AAA LG+PV +VP Y +VA+H L+L L RR LH Sbjct: 62 ALPGLRFVSVLATGYDKVDVAAAGVLGIPVSNVPGYGTDSVAQHVFALLLELCRRTALHD 121 Query: 122 ---RAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPN 178 RA T+ D+ T +L GK +G++G G G RI G ++AY P Sbjct: 122 HRIRAGAWTQSPDWCFWDSTQEELTGKTMGIVGFGNTGRRVGRIANALGMNVIAYAPRSR 181 Query: 179 PRIQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALV 238 ++ LD L +D+VSLHCPLT +T L+DA+RLA+M+PG+ LINT RG L+ Sbjct: 182 FDPDYRPFEHVGLDELFTSADVVSLHCPLTPETEGLVDARRLASMRPGSYLINTARGPLL 241 Query: 239 NAAALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAF 298 + A+ EAL SG+L GLDV +E +D P LLS N ++T H A+ Sbjct: 242 DERAVAEALDSGRLAGAGLDVLSQE-----PPAADNP--------LLSAKNCLITPHLAW 288 Query: 299 LTREALAAIADTTLDNIAAWQDGTPRNRVRA 329 +R A + D+T NI ++ +GTP N V A Sbjct: 289 ASRTARRTLMDSTAANIRSFIEGTPVNVVNA 319 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: 278 Number of extensions: 16 Number of successful extensions: 4 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: 326 Length adjustment: 28 Effective length of query: 301 Effective length of database: 298 Effective search space: 89698 Effective search space used: 89698 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: 48 (23.1 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