Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_011777725.1 MVAN_RS02060 2-hydroxyacid dehydrogenase
Query= BRENDA::A0A0M3KL04 (335 letters) >NCBI__GCF_000015305.1:WP_011777725.1 Length = 318 Score = 140 bits (354), Expect = 3e-38 Identities = 94/266 (35%), Positives = 139/266 (52%), Gaps = 24/266 (9%) Query: 55 HISNPAVYETLQKNG-LRQLTSRTAGYDMIDLEQASERGLVVTNVPAYSPNSVAELALTQ 113 H+ P E L + LR + AG + ID++ A+ RG+ V N+P + SVAE L Sbjct: 52 HVLRPLSGEDLARAPRLRLVHKLGAGVNTIDVDAATARGVAVANMPGANAESVAEGTLLL 111 Query: 114 TMRLIRNLPLFDARGAEQDFRWA-----GLMAREIRSLTVGIIGAGRIGGTVARLFKALG 168 + +R LP+ D R + W G R+I TVG++G G I V R+ A+G Sbjct: 112 MLAALRRLPVLD-RATREGRGWPSDPTLGETVRDIGGCTVGLVGYGNIAKQVERILVAMG 170 Query: 169 ATVIANDIVERVELKDIVTYVSKEELLQAADVVTLHVPLMDSTTQLIDADALALMKNDAV 228 A VI + + S +LL A D+V+LH+PL D+T L+ DALA MK+DAV Sbjct: 171 ADVIHTSTRD----DGSAGWRSLPDLLSACDIVSLHLPLTDATAGLLGRDALARMKSDAV 226 Query: 229 LINASRGPVVDTDALIAALQNKQIAGAALDTLNGEEHFFNQDLCGKELPSEQLKVLRTLP 288 L+N SRGP+VD +AL AL+ ++A A LD E P L LP Sbjct: 227 LVNTSRGPIVDEEALADALRTGKLAAAGLDVFAVE-------------PVPADNPLLRLP 273 Query: 289 NVLITPHIGFYTNKAVQNMVEISLND 314 NV++TPH+ +YT ++ +E ++++ Sbjct: 274 NVVLTPHVTWYTADTMRRYLEFAVDN 299 Lambda K H 0.317 0.133 0.364 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: 244 Number of extensions: 14 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: 335 Length of database: 318 Length adjustment: 28 Effective length of query: 307 Effective length of database: 290 Effective search space: 89030 Effective search space used: 89030 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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