Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_019865275.1 METMI_RS0105575 FAD-binding protein
Query= BRENDA::A0A0G2K1W9 (482 letters) >NCBI__GCF_000384075.1:WP_019865275.1 Length = 476 Score = 243 bits (621), Expect = 8e-69 Identities = 149/462 (32%), Positives = 236/462 (51%), Gaps = 10/462 (2%) Query: 25 LSQDFVEALKAVVGSPHVSTASAVRQHHGHDESMHRCRPPDAVVWPQNVDQVSRLASLCY 84 L F+ AL V + + T +G+D S P AVV+P +QV+ ++C Sbjct: 18 LPAGFIAALAQVFAANGLLTKPEDCWAYGYDNSRRHVLP-QAVVFPATHEQVAATVTVCN 76 Query: 85 NQGVPIIPFGTGTGVEGGVCAVQGGVCISLTHMDQIMELNTEDFSVVVEPGVTRKALNTH 144 + VP+ G GTG G ++GG+ +SL MDQ++E + ++ + V+PG+T + + Sbjct: 77 DYLVPLTTRGRGTGTTGATVPLKGGLVMSLERMDQVLEFSPDNRYIRVQPGITNQQVQDI 136 Query: 145 LRNSGLWFPVDPGADA--SLCGMAATGASGTNAVRYGTMRDNVINLEVVLPDGRLLHTAG 202 ++ G ++P DP + A S+ G A ++G AV+YGT R+N + L V G+ + Sbjct: 137 VKEKGFFWPPDPTSAAFCSIGGNLAYNSAGPRAVKYGTPRENTLGLRAVTGAGKEIKV-- 194 Query: 203 RGRHYRKSAAGYNLTGLFVGSEGTLGIITSATLRLHPAPEATVAATCAFPSVQAAVDSTV 262 G K GY+LT L +GSEGTL +IT ATL+L P PEAT + +V AA + Sbjct: 195 -GVFTSKGVVGYDLTRLIIGSEGTLAVITEATLKLTPLPEATKTLRAVYQNVFAAAKAVA 253 Query: 263 QILQAAVPVARIEFLDEVMMDACNRHSKLNCP--VAPTLFLEFHGSQQALAEQLQRTEAI 320 I+ V +EF+D ++ ++S + P L +E G + L Q+ Sbjct: 254 AIMAQPVVPCALEFIDGNAINMIRQYSTCDLPENAGAILMMEVDGQLEGLDNAAQKVADS 313 Query: 321 TQDNGGSHFSWAKEAEKRNELWAARHNAWYAALALRPGSKAYSTDVCVPISRLPEILVET 380 +++G A+ E+ LW R A + P K + DV VP++ +P ++ Sbjct: 314 AKNDGLLDIRVAQTKEEVAALWQTRKALSPALRKVAP--KKINEDVVVPVTEIPTLIAGL 371 Query: 381 KEELKASKLTGVIVGHVGDGNFHCILLVNPDDVEEQRRVKAFAENLGRRALALHGTCTGE 440 E K +L + GH G+GN H LL+NPDD E+ R + + L L+GT +GE Sbjct: 372 DELSKQYQLPIINFGHAGNGNIHVNLLLNPDDPEQSARAHQCLDEVFSLVLKLNGTLSGE 431 Query: 441 HGIGLGKRQLLQEEVGPVGVETMRQLKDTLDPRGLMNPGKVL 482 HG+GL KR + E+ +E MR +K DP+G++NP K+L Sbjct: 432 HGVGLEKRDFVDRELDANSLELMRNIKHQFDPKGILNPDKML 473 Lambda K H 0.319 0.134 0.407 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: 563 Number of extensions: 25 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: 482 Length of database: 476 Length adjustment: 34 Effective length of query: 448 Effective length of database: 442 Effective search space: 198016 Effective search space used: 198016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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