Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_057507800.1 ABB28_RS06140 dimethylmenaquinone methyltransferase
Query= BRENDA::A0A0G2K1W9 (482 letters) >NCBI__GCF_001431535.1:WP_057507800.1 Length = 462 Score = 258 bits (660), Expect = 2e-73 Identities = 165/456 (36%), Positives = 223/456 (48%), Gaps = 10/456 (2%) Query: 30 VEALKAVVGSPHVSTASAVRQHHGHDESMHRCRPPDAVVWPQNVDQVSRLASLCYNQGVP 89 V L ++G+ T +A R + D S R + P AV P +QV + C V Sbjct: 10 VAELSLLLGTDGWRTDAAARDANAQDNSWRR-QLPLAVALPSTREQVQAIVRACRRHRVA 68 Query: 90 IIPFGTGTGVEGGVCAVQGGVCISLTHMDQIMELNTEDFSVVVEPGVTRKALNTHLRNSG 149 ++ G GTG G +QG V +SL M +I+E+ D VVEPGV L L G Sbjct: 69 VVARGAGTGTTGAAVPLQGSVVLSLARMARILEVRAGDRCAVVEPGVLNGDLQQVLAPHG 128 Query: 150 LWFPVDPGADASLC---GMAATGASGTNAVRYGTMRDNVINLEVVLPDGRLLHTAGRGRH 206 L++P DP + A +C G A A G AV+YGT RDNV+ L V G L+ G Sbjct: 129 LFWPPDPSS-ADICSIGGNLACNAGGPRAVKYGTSRDNVLGLVAVTGSGDLIRCGGA--- 184 Query: 207 YRKSAAGYNLTGLFVGSEGTLGIITSATLRLHPAPEATVAATCAFPSVQAAVDSTVQILQ 266 Y K A GY+LT L VGSEGTL II ATL+L P A + AA + +++ Sbjct: 185 YTKDATGYDLTHLLVGSEGTLAIIVEATLKLTPLAVAQAGLRVLYRDADAAAQAVSRVMG 244 Query: 267 AAVPVARIEFLDEVMMDACNRHSKLNCPVAPTLFLEFHGSQQALAEQLQRTEAITQDNGG 326 V R+EF+D ++ R+ L +E G L LQ + G Sbjct: 245 QPVVPTRLEFMDARSLELLRRNGADVPDAGAMLLIEADGDHDTLPYLLQALANAAEGEGM 304 Query: 327 SHFSWAKEAEKRNELWAARHNAWYAALALRPGSKAYSTDVCVPISRLPEILVETKEELKA 386 A E R +LWAAR A ++ PG + DV VP+SR+PE++ + Sbjct: 305 IALDVAMEGAAREKLWAARKALSPALRSIAPGK--INEDVVVPVSRIPELVRGVQALAAE 362 Query: 387 SKLTGVIVGHVGDGNFHCILLVNPDDVEEQRRVKAFAENLGRRALALHGTCTGEHGIGLG 446 LT V GH G+GN H +L +PDD +E R +A + LAL GT +GEHGIGL Sbjct: 363 FDLTIVTFGHAGNGNLHVNILYHPDDADENARAQAALPRIFALTLALEGTLSGEHGIGLA 422 Query: 447 KRQLLQEEVGPVGVETMRQLKDTLDPRGLMNPGKVL 482 KR + + P + MR +K LDP G++NPGKVL Sbjct: 423 KRDFMAQAFTPETLAAMRAIKAALDPDGILNPGKVL 458 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: 612 Number of extensions: 34 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: 462 Length adjustment: 33 Effective length of query: 449 Effective length of database: 429 Effective search space: 192621 Effective search space used: 192621 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