Align D-lactate dehydrogenase (EC 1.1.1.28); D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate 209326 DVU0390 glycolate oxidase, subunit GlcD, putative
Query= BRENDA::Q9YEU4 (473 letters) >MicrobesOnline__882:209326 Length = 460 Score = 243 bits (621), Expect = 8e-69 Identities = 161/446 (36%), Positives = 226/446 (50%), Gaps = 23/446 (5%) Query: 27 YSREPSGLEGRAEAVVFPESAQDVSRLVRYAYSREVYIYPQGSSTDLAGGAFPERPGVVV 86 Y R+ S L + VV PES + L+R A + P+G T LAGG GVV+ Sbjct: 33 YDRDASELRATPDMVVLPESVGQIQALMRLATEHRFPVIPRGGGTGLAGGCLALMGGVVL 92 Query: 87 SMERMRRVREVSVLDSVAVVEPGVRLWDLNVELSKYRYMFPIDPGSVKVATVGGAINTGA 146 S+ERM RVR + + VA V+ G L + +P DP + +TVGG + T A Sbjct: 93 SVERMNRVRAIDTRNLVAEVDAGCITQTLRDAAAAANLFYPPDPAGMDRSTVGGNVATNA 152 Query: 147 GGMRGARYGTMRDWVLGLEIVLPDEEGTILRVGCRTLKCRQGYDLARLIVGSEGTLAIVT 206 GG +YG RD+VLG+E VLPD G +LR G RT K GYD+A L+ GSEGTL ++T Sbjct: 153 GGPACVKYGVTRDYVLGVEAVLPD--GELLRAGVRTRKGVVGYDMAHLLCGSEGTLGVIT 210 Query: 207 EAILKITPMPENVVVVLAFFPTLRQLVDAVIEVKSRAIDTLLMEFMDVDSARLAAETLGA 266 +K+ P+P V + F + + AV V +EFMD L E L Sbjct: 211 GLTMKLIPLPAATVGMAVAFADMPSAMRAVAAVLGAGHLPSAIEFMDHRCLALVGEMLPF 270 Query: 267 AI---RPDGHMLLVGVPVNREASTRVLEEMVSIAKAAGAASVYTAKSMEEAEEKKLLEIR 323 + RP +L++ + R L+ + +I + GA V A + +AE + +R Sbjct: 271 PVPGARPS--LLIIELDGQRATIEPQLDAVAAICREQGATQVLPAPT--DAERATIWGVR 326 Query: 324 RSLFATQALLTQKQFKGRKVMMLMEDIAVPPSKLLDAVERLKELEAKYGFKTVLGGHIGD 383 R Q L + G + L ED+AVP + D V L E +YG + GH GD Sbjct: 327 R-----QVSLRIHDYAG---LYLSEDVAVPLVAIADLVAELPAFEERYGLEIFAFGHAGD 378 Query: 384 GNLHPTISYPVDDEKAKEAALKWYYDVMRMAIELGGTVSAEHGIGVLKKEALRLELERMG 443 GN+H ++ D +E A + + R +ELGGT+S EHGIG KK + LEL Sbjct: 379 GNIHLNVTSSSTDN--RERAEEGVVALARRVVELGGTISGEHGIGEAKKHLVPLEL---- 432 Query: 444 SVKALEIMAGIKRVFDPKGILNPGKV 469 S +++ + GI+ VFDP GI+NPGKV Sbjct: 433 SARSIALQKGIRGVFDPLGIMNPGKV 458 Lambda K H 0.319 0.136 0.381 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: 539 Number of extensions: 29 Number of successful extensions: 5 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: 473 Length of database: 460 Length adjustment: 33 Effective length of query: 440 Effective length of database: 427 Effective search space: 187880 Effective search space used: 187880 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 (21.7 bits) S2: 51 (24.3 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