Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_084165221.1 N825_RS31190 FAD-binding oxidoreductase
Query= uniprot:Q8EGS3 (934 letters) >NCBI__GCF_000576635.1:WP_084165221.1 Length = 662 Score = 629 bits (1621), Expect = 0.0 Identities = 317/628 (50%), Positives = 420/628 (66%), Gaps = 2/628 (0%) Query: 16 LGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGT 75 LG V DP+R A+ TDAS++R+VP VVV +T ++ L R+ PVTFRAAGT Sbjct: 35 LGADRVILDPLRLLAYGTDASFYRLVPRVVVKVDTEREITAVLAACRRDRLPVTFRAAGT 94 Query: 76 SLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPAT 135 SLSGQA+ + +L++LG +G+ ++ V D K I L V+G+DAN LA RKIGPDPA+ Sbjct: 95 SLSGQAVTDSVLIVLG-EGWNRMVVERDGKLIRLQPGVLGADANRRLATHARKIGPDPAS 153 Query: 136 IASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKL 195 I SAKIGGI ANN+SGMCCGT+ NSY+T+ S +LL ADGT +DTG S F+ +HG L Sbjct: 154 IDSAKIGGIAANNSSGMCCGTSDNSYKTLVSMRLLLADGTLVDTGDAASLVRFSASHGVL 213 Query: 196 LQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLA 255 L+ L+EL T+ N LA RIR K++IKNTTGY IN+L+DF +P DI+ HLM+G EGTL Sbjct: 214 LERLAELGRATKANKELAARIRAKFAIKNTTGYSINALVDFEEPVDILQHLMIGSEGTLG 273 Query: 256 FINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPG 315 FI E+TY TV + KASA+ +F ++ +A RA+ L+ VSA EL+D ++++V KPG Sbjct: 274 FIAEITYRTVPDHAHKASALLLFPDIGEACRAVALLKPAPVSAVELMDRAALRSVEDKPG 333 Query: 316 MPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYW 375 MP + L LL+E+RA+D L+ + LAG + P F++ + K W Sbjct: 334 MPAEIRGLADGVTALLVETRAEDVGGLDANIAAIATVLAGVTTLGPAVFTSRADEFGKLW 393 Query: 376 AMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAG 435 +RKGLFP VG R GT+VIIEDVAF +E LAAA D+ LF KHGY E I+GHAL G Sbjct: 394 KIRKGLFPAVGAVRKAGTTVIIEDVAFRIEDLAAATLDLQALFAKHGYHEAIIFGHALDG 453 Query: 436 NFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDA 495 N HF+ T F ++++R+ AFMDD+ +V+ Y+GS+KAEHGTGR +APFVE EWG+DA Sbjct: 454 NLHFVFTQDFAIDSEVERYAAFMDDVCKLVVETYDGSLKAEHGTGRNMAPFVEMEWGRDA 513 Query: 496 YTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTS 555 Y LM+ IK + DP GILNPGVILNDD H++++KP P D VD CIECGFCE+ CP++ Sbjct: 514 YALMREIKSLLDPLGILNPGVILNDDPKAHLRDLKPMPKADPLVDTCIECGFCERMCPSA 573 Query: 556 ALNFSPRQRIATLREIERL-EQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSM 614 L +PRQRI REI RL ++ GD A ++R Y ++TCAAC LC ACPV+ Sbjct: 574 GLTLTPRQRIVGWREISRLADEGGDTARETELRTLYDYQGLETCAACGLCATACPVEIET 633 Query: 615 GQLVRKLRTPYISTTEQKVLDFQAKHFG 642 G L + LR S +++ A+HFG Sbjct: 634 GMLTKALRGRRQSPARRRIAALAARHFG 661 Lambda K H 0.319 0.135 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: 1444 Number of extensions: 52 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: 934 Length of database: 662 Length adjustment: 41 Effective length of query: 893 Effective length of database: 621 Effective search space: 554553 Effective search space used: 554553 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: 55 (25.8 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