Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate WP_037457682.1 N825_RS23825 FAD-binding protein
Query= SwissProt::F1QXM5 (497 letters) >NCBI__GCF_000576635.1:WP_037457682.1 Length = 466 Score = 535 bits (1378), Expect = e-156 Identities = 262/464 (56%), Positives = 338/464 (72%), Gaps = 5/464 (1%) Query: 27 AKTAAVERVVSSFRSVTGDEGVSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALA 86 A+ A E ++ R + GD +S +AVRE HG+DES H PPD V F +S EEV+A+ Sbjct: 8 ARAPAAEALIEELRGLLGDR-LSTSAAVREHHGKDESYHPVVPPDAVAFVQSTEEVAAVV 66 Query: 87 KICHHYRLPIIPFGTGTGLEGGVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKS 146 C + P+IPFGTGT LEGGV AL GGVC L M V+ + ED DVTV+ GVTRK Sbjct: 67 AACARHDTPVIPFGTGTSLEGGVAALHGGVCIDLSGMNAVLRVSPEDLDVTVQAGVTRKQ 126 Query: 147 LNSYLRDTGLWFPVDPGADASLCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHT 206 LN +LRDTGL+FP+DPGADASL GMA+T ASGTNAVRYGTMRENVL L VV+ADG I+ T Sbjct: 127 LNEHLRDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMRENVLGLTVVMADGRIVKT 186 Query: 207 AGKGRRPRKTAAGYNLTNLFVGSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDS 266 G R RK+AAGY+LT LFVG+EGTLG+IT+ TLRLYG+PE++ +AVC FP+++ AVD+ Sbjct: 187 GG---RARKSAAGYDLTRLFVGAEGTLGVITEVTLRLYGIPEAISAAVCPFPTIKDAVDT 243 Query: 267 TVQILQAGVPIARIEFLDDVMINACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEI 326 + +Q+G+P+ARIE LD+V + A + L YAV PTLF EFHG+ + EQ + I Sbjct: 244 VITTIQSGIPVARIELLDEVQMRAVVAHSKLDYAVAPTLFFEFHGTEAGVTEQAEMVSAI 303 Query: 327 TRDNGGSDFAWAEDEETRSRLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVET 386 + GG+DF WA E RSRLW+ARH+A+YAA+ALRPG K ++TDVCVPISRL + IVET Sbjct: 304 AAEFGGTDFQWAAKAEDRSRLWQARHEAYYAALALRPGSKGWATDVCVPISRLAECIVET 363 Query: 387 KADLISNNITGPIAGHVGDGNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGE 446 KAD+ ++++T P+ GHVGDGNFH + ++DP + E++ ER+ RALAM GTCTGE Sbjct: 364 KADIAASSLTAPLVGHVGDGNFHLVYLVDPANPAELEEAAELNERMVMRALAMGGTCTGE 423 Query: 447 HGIGLGKRALLREEVGPLAIEVMKGLKASLDPRNLMNPGKVLEL 490 HG+G GK L E G A+ VM+ +K +LDP+N+MNPGKV+ + Sbjct: 424 HGVGYGKMHFLPAEHGE-AVSVMRMVKQALDPKNIMNPGKVIRV 466 Lambda K H 0.319 0.135 0.399 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: 591 Number of extensions: 21 Number of successful extensions: 3 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: 497 Length of database: 466 Length adjustment: 34 Effective length of query: 463 Effective length of database: 432 Effective search space: 200016 Effective search space used: 200016 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: 52 (24.6 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