Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate N515DRAFT_1999 N515DRAFT_1999 D-lactate dehydrogenase
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Dyella79:N515DRAFT_1999 Length = 456 Score = 232 bits (591), Expect = 2e-65 Identities = 149/463 (32%), Positives = 229/463 (49%), Gaps = 15/463 (3%) Query: 29 TAAVERVVSSFRSVTGDEGVSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKI 88 TA +E + +SF + +S+G A R + D S R PD VVFP S E+ AL + Sbjct: 5 TALLEALHASFAG----DALSLGEAERLAYAYDNS-RRNALPDAVVFPTSHEQTEALVRA 59 Query: 89 CHHYRLPIIPFGTGTGLEGGVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLN 148 C +R+P++ G GT G + GGV S +M +++ + ++ VEPGV L Sbjct: 60 CREHRVPLVARGRGTNTTGATVPVDGGVVASFERMNRILRIDPDNRLAVVEPGVLNGDLQ 119 Query: 149 SYLRDTGLWFPVDPGAD--ASLCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHT 206 L+ G ++P DP + S+ G A +++G V+YG+ REN L L V G Sbjct: 120 QALKPHGFFWPPDPTSSPWCSIGGNLACNSAGPRTVKYGSPRENTLGLRAVAGTGVGFRC 179 Query: 207 AGKGRRPRKTAAGYNLTNLFVGSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDS 266 G K + GY+LT L +GSEGTL +IT+ATL+L P + + ++ V +A + Sbjct: 180 ---GTYTSKGSTGYDLTRLLIGSEGTLALITEATLKLTPKPSGLRTLRATYRDVSAAARA 236 Query: 267 TVQILQAGVPIARIEFLDDVMINACNRFNNLSYAVT-PTLFLEFHGSSKSMEEQVSVTEE 325 +I+ V +EF+DDV + S V L +E G ++ V Sbjct: 237 VARIMAQPVTPCALEFIDDVALKLARDHGGDSVPVAGAMLMIEVDGEPDTLAGAVEAVSR 296 Query: 326 ITRDNGGSDFAWAEDEETRSRLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVE 385 R +G A+ E LW AR A + P + DV VP+SRLP+++ Sbjct: 297 AARGDGLESLQVAQSAEETQALWSARKALSPAQRTISP--NKINEDVVVPVSRLPELVDG 354 Query: 386 TKADLISNNITGPIAGHVGDGNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTG 445 KA +++ GH G+GN H + L P D E +R H+ + + +DGT +G Sbjct: 355 IKALAAKHDVLIVSFGHAGNGNLH--VNLLPRDEAERERAHACLAEVFALVIRLDGTLSG 412 Query: 446 EHGIGLGKRALLREEVGPLAIEVMKGLKASLDPRNLMNPGKVL 488 EHGIGL KR + + P + +M+G+KA+ DP ++NP K+L Sbjct: 413 EHGIGLVKREFMPLALQPETLGLMRGVKAAFDPDGILNPRKLL 455 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: 488 Number of extensions: 21 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: 497 Length of database: 456 Length adjustment: 33 Effective length of query: 464 Effective length of database: 423 Effective search space: 196272 Effective search space used: 196272 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 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