Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate SM_b21129 SM_b21129 oxidoreductase
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Smeli:SM_b21129 Length = 442 Score = 181 bits (459), Expect = 5e-50 Identities = 139/451 (30%), Positives = 209/451 (46%), Gaps = 28/451 (6%) Query: 51 GSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGGVG 110 G + E+H D S+ P VV P SV EV+ +IC+ +R ++P G TGL GG Sbjct: 4 GDRIAERHRGDASLTGRILPLAVVRPASVAEVADALRICNAHRQAVVPQGGLTGLAGGAN 63 Query: 111 ALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGADAS--L 168 G V SL ++ + ++ +TV G + D G P+D GA S + Sbjct: 64 PCAGDVAISLERLSGIEEIDAAAGTMTVLAGTPLEVAQRAAEDAGFLLPIDLGARGSCQV 123 Query: 169 CGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVG 228 G AT+A G +R G R+NVL LE VLADGT+L + K K GY+L LF+G Sbjct: 124 GGNLATNAGGIRVIRNGVARDNVLGLEAVLADGTVLSSMNK---MIKNNTGYDLRQLFIG 180 Query: 229 SEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMI 288 SEGTLGIIT+A LRL +P ++A+C+ S ++ V + +A +A + + M Sbjct: 181 SEGTLGIITRAVLRLRPLPAGRLTALCALDSYENVV---ALLKRAQKELAGLSAY-EAMW 236 Query: 289 NACNRFNNLS-----YAVTPTLFL----EFHGSSKSMEEQVSVTEEITRDNGGSDFAWAE 339 + RFN ++ + TP + + G E + D D A+ Sbjct: 237 ESYFRFNCVAEGLRLFEATPAFAVIVEEDLQGHEAERERFEAFLGRALEDGVIGDALIAQ 296 Query: 340 DEETRSRLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPI 399 ++ W+ R + L + DV +PI + + E L + + Sbjct: 297 SQKEVQTFWRIREGHALDRLPL-----LLNFDVSLPIGEIGRFADECGKALRAKFPEAHV 351 Query: 400 A--GHVGDGNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALL 457 + GHVGD N H + P T+E H+ + G+ + EHGIGL KR L Sbjct: 352 SFFGHVGDSNLHIAFSV-PGATEET--AHAVDAVVYGLVGIYSGSVSAEHGIGLVKRDFL 408 Query: 458 REEVGPLAIEVMKGLKASLDPRNLMNPGKVL 488 P +E+M+ +K +LDP ++NPGKVL Sbjct: 409 DRSRSPAELELMRRIKNALDPNGILNPGKVL 439 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: 446 Number of extensions: 16 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: 442 Length adjustment: 33 Effective length of query: 464 Effective length of database: 409 Effective search space: 189776 Effective search space used: 189776 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