Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate Synpcc7942_0276 Synpcc7942_0276 glycolate oxidase subunit GlcD
Query= SwissProt::Q7TNG8 (484 letters) >FitnessBrowser__SynE:Synpcc7942_0276 Length = 490 Score = 218 bits (556), Expect = 3e-61 Identities = 145/471 (30%), Positives = 229/471 (48%), Gaps = 26/471 (5%) Query: 33 EALKAVVGSPHVSTASAVREQHGHDESMHR--------C-------QPPDAVVWPQNVDQ 77 + + AV + A A RE G ++ + R C Q P VV P++ ++ Sbjct: 3 QPMTAVAAPNWTAIAQAFREVLGREQVVERREELLVYECDGLTNHRQIPPLVVLPRSTEE 62 Query: 78 VSRVASLCYNQGVPIIPFGTGTGVEGGVCAVQGGVCINLTHMDQITELNTEDFSVVVEPG 137 V+ LC + + G GTG+ GG V+ V I M QI E++ ++ V V+PG Sbjct: 63 VAAAVRLCNQFDLSFVARGAGTGLSGGALPVEDSVLIVTARMRQILEIDYDNLRVRVQPG 122 Query: 138 VTRKALNTHLRDSGLWFPVDPGADA--SLCGMAATGASGTNAVRYGTMRDNVINLEVVLP 195 V + +G ++ DP + + S+ G A + G + +++G ++V+ L +VLP Sbjct: 123 VINSWVTQATTGAGFFYAPDPSSQSVCSIGGNVAENSGGVHCLKHGVTNNHVLGLTLVLP 182 Query: 196 DGRLLHTAGRGRHYRKSAAGYNLTGLFVGSEGTLGIITSTTLRLHPAPEATVAATCAFPS 255 D ++ G GY+L G+FVGSEGTLGI T TLRL P P++ F S Sbjct: 183 DASVIQVGGA----IADLPGYDLCGIFVGSEGTLGIATEVTLRLQPLPQSVQVLLADFSS 238 Query: 256 VQAAVDSTVQILQAAVPVARIEFLDDVMMDACNRHSKLNC---PVAPTLFLEFHGSQQTL 312 ++AA + I+ A + A +E +D+ ++A K +C A L E G + Sbjct: 239 IEAAGAAVSGIIAAGILPAGLELMDNFSINAVEDVVKSDCYPRDAAAILLAELDGRASEV 298 Query: 313 AEQLQRTEAITQDNGGSHFSWAKEAEKRNELWAARHNAWYAALALSPGSKAYSTDVCVPI 372 A+Q++ EA+ + +G + A +AE R LW R A+ A +SP Y D +P Sbjct: 299 AQQIRDVEAVCRQHGARSIAIATDAEDRLRLWKGRKAAFAAVGRISPSY--YVQDGVIPR 356 Query: 373 SRLPEILVETKEEIKASKLTGAIVGHVGDGNFHCILLVDPDDAEEQRRVKAFAENLGRRA 432 S LP +L E ++ + A V H GDGN H ++L D +D RV+A + + Sbjct: 357 STLPFVLHEIEQLGQKHGYRVANVFHAGDGNLHPLILYDRNDPGALERVEALGGEILKLC 416 Query: 433 LALGGTCTGEHGIGLGKRQLLQEEVGPVGVETMRQLKNTLDPRGLMNPGKV 483 + +GG+ +GEHGIG KR + +ETM+ L++ DP NP KV Sbjct: 417 VNVGGSISGEHGIGADKRCYMPAMFSSEDLETMQWLRHAFDPLERANPTKV 467 Lambda K H 0.318 0.133 0.403 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: 586 Number of extensions: 28 Number of successful extensions: 4 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: 484 Length of database: 490 Length adjustment: 34 Effective length of query: 450 Effective length of database: 456 Effective search space: 205200 Effective search space used: 205200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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