Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate AZOBR_RS05725 AZOBR_RS05725 FAD-binding protein
Query= SwissProt::Q7TNG8 (484 letters) >FitnessBrowser__azobra:AZOBR_RS05725 Length = 495 Score = 228 bits (582), Expect = 3e-64 Identities = 141/460 (30%), Positives = 228/460 (49%), Gaps = 12/460 (2%) Query: 29 QDFVEALKAVV-GSPHVSTASAVREQHGHDESMHRCQPPDAVVWPQNVDQVSRVASLCYN 87 ++ + AL+A+V G ++ S +R + +R Q P VV P V+QVSRV C Sbjct: 15 REIIAALRAIVPGEGVIADESELRAYECDGLTAYR-QLPMVVVLPSTVEQVSRVLRTCKE 73 Query: 88 QGVPIIPFGTGTGVEGGVCAVQGGVCINLTHMDQITELNTEDFSVVVEPGVTRKALNTHL 147 GV ++P G GT + GG + GV + + ++I +++ + VV +PGVT ++T + Sbjct: 74 MGVKVVPRGAGTSLSGGALPLADGVLLGMGKFNRILDIDFANRCVVTQPGVTNLGISTAV 133 Query: 148 RDSGLWFPVDPGAD--ASLCGMAATGASGTNAVRYGTMRDNVINLEVVLPDGRLLHTAGR 205 G ++ DP + ++ G A + G + ++YG +NV+ LE+VL DG +L G+ Sbjct: 134 AHEGFYYAPDPSSQIACTIGGNIAENSGGVHCLKYGLTTNNVLGLEMVLMDGTVLRLGGK 193 Query: 206 GRHYRKSAAGYNLTGLFVGSEGTLGIITSTTLRLHPAPEATVAATCAFPSVQAAVDSTVQ 265 A GY+L G+ GSEG LG++T T+R+ P A FP+ + D Sbjct: 194 ----HLDAGGYDLMGVVTGSEGLLGVVTEVTVRILKKPATARAVLIGFPTSEQGGDCVAA 249 Query: 266 ILQAAVPVARIEFLDDVMMDACNR--HSKLNCPVAPTLFLEFHGSQQTLAEQLQRTEAIT 323 I+ A + +E +D + A H+ V L +E G + + + I Sbjct: 250 IIAAGIIPGGMEMMDKPAIHAAEDFVHAGYPLDVEALLIVELDGPAAEVDHLIDQVAEIA 309 Query: 324 QDNGGSHFSWAKEAEKRNELWAARHNAWYAALALSPGSKAYSTDVCVPISRLPEILVETK 383 + G + + E+R WA R A+ A +SP Y D +P LP +L + Sbjct: 310 RSKGCCYSRVSTSEEERLSFWAGRKAAFPAVGRISPDY--YCMDGTIPRKALPLVLHRMQ 367 Query: 384 EEIKASKLTGAIVGHVGDGNFHCILLVDPDDAEEQRRVKAFAENLGRRALALGGTCTGEH 443 E L A V H GDGN H ++L D + E R +AF ++ R + +GG TGEH Sbjct: 368 EMSDRYALRVANVFHAGDGNLHPLILYDANKPGELERAEAFGNDILRLCVEVGGVLTGEH 427 Query: 444 GIGLGKRQLLQEEVGPVGVETMRQLKNTLDPRGLMNPGKV 483 G+G+ KR L+ ++ V ++ +++K DP GL+NPGKV Sbjct: 428 GVGVEKRDLMTDQFDEVDLDQQQRIKCAFDPDGLLNPGKV 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: 608 Number of extensions: 28 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: 484 Length of database: 495 Length adjustment: 34 Effective length of query: 450 Effective length of database: 461 Effective search space: 207450 Effective search space used: 207450 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