Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate 8502165 DvMF_2875 FAD linked oxidase domain protein (RefSeq)
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Miya:8502165 Length = 474 Score = 218 bits (554), Expect = 5e-61 Identities = 142/437 (32%), Positives = 218/437 (49%), Gaps = 22/437 (5%) Query: 66 RCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGGVGALQGGVCFSLRKMEQ 125 R P VV P + +V L ++ RLP+ G + G + G+ SL M + Sbjct: 42 RMGTPLAVVRPTTEAQVVELLRLAQAERLPVYARGRASNQVGACVPDRPGIVVSLLHMNR 101 Query: 126 VVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGAD--ASLCGMAATSASGTNAVR 183 ++D+ +DF VEPGV L + GL++P DP + +++ G AT A G A++ Sbjct: 102 ILDIADDDFVAEVEPGVVTSDLQRAVEARGLFYPPDPASIDISTIGGNVATCAGGMRALK 161 Query: 184 YGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVGSEGTLGIITKATLRL 243 YG RE VL L VL G +LHT G R K G +LT LFVGSEGTLGI+T+ TL+L Sbjct: 162 YGVTREYVLGLTAVLPGGRVLHTGG---RCHKNVVGLDLTRLFVGSEGTLGIVTRITLKL 218 Query: 244 YGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMINACNRFNNLSY--AV 301 +P++ + + F S+++A+ +I +AG+ +EFL +++ R + +V Sbjct: 219 LPLPQATATLLAGFGSMEAAMHGVRRIFRAGILPVALEFLSPEVLDCVARRQTPPWPDSV 278 Query: 302 TPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRLWKAR---HDAWYAA 358 L + GS +S+ +V + G + A + +E LW A HD Sbjct: 279 RGALLIRLDGSRESLPLEVRRMHDALHSPGNAAGATSGNEPP---LWSAHGVGHDEEEPL 335 Query: 359 MALRPGCKAYS---------TDVCVPISRLPQIIVETKADLISNNITGPIAGHVGDGNFH 409 A+R G S D+ VP RL + +A ++++ GHVGDGN H Sbjct: 336 WAMRRGISPSSYLVRPNKIGEDIAVPRGRLLDALTGIRAIAQAHDLPILTYGHVGDGNIH 395 Query: 410 CLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIEVM 469 I+ D D E R + T + R +MDGT +GEHG+G+ K+ L ++ PL E+M Sbjct: 396 VNIMYDGADPSETTRADAATVEVMRLVRSMDGTLSGEHGVGMAKKEFLHLQLSPLETELM 455 Query: 470 KGLKASLDPRNLMNPGK 486 + +K + DP +MNP K Sbjct: 456 RQVKHAFDPLGIMNPDK 472 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: 517 Number of extensions: 20 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: 497 Length of database: 474 Length adjustment: 34 Effective length of query: 463 Effective length of database: 440 Effective search space: 203720 Effective search space used: 203720 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 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