Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate Ac3H11_4909 D-Lactate dehydrogenase, cytochrome c-dependent (EC 1.1.2.4)
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4909 Length = 474 Score = 469 bits (1206), Expect = e-136 Identities = 222/442 (50%), Positives = 313/442 (70%), Gaps = 3/442 (0%) Query: 49 SVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGG 108 S+ AVREQHGRDE + PP VVF S ++V+ K+ Y +P+IP+G G+ LEG Sbjct: 36 SLAQAVREQHGRDEGSLQAPPPSAVVFAESTQDVADAVKLASQYEVPVIPYGAGSSLEGH 95 Query: 109 VGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGADASL 168 + A+QGG+ + +M QV+ ++ ED VTV+PG+TRK+LN ++DTGL+FP+DPGADAS+ Sbjct: 96 LLAVQGGISIDVSRMNQVLSINAEDLTVTVQPGITRKALNEAIKDTGLFFPIDPGADASI 155 Query: 169 CGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVG 228 GM AT ASGTNAVRYGTMRENVL LEVV A G ++HT G R +K++AGY+LT L VG Sbjct: 156 GGMCATRASGTNAVRYGTMRENVLALEVVTASGEVIHT---GTRAKKSSAGYDLTRLMVG 212 Query: 229 SEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMI 288 SEGTLGI+T+ T+RLY +PE++ +A+CSFPS+++AV +T+Q +Q GVPIAR+E +D + Sbjct: 213 SEGTLGIMTEITVRLYPLPEAVSAAICSFPSIEAAVRTTIQTIQIGVPIARVELIDHHTV 272 Query: 289 NACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRLW 348 N + L+ P L +EFHGS S++EQ + ++I + GG F WA E R+RLW Sbjct: 273 RMVNAHSKLTLREEPMLLMEFHGSPASVKEQAEMVQDIASEFGGQAFEWASTPEERTRLW 332 Query: 349 KARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGDGNF 408 ARH+A++AA+ RPGC+A STD CVPISRL ++E+ ++ ++ I + GHVGDGNF Sbjct: 333 TARHNAYFAAVQSRPGCRAISTDTCVPISRLADCLLESVDEVEASGIPYFLVGHVGDGNF 392 Query: 409 HCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIEV 468 H ++DPN +E + + L RAL+M GTCTGEHG+G+ K L +E G A+++ Sbjct: 393 HFGYLIDPNSAEERTKAEAMNHTLVARALSMGGTCTGEHGVGVHKMGFLLDETGTGAVDM 452 Query: 469 MKGLKASLDPRNLMNPGKVLEL 490 M+ +K +LDP+N++NPGK+ L Sbjct: 453 MRAIKRALDPKNILNPGKIFAL 474 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: 553 Number of extensions: 20 Number of successful extensions: 2 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