Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate SMc02479 SMc02479 malate dehydrogenase
Query= BRENDA::Q8I8U5 (330 letters) >FitnessBrowser__Smeli:SMc02479 Length = 320 Score = 339 bits (870), Expect = 5e-98 Identities = 167/314 (53%), Positives = 230/314 (73%), Gaps = 5/314 (1%) Query: 9 RPKIAMVGSGMIGGTMAFLCSLRELGDVVLFDVVPNMPMGKAMDISHNSSVVDTGITVYG 68 R KIA++GSGMIGGT+A L L+ELGD+VLFD+ +P GK +DI+ +S V ++ G Sbjct: 3 RNKIALIGSGMIGGTLAHLAGLKELGDIVLFDIADGIPQGKGLDIAQSSPVEGFDASLTG 62 Query: 69 SNSYECLKGADVVIITAGITKIPGKSDKEWSRMDLLPVNIKIMREVGAAIKSYCPNAFVI 128 ++ Y ++GADV I+TAG+ + PG S R DLL +N+K+M +VGA IK Y PNAFVI Sbjct: 63 ASDYSAIEGADVCIVTAGVPRKPGMS-----RDDLLGINLKVMEQVGAGIKKYAPNAFVI 117 Query: 129 NITNPLDVMVAALQESSGLPHHRICGMAGMLDSSRFRRMIADKLEVSPRDVQGMVIGVHG 188 ITNPLD MV ALQ+ SGLP +++ GMAG+LDSSRFR +A++ VS +D+ V+G HG Sbjct: 118 CITNPLDAMVWALQKFSGLPKNKVVGMAGVLDSSRFRLFLAEEFNVSVKDITAFVLGGHG 177 Query: 189 DHMVPLSRYATVNGIPLSEFVKKGWIKQEEVDDIVQKTKVAGGEIVRLLGQGSAYYAPGA 248 D MVPL+RY+TV GIPL + ++ GW +E++D I+Q+T+ G EIV LL GSAYYAP A Sbjct: 178 DTMVPLARYSTVAGIPLPDLIQMGWTTKEKLDQIIQRTRDGGAEIVGLLKTGSAYYAPAA 237 Query: 249 SAIQMAESYLKDRKRVMVCSCYLQGQYGVQNHYLGVPCVIGGRGVEKIIELELTAQERQE 308 SAI+MAE+YLKD+KRV+ C+ +L GQYGV++ Y+GVP VIG G+E+IIE++L E++ Sbjct: 238 SAIEMAEAYLKDKKRVLPCAAHLSGQYGVKDMYVGVPTVIGAGGIERIIEIDLNKGEKEA 297 Query: 309 LQGSIDEVKEMQKA 322 S+ V + +A Sbjct: 298 FDKSVAAVAGLCEA 311 Lambda K H 0.319 0.136 0.394 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: 350 Number of extensions: 15 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: 330 Length of database: 320 Length adjustment: 28 Effective length of query: 302 Effective length of database: 292 Effective search space: 88184 Effective search space used: 88184 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: 48 (23.1 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