Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate GFF354 PGA1_c03650 malate dehydrogenase Mdh
Query= BRENDA::Q8I8U5 (330 letters) >FitnessBrowser__Phaeo:GFF354 Length = 320 Score = 338 bits (867), Expect = 1e-97 Identities = 166/321 (51%), Positives = 230/321 (71%), Gaps = 5/321 (1%) Query: 9 RPKIAMVGSGMIGGTMAFLCSLRELGDVVLFDVVPNMPMGKAMDISHNSSVVDTGITVYG 68 RPKIA++G+G IGGT+A L +L+ELGDVVLFD+ P GKA+DI+ + + G Sbjct: 3 RPKIALIGAGQIGGTLAHLAALKELGDVVLFDIAEGTPEGKALDIAESGPSEGFDAKLKG 62 Query: 69 SNSYECLKGADVVIITAGITKIPGKSDKEWSRMDLLPVNIKIMREVGAAIKSYCPNAFVI 128 + SYE + GADV I+TAG+ + PG S R DLL +N+K+M+ VG I+ + P+AFVI Sbjct: 63 TQSYEDIAGADVCIVTAGVPRKPGMS-----RDDLLGINLKVMKSVGEGIRDHAPDAFVI 117 Query: 129 NITNPLDVMVAALQESSGLPHHRICGMAGMLDSSRFRRMIADKLEVSPRDVQGMVIGVHG 188 ITNPLD MV AL+E SGLPH ++CGMAG+LDS+RFR +A++ VS +DV V+G HG Sbjct: 118 CITNPLDAMVWALREFSGLPHEKVCGMAGVLDSARFRHFLAEEFNVSMKDVTAFVLGGHG 177 Query: 189 DHMVPLSRYATVNGIPLSEFVKKGWIKQEEVDDIVQKTKVAGGEIVRLLGQGSAYYAPGA 248 D MVPL+RY+TV GIPL + VK GW QE++D IVQ+T+ G EIV LL GSA+YAP Sbjct: 178 DTMVPLTRYSTVAGIPLPDLVKMGWTSQEKLDAIVQRTRDGGAEIVGLLKTGSAFYAPAT 237 Query: 249 SAIQMAESYLKDRKRVMVCSCYLQGQYGVQNHYLGVPCVIGGRGVEKIIELELTAQERQE 308 SAI+MAE+YLKD+KRV+ C+ Y+ G G++ Y+GVP VIG G+E++I++++T+ E+ Sbjct: 238 SAIEMAEAYLKDQKRVLPCAAYVDGALGLKGMYVGVPTVIGAGGIERVIDIKMTSDEQTM 297 Query: 309 LQGSIDEVKEMQKAIAALDAS 329 S++ VK + +A +D S Sbjct: 298 FDNSVNAVKGLVEACKGIDGS 318 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: 323 Number of extensions: 14 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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