Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_002721256.1 RSPH17029_RS13255 malate dehydrogenase
Query= BRENDA::Q8I8U5 (330 letters) >NCBI__GCF_000015985.1:WP_002721256.1 Length = 320 Score = 330 bits (845), Expect = 4e-95 Identities = 163/321 (50%), Positives = 227/321 (70%), Gaps = 5/321 (1%) Query: 9 RPKIAMVGSGMIGGTMAFLCSLRELGDVVLFDVVPNMPMGKAMDISHNSSVVDTGITVYG 68 RPKIA++G+G IGGT+A L +++ELGDVVLFD+ P GKA+DI+ + + G Sbjct: 3 RPKIALIGAGQIGGTLAHLAAIKELGDVVLFDIAEGTPQGKALDIAQSGPSEGFDAVMKG 62 Query: 69 SNSYECLKGADVVIITAGITKIPGKSDKEWSRMDLLPVNIKIMREVGAAIKSYCPNAFVI 128 +NSYE + GADV I+TAG+ + PG S R DL+ +N+K+M+ VG IK++ PNAFVI Sbjct: 63 ANSYEEIAGADVCIVTAGVPRKPGMS-----RDDLIGINLKVMKSVGEGIKAHAPNAFVI 117 Query: 129 NITNPLDVMVAALQESSGLPHHRICGMAGMLDSSRFRRMIADKLEVSPRDVQGMVIGVHG 188 ITNPLD MV ALQ+ SGLP ++ GMAG+LDS+RFR ++ + VS RDV V+G HG Sbjct: 118 CITNPLDAMVWALQQFSGLPAEKVVGMAGVLDSARFRHFLSVEFNVSMRDVTAFVLGGHG 177 Query: 189 DHMVPLSRYATVNGIPLSEFVKKGWIKQEEVDDIVQKTKVAGGEIVRLLGQGSAYYAPGA 248 D MVPL RY+TV GIPL + V+ GW QE++D IVQ+T+ G EIV LL GSA+YAP Sbjct: 178 DTMVPLVRYSTVAGIPLPDLVQMGWTTQEKLDQIVQRTRDGGAEIVGLLKTGSAFYAPAT 237 Query: 249 SAIQMAESYLKDRKRVMVCSCYLQGQYGVQNHYLGVPCVIGGRGVEKIIELELTAQERQE 308 SAI+MAE+YLKD+KR++ C+ Y+ G +G+ Y+GVP +IG G+EKI++++L E+ Sbjct: 238 SAIEMAEAYLKDQKRLLPCAAYVDGAFGLNGMYVGVPTIIGAGGIEKIVDIKLNDDEQAM 297 Query: 309 LQGSIDEVKEMQKAIAALDAS 329 S++ VK + +A +D+S Sbjct: 298 FDKSVNAVKGLVEACKGIDSS 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: 330 Number of extensions: 12 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 Apr 10 2024. 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