Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_012469683.1 GLOV_RS08065 malate dehydrogenase
Query= BRENDA::Q8I8U5 (330 letters) >NCBI__GCF_000020385.1:WP_012469683.1 Length = 321 Score = 296 bits (759), Expect = 4e-85 Identities = 157/321 (48%), Positives = 218/321 (67%), Gaps = 8/321 (2%) Query: 9 RPKIAMVGSGMIGGTMAFLCSLRELGDVVLFDVVPNMPMGKAMDISHNSSVVDTGITVYG 68 R KI+++G G IGG +A LC+LRELGDVV+FD+V MP GK +DI+ S V + + G Sbjct: 3 RKKISLIGGGQIGGVLAQLCALRELGDVVMFDIVEGMPQGKMLDIAEASPVDGFDVCLQG 62 Query: 69 SNSYECLKGADVVIITAGITKIPGKSDKEWSRMDLLPVNIKIMREVGAAIKSYCPNAFVI 128 + Y+ + G+DVVI+TAG+ + PG S R DL+ N KIM V IK Y NAFVI Sbjct: 63 TQDYKDIAGSDVVIVTAGLPRKPGMS-----RDDLIATNSKIMTSVAEGIKQYASNAFVI 117 Query: 129 NITNPLDVMVAALQESSGLPHHRICGMAGMLDSSRFRRMIADKLEVSPRDVQGMVIGVHG 188 I+NPLD MV Q+ +G+P +R+ G AG+LDS+RF+ IA +L VS +DV M +G HG Sbjct: 118 IISNPLDAMVTLCQKITGMPANRVVGQAGVLDSARFKAFIAWELGVSVKDVSAMTLGGHG 177 Query: 189 DHMVPLSRYATVNGIPLSEFV--KKGWIKQEEV-DDIVQKTKVAGGEIVRLLGQGSAYYA 245 D MVPL RYA VNGIP+ E + K G K +EV + +V +T++AGGE+V LL GSA+Y+ Sbjct: 178 DDMVPLVRYAAVNGIPVMELLEQKYGAEKAKEVMEAMVNRTRLAGGEVVALLKTGSAFYS 237 Query: 246 PGASAIQMAESYLKDRKRVMVCSCYLQGQYGVQNHYLGVPCVIGGRGVEKIIELELTAQE 305 P +SAI MAES LKD+KRV+ C L G++GV +Y+GVP V+G GVEKI++ +L A E Sbjct: 238 PASSAIAMAESVLKDQKRVLPTCCLLNGEFGVNGYYVGVPAVLGASGVEKILQFKLDATE 297 Query: 306 RQELQGSIDEVKEMQKAIAAL 326 + + S+ VK + ++ ++ Sbjct: 298 QAMMDKSVAAVKGLVDSLDSI 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: 342 Number of extensions: 11 Number of successful extensions: 3 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: 321 Length adjustment: 28 Effective length of query: 302 Effective length of database: 293 Effective search space: 88486 Effective search space used: 88486 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 24 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