Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.110) (characterized)
to candidate WP_012592569.1 MSIL_RS18370 electron transfer flavoprotein subunit beta/FixA family protein
Query= BRENDA::H6LBB0 (264 letters) >NCBI__GCF_000021745.1:WP_012592569.1 Length = 283 Score = 173 bits (439), Expect = 3e-48 Identities = 99/264 (37%), Positives = 153/264 (57%), Gaps = 7/264 (2%) Query: 1 MKILVCIKQVPGTSNVEVDPETGVLIRDGVESKLNPYDLFGLETAFRLKEQLGGTITTLS 60 M ILVCIKQVP ++ + ++P T ++R GV + +NPYDLF LE A RL++Q GG +T L+ Sbjct: 1 MHILVCIKQVPDSAQIRINPVTQTIMRQGVPTIINPYDLFSLEEALRLRDQFGGEVTVLT 60 Query: 61 MGPMQSKEVLMESFYMGADEGCLLSDRKFGGADVVATSYTLAQG----TKRLGDFDLIIC 116 MGP + + L ++ +GAD LL+DR F G+D +ATS+ L Q ++ G D++ Sbjct: 61 MGPPMASDSLRKALAIGADRAVLLTDRFFAGSDTLATSFALTQAIVKISETFGAPDIVFT 120 Query: 117 GKQTTDGDTAQVGPEMAEFLGIPHVTNVIKILAA--DEKGLTLQMNMEESLEIQRVPYPC 174 GKQT DGDTAQVGP +A+ L + +T V KI+ D++ + ++ E + + + PC Sbjct: 121 GKQTIDGDTAQVGPGIAKRLDLLQLTYVAKIVECNPDKREIIVERRSEGGVHVLKTKLPC 180 Query: 175 LITVDKDIYTPRLPSYKRKLDISKNPEIKILTLKDMYDTNEKKYGLSGSPTQVERIFPPE 234 LIT+ + R + K L ++ EI + KD + K GL GSPT V+++F P Sbjct: 181 LITMLEGSNEVRRGAMKDALRAAR-AEIVTWSAKDAGIADITKCGLKGSPTVVKKVFAPP 239 Query: 235 SNVEKTSFEGDGKVLAKALLGILT 258 E+ F V ++ ++T Sbjct: 240 PRSERAFFVPTADVASQEAENLIT 263 Lambda K H 0.316 0.137 0.386 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: 182 Number of extensions: 7 Number of successful extensions: 4 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: 264 Length of database: 283 Length adjustment: 25 Effective length of query: 239 Effective length of database: 258 Effective search space: 61662 Effective search space used: 61662 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 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