Align dihydrolipoamide dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_090440669.1 BLS63_RS05065 dihydrolipoyllysine-residue acetyltransferase
Query= metacyc::MONOMER-18551 (613 letters) >NCBI__GCF_900100495.1:WP_090440669.1 Length = 553 Score = 100 bits (249), Expect = 2e-25 Identities = 61/129 (47%), Positives = 83/129 (64%), Gaps = 2/129 (1%) Query: 6 IKVPDIGDFDAVEVIEVLVAQGDTVKEEQSLITVESDKASMEIPSSAAGKVVSLSVKVGD 65 I+VPDIG + EVIE++V GD ++ +QSL+T+ESDKASMEIP+ AG + SL VK+GD Sbjct: 5 IRVPDIGSGEG-EVIELMVKVGDRIEADQSLLTLESDKASMEIPAPKAGVIKSLKVKLGD 63 Query: 66 KVSEGTVILMLEAAAAGAQAAASDKAAAQPAAKSEAAAQKPAASSAAAEQASAAADQRPA 125 ++ EG +L LE A A AA +AAA PAA +AAA P A+ AA +S P Sbjct: 64 RLKEGDELLELEVEGASAPAAQPAQAAA-PAAAPQAAAAAPVAAPAAPVASSVQDVHVPD 122 Query: 126 QAAADSSEV 134 +A ++V Sbjct: 123 IGSAGKAKV 131 Score = 98.6 bits (244), Expect = 6e-25 Identities = 71/164 (43%), Positives = 91/164 (55%), Gaps = 13/164 (7%) Query: 5 EIKVPDIGDFDAVEVIEVLVAQGDTVKEEQSLITVESDKASMEIPSSAAGKVVSLSVKVG 64 ++ VPDIG +VIEVLV GDTV+ +QSLIT+ESDKASMEIPS AAG V S+ VK+ Sbjct: 117 DVHVPDIGSAGKAKVIEVLVKAGDTVETDQSLITLESDKASMEIPSPAAGVVESVEVKLD 176 Query: 65 DKVSEGTVILMLEAAAAGAQAAASDKAAAQPAAKSEAAAQKPAAS-------SAAAEQAS 117 +V G +IL L+ AGA AAA+ AA PAA P A+ +A A+ A+ Sbjct: 177 AEVGTGDLILKLK--VAGAAAAAAPAAAPAPAAAPALHTTPPGAAPEVVAEVNAIAKLAA 234 Query: 118 AAADQRPAQAAADSSEVRYSPPASAPADGCDV---LVLGAGPGG 158 AAA P + + V P A V + G+GP G Sbjct: 235 AAASVAP-PTLSSGARVHAGPAVRQLARDFGVELGAIGGSGPKG 277 Lambda K H 0.314 0.131 0.364 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: 714 Number of extensions: 38 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 613 Length of database: 553 Length adjustment: 36 Effective length of query: 577 Effective length of database: 517 Effective search space: 298309 Effective search space used: 298309 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 53 (25.0 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