Align Putative L-lactate dehydrogenase, Fe-S oxidoreductase subunit YkgE (characterized, see rationale)
to candidate WP_027458587.1 K420_RS0113820 (Fe-S)-binding protein
Query= uniprot:A0A0C4YIN5 (262 letters) >NCBI__GCF_000519045.1:WP_027458587.1 Length = 261 Score = 288 bits (738), Expect = 6e-83 Identities = 153/263 (58%), Positives = 185/263 (70%), Gaps = 14/263 (5%) Query: 7 PPAPAQVYLFATCLVDMFVPQAGLDAVRLLEREGLTVHFPRGQSCCGQPAYSSGNPEQAR 66 P P VY FATC+VD F P AG+DA+ LLER+G+ VHFP Q+CCGQPAY+SG P++AR Sbjct: 5 PARPTDVYFFATCVVDQFFPGAGMDAITLLERQGIRVHFPEEQTCCGQPAYTSGFPDEAR 64 Query: 67 AVALAQLDLFAEPWPVIVPSGSCAGMMRHHWPQLFAQDPVAGPKAALLAERVYELSEFLL 126 VA QL LF WPV+VPSGSCAGMM+HH+P LFAQDPV AA L+ R+YE ++FL+ Sbjct: 65 KVAAHQLTLFPNDWPVVVPSGSCAGMMKHHYPTLFAQDPVRQAAAAKLSARIYEFTQFLV 124 Query: 127 HVLKVRFDVSGVAGQPPETVVLHTSCAARREMGTRDHGVALVDALPGVTRTEHQRESECC 186 VL + + G TVVLHTSC+ARREMG G L+ L VT + ESECC Sbjct: 125 DVLNFKPEDVG----SDCTVVLHTSCSARREMGVHLTGRKLLGDLNHVTIAQQDHESECC 180 Query: 187 GFGGTFSLKHPDISGAMVQDKIASACATGCDRLVSADCGCLLNI-GHAA---RHQG---A 239 GFGGTFS+K P+IS AMV+DK+ S ATG +R+VSADCGCL+NI GHAA + +G Sbjct: 181 GFGGTFSVKQPEISAAMVEDKVKSLKATGAERVVSADCGCLMNILGHAAWKDQQEGRTTP 240 Query: 240 PLPVEHIASFLWRRTGGAAKEQA 262 LP EHIA+FL RRT AKE A Sbjct: 241 SLPGEHIATFLLRRT---AKENA 260 Lambda K H 0.323 0.136 0.433 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: 290 Number of extensions: 4 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: 262 Length of database: 261 Length adjustment: 25 Effective length of query: 237 Effective length of database: 236 Effective search space: 55932 Effective search space used: 55932 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 (22.0 bits) S2: 47 (22.7 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