Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate WP_012404619.1 BPHY_RS26900 lactate utilization protein C
Query= uniprot:A0A0C4YFN9 (234 letters) >NCBI__GCF_000020045.1:WP_012404619.1 Length = 235 Score = 293 bits (750), Expect = 2e-84 Identities = 151/227 (66%), Positives = 177/227 (77%), Gaps = 2/227 (0%) Query: 4 LSARERMLGRLRAAAPATTA--DASQLDARIDAHYDARREAATPAELAQAMQAALGASHA 61 ++ARERMLGRLRAA P + D +LDA ID HYD RR A L ++MQAAL ASHA Sbjct: 1 MNARERMLGRLRAAVPTHVSGDDLKRLDAGIDLHYDGRRVTAPTQTLVESMQAALQASHA 60 Query: 62 LAWCASAEAWPAQLAGKLAAAGVRRLLLDPAAEQGAALMRALPASVAPLSYARPIEAWKA 121 A+ WPA LA +L A V+R+LLD + +GAAL +AL SVA +Y +PIE WKA Sbjct: 61 DVIRATERTWPALLAQRLLDANVKRVLLDTSRAEGAALHQALAPSVATRNYDQPIENWKA 120 Query: 122 ELFDTVDAGFTVARSGIAATGTLVLAPDAQTPRTVSLVPPLHIALVYAETLHPDLHCAAR 181 ELFDT+DAGFTVARSG+AATGTL++APDA +PRT+SLVPP+HIALVYA TLH DLH A R Sbjct: 121 ELFDTIDAGFTVARSGLAATGTLIVAPDAGSPRTMSLVPPVHIALVYAHTLHADLHAAMR 180 Query: 182 AERWSAGMPTNLVLVSGPSKTSDIQQTLAYGAHGPRELWVIIVTGSA 228 AE+W AGMPTNLV++SGPSKTSDIQQTLAYGAHGPRELWV+IV A Sbjct: 181 AEQWQAGMPTNLVMISGPSKTSDIQQTLAYGAHGPRELWVVIVEHQA 227 Lambda K H 0.317 0.127 0.375 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: 266 Number of extensions: 4 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: 234 Length of database: 235 Length adjustment: 23 Effective length of query: 211 Effective length of database: 212 Effective search space: 44732 Effective search space used: 44732 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: 41 (21.7 bits) S2: 46 (22.3 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