Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate WP_009156708.1 SACMADRAFT_RS25300 lactate utilization protein C
Query= uniprot:A0A0C4YFN9 (234 letters) >NCBI__GCF_000244955.1:WP_009156708.1 Length = 199 Score = 79.7 bits (195), Expect = 4e-20 Identities = 78/231 (33%), Positives = 101/231 (43%), Gaps = 43/231 (18%) Query: 5 SARERMLGRLRAAAPATTADASQLDARIDAHYDARREAATPAELAQAMQAALGASHALAW 64 SARE +L R+RAA A + + Y R A P AL A + Sbjct: 3 SAREEILVRIRAAGAARSVT-------VPREYRRERRVADPV--------ALFAERVADY 47 Query: 65 CASAEAWPAQLAGK-LAAAGVRRLLLDPAAEQGAALMRALPASVAPLSYARPIEAWKAE- 122 A P +L G+ L A GVR + A+PA V P + P W A+ Sbjct: 48 RAVVRRGPVELIGECLRARGVRTM--------------AVPADV-PAHWRAPGVRWLADD 92 Query: 123 ------LFDTVDAGFTVARSGIAATGTLVL-APDAQTPRTVSLVPPLHIALVYAETLHPD 175 + D VD T IA TGT+VL A AQ R +SLVP H+ +V A+ + + Sbjct: 93 PPLELAVVDGVDGVLTGCAVAIAETGTIVLDAGQAQGRRLLSLVPDYHLCVVRADQI--E 150 Query: 176 LHCAARAERWSAGMPTNLVLVSGPSKTSDIQQTLAYGAHGPRELWVIIVTG 226 + A R P L VSGPS TSDI+ G HGPR L V++V G Sbjct: 151 VTVAQALARLDPVRP--LTFVSGPSATSDIELDRVEGVHGPRTLEVLVVAG 199 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: 144 Number of extensions: 8 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: 199 Length adjustment: 22 Effective length of query: 212 Effective length of database: 177 Effective search space: 37524 Effective search space used: 37524 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: 45 (21.9 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