Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 138 bits (347), Expect = 2e-37 Identities = 89/220 (40%), Positives = 127/220 (57%), Gaps = 6/220 (2%) Query: 17 PPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGG-TVVNDLPARE 75 PPVL ++L+I G+ ++G SGCGKST+L+MIAGL S G +RI G TVV P+ + Sbjct: 22 PPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRINGKTVVK--PSAK 79 Query: 76 RNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAM 135 N M+FQ +LYP MSV +N A GL + DR V E+ ++ L ++ + + Sbjct: 80 WN--MMFQKPSLYPWMSVRENAALGLVFAGTYKQKQDR-VEELLDMVGLSEHKDKNVQEL 136 Query: 136 SGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQ 195 SGGQQQR A+AR++ P + L DEP S LDA R L+ ++ ++ T + VTHD Sbjct: 137 SGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQGITMIMVTHDI 196 Query: 196 LEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235 EA+ +AD+V++M G YPR+ AA FI Sbjct: 197 EEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236 Lambda K H 0.321 0.137 0.403 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: 193 Number of extensions: 12 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: 406 Length of database: 263 Length adjustment: 28 Effective length of query: 378 Effective length of database: 235 Effective search space: 88830 Effective search space used: 88830 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 (21.8 bits) S2: 48 (23.1 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