Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate PP_1722 PP_1722 ABC transporter, ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Putida:PP_1722 Length = 329 Score = 228 bits (582), Expect = 2e-64 Identities = 120/236 (50%), Positives = 156/236 (66%), Gaps = 1/236 (0%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 M+ + Q L K YAG P V +D HI GEFV LLGPSGCGKST+LR IAGL + G Sbjct: 1 MSFVSVQKLQKSYAGSP-VFERIDCHIERGEFVTLLGPSGCGKSTLLRCIAGLTSVDSGQ 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + + G + L ++R + MVFQ+YAL+P+M+V N+AFGLR K A E RVREV Sbjct: 60 ILLDGHDIVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVKADESQLRVREVLE 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 L+ L R P +SGGQ QR A+AR+++ P + L DEPLS LDA++R LR I+ + Sbjct: 120 LVELGKFAGRYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRAI 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIG 236 + L TT++VTHDQ EA+T++DR+ LM GRIVQ+G LY P +LFAAGFIG Sbjct: 180 QRELGLTTIFVTHDQEEALTMSDRIFLMNQGRIVQSGDAETLYTAPVDLFAAGFIG 235 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: 329 Number of extensions: 11 Number of successful extensions: 1 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: 329 Length adjustment: 30 Effective length of query: 376 Effective length of database: 299 Effective search space: 112424 Effective search space used: 112424 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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