Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 204 bits (520), Expect = 3e-57 Identities = 107/221 (48%), Positives = 146/221 (66%), Gaps = 4/221 (1%) Query: 20 LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79 L PL+L I +GE + LLGPSG GK+T+LR+IAGLE G + G V + R+R V Sbjct: 18 LSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFGNRDVTQVHVRDRRVG 77 Query: 80 MVFQNYALYPHMSVYDNIAFGLR---RLKRPA-AEIDRRVREVAALLNLEALLERKPRAM 135 VFQNYAL+ HM+V DN+AFGL + +RP+ AEI +RV + ++ L L +R P + Sbjct: 78 FVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLEMVQLGHLAQRYPEQL 137 Query: 136 SGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQ 195 SGGQ+QR A+ARA+ P V L DEP LDAK+R +LR ++ LH L+ T+V+VTHDQ Sbjct: 138 SGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKFTSVFVTHDQ 197 Query: 196 LEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIG 236 EA+ L+DRV++M +G I Q +P ELY P + F F+G Sbjct: 198 DEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLG 238 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: 324 Number of extensions: 7 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: 406 Length of database: 376 Length adjustment: 31 Effective length of query: 375 Effective length of database: 345 Effective search space: 129375 Effective search space used: 129375 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: 50 (23.9 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