Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 211 bits (536), Expect = 4e-59 Identities = 127/287 (44%), Positives = 178/287 (62%), Gaps = 14/287 (4%) Query: 9 LAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVV 68 L + Y G L L I +GEFV LLGPSG GKS++LR++AGL+D G + GT + Sbjct: 8 LTRRY-GAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRDGTDL 66 Query: 69 NDLPARERNVAMVFQNYALYPHMSVYDNIAFGLR---RLKRPAA-EIDRRVREVAALLNL 124 LPA+ R++ +VFQ+YAL+PHM+V DNIAFGLR R +RP+ +I RV ++ + L Sbjct: 67 LALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQL 126 Query: 125 EALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRL 184 E L R P +SGGQ+QR A+ARA+ PS+ L DEP LDA++R LR ++ L + L Sbjct: 127 EELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRSL 186 Query: 185 RTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLS 244 TTV VTHDQ EA+ LADRV++M GRI Q G+P+E+YR P F GF+G N + Sbjct: 187 GLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVG--RANRIR 244 Query: 245 GTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIA 291 G V+R +L + + L G+ R ++ +RP+H+ +A Sbjct: 245 GHVERD--RLHLGGHSFQGELPGDLAGR-----EIEAWLRPEHLALA 284 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: 380 Number of extensions: 13 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: 384 Length adjustment: 31 Effective length of query: 375 Effective length of database: 353 Effective search space: 132375 Effective search space used: 132375 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