Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate RR42_RS12250 RR42_RS12250 sulfate ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Cup4G11:RR42_RS12250 Length = 374 Score = 217 bits (553), Expect = 4e-61 Identities = 124/338 (36%), Positives = 194/338 (57%), Gaps = 14/338 (4%) Query: 3 SVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTI 62 S+ ++N++K + + D+ LD +G+ +GPSGCGK+TL+R+IAGLE G + + Sbjct: 2 SIQVKNVQKHFGNFVALDDVTLDFDEGQLTALLGPSGCGKTTLLRIIAGLERADAGQILL 61 Query: 63 DGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKIL- 121 +G + +R + VFQ YAL+ HMT+++N+AFGL++ + +A +R+ + L Sbjct: 62 EGRDASHQHVRQRQVGFVFQHYALFKHMTVFENVAFGLRVKPRAERPGEAQIRDKVRALL 121 Query: 122 ---HIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178 +D L DR P QLSGGQRQR+A+ RA+ +P+V L DEP LDA +R ++R R Sbjct: 122 ELVQLDWLADRYPPQLSGGQRQRIALARALAVEPRVLLLDEPFGALDAKVRKELRRWLRR 181 Query: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238 LHDEL T ++VTHDQ EA+ +AD++V+++ G++EQ G+P +Y+ PA FV GF+G+ Sbjct: 182 LHDELHVTSVFVTHDQEEALEVADQVVLMNRGHVEQAGTPEAVYNHPATPFVFGFLGN-- 239 Query: 239 MNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHV---GMAED 295 +N G ++ G+ TG++ + GD V +RP L + D Sbjct: 240 VNLFHGRLEVGERGGL---LHTGDSILPVIGSGHETAGDAVAY-VRPHDLDLERYSPGTD 295 Query: 296 GISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLER 333 GI+ +LG A L E + +I PLER Sbjct: 296 GIAVTLRRALTLGPVAQLELEREDTQE-VIEVALPLER 332 Lambda K H 0.320 0.135 0.384 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: 364 Number of extensions: 14 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: 369 Length of database: 374 Length adjustment: 30 Effective length of query: 339 Effective length of database: 344 Effective search space: 116616 Effective search space used: 116616 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