Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Burk376:H281DRAFT_03228 Length = 383 Score = 369 bits (947), Expect = e-107 Identities = 205/375 (54%), Positives = 265/375 (70%), Gaps = 20/375 (5%) Query: 1 MASVTLRNIRKAY-DENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGD 59 MAS++LR ++KAY D V+RD++L+I + EF VF+GPSGCGKSTL+RMIAGLED++ GD Sbjct: 1 MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 LTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAK 119 L I G +NDV A+RG+AMVFQSYAL+PHMT+++NMAFGLKLA T K EID VR AA+ Sbjct: 61 LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120 Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 IL ++ LL+R+PK LSGGQRQRVAIGRAI R+P VFLFDEPLSNLDA LR + R+E ARL Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HDEL-KTTMIYVTHDQVEAMTLADKIVVLSA-------GNLEQVGSPTMLYHAPANRFVA 231 H + K +++YVTHDQ+EAMTLADKIV+L A G++ Q+G+P LYH P +RFVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240 Query: 232 GFIGSPKMNFMEGVVQSVTHDGVTVRYE-TGETQRVAVEPAAVKQGDKVTVGIRPEHLHV 290 GFIGSP+MNF+ G + SV GV V + T E RV + AA++ VT+G+RPEHL Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300 Query: 291 ----GMAEDGISARTMA-VESLGDAAYLYAESSVAPDG--LIARIPPLERHTKGETQKLG 343 +D + +RT++ VE LG+ +Y++ + P G LIA+ P R G+ L Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQ---PGGVALIAKAPGDTRLAPGDRANLR 357 Query: 344 ATPEHCHLFDSAGKA 358 HLF G A Sbjct: 358 VPRHATHLFTEDGFA 372 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: 457 Number of extensions: 21 Number of successful extensions: 5 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: 383 Length adjustment: 30 Effective length of query: 339 Effective length of database: 353 Effective search space: 119667 Effective search space used: 119667 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