Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Burk376:H281DRAFT_02629 Length = 381 Score = 379 bits (974), Expect = e-110 Identities = 203/373 (54%), Positives = 263/373 (70%), Gaps = 12/373 (3%) Query: 1 MASVTLRNIRKAYDENE-VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGD 59 MA+++LR I+K +D N V+RD+NL+I + EF VF+GPSGCGKSTL+R++AGLED + GD Sbjct: 1 MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60 Query: 60 LTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAK 119 ++I G +N V A+RG+AMVFQSYAL+PHMT+Y+NMAFGLKLA T K EID VR AA Sbjct: 61 VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120 Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 +L +D LL RKP++LSGGQRQRVAIGRAI R+P VFLFDEPLSNLDAALR + R+E ARL Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180 Query: 180 HDE-LKTTMIYVTHDQVEAMTLADKIVVLSA-------GNLEQVGSPTMLYHAPANRFVA 231 H + +++YVTHDQ+EAMTLADKIV+L A G++ Q+G+P LYH P ++FVA Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240 Query: 232 GFIGSPKMNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVG 291 GFIGSP+MNF++GVV+ + D V V G RV V+ +K G +VT+GIRPEH+ Sbjct: 241 GFIGSPRMNFIDGVVERIADDSVEVSM-PGTALRVLVDGRRLKPGQRVTLGIRPEHVRFD 299 Query: 292 MAEDGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHL 351 ++ + E LG+ +YL+A+ A LIA+ P GE L + CHL Sbjct: 300 GGTQTLAVNALLTEQLGEHSYLHADH--AGGTLIAKAPGDLHVRNGERLALHLPADACHL 357 Query: 352 FDSAGKAFQRKIV 364 FD G A R IV Sbjct: 358 FDEDGIALHRTIV 370 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: 451 Number of extensions: 17 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: 381 Length adjustment: 30 Effective length of query: 339 Effective length of database: 351 Effective search space: 118989 Effective search space used: 118989 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