Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Keio:14980 Length = 377 Score = 229 bits (583), Expect = 1e-64 Identities = 134/338 (39%), Positives = 193/338 (57%), Gaps = 10/338 (2%) Query: 6 LRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGM 65 +RN+ K+YD + D++L I GE +G SGCGKSTL+RM+AG E S G + +DG+ Sbjct: 22 IRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGV 81 Query: 66 RVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILHIDH 125 ++ V P R I M+FQSYAL+PHMT+ N+AFGLK K EI + V ++H+ Sbjct: 82 DLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQE 141 Query: 126 LLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKT 185 RKP QLSGGQRQRVA+ R++ ++PK+ L DEP+ LD LR +M+LE + + + Sbjct: 142 FAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGV 201 Query: 186 TMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFMEGV 245 T + VTHDQ EAMT+A +I +++ G Q+G P +Y P R+ A FIGS +N EGV Sbjct: 202 TCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS--VNVFEGV 259 Query: 246 VQSVTHDGVTVRYETGETQRVAVE-PAAVKQGDKVTVGIRPEHLHVGMAEDGISARTMAV 304 ++ DG+ V G + V+ A+V V V +RPE + + E + AV Sbjct: 260 LKERQEDGL-VLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIML-CEEPPANGCNFAV 317 Query: 305 ESLGDAAYL-----YAESSVAPDGLIARIPPLERHTKG 337 + AYL Y + + A++ RH KG Sbjct: 318 GEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKG 355 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: 347 Number of extensions: 11 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 339 Effective length of database: 347 Effective search space: 117633 Effective search space used: 117633 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