Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 375 bits (963), Expect = e-108 Identities = 202/375 (53%), Positives = 260/375 (69%), Gaps = 11/375 (2%) Query: 1 MASVTLRNIRKAY-DENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGD 59 MAS+TLR +KAY D V+R+++LDI + EF VF+GPSGCGKSTL+R IAGLED++ GD Sbjct: 1 MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD 60 Query: 60 LTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAK 119 L I G RVNDV A+R +AMVFQSYAL+PHMT+Y+NM+FGL LA K EI+ VR AA+ Sbjct: 61 LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR 120 Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 IL ++ LL RKPK+LSGGQRQRVAIGRAI R+P VFLFDEPLSNLDA LR + R+E ARL Sbjct: 121 ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL 180 Query: 180 HDEL-KTTMIYVTHDQVEAMTLADKIVVLSA-------GNLEQVGSPTMLYHAPANRFVA 231 H + + +++YVTHDQVEAMTLAD+IV+L A G++ QVG+P LYH P NRFVA Sbjct: 181 HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA 240 Query: 232 GFIGSPKMNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVG 291 GFIGSP+MNF+ V V +G+ VR E + A++ G VTVG+RPEH+ +G Sbjct: 241 GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG 300 Query: 292 -MAEDGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCH 350 + GI + VE LG+ Y++ + A L+A+ R T+GE ++ P + Sbjct: 301 SQGQYGIHREVVLVERLGEQTYVHLDEP-AGQPLVAKAAGDARITRGERVRVAIAPACAY 359 Query: 351 LFDSAGKAFQRKIVE 365 LFD G A R V+ Sbjct: 360 LFDQDGLALTRTQVQ 374 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: 415 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