Align ABC transporter for D-Sorbitol, periplasmic substrate-binding component (characterized)
to candidate GFF1305 PGA1_c13210 extracellular solute-binding protein
Query= reanno::Phaeo:GFF1305 (433 letters) >FitnessBrowser__Phaeo:GFF1305 Length = 433 Score = 883 bits (2281), Expect = 0.0 Identities = 433/433 (100%), Positives = 433/433 (100%) Query: 1 MYLKSALRAATALTVFASTAAFADTITIATVNNGDMIRMQGLTEDFTAKTGHEVEWVTLE 60 MYLKSALRAATALTVFASTAAFADTITIATVNNGDMIRMQGLTEDFTAKTGHEVEWVTLE Sbjct: 1 MYLKSALRAATALTVFASTAAFADTITIATVNNGDMIRMQGLTEDFTAKTGHEVEWVTLE 60 Query: 61 ENVLRQRVTTDISAKGGQFDIMTIGMYETPIWGKNGWLVPLNDLPADYDVDDILPAMRGG 120 ENVLRQRVTTDISAKGGQFDIMTIGMYETPIWGKNGWLVPLNDLPADYDVDDILPAMRGG Sbjct: 61 ENVLRQRVTTDISAKGGQFDIMTIGMYETPIWGKNGWLVPLNDLPADYDVDDILPAMRGG 120 Query: 121 LSHDGTLFAAPFYGESSMIMYRTDLMEKAGLEMPAAPTWDFVADAARQMTDKDNETYGIC 180 LSHDGTLFAAPFYGESSMIMYRTDLMEKAGLEMPAAPTWDFVADAARQMTDKDNETYGIC Sbjct: 121 LSHDGTLFAAPFYGESSMIMYRTDLMEKAGLEMPAAPTWDFVADAARQMTDKDNETYGIC 180 Query: 181 LRGKAGWGENAAFITAMSNSFGARWFDENWAPQFDSEAWSNTLNFYINLLNDAGPPGASN 240 LRGKAGWGENAAFITAMSNSFGARWFDENWAPQFDSEAWSNTLNFYINLLNDAGPPGASN Sbjct: 181 LRGKAGWGENAAFITAMSNSFGARWFDENWAPQFDSEAWSNTLNFYINLLNDAGPPGASN 240 Query: 241 NGFNENLSLFQQGKCGMWIDATVAASFVTNPNDSTVADKVGFALAPDTGLGKRSNWLWAW 300 NGFNENLSLFQQGKCGMWIDATVAASFVTNPNDSTVADKVGFALAPDTGLGKRSNWLWAW Sbjct: 241 NGFNENLSLFQQGKCGMWIDATVAASFVTNPNDSTVADKVGFALAPDTGLGKRSNWLWAW 300 Query: 301 ALAIPAGTQKEAAAKEFIQWATSKDYIELVAENEGWANVPPGARISLYENANYKDIPFAK 360 ALAIPAGTQKEAAAKEFIQWATSKDYIELVAENEGWANVPPGARISLYENANYKDIPFAK Sbjct: 301 ALAIPAGTQKEAAAKEFIQWATSKDYIELVAENEGWANVPPGARISLYENANYKDIPFAK 360 Query: 361 MTLESILSADPNNPTVDPVPYVGIQFAAIPEFAGIATQVGQEFSAALAGQQTAEEALAKA 420 MTLESILSADPNNPTVDPVPYVGIQFAAIPEFAGIATQVGQEFSAALAGQQTAEEALAKA Sbjct: 361 MTLESILSADPNNPTVDPVPYVGIQFAAIPEFAGIATQVGQEFSAALAGQQTAEEALAKA 420 Query: 421 QALTADEMEAAGY 433 QALTADEMEAAGY Sbjct: 421 QALTADEMEAAGY 433 Lambda K H 0.316 0.131 0.400 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: 905 Number of extensions: 19 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: 433 Length of database: 433 Length adjustment: 32 Effective length of query: 401 Effective length of database: 401 Effective search space: 160801 Effective search space used: 160801 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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