Align Sugar ABC transporter permease (characterized, see rationale)
to candidate RR42_RS22885 RR42_RS22885 sugar ABC transporter permease
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__Cup4G11:RR42_RS22885 Length = 288 Score = 149 bits (376), Expect = 7e-41 Identities = 89/275 (32%), Positives = 145/275 (52%), Gaps = 11/275 (4%) Query: 12 RLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVS----YWIENPDFSNYAAVLNQAS 67 R G ++ V + FPFY+ ++T+ K L + + + P N + + Sbjct: 18 RFGHVAILAVFAGFCAFPFYWMLITTFKDVHDLINTANNPFLFNQPPTLDNLRVLFLETQ 77 Query: 68 FLRAIGNSLVVALCVVTLALFLSLTAAYALGRVK-FRGRGTVLMMVLGVSMFPQVAVLSG 126 +LR I N+L+V VV + L L++ A Y+L R+ RGR + + L + P + Sbjct: 78 YLRWIANTLLVGAMVVAITLLLAVPAGYSLARLAGSRGRQLAIAIFL-TYLIPPTILFIP 136 Query: 127 LFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLT 186 +I ALGL ++ W+L+L Y FT+PF W++ F +P ++EEAA+MDG S + Sbjct: 137 FSRIIGALGLQDSLWSLVLVYPSFTVPFCTWLMMGFFKAVPRDIEEAAMMDGLSRFGAFL 196 Query: 187 RVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIA--LISGGSPHELPW 244 +V++PL ++T + EF++ALTF + +Q TV V + L+ G W Sbjct: 197 KVVVPLSSAGILTVVIFTLTLVMQEFVYALTFITSSSQYTVSVGVPTFLVRGDVYF---W 253 Query: 245 GLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALK 279 G LM A +VV+VP+ +L +F R V+G T GA+K Sbjct: 254 GSLMGACLVVSVPVAVLYNLFVDRFVAGFTVGAVK 288 Lambda K H 0.329 0.141 0.433 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: 217 Number of extensions: 8 Number of successful extensions: 4 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: 280 Length of database: 288 Length adjustment: 26 Effective length of query: 254 Effective length of database: 262 Effective search space: 66548 Effective search space used: 66548 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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