Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate RR42_RS22885 RR42_RS22885 sugar ABC transporter permease
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__Cup4G11:RR42_RS22885 Length = 288 Score = 119 bits (298), Expect = 7e-32 Identities = 78/256 (30%), Positives = 127/256 (49%), Gaps = 11/256 (4%) Query: 7 RCAVWGV--GIVLVLVA-----VFPLLWALLNSVKTLLDIV-TPTPRFLFT--PTLENYR 56 R A WG G V +L FP W L+ + K + D++ T FLF PTL+N R Sbjct: 11 RGARWGARFGHVAILAVFAGFCAFPFYWMLITTFKDVHDLINTANNPFLFNQPPTLDNLR 70 Query: 57 QVIGSPEVLVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLSLRFLPP 116 + + L + N+ ++ V + + VPA Y +AR R + + +PP Sbjct: 71 VLFLETQYLRWIANTLLVGAMVVAITLLLAVPAGYSLARLAGSRGRQLAIAIFLTYLIPP 130 Query: 117 VAVAIPLIAIWVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYG 176 + IP I LGL D+ +S+++ Y T+ TWL + F+ +PR+IEEAA +DG Sbjct: 131 TILFIPFSRIIGALGLQDSLWSLVLVYPSFTVPFCTWLMMGFFKAVPRDIEEAAMMDGLS 190 Query: 177 PYAVFWKIALPNCATTLLGGIIFSFVLVWNELMIALA-LTSSNSATLPVVASAFTSMGQE 235 + F K+ +P + +L +IF+ LV E + AL +TSS+ T+ V F G Sbjct: 191 RFGAFLKVVVPLSSAGILTVVIFTLTLVMQEFVYALTFITSSSQYTVSVGVPTFLVRGDV 250 Query: 236 VPWGVINASTVLLALP 251 WG + + +++++P Sbjct: 251 YFWGSLMGACLVVSVP 266 Lambda K H 0.327 0.142 0.434 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: 225 Number of extensions: 13 Number of successful extensions: 3 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: 270 Length of database: 288 Length adjustment: 26 Effective length of query: 244 Effective length of database: 262 Effective search space: 63928 Effective search space used: 63928 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 (21.7 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