Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PfGW456L13_3040 Various polyols ABC transporter, permease component 2
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3040 Length = 276 Score = 148 bits (373), Expect = 1e-40 Identities = 87/252 (34%), Positives = 130/252 (51%), Gaps = 5/252 (1%) Query: 4 LITRCAVWGVGIVLVLVAVFPLLWALLNSVKTLLDIVTPTPRFLFTPTLENYRQVIGSPE 63 L+ W + I++ FP+ W +L S KT +D P+F+F PTLENY + + Sbjct: 12 LLLGTLAWAIAILIF----FPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHINERSD 67 Query: 64 VLVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLSLRFLPPVAVAIPL 123 NS VI SA L + VPAAY +A Y R ++LS + LPPV V +P+ Sbjct: 68 YFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTRGTLLWMLSTKMLPPVGVLMPI 127 Query: 124 IAIWVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYGPYAVFWK 183 + GL DTR ++IV Y L L + W+ F+ +PR+I EAA LDG + Sbjct: 128 YLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPRDILEAARLDGATLAQEMLR 187 Query: 184 IALPNCATTLLGGIIFSFVLVWNELMIALALTSSNSATLPVVASAFTSMGQEVPWGVINA 243 + LP L ++ S +L WNE +L LTSS +A L + ++++S + + W ++A Sbjct: 188 VLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSS-PEGLFWAKLSA 246 Query: 244 STVLLALPPLIF 255 + L P LIF Sbjct: 247 VSTLACAPILIF 258 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: 204 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: 270 Length of database: 276 Length adjustment: 25 Effective length of query: 245 Effective length of database: 251 Effective search space: 61495 Effective search space used: 61495 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 Apr 09 2024. 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