Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 196 bits (499), Expect = 5e-55 Identities = 115/320 (35%), Positives = 182/320 (56%), Gaps = 10/320 (3%) Query: 13 VPPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQ 72 +P G S ++ +G+L V+ +LYL+F L+ G F S N MN+LR Sbjct: 8 LPQGKSVSLKQFVSRHINEIGLLVVIAILYLVFS-----LNAPG---FISLNNQMNVLRD 59 Query: 73 VAINLVLAAGMTFVILTAGIDLSVGSVLA-VSAVLGMQVSLGAAPGWAIPMFIFSGLVMG 131 A + A MT +I++ ID+SVG ++A VS L + A + + G +MG Sbjct: 60 AATIGIAAWAMTLIIISGEIDVSVGPMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMG 119 Query: 132 MVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWL 191 + G + + N+ +FV TLG +A RG + + V ++ +W+G G FL VP Sbjct: 120 TLAGVLRGVFNVPSFVATLGLWSALRGMGLFMTNALPVPIDENEVLDWLG-GQFLGVPVS 178 Query: 192 IWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAG 251 + + + L I RKT G ++A+GGN AA+L GI V V + ++++SGL + + G Sbjct: 179 ALIMIVLFALFVFISRKTAFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTG 238 Query: 252 AMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTIL 311 + A+RL N +G E D IAAVV+GGT+L GG GS++GT++G L+I ++ NGL +L Sbjct: 239 ILLAARLGSGNAGAANGLEFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLL 298 Query: 312 GLSSFWQYVAKGAVIVLAVI 331 G++SF+Q V +G +IV+AV+ Sbjct: 299 GINSFFQQVVRGVIIVVAVL 318 Lambda K H 0.324 0.138 0.417 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: 312 Number of extensions: 12 Number of successful extensions: 2 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: 344 Length of database: 332 Length adjustment: 28 Effective length of query: 316 Effective length of database: 304 Effective search space: 96064 Effective search space used: 96064 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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