Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 180 bits (456), Expect = 5e-50 Identities = 109/302 (36%), Positives = 174/302 (57%), Gaps = 9/302 (2%) Query: 40 VLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSV 99 V LL L ++G G F S EN +NI Q I L++A MT +I+T G+DLS+G+V Sbjct: 22 VWVLLLLSLGFSVTGPG---FLSVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGAV 78 Query: 100 LAV-SAVLGMQVSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRG 158 L + VL M + + A+ + +GL G++NGA+V+ L I FV TLGT+ +G Sbjct: 79 LTLCGVVLAMVMVATESLPLALGAALLTGLAFGLLNGALVSWLEIPPFVATLGTLGVAQG 138 Query: 159 AAYLLADGTTV--LNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIY 216 A + DG +V + IP I G L VP IW+A L +L T G +++ Sbjct: 139 LALVATDGQSVTGIGEAIPL---IYAGQLLGVPLPIWIAAVFYGLFHWLLYHTRFGAYVF 195 Query: 217 AIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAA 276 A+GGN +A + +G+R+ + L+ VY++ GL +G+A + +R+ + G E DAIAA Sbjct: 196 ALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAAIGLEFDAIAA 255 Query: 277 VVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWR 336 V +GGT+ G G + GTV+G L +GV+ NGL ++G+ S Q A G ++++ ++++ ++ Sbjct: 256 VAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAIGLLVLVVLLIESFK 315 Query: 337 QK 338 K Sbjct: 316 GK 317 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: 332 Number of extensions: 24 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: 344 Length of database: 318 Length adjustment: 28 Effective length of query: 316 Effective length of database: 290 Effective search space: 91640 Effective search space used: 91640 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