Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 195 bits (495), Expect = 2e-54 Identities = 117/305 (38%), Positives = 177/305 (58%), Gaps = 15/305 (4%) Query: 42 YLLF-YGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVL 100 Y LF GL L + F + N +N+LRQ ++ +LA+G+T VILT G+DLSVG+ + Sbjct: 19 YRLFALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLSVGANV 78 Query: 101 AVSAVLGMQVS-------LGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTM 153 A+SA + V LG G + +G ++G+ NG +VA+L I F+ T G + Sbjct: 79 AMSACVAATVMKATGSTMLGVGAG------LGTGALIGLANGLLVAMLRIPPFIATYGML 132 Query: 154 TAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGM 213 G Y G T+ + P+F IG+G VP +++ + ++ + +KT G Sbjct: 133 WVLHGVTYWFMAGETI-HGFPPAFRAIGSGYLWGVPIPVYLMLVFLVAGTAMSQKTTYGQ 191 Query: 214 HIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDA 273 IYAIG N AARL+G+ V L+ VY +SG +G+A + +RL A G+ G L A Sbjct: 192 EIYAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDIGEALTLPA 251 Query: 274 IAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILD 333 IAAV++GGTSL GGVG + GT+VGA+I+ ++ NG+ +L +S+ WQ + G ++VLAV LD Sbjct: 252 IAAVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVIVVLAVFLD 311 Query: 334 KWRQK 338 +K Sbjct: 312 TLSRK 316 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: 327 Number of extensions: 20 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: 322 Length adjustment: 28 Effective length of query: 316 Effective length of database: 294 Effective search space: 92904 Effective search space used: 92904 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