Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 264 bits (675), Expect = 2e-75 Identities = 150/332 (45%), Positives = 215/332 (64%), Gaps = 27/332 (8%) Query: 25 AQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMT 84 A+W R+G+L VL+VL L L NF +N +NI R +++N +LAAGMT Sbjct: 19 AKWW-DRVGILIVLLVL--------LILMSTFAPNFNRVDNLLNIARSISVNAILAAGMT 69 Query: 85 FVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFSGL----VMGMVNGAMVAL 140 FVILT+GIDLSVGS++AVS V+ + ++ P P+ I +G+ + G++NG + A Sbjct: 70 FVILTSGIDLSVGSIVAVSGVVSVVAAMAGIPA---PLAILAGVGVGALCGLLNGVLTAY 126 Query: 141 LNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVL 200 L + F+VTLGTMT RG AY + +G ++++ + SF +GNG + +P + + + V L Sbjct: 127 LALAPFIVTLGTMTFLRGMAYTITEGQPIVSSSL-SFRELGNGYLIGIPIPVIIMLVVYL 185 Query: 201 LSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYG 260 L+W IL +T G HIYA+GGN QAARL G+RV VL VY I+G+ +GLAG + A+R+ Sbjct: 186 LAWFILERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVIS 245 Query: 261 ANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYV 320 A G+GYELDAIAAVVLGGTSL GG G I GT++G++I+GV++ GL +L + F Q + Sbjct: 246 AQPTAGTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLL 305 Query: 321 AKGAVIVLAVILDK----------WRQKDAAQ 342 KG VI+LAV +D WR+K+ A+ Sbjct: 306 IKGIVIILAVAIDGLKQHPELFTFWRKKEIAR 337 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: 331 Number of extensions: 10 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: 339 Length adjustment: 29 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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 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