Align Inner-membrane translocator (characterized, see rationale)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 182 bits (462), Expect = 1e-50 Identities = 107/308 (34%), Positives = 185/308 (60%), Gaps = 14/308 (4%) Query: 66 LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDL 125 L+AL +L+ + +FF I+ +L +IL +++ A++++GM+LVI T GIDL Sbjct: 23 LIALLVLIAIVSTLSPNFFTIN--------NLFNILQQTSVNAIMAVGMTLVILTSGIDL 74 Query: 126 SVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLLL 185 SVG+++A+ GAV A+++ + +++ + +AA L +G G + G +V+ +Q +ATL++ Sbjct: 75 SVGSLLALTGAVAASIVGI-EVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVM 133 Query: 186 MVAGRGVAQLINQGQII----TFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKT 241 M+ RGV + G + T F G+G+ LG+P PVWI+ + + +L T Sbjct: 134 MLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHT 193 Query: 242 ALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLW 301 LG +I A+G N A+R GIN IK+ Y + GL A+LAG+I A + + AG Sbjct: 194 RLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQP-TAGTG 252 Query: 302 LELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILT 361 ELDA+ AVV+GG +L GG+ ++ +++GALI+ L + + G+ + + +++KA+VIL Sbjct: 253 YELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILL 312 Query: 362 VLLLQSAK 369 +L+ + K Sbjct: 313 AVLVDNKK 320 Lambda K H 0.323 0.136 0.379 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: 283 Number of extensions: 19 Number of successful extensions: 4 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: 405 Length of database: 321 Length adjustment: 29 Effective length of query: 376 Effective length of database: 292 Effective search space: 109792 Effective search space used: 109792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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