Align Fructose import permease protein FruF (characterized)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 179 bits (455), Expect = 7e-50 Identities = 104/271 (38%), Positives = 165/271 (60%), Gaps = 6/271 (2%) Query: 43 LALSWNSNTGGLAG--PLITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAM 100 L + ++ T AG L + Q+++ +++A GMT VI T GIDLSVGS+++++ AM Sbjct: 38 LCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAVVAM 97 Query: 101 QTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGE 160 LS+ AL GL G VNGALV+F+ L PFI TL + A RG+A+++ Sbjct: 98 LVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLV---- 153 Query: 161 NTDASAVAGNEPLKWFANGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEA 220 D++ + + NG +LG+P +IA +V + + R+T +G+ I AVG N EA Sbjct: 154 GNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEA 213 Query: 221 SRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTS 280 +R++GIK +L VYA+SG LA + G+ ++A + + ++ GQ E+ AI AV++GGTS Sbjct: 214 ARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTS 273 Query: 281 LLGGKFSLAGSAVGAVIIAMIRKTIITLGVN 311 +GG S+ G+ VGA+IIA++ ++ LGV+ Sbjct: 274 FVGGTGSIVGTLVGALIIAVLSNGLVLLGVS 304 Lambda K H 0.325 0.136 0.384 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: 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: 356 Length of database: 333 Length adjustment: 29 Effective length of query: 327 Effective length of database: 304 Effective search space: 99408 Effective search space used: 99408 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