Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 487 bits (1253), Expect = e-142 Identities = 247/339 (72%), Positives = 291/339 (85%) Query: 7 SATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSI 66 ++ S ++ + N + GLRAR+F P A QKLLAF SL+L+++FFSFASP FM++DN++ I Sbjct: 2 TSQSDTSALGNKKTFSGLRARVFTPTALQKLLAFGSLILLLVFFSFASPAFMQMDNMLGI 61 Query: 67 LQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFG 126 LQ+TAVNGVLAIACT+VIIT GIDLSVGT+MTF AV+ GV LT W +P+ G+ AAI G Sbjct: 62 LQATAVNGVLAIACTFVIITGGIDLSVGTLMTFTAVICGVFLTYWHLPMWTGVLAAIGTG 121 Query: 127 ALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIG 186 A+ G +SG + AK+K+PPFIATLGMMMLLKGLSLV+S +PIYF DTE F I+QDSLIG Sbjct: 122 AICGTVSGTLTAKMKIPPFIATLGMMMLLKGLSLVVSADKPIYFTDTENFYMISQDSLIG 181 Query: 187 DLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVY 246 DL+PSLP+PNAVLILF +A+ +SI LN+T GRYTFALGSNEEA+RLSGV VD WK+A+Y Sbjct: 182 DLLPSLPVPNAVLILFFLAVVSSITLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIY 241 Query: 247 TFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFI 306 SGAICGIAGL+IASRLNSAQPALGQGYEL+AIAAVVIGGTSLSGG GTILGTIIGAFI Sbjct: 242 GLSGAICGIAGLLIASRLNSAQPALGQGYELEAIAAVVIGGTSLSGGAGTILGTIIGAFI 301 Query: 307 MSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345 MSVL NGLRIMSVAQEWQ VVTG+IIILAVY DILRR++ Sbjct: 302 MSVLTNGLRIMSVAQEWQIVVTGLIIILAVYGDILRRKK 340 Lambda K H 0.326 0.139 0.398 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: 362 Number of extensions: 10 Number of successful extensions: 1 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: 347 Length of database: 341 Length adjustment: 29 Effective length of query: 318 Effective length of database: 312 Effective search space: 99216 Effective search space used: 99216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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