Align Fructose import permease protein FruF (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 177 bits (448), Expect = 4e-49 Identities = 106/310 (34%), Positives = 172/310 (55%), Gaps = 11/310 (3%) Query: 24 SIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAG 83 S++A ++L+ I + +F ++ L +LQ+++ ++A GMTLVI T+G Sbjct: 22 SLIALLVLIAIVSTMSPNFFTVN----------NLFNILQQTSVNAIMAVGMTLVILTSG 71 Query: 84 IDLSVGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTL 143 IDLSVGS++A+ GA A + +N +++ ALA+G AIG V G +V+ +Q FI TL Sbjct: 72 IDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATL 131 Query: 144 IMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIVILVGLLCR 203 +MML RG+ V T+G + + WF G LGIP I I+ + + Sbjct: 132 VMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFLAAWYMLH 191 Query: 204 KTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTG 263 T +G I A+G N+ A+R++GI K+ +VY++ G LA++AG+ A + G Sbjct: 192 HTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPT-AG 250 Query: 264 QDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVV 323 E+ AI AVV+GGTSL GGK + G+ +GA+I+ + + LGV++ AVV+ Sbjct: 251 TGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVI 310 Query: 324 IVICVMQAPK 333 ++ ++ K Sbjct: 311 LLAVLVDNKK 320 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: 302 Number of extensions: 15 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: 321 Length adjustment: 28 Effective length of query: 328 Effective length of database: 293 Effective search space: 96104 Effective search space used: 96104 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