Align Fructose import permease protein FruF (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 162 bits (410), Expect = 1e-44 Identities = 101/303 (33%), Positives = 167/303 (55%), Gaps = 34/303 (11%) Query: 24 SIVAFILLVIICTIFQHDFLALS--WNSNTGGLAGPLITMLQESARYLMIATGMTLVIST 81 S++A I+L ++ ++ FL L+ WN ++++ + + I+ GMTLVI T Sbjct: 9 SLIALIILCLVLSLLSDRFLTLANGWN------------VMRQVSVNICISVGMTLVILT 56 Query: 82 AGIDLSVGSVMAVAGAAAMQTLSNG-----MNVWL------SILIALAVGLAIGCVNGAL 130 AGIDLSVGS++A+ GA + NG +N+ + ++++ + +G +G NG Sbjct: 57 AGIDLSVGSILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWT 116 Query: 131 VSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVI 190 ++ + PF+ TL M+ RG+ + T G + E + G+ LGIP I Sbjct: 117 ITRFKVPPFVATLAMLTIARGLTMLWTGGFPINGLG----EDFAFLGTGWFLGIPMPVWI 172 Query: 191 AVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFA 250 +IV L LL +KT G + A+G N+ A+R++GI ++ VYAI+G LAA+ G+ Sbjct: 173 TAVIVALAVLLTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIV 232 Query: 251 TASVMRVDVVK--TGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITL 308 T+ R+D + G E+ AI AVVIGGTSL GGK ++ G+ +G +II ++ ++ L Sbjct: 233 TS---RLDSAQPNAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLL 289 Query: 309 GVN 311 V+ Sbjct: 290 NVS 292 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: 337 Number of extensions: 26 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: 356 Length of database: 318 Length adjustment: 28 Effective length of query: 328 Effective length of database: 290 Effective search space: 95120 Effective search space used: 95120 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