Align Fructose import permease protein FruF (characterized)
to candidate H281DRAFT_02175 H281DRAFT_02175 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Burk376:H281DRAFT_02175 Length = 353 Score = 157 bits (397), Expect = 4e-43 Identities = 96/311 (30%), Positives = 165/311 (53%), Gaps = 21/311 (6%) Query: 25 IVAFILLVIICTIFQHDFLAL-SWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAG 83 ++ + +V+ IF F +L ++N N L + +++ GMTLV++T G Sbjct: 55 VIVLLAMVLFNLIFTPHFWSLQTFNVN-----------LTQVVTIVIVGIGMTLVVATGG 103 Query: 84 IDLSVGSVMAVAGAAAMQTLSN---GMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFI 140 IDLSVG+ MA++GA A N + L+ ++ + G NG LV+ L +QP + Sbjct: 104 IDLSVGASMAISGALAPMLFLNIPVPGGIALAFVLPVLAAALCGVFNGLLVTRLAVQPIV 163 Query: 141 TTLIMMLAGRGMAKVITSGENTDASAVAGNEP-LKWFANGFILGIPANFVIAVIIVILVG 199 TL++ +AGRG+A+V+T G S A N P +W A G + G+P ++ + +V+ Sbjct: 164 ATLVLFIAGRGIAQVVTDG-----SLQAFNTPAFQWIALGKVAGVPFQVLLMLALVVAFA 218 Query: 200 LLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDV 259 + RKT G + G N++A+ ++G+ + + Y + LA +AGL + + D Sbjct: 219 WVVRKTLFGQYLLITGGNEKAAYLSGVPTASVKLIAYTLCAALAGLAGLISISVNSSSDA 278 Query: 260 VKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFF 319 G +E+ AI AV +GGT+L GGK + G+ VGA+II ++R T++ G+ A Sbjct: 279 NVVGLGIELDAIAAVAVGGTALTGGKAFIGGTLVGALIIQLLRYTLLAHGIPDAAALVVK 338 Query: 320 AVVVIVICVMQ 330 A +++ +Q Sbjct: 339 AGIIVAAVYVQ 349 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: 312 Number of extensions: 19 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: 353 Length adjustment: 29 Effective length of query: 327 Effective length of database: 324 Effective search space: 105948 Effective search space used: 105948 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