Align Fructose import permease protein FrcC (characterized)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 142 bits (357), Expect = 2e-38 Identities = 94/303 (31%), Positives = 154/303 (50%), Gaps = 9/303 (2%) Query: 52 LIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMV 111 LI +L L+A F + + + + + ++ Q +VILT IDLSV A + Sbjct: 13 LIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANLA 72 Query: 112 LSSVIMGQFTFRY-GFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170 L+ +++ G P + + +G+G L G NG LV ++++PP +VTLG I Sbjct: 73 LTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFRG 132 Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAW 230 FL S + + + ++S + F + +G V ++ + +L V L V+ RT Sbjct: 133 IIFLISDGKWVNSHEMSP---AFKAFPRAELLGLPVLSW---IAILAVILFTIVMTRTTL 186 Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIG-SVSPTAGQFAN 289 GR YA G +P AA AG++V + +T+SG + L G+ + R S AG F Sbjct: 187 GRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGF-E 245 Query: 290 IESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAV 349 ++ + A VIGG+S+ GG G++ G L GAL +G+ L ++ P W + G IIIAV Sbjct: 246 LDVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAV 305 Query: 350 AID 352 A++ Sbjct: 306 ALN 308 Lambda K H 0.327 0.141 0.420 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: 321 Number of extensions: 21 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: 360 Length of database: 327 Length adjustment: 29 Effective length of query: 331 Effective length of database: 298 Effective search space: 98638 Effective search space used: 98638 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