Align Fructose import permease protein FrcC (characterized)
to candidate SMc03814 SMc03814 ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Smeli:SMc03814 Length = 335 Score = 173 bits (438), Expect = 7e-48 Identities = 97/304 (31%), Positives = 166/304 (54%), Gaps = 8/304 (2%) Query: 50 VPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAI 109 + L +LV+ L+ ++ KF ++ + I Q +GI+ T V+++ GID+SVG+I Sbjct: 34 IALAILVIGLVVS--VISAKFATSGNLLNIFQNACFIGIMALGMTPVLISGGIDISVGSI 91 Query: 110 MVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVL 169 + + V +G P A+ ++ L +G CG +NG +++ +KLPPFIVTL I Sbjct: 92 LGMCGVTLG-IVLNSDMPLAVGILATLAMGVACGMVNGIIISYVKLPPFIVTLATLSIGR 150 Query: 170 ASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTA 229 + + + NE + N I G +F + N V+ +V V +L ++L T Sbjct: 151 SLALVLTNNEVFYEFGRATNGIIALGGGYSFGLPNVVYA-----LVAGVIILHFLLTMTR 205 Query: 230 WGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFAN 289 WGRY++A+G + AA+LAG+ V + +S Y +GL+ A+ L+G +G+V+ G Sbjct: 206 WGRYLFAIGGNEAAARLAGIPVDLIKVSAYAFNGLMVAITAVFLVGWLGAVTNAIGTGYE 265 Query: 290 IESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAV 349 ++ I + VIGG SL GG G+ +G GA++V V L + G +P W + +G I+ AV Sbjct: 266 LQVIASTVIGGASLTGGFGTALGAAIGAILVEVIRNALLIAGVNPFWQGMFVGSFILAAV 325 Query: 350 AIDQ 353 +++ Sbjct: 326 LLER 329 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: 360 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: 360 Length of database: 335 Length adjustment: 29 Effective length of query: 331 Effective length of database: 306 Effective search space: 101286 Effective search space used: 101286 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