Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate SM_b20930 SM_b20930 sugar uptake ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Smeli:SM_b20930 Length = 246 Score = 178 bits (452), Expect = 8e-50 Identities = 106/247 (42%), Positives = 148/247 (59%), Gaps = 5/247 (2%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +L + K +G + A+ L GE++ ++GDNGAGKS+++K ++G P G IRL Sbjct: 3 VLELVNISKHFGAIQAVSDVSLSLERGEVVGLMGDNGAGKSTLVKMMAGNFRPSHGTIRL 62 Query: 66 EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125 +G + P+EARQ GIE VYQ+LAL L+ A N+FLGREIR+ GI R LD A Sbjct: 63 DGAELVMHRPVEARQHGIEIVYQDLALCDNLTAAANVFLGREIRR-GIGP--LRILDYKA 119 Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185 M ++A EL T V +SGGQRQ VA+AR +K+V+MDEPTAA+ V+ Sbjct: 120 MYRRAGEIFRELKSETPP--RNLVRQMSGGQRQAVAIARTMLSEAKIVLMDEPTAAISVR 177 Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVA 245 + VL LI ++R RG+ +VLISH MP VF VADR+ + R GR++ + + Sbjct: 178 QVAEVLNLIRELRDRGIAVVLISHRMPDVFTVADRVIVMRRGRKVADKPIAASSPEEVTG 237 Query: 246 FMTGAKE 252 +TGA E Sbjct: 238 LITGAIE 244 Lambda K H 0.321 0.136 0.383 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: 183 Number of extensions: 6 Number of successful extensions: 2 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: 260 Length of database: 246 Length adjustment: 24 Effective length of query: 236 Effective length of database: 222 Effective search space: 52392 Effective search space used: 52392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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