Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_011383886.1 AMB_RS07455 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_000009985.1:WP_011383886.1 Length = 261 Score = 117 bits (292), Expect = 3e-31 Identities = 78/249 (31%), Positives = 123/249 (49%), Gaps = 27/249 (10%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 M+Q L+ RGL K YG V A+ DFDL PGEILA+IG NGAGKS+ ++G P Sbjct: 1 MSQNQTLSVRGLSKNYGGVAAVTNVDFDLAPGEILALIGPNGAGKSTCFNMLNGQFPPTA 60 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKW--- 117 G I+L G+ + + P E + G+ +Q A ++++ +N+ + + W Sbjct: 61 GSIKLFGEELVGKKPREIWRLGVGRTFQITATFGSMTVLENVQMALISFHNRLRALWPFA 120 Query: 118 --------FRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFG 169 F+ L+ ME QA ++ L+ G + V +A A A Sbjct: 121 GGLYQDEAFQLLELVGMEAQA---------------SRPCSVLAYGDLKRVELAVALANA 165 Query: 170 SKVVIMDEPTAALGVKESRRVLELILD-VRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228 K+++MDEPTA + KE +++L D VR RG+ ++ H+M VF A+RI + G Sbjct: 166 PKLLLMDEPTAGMAPKERIELMQLTADIVRERGISVLFTEHDMDVVFTHANRIMVLSRGH 225 Query: 229 RLCVINPKD 237 + P++ Sbjct: 226 VVAEGKPQE 234 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: 144 Number of extensions: 4 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: 260 Length of database: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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: 47 (22.7 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