Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_086511522.1 BZY95_RS19340 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_002151265.1:WP_086511522.1 Length = 264 Score = 135 bits (341), Expect = 7e-37 Identities = 77/223 (34%), Positives = 124/223 (55%), Gaps = 3/223 (1%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 + + P+L +GL +R+G + A++ DF L GEI A++G NGAGKS++I +SG P E Sbjct: 10 LLETPLLETKGLTRRFGGLVAVNDVDFTLRQGEIHAILGPNGAGKSTLINLLSGEFPPSE 69 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRS 120 GEI +G+PIQ R + + GI +Q + P L+ N L I G+ G W RS Sbjct: 70 GEILFQGQPIQGRKARQIARMGIGRSHQKTNIFPRLTCLQNCQLAARIHLGGVFGSW-RS 128 Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 RA + ++ E + + +S G+++ + +A A K++++DEP A Sbjct: 129 RHRAREVDERALEVLET-CQLVHRAHTPASAMSYGEQRQLQIAMVLATAPKLMLLDEPMA 187 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHI 223 +G +E+ +V EL+ + R P+VLI H+M VF +ADRI + Sbjct: 188 GMGREETAQVTELLKGLSDR-YPLVLIEHDMDSVFRLADRITV 229 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: 153 Number of extensions: 6 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: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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 24 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