Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_002723117.1 RSPH17029_RS17245 ATP-binding cassette domain-containing protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_000015985.1:WP_002723117.1 Length = 261 Score = 192 bits (487), Expect = 8e-54 Identities = 107/249 (42%), Positives = 151/249 (60%), Gaps = 8/249 (3%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 ++ PIL+ R + K +G AL D D+ PGE L +IGDN AGKS++ K ISG PDE Sbjct: 17 LSAAPILSLRNIHKTFGSHQALRGVDLDIRPGECLGLIGDNAAGKSTLSKVISGTYIPDE 76 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRS 120 GEI +EGKP++F +P EAR IE VYQ+LAL + + N+FLGRE+++ Sbjct: 77 GEITMEGKPVRFATPSEARALNIEMVYQDLALCDHVDVVGNLFLGRELKRGPF------- 129 Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 LD+ M +A L+ L + I + VE LSGGQRQ +A+ARAA+F KV++MDEPT+ Sbjct: 130 LDQKRMLAEAERMLAALEI-RIPRLTAKVEKLSGGQRQAIAIARAASFEPKVLLMDEPTS 188 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTM 240 AL V E VL LI V+ RG+ +VL++H M +F V DR+ + G ++ D + Sbjct: 189 ALAVAEVEAVLGLINRVKARGVAVVLVTHRMQDLFRVCDRVAVMYEGTKVAERAIADTNL 248 Query: 241 SDAVAFMTG 249 + V + G Sbjct: 249 QELVDLIVG 257 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: 176 Number of extensions: 4 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: 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 Apr 10 2024. 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