Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_002117405.1:WP_085770502.1 Length = 293 Score = 115 bits (288), Expect = 1e-30 Identities = 80/235 (34%), Positives = 117/235 (49%), Gaps = 8/235 (3%) Query: 16 YGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSP 75 +G + AL DF + GEI ++IG NGAGKSS+I I+G PD G I+L+ Sbjct: 44 FGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLDKNSFSRMPT 103 Query: 76 MEARQAGIETVYQNLALSPALSIADNMFLGREIRKPG-----IMGKWFRSLDRAAMEKQA 130 G+ +QNLAL LS+ DN+ +GR + G DR A E Sbjct: 104 ERLASLGVARTFQNLALFRGLSVFDNIAVGRVSATRSHWLEQVFGLPRARADRLATEIIV 163 Query: 131 RAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRV 190 L LGL ++ N+ TL G ++ V +ARA A +++++DEP A + E + Sbjct: 164 EEMLVFLGLGQVR--NRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGMTAGEKAEM 221 Query: 191 LELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 E I R R G IVLI H++ V E++DR+ + GR++ P D +AV Sbjct: 222 GEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMNDEAV 276 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: 169 Number of extensions: 10 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: 293 Length adjustment: 25 Effective length of query: 235 Effective length of database: 268 Effective search space: 62980 Effective search space used: 62980 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 09 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