Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Ac3H11_3037 Fructose ABC transporter, ATP-binding component FrcA
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3037 Length = 268 Score = 328 bits (841), Expect = 7e-95 Identities = 170/257 (66%), Positives = 213/257 (82%), Gaps = 4/257 (1%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 ++ A+GLVKRYG+VTALD ADF+L GEILAVIGDNGAGKSS+IKA+SGA PDEGEI L Sbjct: 13 VMQAKGLVKRYGQVTALDGADFELRAGEILAVIGDNGAGKSSLIKALSGATVPDEGEILL 72 Query: 66 EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125 +G+ IQF+SP+EAR+AGIETVYQ+LA++PA++IA+N+FLGRE+R+PG++G R LD+ Sbjct: 73 DGQRIQFKSPIEARRAGIETVYQDLAVAPAMTIAENLFLGRELRRPGLLGTALRMLDKKK 132 Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185 M +++ A+++EL + I+++ QAVETLSGGQRQ VAVARAAAF VVIMDEPTAALGVK Sbjct: 133 MLEESVARMAEL-KVGIRSMTQAVETLSGGQRQCVAVARAAAFARHVVIMDEPTAALGVK 191 Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVA 245 E VLELI VR +GLP++LISHNMPHVFE+ADRIHI RLG+R V+NPK +MSD VA Sbjct: 192 EGNMVLELIRRVRDKGLPVILISHNMPHVFEIADRIHIARLGKRAAVVNPKKISMSDTVA 251 Query: 246 FMTG---AKEPPREAIA 259 MTG A + P E +A Sbjct: 252 VMTGAMAASDLPAECLA 268 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: 232 Number of extensions: 9 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: 268 Length adjustment: 25 Effective length of query: 235 Effective length of database: 243 Effective search space: 57105 Effective search space used: 57105 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