Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 106 bits (264), Expect = 5e-28 Identities = 73/229 (31%), Positives = 120/229 (52%), Gaps = 12/229 (5%) Query: 11 GLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL-EGKP 69 G+ K YG AL D+ GE + + G +G+GKS++I+ I+G T DEG IR+ E + Sbjct: 6 GVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEV 65 Query: 70 IQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQ 129 R ++ +A + V+Q+ L P L+I +N L R L R A E Sbjct: 66 RPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAP---------MKVRGLARDAAEAL 116 Query: 130 ARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRR 189 AR L + + ++ LSGGQ+Q A+ARA A ++++ DEPT+AL + + Sbjct: 117 ARELLERVRIA--DQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKE 174 Query: 190 VLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDY 238 VL+++ + G+ ++ ++H M EVADRI G+ + +P+D+ Sbjct: 175 VLDIMKALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDF 223 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: 146 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: 241 Length adjustment: 24 Effective length of query: 236 Effective length of database: 217 Effective search space: 51212 Effective search space used: 51212 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: 46 (22.3 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