Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 3606961 Dshi_0388 ABC transporter related (RefSeq)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Dino:3606961 Length = 261 Score = 427 bits (1097), Expect = e-124 Identities = 215/256 (83%), Positives = 235/256 (91%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 +Q+PIL R LVKRYGRVTALD DF+LYPGEILAVIGDNGAGKSS+IKA+SGAV PDEG Sbjct: 5 SQQPILAGRNLVKRYGRVTALDHCDFELYPGEILAVIGDNGAGKSSLIKAVSGAVIPDEG 64 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121 E+ LEGK ++F+SP++AR AGIETVYQ LA+SPALSIADNMF+GRE+RKPG GKW R L Sbjct: 65 EVFLEGKRVRFQSPLDARAAGIETVYQQLAMSPALSIADNMFMGRELRKPGWRGKWLRQL 124 Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181 DRAAMEK AR KLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKV+I+DEPTAA Sbjct: 125 DRAAMEKFARDKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVIILDEPTAA 184 Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241 LGVKESRRVLELILDVR RG+PIVLISHNMPHVFEVADRIHIHRLG+RLCVI+PKD+ MS Sbjct: 185 LGVKESRRVLELILDVRARGIPIVLISHNMPHVFEVADRIHIHRLGKRLCVIDPKDHDMS 244 Query: 242 DAVAFMTGAKEPPREA 257 DAVAFMTGAKEP A Sbjct: 245 DAVAFMTGAKEPESAA 260 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: 280 Number of extensions: 4 Number of successful extensions: 1 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 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