Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 3607868 Dshi_1276 ABC transporter related (RefSeq)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Dino:3607868 Length = 264 Score = 188 bits (477), Expect = 1e-52 Identities = 102/248 (41%), Positives = 155/248 (62%), Gaps = 4/248 (1%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 PI+ + + K +G V AL D++PGE ++GDNGAGKS+ IK +SG P +GEI Sbjct: 9 PIIQMKNIEKHFGAVIALAGVSIDIFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGEII 68 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 EG+P+ F P +A +AGI TV+Q+LA+ P +S++ N F+G E K I G F LDR Sbjct: 69 FEGRPMHFEDPRDAMEAGIATVHQHLAMIPLMSVSRNFFMGNEPVKK-IAGINF--LDRE 125 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 ++ ++ ++G+ ++ +QAV TLSGG+RQ VA++RA FG+KV+I+DEPT+ALGV Sbjct: 126 FADRVTMEEMRKMGI-NLRGPDQAVGTLSGGERQTVAISRAVYFGAKVLILDEPTSALGV 184 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 +++ VL I VR++G+ +V I+HN+ H V DR + G+ L + T + Sbjct: 185 RQTSNVLATIDKVRKQGVAVVFITHNVRHAMAVGDRFTVLNRGQTLGTAERGEITPEELQ 244 Query: 245 AFMTGAKE 252 M G +E Sbjct: 245 DMMAGGQE 252 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: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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