Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 7023263 Shewana3_0497 ABC transporter related (RefSeq)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__ANA3:7023263 Length = 348 Score = 96.3 bits (238), Expect = 8e-25 Identities = 71/224 (31%), Positives = 114/224 (50%), Gaps = 18/224 (8%) Query: 7 LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66 + A GL KRY AL F+L+ G+ LA++G NGAGKS++IK I G V+P +GE+ ++ Sbjct: 29 IKAIGLCKRYATFEALTDLHFELHAGQTLALLGHNGAGKSTLIKMILGLVSPSQGELFVQ 88 Query: 67 GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126 G+P+ + A + Y L +S DNM +EI +F L + Sbjct: 89 GQPLH----TKRANANLSLGY----LPENVSFYDNM-TAQEIL------SYFAKL-KGVA 132 Query: 127 EKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKE 186 K+ L E GLM + ++ + T S G RQ + +A+A KV+++DEPT L Sbjct: 133 PKRVSILLEEFGLMAAK--DKRLSTFSKGMRQRLGLAQAVLADPKVLLLDEPTVGLDPLA 190 Query: 187 SRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRL 230 S + + + ++ +G I++ +H + V + D I GR L Sbjct: 191 SAFLYQKMAQLKAQGCAIIISTHELGLVQDQMDSALILGQGRLL 234 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: 162 Number of extensions: 6 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: 348 Length adjustment: 27 Effective length of query: 233 Effective length of database: 321 Effective search space: 74793 Effective search space used: 74793 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: 48 (23.1 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