Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 97.1 bits (240), Expect = 4e-25 Identities = 67/227 (29%), Positives = 125/227 (55%), Gaps = 24/227 (10%) Query: 7 LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66 LT + Y T L D L+ GEI A++G +G GK++++KAI+G +G I + Sbjct: 4 LTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISIN 63 Query: 67 GKPI---QFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123 G+ + + P E R+ G+ ++Q+ AL P L++A+N+ G + LD+ Sbjct: 64 GRLLSGPETFVPSERREVGM--IFQDYALFPHLTVAENILFG------------VKGLDK 109 Query: 124 AAMEKQARAKLSE-LGLMTIQNI-NQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181 AA + A+L E L L+ ++ + + LSGGQ+Q V++ARA A+ +++++DEP + Sbjct: 110 AARQ----ARLGEMLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSN 165 Query: 182 LGVK-ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLG 227 + K ++E+ +++RG+ V ++H+ F AD++ + + G Sbjct: 166 IDAKVRGEMMVEIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDG 212 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: 182 Number of extensions: 9 Number of successful extensions: 3 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: 342 Length adjustment: 26 Effective length of query: 234 Effective length of database: 316 Effective search space: 73944 Effective search space used: 73944 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