Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Keio:1937256 Length = 500 Score = 158 bits (400), Expect = 2e-43 Identities = 88/224 (39%), Positives = 138/224 (61%), Gaps = 9/224 (4%) Query: 4 EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63 + IL GL K + V ALD DF L GEI+A++G+NGAGKS++IKA++G D G I Sbjct: 7 QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66 Query: 64 RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123 LEG+ I ++ A+Q GI TVYQ + L P +S+ADN+F+GRE ++ G+ L R Sbjct: 67 WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGL-------LRR 119 Query: 124 AAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183 MEK+A ++ G ++ + + S +Q VA+ RA +KV+I+DEPTA+L Sbjct: 120 KEMEKRATELMASYGFSL--DVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLD 177 Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLG 227 +E + +L+ +R RG+ ++ ++H + V++V+DRI + R G Sbjct: 178 TQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNG 221 Score = 92.4 bits (228), Expect = 2e-23 Identities = 61/215 (28%), Positives = 107/215 (49%), Gaps = 9/215 (4%) Query: 14 KRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFR 73 K YG+ + D ++ PGEI+ + G G+G++ + I G D G ++GKP R Sbjct: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327 Query: 74 SPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQA 130 SP +A GI ++ + A S+ +N+ L + ++ W R + R ++ A Sbjct: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR-----GWLRPISRKEQQEIA 382 Query: 131 RAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRV 190 + +LG+ T + Q +E LSGG +Q V ++R + +I+DEPT + V + Sbjct: 383 ERFIRQLGIRT-PSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEI 441 Query: 191 LELILDVRRRGLPIVLISHNMPHVFEVADRIHIHR 225 + LI + GL +++IS + + ADR+ I R Sbjct: 442 IRLIETLCADGLALLVISSELEELVGYADRVIIMR 476 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: 296 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 500 Length adjustment: 29 Effective length of query: 231 Effective length of database: 471 Effective search space: 108801 Effective search space used: 108801 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: 49 (23.5 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