Align CBP protein aka CebF, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= TCDB::Q9X9R6 (306 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 158 bits (400), Expect = 1e-43 Identities = 91/285 (31%), Positives = 154/285 (54%), Gaps = 11/285 (3%) Query: 16 KASPYAFVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFW 75 + SPY F+AP + G P L ++S + W GL+N++ LL+ FW Sbjct: 7 RLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDAVFW 66 Query: 76 NALKNTLTIGIISTVPQLL-AALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTL 134 L NT I +I VP L+ L LA L+N LRG T +R+ TP S+ A + + Sbjct: 67 KTLGNTF-IYLIGVVPLLVFLPLGLAILVNRPLRGITLFRLAYYTPVIVSIVVAGIAWRW 125 Query: 135 LYSWDGGMVNWILDFF---GVDPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAI 191 LY+ + G++N + G P+ W S + F+V ++ +W+ GY +IYLA +Q I Sbjct: 126 LYA-ETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLAGLQGI 184 Query: 192 PADLYESAALDGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGEPLLFGGVSGSKG 251 P +LYE+AALDG++ W++ +T+P +RP ++ V+S I AT++F E + ++G Sbjct: 185 PLELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIM-----TQG 239 Query: 252 GSEHQYQTLGLYMYDQGWIIGNLGKASAIAWSMFLILLIVAAVNL 296 G + +T+ Y+Y Q + + A + ++FL++L ++ + L Sbjct: 240 GPLNSSKTVVYYVYQQAFQKLEVSYACTVGLALFLVVLTLSLLRL 284 Lambda K H 0.324 0.137 0.441 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: 270 Number of extensions: 18 Number of successful extensions: 4 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: 306 Length of database: 293 Length adjustment: 27 Effective length of query: 279 Effective length of database: 266 Effective search space: 74214 Effective search space used: 74214 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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