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 SM_b21653 SM_b21653 lactose ABC transporter permease
Query= TCDB::Q9X9R6 (306 letters) >FitnessBrowser__Smeli:SM_b21653 Length = 298 Score = 156 bits (395), Expect = 5e-43 Identities = 96/285 (33%), Positives = 153/285 (53%), Gaps = 11/285 (3%) Query: 20 YAFVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWNALK 79 + FVAP L F + P+ ++ W S + + L +AG N L + F AL Sbjct: 17 WLFVAPALGLITLFMVYPIAWSLWMSFQSGRGMTLK---FAGFANIVRLWNDPVFIKALT 73 Query: 80 NTLTIGIISTVPQLLAALALAHLLNY-KLRGSTAWRVVMLTPYATSVAAATLVFTLLYSW 138 NT+T ++ +L AL LA LLN +L G +R + P +S+ A +++F +++ Sbjct: 74 NTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFAT 133 Query: 139 DGGMVNWILDFFGV--DPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLY 196 DG +VN L G+ P+ W + ++ V + WRWTGYN + YLAA+Q I +Y Sbjct: 134 DG-IVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIY 192 Query: 197 ESAALDGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGEPLLFGGVSGSKGGSEHQ 256 E A +DG W + H+T+P L+P ILFT V+STIG QLF E ++ KGG + Sbjct: 193 EVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVY---NLTEGKGGPSNA 249 Query: 257 YQTLGLYMYDQGW-IIGNLGKASAIAWSMFLILLIVAAVNLLLTR 300 TL LY+Y+ + + NLG A+ +++ + +++ ++A V R Sbjct: 250 TLTLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQFFAAR 294 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: 245 Number of extensions: 12 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: 298 Length adjustment: 27 Effective length of query: 279 Effective length of database: 271 Effective search space: 75609 Effective search space used: 75609 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