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 17513 b3452 glycerol-3-phosphate transporter subunit (NCBI)
Query= TCDB::Q9X9R6 (306 letters) >FitnessBrowser__Keio:17513 Length = 295 Score = 122 bits (305), Expect = 1e-32 Identities = 84/274 (30%), Positives = 138/274 (50%), Gaps = 10/274 (3%) Query: 19 PYAFVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWNAL 78 PY VAP ++ F + P WYSL +V + + GLDN+ L ++ ++ Sbjct: 14 PYLLVAPQLIITVIFFIWPAGEALWYSLQSVDPFGFSSQ-FVGLDNFVTLFHDSYYLDSF 72 Query: 79 KNTLTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTLLYSW 138 T+ TV LL +L A L+ Y +RGS ++ +ML PYA + A A +++ L++ Sbjct: 73 WTTIKFSTFVTVSGLLVSLFFAALVEYIVRGSRFYQTLMLLPYAVAPAVAAVLWIFLFNP 132 Query: 139 DGGMVNWILDFFGVDPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLYES 198 G++ L FG D N ++ + F V +W+ YN L + AA+Q+IP L E+ Sbjct: 133 GRGLITHFLAEFGYD-WNHAQNSGQAMFLVVFASVWKQISYNFLFFYAALQSIPRSLIEA 191 Query: 199 AALDGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGE-PLLFGGVSGSKGGSEHQY 257 AA+DGA ++F + +P + P F +VV+ + A F P++ S GG Sbjct: 192 AAIDGAGPIRRFFKIALPLIAPVSFFLLVVNLVYA--FFDTFPVIDAATS---GGPVQAT 246 Query: 258 QTLGLYMYDQGWIIGNLGKASAIAWSMFLILLIV 291 TL +Y +G+ L AS+ A S+ L+ L++ Sbjct: 247 TTLIYKIYREGFT--GLDLASSAAQSVVLMFLVI 278 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: 234 Number of extensions: 16 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: 306 Length of database: 295 Length adjustment: 27 Effective length of query: 279 Effective length of database: 268 Effective search space: 74772 Effective search space used: 74772 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