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 BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease
Query= TCDB::Q9X9R6 (306 letters) >FitnessBrowser__Koxy:BWI76_RS23380 Length = 296 Score = 139 bits (351), Expect = 6e-38 Identities = 86/277 (31%), Positives = 148/277 (53%), Gaps = 13/277 (4%) Query: 21 AFVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSD-FFWNALK 79 A+++P+ + F+ P + + + S L + + G++NY +L+ D FW ++ Sbjct: 10 AWISPYIIGLIVFTAFPFVSSFFLSFTEYDL--MSPPVFNGIENYRYMLTEDGLFWKSMG 67 Query: 80 NTLTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTP--YATSVAAATLVFTLLYS 137 T ++ +L AL +A +LN+KLRG +R P +SVA A L + L++ Sbjct: 68 VTFAYVFLTIPLKLAFALGIAFVLNFKLRGIGFFRTAYYIPSILGSSVAIAVL-WRALFA 126 Query: 138 WDGGMVNWILDFFGVDPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLYE 197 DG ++N + G DPVNW + +V+ + +W++ G +I+LAA+Q +P YE Sbjct: 127 IDG-LLNSFIGVLGFDPVNWLGEPSLALMSVTLLRVWQF-GSAMVIFLAALQNVPQSQYE 184 Query: 198 SAALDGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGEPLLFGGVSGSKGGSEHQY 257 +A +DGA++WQ F VTVP + P I F ++ T A Q F P + G GG + Sbjct: 185 AAMIDGASKWQMFMKVTVPLITPVIFFNFIMQTTQAFQEFTGPYVITG-----GGPTYST 239 Query: 258 QTLGLYMYDQGWIIGNLGKASAIAWSMFLILLIVAAV 294 LY+YD + ++G +A+AW +FL++ + AA+ Sbjct: 240 YLFSLYIYDTAFKYFDMGYGAALAWVLFLVVAVFAAI 276 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: 311 Number of extensions: 19 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: 296 Length adjustment: 27 Effective length of query: 279 Effective length of database: 269 Effective search space: 75051 Effective search space used: 75051 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