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_RS03135 BWI76_RS03135 sugar ABC transporter permease
Query= TCDB::Q9X9R6 (306 letters) >FitnessBrowser__Koxy:BWI76_RS03135 Length = 290 Score = 117 bits (294), Expect = 2e-31 Identities = 79/285 (27%), Positives = 140/285 (49%), Gaps = 9/285 (3%) Query: 19 PYAFVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWNAL 78 P+ ++P L F+ PL + + SL + ++ + D + GL+N+ L + FW +L Sbjct: 7 PWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVS-DGGQYVGLENFSRLFADSVFWQSL 65 Query: 79 KNTLTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTLLYSW 138 N L +++ VP + AL LA L R + R P + +A ++ ++ Sbjct: 66 VNNLLYILLTVVPGVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVSAAALWLFIFMP 125 Query: 139 DGGMVN-WILDFFGVDPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLYE 197 G+++ ++ FG NW + A++ I +W++ GY L +LA +Q+IPA E Sbjct: 126 GLGLLDHYLAKLFGPMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQSIPASTRE 185 Query: 198 SAALDGANRWQQFRHVTVPQLRPTILFTVVVSTI-GATQLFGEPLLFGGVSGSKGGSEHQ 256 +A ++GA R Q F VT+P LRPT+ F + + I TQ+ ++ ++GG ++ Sbjct: 186 AAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVM------TRGGPDNA 239 Query: 257 YQTLGLYMYDQGWIIGNLGKASAIAWSMFLILLIVAAVNLLLTRR 301 L Y+ + W +LGKASA + L + +NL L + Sbjct: 240 TTVLLYYIQNLAWDTHDLGKASAATFLTLAGLFAFSLINLKLLEK 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: 265 Number of extensions: 15 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: 290 Length adjustment: 26 Effective length of query: 280 Effective length of database: 264 Effective search space: 73920 Effective search space used: 73920 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