Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate BPHYT_RS22035 BPHYT_RS22035 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__BFirm:BPHYT_RS22035 Length = 332 Score = 157 bits (396), Expect = 4e-43 Identities = 90/244 (36%), Positives = 145/244 (59%), Gaps = 9/244 (3%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP---PTSGEIYFEGKDIWKDIK 79 ++AV+ VSF ++ + +VGESGSGK+ T +L LL SG + G+++ Sbjct: 21 VDAVQGVSFSLEAGRTLGIVGESGSGKSQTVMALLGLLAGNGKVSGSATYRGENLLT--M 78 Query: 80 DRESLVEFRR-KVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLF 138 + SL + R ++ +FQDP S NPF +ER + + + L ++ +++EA E+L Sbjct: 79 NEASLNKIRGDRIGMIFQDPMTSLNPFLTIERQMTETLQL--HRKMSRREARRRAIETLE 136 Query: 139 RVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLL 197 V I D +G YPH+ SGG +QR+MIA + P +++ADEPT+ +D + + II+LL Sbjct: 137 SVRIPDAARRIGMYPHEFSGGMRQRVMIAMALLSEPEILIADEPTTALDVTVQAQIIELL 196 Query: 198 EELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGS 257 EL E+GT+II ITHD+G+ + D++ VM G+ VE+ + PTH YT L+ + Sbjct: 197 RELNRERGTAIILITHDMGVVAGLCDDVMVMYAGQTVEQASAAALFAAPTHPYTLGLLNA 256 Query: 258 IPKL 261 +P+L Sbjct: 257 LPRL 260 Lambda K H 0.319 0.139 0.397 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: 203 Number of extensions: 5 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: 268 Length of database: 332 Length adjustment: 27 Effective length of query: 241 Effective length of database: 305 Effective search space: 73505 Effective search space used: 73505 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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