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 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 115 bits (289), Expect = 1e-30 Identities = 79/236 (33%), Positives = 126/236 (53%), Gaps = 8/236 (3%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESL 84 AVK+ + + E EI ++G SGSGK+T + I RL+ PTSGE+ G DI K + D+E L Sbjct: 42 AVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAK-VSDKELL 100 Query: 85 VEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGIDP 144 R+++ VFQ+ P L LE + K E + ES+ VG+ Sbjct: 101 QIRRKELAMVFQN-----FGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQLVGL-- 153 Query: 145 KDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQ 204 K + ++SGG +QR+ +AR P +++ DE S +D R + L L+ + Sbjct: 154 KGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKM 213 Query: 205 GTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIPK 260 +I+FITHDL A + D I +MK+GEIV+ G ++++ EP + Y + V ++ + Sbjct: 214 KKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFVENVDR 269 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: 275 Number of extensions: 13 Number of successful extensions: 2 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: 408 Length adjustment: 28 Effective length of query: 240 Effective length of database: 380 Effective search space: 91200 Effective search space used: 91200 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: 49 (23.5 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