Align TM0028, 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::Q9WXN5 (330 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 89.0 bits (219), Expect = 2e-22 Identities = 76/244 (31%), Positives = 125/244 (51%), Gaps = 23/244 (9%) Query: 24 AVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNG-EFVELS 82 AV + I E E+ ++G SG GK+TL I +++P + G++ +NG + ++S Sbjct: 42 AVKDANLSINEGEIFVIMGLSGSGKSTLLRCI-NRLIRPTS---GEVI--INGTDIAKVS 95 Query: 83 SMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFE 142 +++RK E+ ++ Q L+P + + E G+ + E KA + Sbjct: 96 DKELLQIRRK----ELAMVFQNF--GLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQ 149 Query: 143 EVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALD----VVNQKVLLK 198 VGL + + ELSGGM+QR +A A NP +L+ DE SALD V Q LL Sbjct: 150 LVGLKG-YENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLT 208 Query: 199 VLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGL 258 + +MK K+I+FITHD++ ++ DR+ IM G+IV+ E +L +P + Y + Sbjct: 209 LQSKMK-----KTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERF 263 Query: 259 FNSV 262 +V Sbjct: 264 VENV 267 Lambda K H 0.321 0.138 0.405 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: 296 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: 330 Length of database: 408 Length adjustment: 30 Effective length of query: 300 Effective length of database: 378 Effective search space: 113400 Effective search space used: 113400 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 (21.8 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