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 Dsui_0415 Dsui_0415 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__PS:Dsui_0415 Length = 326 Score = 152 bits (383), Expect = 1e-41 Identities = 96/247 (38%), Positives = 146/247 (59%), Gaps = 10/247 (4%) Query: 17 FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP----TSGEIYFEGK 72 F RR A+ VS E+ + E++ L+GESGSGK+ T + +LRL P T+G I +G+ Sbjct: 15 FNGARRASALNQVSLELGQGEVLGLLGESGSGKSVTLRTLLRLHPERHTRTAGRIRVDGQ 74 Query: 73 DIWKDIKDRESLVEFRR-KVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALE 131 D+ ++ RE L +R V VFQ+P +++P Y + + + +A+ + E A Sbjct: 75 DVLA-LRGRE-LDRYRGGTVSMVFQEPGLAFDPVYTIGQQISEAVRVHEGVDQATAAARA 132 Query: 132 LIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSR 190 L L RV I + YPH++SGG +QR MIA +P L++ADEPT+ +DA+ + Sbjct: 133 LAM--LERVQIPQARRRFDAYPHELSGGMRQRAMIALALACKPKLLLADEPTTALDATVQ 190 Query: 191 GGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEY 250 I+ LL EL+ E G S+IF+THD+G A V+D I VM G IVE+G ++V +P H Y Sbjct: 191 IQILLLLRELQRETGMSVIFVTHDIGAAVEVADRIAVMYAGRIVEQGPVGQLVRQPCHPY 250 Query: 251 TKLLVGS 257 T+ L+ + Sbjct: 251 TRGLLAA 257 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: 206 Number of extensions: 6 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: 326 Length adjustment: 26 Effective length of query: 242 Effective length of database: 300 Effective search space: 72600 Effective search space used: 72600 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