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 200963 SO1801 peptide ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__MR1:200963 Length = 261 Score = 158 bits (400), Expect = 1e-43 Identities = 92/254 (36%), Positives = 153/254 (60%), Gaps = 10/254 (3%) Query: 4 LVVKNLTKIFSLGF--FSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP 61 L V +L K + G+ F+++ +A+ VSFE+ E +++VGE+GSGK+T A++++ P Sbjct: 6 LKVNDLFKRYDTGYKGFTRQYNDALAPVSFELNRGETLAIVGEAGSGKSTLARILVGAEP 65 Query: 62 PTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLEN 121 + GEIYFEG+ + D ++ + R + +FQDP S NP + + L + + N Sbjct: 66 RSGGEIYFEGEAL-----DSRNIKQRCRLIRMIFQDPNTSLNPRLTIGQLLDEPLRF--N 118 Query: 122 KPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEP 181 + KE + ++L +VG+ P+ YPH IS GQKQR+ +AR +L P +I+ADE Sbjct: 119 TQLSAKERNTQVIDTLRKVGLLPEHS-DFYPHMISEGQKQRVAVARALMLNPKIIIADEA 177 Query: 182 TSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDK 241 + +D S R I+ LL +L+++ G S IF++H+L + +VSD I V+ G +VE+ ++ Sbjct: 178 LTALDLSVRSQILNLLLKLQKDLGLSYIFVSHNLNIIRHVSDKIMVLHKGVMVEKAPTEQ 237 Query: 242 VVLEPTHEYTKLLV 255 + P HEYT+ LV Sbjct: 238 IFNSPQHEYTQRLV 251 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: 178 Number of extensions: 11 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: 261 Length adjustment: 25 Effective length of query: 243 Effective length of database: 236 Effective search space: 57348 Effective search space used: 57348 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: 47 (22.7 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