Align TM0029, 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 SMc02028 SMc02028 peptide ABC transporter permease
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__Smeli:SMc02028 Length = 272 Score = 115 bits (289), Expect = 8e-31 Identities = 79/267 (29%), Positives = 131/267 (49%), Gaps = 10/267 (3%) Query: 16 IIGFSIFLFFLFLGIFGPMFYRVDPTEMTWDYE-QPPSSAHPLGTDTYGRDVLAQLLHGI 74 +IG + L G + DP ++++ P AH LGTD +GRDVL++L+ G Sbjct: 9 LIGGILIAILLVTAAVGLFWTPFDPMKLSFTARLAAPGPAHLLGTDEFGRDVLSRLMVGA 68 Query: 75 RSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLTTPSILIAILIASYLK 134 R+S++IG L + V GT+IG S RG VD V+M + N +L P IL+A+ + + Sbjct: 69 RASVWIGVLTVGFATVCGTLIGLISGYARGWVDGVIMAVNNALLAFPGILLALGLLAVFG 128 Query: 135 VRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYSDLRLVIEDLIPTIAT 194 ++ LG+ P AR +R ++S+ RE++ S + G +L ++ ++P Sbjct: 129 ANQYGII-FALGIAYTPSMARVVRGAVLSLREREFIEASRVMGNGELYTMLRHILPNCVA 187 Query: 195 YAFMSFVLFINGGIMGEAGLSLIGLG-PTQGISLGIMLQWA--VLMEAVRRGLWWWFVPP 251 + I+ E+ LS +GLG P + G ML L +A GL+ P Sbjct: 188 PITVLATSMFGWAILSESALSFLGLGVPPPAPTWGNMLAAGRPFLQQAAWLGLF-----P 242 Query: 252 GLAIVAVTASLLVISTAMDEVFNPRLR 278 GL I + ++ A+ + +PR+R Sbjct: 243 GLCIALTLLGINLLGDALRDRLDPRMR 269 Lambda K H 0.330 0.144 0.441 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: 177 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: 280 Length of database: 272 Length adjustment: 25 Effective length of query: 255 Effective length of database: 247 Effective search space: 62985 Effective search space used: 62985 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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