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 207956 DVU2462 oligopeptide ABC transporter, permease protein
Query= TCDB::Q9WXN6 (280 letters) >MicrobesOnline__882:207956 Length = 300 Score = 139 bits (349), Expect = 1e-37 Identities = 83/272 (30%), Positives = 147/272 (54%), Gaps = 8/272 (2%) Query: 11 KNKKFIIGFSIFLFFLFLGIFGPMFYRVDPTEMTWD-YEQPPSSAHPLGTDTYGRDVLAQ 69 +N F IGF+I L + P DPT + D PS+ H LGTD GRDVL++ Sbjct: 34 RNILFAIGFAIVGSMSLLALLAPWIAPYDPTALHLDTILSGPSATHLLGTDALGRDVLSR 93 Query: 70 LLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLTTPSILIAILI 129 LL+G R SL++GF++ I++ IG +G + GI+D++ M + +I+L PS + + + Sbjct: 94 LLYGARVSLWVGFVSVGIAVAIGLAVGLVAGYFGGIIDELAMRLVDIMLCFPSFFLILAV 153 Query: 130 ASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYSDLRLVIEDLI 189 ++L+ S+ + ++GL W AR +RA+ +S+ RE+V + +AG R+++ ++ Sbjct: 154 IAFLE-PSLGNIMAVIGLTSWMGVARLVRAETLSLREREFVAAARLAGAGRTRIILTHIL 212 Query: 190 PTIATYAFMSFVLFINGGIMGEAGLSLIGLG--PTQGISLGIMLQWAVLMEAVRRGLWWW 247 P +S L + G I+ E+ LS +GLG P ++L+ ++E W Sbjct: 213 PNAMAPVLVSATLGVAGAILTESALSFLGLGVQPPDPSWGNMLLEGKDVLEIAP----WM 268 Query: 248 FVPPGLAIVAVTASLLVISTAMDEVFNPRLRE 279 + PGLAI+ ++ ++ + +PRL++ Sbjct: 269 SLFPGLAILVTVLGYNLLGESLRDFLDPRLKK 300 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: 213 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: 280 Length of database: 300 Length adjustment: 26 Effective length of query: 254 Effective length of database: 274 Effective search space: 69596 Effective search space used: 69596 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: 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