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 H281DRAFT_06102 H281DRAFT_06102 peptide/nickel transport system permease protein
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__Burk376:H281DRAFT_06102 Length = 304 Score = 132 bits (332), Expect = 9e-36 Identities = 80/270 (29%), Positives = 146/270 (54%), Gaps = 11/270 (4%) Query: 12 NKKFIIGFSIFLFFLFLGIFGPMFYRVDPT-EMTWDYEQPPSS-AHPLGTDTYGRDVLAQ 69 N + GF+I + + + I GP DP ++ D PP S +H LGTD GRD+L++ Sbjct: 38 NPLSVFGFAILMVLVIVAIIGPWIAPHDPLRQVLSDRLLPPGSPSHWLGTDQLGRDILSR 97 Query: 70 LLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLTTPSILIAILI 129 +++G R +L I L ++ + IG +IG+ + G VD+VLM +T+I L P I++A+ Sbjct: 98 IIYGSRLTLSIAILVVVVVVPIGLMIGTTAGFFGGWVDNVLMRVTDIALAFPKIVLALAF 157 Query: 130 ASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYSDLRLVIEDLI 189 A+ L + V + + + WP +AR RA+ + ++ +++ ++ + G S+LR+++ ++ Sbjct: 158 AAALGPGVINAV-IAISITAWPAYARLARAETLRLVQADFIQVARLQGASNLRILLRYVV 216 Query: 190 PTIATYAFMSFVLFINGGIMGEAGLSLIGLGPTQGISLGIMLQWAVLMEAVRRGL---WW 246 P + + L + G I+ AGL +GLG +W ++ + R L WW Sbjct: 217 PLCMSSVIVRATLDMAGIILTVAGLGFLGLGAQPPSP-----EWGFMVASGRNVLLDSWW 271 Query: 247 WFVPPGLAIVAVTASLLVISTAMDEVFNPR 276 PG AI+ V+ + ++ + +VF+PR Sbjct: 272 VATIPGFAILLVSLAFNLLGDGLRDVFDPR 301 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: 196 Number of extensions: 16 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: 304 Length adjustment: 26 Effective length of query: 254 Effective length of database: 278 Effective search space: 70612 Effective search space used: 70612 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