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 SMc04035 SMc04035 peptide ABC transporter permease
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__Smeli:SMc04035 Length = 283 Score = 123 bits (308), Expect = 5e-33 Identities = 79/265 (29%), Positives = 133/265 (50%), Gaps = 18/265 (6%) Query: 16 IIGFSIFLFFLFLGIFGPMFYRVDPTEMTWDYE-QPPSSAHPLGTDTYGRDVLAQLLHGI 74 +IG I LFFL L I P+ DP QPPS HP GTD +GRD+L++++ G Sbjct: 24 VIGAGILLFFLLLAIGAPVVAPYDPILQNGAARLQPPSLLHPFGTDNFGRDLLSRVIWGT 83 Query: 75 RSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLTTPSILIAILIASYLK 134 R L I + VIGTI+G+ + GIVD + M + +I+L P +++ + I + L Sbjct: 84 RIDLQIALIGVAFPFVIGTIVGTIAGFFGGIVDALFMRLVDIILAFPFLVLMLSIIAILG 143 Query: 135 VRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYSDLRLVIEDLIPTI-- 192 + + + L W +AR IRAQ++ + + +Y +V G+ R++ L+P Sbjct: 144 -PGLGSFYIAMALVGWVSYARLIRAQILVLKNSDYAVAAVSLGFGRFRIMFRHLLPNAIA 202 Query: 193 --ATYAFMSFVLFINGGIMGEAGLSLIGLGPTQGISLGIMLQWAVLM---EAVRRGLWWW 247 +A VL + G A +S +GLG ++ +W V++ ++ WW Sbjct: 203 GSIVFAMSDAVLVLLSG----AAVSYLGLGVQPPVA-----EWGVMVAEGQSFITTAWWI 253 Query: 248 FVPPGLAIVAVTASLLVISTAMDEV 272 + PGL+IV++ ++ A+ E+ Sbjct: 254 TLFPGLSIVSLAFGFSMLGDALGEL 278 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: 219 Number of extensions: 18 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: 283 Length adjustment: 26 Effective length of query: 254 Effective length of database: 257 Effective search space: 65278 Effective search space used: 65278 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