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 WP_011386732.1 AMB_RS22190 ABC transporter permease
Query= TCDB::Q9WXN6 (280 letters) >NCBI__GCF_000009985.1:WP_011386732.1 Length = 342 Score = 110 bits (276), Expect = 3e-29 Identities = 82/249 (32%), Positives = 124/249 (49%), Gaps = 14/249 (5%) Query: 33 PMFYRVDPTEMTWDYEQPPSSAHPLGTDTYGRDVLAQLLHGIRSSLYIGFLAAIISLVIG 92 P YR + + PPS ++ LGTD GRDVLA+L++G+R S+ G ++S V+G Sbjct: 100 PFDYRAINYDPMVKHPSPPSRSNWLGTDDQGRDVLARLIYGLRLSICFGLALTLVSTVVG 159 Query: 93 TIIGSFSAVKRGIVDDVLMGITNIVLTTPSILIAILIASYLKVRSVEMVAVILGLFQWPW 152 G+ G VD V I P +LI I+IAS +K ++ V++ LF W Sbjct: 160 VAAGAVQGYFGGKVDLVFQRFLEIWGGLPELLILIIIASIIKPGFWTLLLVLV-LFSWTN 218 Query: 153 FARAIRAQLMSVMSREYVYLSVMAGYSDLRLVIEDLIPT--IATYAFMSFVLFINGGIMG 210 +RA+ + + +YV + G SD R++ ++P +AT FM F+L N I+ Sbjct: 219 LVGVVRAEFLRARNFDYVRAARTLGMSDARIMARHVLPNAMVATVTFMPFIL--NSSIVS 276 Query: 211 EAGLSLIGLG-PTQGISLGIML-QWAVLMEAVRRGLWWWFVPPGLAIVAVTASLLV-IST 267 L +GLG P SLG +L Q ++A W G +VA SLLV + Sbjct: 277 LTALDFLGLGLPPGSASLGDLLRQGKENLQAP------WLGLTGFLVVATLLSLLVFVGE 330 Query: 268 AMDEVFNPR 276 A+ + F+PR Sbjct: 331 AVRDAFDPR 339 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: 197 Number of extensions: 9 Number of successful extensions: 2 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: 342 Length adjustment: 27 Effective length of query: 253 Effective length of database: 315 Effective search space: 79695 Effective search space used: 79695 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