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 Ac3H11_4826 Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4826 Length = 290 Score = 130 bits (328), Expect = 3e-35 Identities = 88/272 (32%), Positives = 140/272 (51%), Gaps = 12/272 (4%) Query: 11 KNKKFIIGFSIFLFFLFLGIFGPMFYRVDPTEMTWDYEQP-PSSAHPLGTDTYGRDVLAQ 69 +++ F+IG + L + ++ P EM + PS H LGTD +GRDV + Sbjct: 22 RHRSFVIGAVLSLLLILAAALSLVWTPWSPYEMDLANKLAGPSGTHWLGTDAFGRDVASL 81 Query: 70 LLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLTTPSILIAILI 129 LL G R+S+ +G +A I L IGT +G +A KRG V++++M + + P+IL AI++ Sbjct: 82 LLVGARNSILVGVIAVGIGLTIGTALGLLAAAKRGWVEELIMRLADFTFAFPAILSAIMM 141 Query: 130 ASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYSDLRLVIEDLI 189 + V + + +G+F P FAR RA +V SREY+ S G R+ IE ++ Sbjct: 142 TAVFGAGIVNSI-IAIGIFNIPTFARVTRASANAVWSREYIMASRACGKGSWRITIEHVL 200 Query: 190 PTIATYAFMSFVLFINGGIMGEAGLSLIGLG--PTQGISLGIMLQWA--VLMEAVRRGLW 245 P I + + + I+ EA LS +GLG P Q S G ML A ++ +A +W Sbjct: 201 PNILSVLIVQATIQFAIAILAEAALSYLGLGTQPPQP-SWGRMLSEAQTLMFQAPLLAVW 259 Query: 246 WWFVPPGLAIVAVTASLLVISTAMDEVFNPRL 277 PG+AI L ++ + ++ +PRL Sbjct: 260 -----PGVAIALAVLGLNLLGDGLRDLLDPRL 286 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: 179 Number of extensions: 15 Number of successful extensions: 4 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: 290 Length adjustment: 26 Effective length of query: 254 Effective length of database: 264 Effective search space: 67056 Effective search space used: 67056 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