Align TM0030, 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_2047 Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2047 Length = 326 Score = 163 bits (412), Expect = 6e-45 Identities = 110/338 (32%), Positives = 182/338 (53%), Gaps = 23/338 (6%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M ++LRR I ++ I I F+L + + G+P+ +L A PE IR +L Sbjct: 1 MLAFILRRLIQAVIVMITVAFISFMLFQYV-GDPVVFLLG-----QDATPEQIRELRASL 54 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 GL KP++VQ+ F+ A +G+ G S+ KV LI P TL L L A +A Sbjct: 55 ----GLDKPFFVQFGHFLVNAAQGEFGLSLR-QGAKVSRLIAERFPATLELALVAAFLAL 109 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 +G +G AA KR T+ + +T SL+ +P + +G++ I +F V LGW P ++ + Sbjct: 110 AIGVPMGVYAALKRGTFTSQLFMTLSLLGVSLPTFLIGILLILVFAVTLGWFP---SFGR 166 Query: 186 GTIPNLSWSFFVDVLK-----HYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEY 240 G + + W + +LK H I+P ++ + + +R ++ L +DY F+ Sbjct: 167 GEVVQMGW-WSTGLLKAKGWHHIILPAVTLAIFQLTLIMRLVRAEMLEVLRTDYIKFARA 225 Query: 241 LGMKDKRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLD 299 G+ ++ I F + +N+L+P +T L LGG++ A+ITE VF +PG G L +A+T D Sbjct: 226 RGLSNRAIHFGHALKNTLVPVMTITGLQLGGLIAFAIITETVFQWPGMGLLFIQAVTFAD 285 Query: 300 YPLIQGIFVILIASIYLA-NFIVDFLYALIDPRIRLGQ 336 P + ++ LIA I++ N +VD LY +DPR+R+G+ Sbjct: 286 IP-VMAAYLCLIALIFVVINLVVDLLYFAVDPRLRVGK 322 Lambda K H 0.329 0.146 0.449 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: 283 Number of extensions: 17 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: 338 Length of database: 326 Length adjustment: 28 Effective length of query: 310 Effective length of database: 298 Effective search space: 92380 Effective search space used: 92380 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: 49 (23.5 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