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_697 Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_697 Length = 316 Score = 169 bits (428), Expect = 9e-47 Identities = 113/332 (34%), Positives = 177/332 (53%), Gaps = 22/332 (6%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M ++LL+R +V + +VF L R G+P++ +L QA I A Sbjct: 1 MMRFLLKRLGGAVVVLALVAVLVFCLTRLASGDPVALLLGD-----QATAADIAQARA-- 53 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 ++GL KP VQ+ ++ + L+G+LG S+ F R V ++ TL L L A +A Sbjct: 54 --QYGLDKPLPVQFGLWVGELLQGNLGQSL-FLQRPVAQALLERAEPTLFLALFAVGIAA 110 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 ++G G AA R + D+ V +++ + +P +WLG+I I LF VKLGW P G Y Sbjct: 111 LVGVPCGMAAAVWRGSATDQAVSGVAMLGASVPSFWLGLILIQLFAVKLGWFPASG-YGD 169 Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAI--GMRLMVIYELGSDYAMFSEYLGM 243 T + + L H ++P ++V+ + I R ++ LG DY + G+ Sbjct: 170 PT------ATLGERLSHLMLP--ALVLGLLNSALIIRFTRASMLDILGEDYVRTARAKGL 221 Query: 244 KDKRIF-KYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPL 302 + I K+V RN+L+P +T L L++ ++GG ++TE VFN PG G L+ RA+ DYP+ Sbjct: 222 PEGTIMVKHVLRNALVPIVTVLGLTMALMIGGTVVTETVFNLPGVGNLVVRAVLRRDYPV 281 Query: 303 IQGIFVILIASIYLANFIVDFLYALIDPRIRL 334 IQG +++ A N +DFLY L+DPRIRL Sbjct: 282 IQGTLLVIAAIYVFINLAIDFLYTLVDPRIRL 313 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: 271 Number of extensions: 18 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: 316 Length adjustment: 28 Effective length of query: 310 Effective length of database: 288 Effective search space: 89280 Effective search space used: 89280 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