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 207955 DVU2461 oligopeptide ABC transporter, permease protein
Query= TCDB::Q9WXN7 (338 letters) >MicrobesOnline__882:207955 Length = 339 Score = 180 bits (457), Expect = 4e-50 Identities = 104/330 (31%), Positives = 171/330 (51%), Gaps = 8/330 (2%) Query: 5 SMFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERT 64 ++ + +LR+ +++V ++ T I F + PG+P + NP A A + Sbjct: 11 ALARRMLRKLAWMVVVFLGITVICFWVIHLAPGSPTDLETT-------MNPLAGAEARKR 63 Query: 65 LMEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVA 124 L +GL +P YVQY +++ + +R D G S++ R V++ I +P T+ + + A + Sbjct: 64 LESIYGLDQPLYVQYAQWLGRLVRLDFGNSMSSDGRPVMERIRERLPLTVGMNVAALFLT 123 Query: 125 WILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYS 184 +L +G +A+ + W D+G+ I +P +WL ++ + FG+ LGWLP+ G S Sbjct: 124 LLLAVPIGVASAHWQGGWFDRGMTVLVFIGFAMPGFWLALLLMLFFGIHLGWLPLSGLTS 183 Query: 185 QGTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMK 244 W F+DV +H +P ++ G + MR ++ L DY + + G+ Sbjct: 184 LDYATLSPWGKFLDVARHLALPLFIYTFGSLAGMSRFMRSAMLEVLRQDYILTARAKGLP 243 Query: 245 DKR-IFKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLI 303 + IF++ RN+LLP IT L LSL G++GG++I E +F PG G L + A+ DYPLI Sbjct: 244 TRTVIFRHALRNALLPVITILGLSLPGLIGGSVIIESIFALPGLGQLFYTAVMARDYPLI 303 Query: 304 QGIFVILIASIYLANFIVDFLYALIDPRIR 333 G V+ N I D Y L DPRIR Sbjct: 304 MGNLVLGAVLTQAGNLIADLCYGLADPRIR 333 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: 332 Number of extensions: 23 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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