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 14956 b0831 predicted peptide transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Keio:14956 Length = 306 Score = 167 bits (422), Expect = 4e-46 Identities = 104/329 (31%), Positives = 167/329 (50%), Gaps = 26/329 (7%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M Y+++R + L+ T + + +VF+ +PG+P I A PEA + Sbjct: 1 MLNYVIKRLLGLIPTLFIVSVLVFLFVHMLPGDPARLI---------AGPEADAQVIELV 51 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 ++ GL +P Y Q++ +I+ A++GD G S+ R V D I TL L + + + A Sbjct: 52 RQQLGLDQPLYHQFWHYISNAVQGDFGLSMVSR-RPVADEIASRFMPTLWLTITSMVWAV 110 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 I G + G +AA RN W D+ +T ++ P + LGM+ I +F V+LGWLP GA Sbjct: 111 IFGMAAGIIAAVWRNRWPDRLSMTIAVSGISFPAFALGMLLIQVFSVELGWLPTVGA--- 167 Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKD 245 D +HYI+P ++ + A R + L DY + G+ + Sbjct: 168 ------------DSWQHYILPSLTLGAAVAAVMARFTRASFVDVLSEDYMRTARAKGVSE 215 Query: 246 KRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQ 304 + K+ RN+++P +T + L G +LGG+++ E VFN+PG G LL ++ DYP+IQ Sbjct: 216 TWVVLKHGLRNAMIPVVTMMGLQFGFLLGGSIVVEKVFNWPGLGRLLVDSVEMRDYPVIQ 275 Query: 305 GIFVILIASIYLANFIVDFLYALIDPRIR 333 ++ L N +VD LYA I+P IR Sbjct: 276 AEILLFSLEFILINLVVDVLYAAINPAIR 304 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: 306 Number of extensions: 14 Number of successful extensions: 5 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: 306 Length adjustment: 28 Effective length of query: 310 Effective length of database: 278 Effective search space: 86180 Effective search space used: 86180 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