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 PP_4455 PP_4455 glutathione ABC transporter permease subunit
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Putida:PP_4455 Length = 313 Score = 171 bits (432), Expect = 3e-47 Identities = 102/330 (30%), Positives = 170/330 (51%), Gaps = 19/330 (5%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M ++ ++R + + T + T VF+L R +PG+P + IL QA+ E++ A + Sbjct: 1 MIQFAIKRLMLAIPTLLAMLTAVFVLVRLVPGDPAAVILGD-----QASAESLAA----M 51 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 E+ GL +P +QY F+ L G+ G S+T R V+ + V+PWTL L + ++ Sbjct: 52 REQLGLNQPIAMQYIHFLGDMLSGNFGVSMTS-GRTVLQEVSLVLPWTLQLTFASVLIGL 110 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 + G LG AA +RN W D SL P + M+ + +F + W PV G+ Sbjct: 111 VFGLPLGVWAALRRNAWPDYVGRILSLTGLSFPAFVSAMLMLLVFAIHFRWFPVIGSLVD 170 Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKD 245 G F+ L +P ++ + R +I LG DY ++ G++ Sbjct: 171 GG--------FLSQLHALTLPALNLGLIMTAYVMRVTRSSMISVLGEDYIRTAKAKGVRP 222 Query: 246 KR-IFKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQ 304 R + ++ RN+L+P +T + L G ++G +++TEIVFN PG G L+ AL T DY L+Q Sbjct: 223 MRLVLRHGLRNALIPIVTVVGLYFGTLIGNSVLTEIVFNRPGLGKLILGALNTRDYTLLQ 282 Query: 305 GIFVILIASIYLANFIVDFLYALIDPRIRL 334 G+ V+ + + N I D +Y L+DPR+++ Sbjct: 283 GLMVVFALCVIVVNIITDIVYGLVDPRVKI 312 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: 288 Number of extensions: 20 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: 313 Length adjustment: 28 Effective length of query: 310 Effective length of database: 285 Effective search space: 88350 Effective search space used: 88350 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