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 WP_011973229.1 MAEO_RS02540 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >NCBI__GCF_000017185.1:WP_011973229.1 Length = 314 Score = 156 bits (394), Expect = 7e-43 Identities = 102/329 (31%), Positives = 166/329 (50%), Gaps = 21/329 (6%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M ++LRR + I + I F L PGNP IL S + + AI+ E+ L Sbjct: 1 MKNFILRRLFLAIPMAIAVSLISFSLLYFSPGNPAEIILEQKSPDSSPDENAIKEYEKKL 60 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 GL KP+Y Y +++KAL GD G S+ VID + P+T+++++ AT V + Sbjct: 61 ----GLDKPFYDLYVIWLSKALTGDFGVSLQ-NGEPVIDEFMARFPYTVMIMVGATTVYF 115 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 +LG +G L+A ++ ID V + + IP +WL ++ I++F VKL Sbjct: 116 VLGVVMGILSALNKDGIIDNIVRAYASLKMAIPSFWLALLLIWVFSVKL----------- 164 Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKD 245 + +F + L I+P ++ + G A +R ++ + SDY + + G+ + Sbjct: 165 ----KIISAFGYNGLDSLILPSFALGLGMAGSLARVLRTCILEVMSSDYILTARAKGLSN 220 Query: 246 KRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQ 304 K + K+V +N+ LP IT + + +LGGA+I E +F +PG G + DYP + Sbjct: 221 KVVVLKHVLKNAFLPVITLMGMKTAYLLGGAVIIESIFGWPGIGSYFIDIINAKDYPAVS 280 Query: 305 GIFVILIASIYLANFIVDFLYALIDPRIR 333 G+ I L N IVD YA++DPR+R Sbjct: 281 GLVFIFGILFVLVNLIVDISYAILDPRVR 309 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: 336 Number of extensions: 26 Number of successful extensions: 6 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: 314 Length adjustment: 28 Effective length of query: 310 Effective length of database: 286 Effective search space: 88660 Effective search space used: 88660 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 Apr 09 2024. 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