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_050750808.1 AMB_RS09975 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >NCBI__GCF_000009985.1:WP_050750808.1 Length = 299 Score = 154 bits (388), Expect = 4e-42 Identities = 96/307 (31%), Positives = 161/307 (52%), Gaps = 15/307 (4%) Query: 27 IVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLMEEFGLGKPWYVQYFEFITKA 86 +V+ L +PG+P+ +++G R+ +A+R L +GL +PW ++ ++ + Sbjct: 4 VVYGLMGLMPGDPIDLMIAGDPRLTPE--DAVR-----LKVLYGLDRPWTERWLRWLGQV 56 Query: 87 LRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWILGNSLGALAAYKRNTWIDKG 146 L+G+LG S Y R V+D + P + + +L+L A ++ L LG LA+ + +D+ Sbjct: 57 LQGELGYS-RLYARPVLDAMAPALGNSALLMLSAMALSLSLAIPLGILASLRPGGLVDRL 115 Query: 147 VLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQGTIPNLSWSFFVDVLKHYIMP 206 V + +P +WLG++ I +F V LGWLP G S G D L+H ++P Sbjct: 116 VNLAAFASVSVPVFWLGLMLIVVFAVSLGWLPAGGVESVGD------GGPTDRLRHMVLP 169 Query: 207 FASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDKRI-FKYVFRNSLLPQITGLA 265 +++ ++ +G MR +I E G+DY + G RI ++ RN+LLP T +A Sbjct: 170 VSALALAGIGQATRHMRAAMIGEAGADYIRTARAKGCGPARIVLRHQLRNALLPITTIIA 229 Query: 266 LSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQGIFVILIASIYLANFIVDFLY 325 L GG+ GALITE VF +PG G L++ A+ D+ L ++ A + + D Y Sbjct: 230 LEFGGLFSGALITETVFAWPGMGRLIYEAVMGNDFNLALSGLLLATAMTLAGSILADMAY 289 Query: 326 ALIDPRI 332 +DPRI Sbjct: 290 QRLDPRI 296 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: 272 Number of extensions: 15 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: 299 Length adjustment: 27 Effective length of query: 311 Effective length of database: 272 Effective search space: 84592 Effective search space used: 84592 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