Align TM0028, 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 209099 DVU0166 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >MicrobesOnline__882:209099 Length = 328 Score = 173 bits (438), Expect = 6e-48 Identities = 118/335 (35%), Positives = 170/335 (50%), Gaps = 23/335 (6%) Query: 3 EILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKP 62 E LL +N+ + L ++ AV+ +SF + E +G+VGESG GK+ I + KP Sbjct: 2 EALLDVQNLTVKFALRDEALTAVNDVSFTLGRGERLGLVGESGAGKSVTGFSIINLISKP 61 Query: 63 LTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRM-----EK 117 + G + N T E R G I++I Q M L P + + E Sbjct: 62 GFIAGGSVLFEGNDLVT-----TDAETLRDIRGNRISMIFQDPMMTLNPVLTIGSQMVET 116 Query: 118 YVRHLAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPS 177 + H S EE LDK R+ + + +K+YP E SGGMRQR VIAIA + +PS Sbjct: 117 ILAHQKMSRREAEEIALDKLRKVY--IPSPEKRLKQYPHEFSGGMRQRIVIAIALLTSPS 174 Query: 178 LLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237 L+IADEPT+ALDV Q ++ +L+++ + +I ITHD+ V Q+ ++ +MYAG+I Sbjct: 175 LIIADEPTTALDVTIQAEIMDLLLEL-CESEKMGLILITHDLGVVSQVTQKIAVMYAGRI 233 Query: 238 VEFAPVESLLEKPLHPYTQGLFNSVLTPEPEV-------KKRGITTIPGAPPNLINPPSG 290 VE ++ P HPYT+GL ++ P+ K+ + IPGA P+L G Sbjct: 234 VEMGETARIVADPQHPYTKGLLAAL--PQGNSCGGGCVGKRHRLNQIPGAMPSLSEIAHG 291 Query: 291 -CRFHPRCPHAMDVCKEKEPPLTEIEPGRRVACWL 324 C FH RC DVC+ P L G VAC L Sbjct: 292 ICPFHNRCELCQDVCRTSRPRLLPKRNGGLVACHL 326 Lambda K H 0.321 0.138 0.405 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: 249 Number of extensions: 8 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: 330 Length of database: 328 Length adjustment: 28 Effective length of query: 302 Effective length of database: 300 Effective search space: 90600 Effective search space used: 90600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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