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 WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 93.2 bits (230), Expect = 5e-24 Identities = 70/233 (30%), Positives = 128/233 (54%), Gaps = 18/233 (7%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64 ++K +N++ Y E S+ A++ + EI E + ++G SG GK+TL +NM+ L Sbjct: 6 IIKIKNLKKEY--EDGSIIALNNVDLEIERGESVSIIGPSGSGKSTL-----LNMIGGLD 58 Query: 65 LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAE 124 + ++ S ++ F EI + Q ++ L+P + + + V+ Sbjct: 59 KANEGQISVAGVNLMDNSDLSN------FRSNEIGFVFQ--LHNLIPNLTVLENVQIPLL 110 Query: 125 SHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEP 184 ID++++ ++A + + V L+ + + P +LSGG RQR IA A + +PS+++ADEP Sbjct: 111 GTDIDDKKMEERALKLLKSVNLENK-VDQKPTKLSGGERQRVAIARALVNHPSIILADEP 169 Query: 185 TSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237 T ALD Q+V+LK+L+ + ++ V ++I +TH+ +Q ADR I + GKI Sbjct: 170 TGALDSETQEVILKLLLDIHKKENV-TLIMVTHEPYVAKQ-ADRSIYVLDGKI 220 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: 168 Number of extensions: 8 Number of successful extensions: 2 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: 223 Length adjustment: 25 Effective length of query: 305 Effective length of database: 198 Effective search space: 60390 Effective search space used: 60390 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: 47 (22.7 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