Align TM0027, 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_094505271.1 CEV31_RS02295 dipeptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_002252445.1:WP_094505271.1 Length = 282 Score = 180 bits (456), Expect = 3e-50 Identities = 98/246 (39%), Positives = 151/246 (61%), Gaps = 6/246 (2%) Query: 16 GFFSKRRI-EAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDI 74 G F K ++ AVK VSF++++ + +++VGESG GK+T A+++ + P TSGE+ G+D+ Sbjct: 20 GLFGKPKVVHAVKGVSFKLEKGKTLAIVGESGCGKSTLARILTMIDPQTSGELLIAGEDV 79 Query: 75 WKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIK 134 +I + R+KV VFQ+P+ S NP + L A LL N + KE E Sbjct: 80 --NIARDGLTADMRQKVQIVFQNPYGSLNPRQKIGDVL--AEPLLLNTKMSAKERRERAM 135 Query: 135 ESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGII 194 E L +VG+ K+ +YPH SGGQ+QRI IAR +L P L++ DEP S +D S + ++ Sbjct: 136 EMLLKVGLG-KEHFNRYPHMFSGGQRQRIAIARALMLNPKLLILDEPVSALDLSVQAQVL 194 Query: 195 KLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLL 254 +L +L+EE G + +FI+HDL + Y++D + VM GE+VE G ++V P H+YTK L Sbjct: 195 NILSDLQEEFGLTYVFISHDLSVVRYIADEVMVMYYGEVVEYGPREQVFSNPQHDYTKKL 254 Query: 255 VGSIPK 260 + P+ Sbjct: 255 FAATPR 260 Lambda K H 0.319 0.139 0.397 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: 190 Number of extensions: 7 Number of successful extensions: 3 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: 268 Length of database: 282 Length adjustment: 25 Effective length of query: 243 Effective length of database: 257 Effective search space: 62451 Effective search space used: 62451 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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