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 6937061 Sama_1232 peptide ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__SB2B:6937061 Length = 335 Score = 131 bits (330), Expect = 2e-35 Identities = 80/245 (32%), Positives = 142/245 (57%), Gaps = 8/245 (3%) Query: 22 RIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP----TSGEIYFEGKDIWKD 77 R++A++ VS + EI LVGESGSG++ A+ +L + P T+ + ++G+++ + Sbjct: 19 RVKALEKVSLMLHAGEIHGLVGESGSGRSLLARAVLGIPGPNWTITADRMMWDGRNLM-E 77 Query: 78 IKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKP--SNKKEALELIKE 135 + D E + + +FQDP S +P + L +A+ +N P +E ++ Sbjct: 78 MSDVERRNLMGKDMAMIFQDPSGSLDPVITIGAQLIEAMPADKNVPFWRRGRERRLTAQK 137 Query: 136 SLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGII 194 L +VGI DPK V+ YP + S G+ Q++MIA +P L++ADEPT+ ++ S++ I Sbjct: 138 WLHKVGIKDPKRVMASYPWETSEGECQKVMIAMALANQPRLLIADEPTNSMEPSTQAQIF 197 Query: 195 KLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLL 254 +LL +L + QG +I+ I+H+L +N+ V+ G+++E G D+++ EP H YTK L Sbjct: 198 RLLAQLNQLQGVTIMMISHELETLADWCNNLTVLYCGQVMESGPIDELIREPLHPYTKAL 257 Query: 255 VGSIP 259 + +P Sbjct: 258 MDHLP 262 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: 199 Number of extensions: 10 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: 335 Length adjustment: 27 Effective length of query: 241 Effective length of database: 308 Effective search space: 74228 Effective search space used: 74228 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: 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