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 8501090 DvMF_1826 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Miya:8501090 Length = 333 Score = 160 bits (404), Expect = 4e-44 Identities = 105/269 (39%), Positives = 153/269 (56%), Gaps = 13/269 (4%) Query: 4 LVVKNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP- 62 L V NLT F+L + AV +VSF + + E + LVGESG+GK+ T IL L+ Sbjct: 5 LDVSNLTVKFAL---RDTALTAVNDVSFTLAKGERLGLVGESGAGKSVTGFSILNLVSKP 61 Query: 63 ---TSGEIYFEGKDIWKDIKDRESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISL 118 G + FEGKD+ + D E+L + R ++ +FQDP + NP V + + I Sbjct: 62 GFIAGGSVLFEGKDLTR--ADAETLRDIRGNRISMIFQDPMMTLNPVLTVGTQMIETI-- 117 Query: 119 LENKPSNKKEALELIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIV 177 L +K +KEA + + L +V I P+ L +YPH+ SGG +QRI+IA + P LI+ Sbjct: 118 LAHKKVTRKEAEAIALDKLRKVYIPSPERRLAQYPHEFSGGMRQRIVIAIALLTSPSLII 177 Query: 178 ADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERG 237 ADEPT+ +D + + I+ LL EL + + +I ITHDLG+ V+ I VM G IVE G Sbjct: 178 ADEPTTALDVTIQAEIMDLLLELCQSEDMGLILITHDLGVVSQVTQKIAVMYAGGIVEMG 237 Query: 238 HPDKVVLEPTHEYTKLLVGSIPKLYRKLE 266 VV EP H YT+ L+G++P+ K + Sbjct: 238 DTAMVVGEPLHPYTRGLLGALPQCADKAD 266 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: 206 Number of extensions: 12 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: 333 Length adjustment: 27 Effective length of query: 241 Effective length of database: 306 Effective search space: 73746 Effective search space used: 73746 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