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 3610414 Dshi_3795 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Dino:3610414 Length = 331 Score = 176 bits (447), Expect = 4e-49 Identities = 102/261 (39%), Positives = 155/261 (59%), Gaps = 11/261 (4%) Query: 4 LVVKNLTKIFSLGFFSKRR--IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP 61 L NL K F LG + K R + AV +V+FEV E + +VGESG GK+TTA+++++LL Sbjct: 11 LSAHNLVKHFPLGGWGKNRRVVRAVDDVTFEVAPGETLGVVGESGCGKSTTARLLVQLLG 70 Query: 62 PTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLEN 121 SGE+ F+G ++ L EFRR V VFQD +AS NP ++ AI+ Sbjct: 71 ADSGEVRFQGHVAGTEMP----LKEFRRHVQMVFQDSYASLNP----RMSMLDAIAFGPT 122 Query: 122 KPS-NKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADE 180 ++ EA + ++ L RVG+DP +YPH++SGGQ+QR+ IAR +P +IV DE Sbjct: 123 VHGVSEAEAQRIARDLLDRVGLDPSRFGPRYPHELSGGQRQRVNIARALAFQPEVIVLDE 182 Query: 181 PTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPD 240 S +D S ++ LL +L+ E+ + +FI+HDL + +VSD + VM GE+ E G Sbjct: 183 AVSALDKSVEAQVLNLLMDLKRERNLTYVFISHDLNVVRHVSDRVMVMYLGEVAEIGPTA 242 Query: 241 KVVLEPTHEYTKLLVGSIPKL 261 ++ +P H YT+ L+ ++P L Sbjct: 243 EMYADPRHPYTRALLAAMPSL 263 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: 11 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: 331 Length adjustment: 26 Effective length of query: 242 Effective length of database: 305 Effective search space: 73810 Effective search space used: 73810 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