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 HSERO_RS07880 HSERO_RS07880 peptide ABC transporter substrate-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__HerbieS:HSERO_RS07880 Length = 330 Score = 165 bits (417), Expect = 1e-45 Identities = 101/267 (37%), Positives = 160/267 (59%), Gaps = 13/267 (4%) Query: 4 LVVKNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP- 62 L V+NL F F + + AV +VS V I+ LVGESGSGK+ T IL ++ Sbjct: 6 LEVRNLRTHF---FTPEGVLPAVDDVSLSVGRGRILGLVGESGSGKSVTGFSILGMVDAP 62 Query: 63 ---TSGEIYFEGKDIWKDIKDRESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISL 118 GEI F+G+D+ + D+ SL E + ++ +FQDP + NP VE + A+ Sbjct: 63 GRIVGGEILFQGRDLVR--MDKTSLRELQGNRIAMIFQDPMMTLNPVLKVEAQMVDAV-- 118 Query: 119 LENKPSNKKEALELIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIV 177 L + ++++A EL +++L +GI P++ L YPHQ+SGG +QR+ IA + +P LI+ Sbjct: 119 LAHSKVSRQQARELARDTLGMMGIASPEERLQAYPHQLSGGMRQRVAIAIAMLHKPDLII 178 Query: 178 ADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERG 237 ADEPT+ +D + + I+ +++L + GT++I+ITHDL + ++D + VM G IVE+G Sbjct: 179 ADEPTTALDVTIQAQILSEVQKLARQHGTALIWITHDLSVVAGLADEVAVMYAGRIVEQG 238 Query: 238 HPDKVVLEPTHEYTKLLVGSIPKLYRK 264 D V+ P H YT+ L+GS+P R+ Sbjct: 239 SVDAVLDAPLHPYTQGLIGSLPSNNRR 265 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: 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: 330 Length adjustment: 26 Effective length of query: 242 Effective length of database: 304 Effective search space: 73568 Effective search space used: 73568 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