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_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_000012965.1:WP_011373501.1 Length = 261 Score = 111 bits (278), Expect = 1e-29 Identities = 81/242 (33%), Positives = 131/242 (54%), Gaps = 17/242 (7%) Query: 18 FSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRL--LPPT---SGEIYFEGK 72 ++K + +VK +S V + I +L+G SG GKTT + R+ L P SGEI F+ + Sbjct: 22 YAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHDLYPNNKYSGEITFKDR 81 Query: 73 DIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALEL 132 +I + +E L++ R ++ +FQ P A +P+ A L N+ E Sbjct: 82 NI---LTSKEDLIKLRIQIGMIFQKPTA-----FPMSIFDNVAYGLKLQGIKNRTELSGR 133 Query: 133 IKESLFRVGI--DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSR 190 ++++L I + KD L + +SGGQ+QR+ IAR + P +++ DEPTS +D S Sbjct: 134 VEKALKDAAIWNEVKDRLKHDANGLSGGQQQRLCIARAVAVEPEVLLFDEPTSALDPIST 193 Query: 191 GGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEY 250 GGI +L+ ELRE SII +TH++ A VSD M GE++E G +++ + P + Sbjct: 194 GGIEELIVELRER--VSIIIVTHNMQQAARVSDYTGFMYLGELIELGKTEEIFVTPKEKL 251 Query: 251 TK 252 T+ Sbjct: 252 TE 253 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: 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: 261 Length adjustment: 25 Effective length of query: 243 Effective length of database: 236 Effective search space: 57348 Effective search space used: 57348 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 Apr 09 2024. 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