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_RS15935 HSERO_RS15935 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__HerbieS:HSERO_RS15935 Length = 280 Score = 170 bits (430), Expect = 3e-47 Identities = 100/252 (39%), Positives = 154/252 (61%), Gaps = 11/252 (4%) Query: 9 LTKIFSL--GFFSKR-RIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSG 65 LTK++ L G F +++AV +VS + E + LVGESG GK+T AKM+L LLPPTSG Sbjct: 21 LTKVYPLKRGLFQPPGQLKAVNDVSLRLYRGETLGLVGESGCGKSTLAKMLLGLLPPTSG 80 Query: 66 EIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSN 125 + G+++ D +R++ R + +FQDP++S NP V + + L + N Sbjct: 81 NVLINGQEV--DPTERKA---HARHIQPIFQDPYSSLNPRKTVAEIVGLPLKL--HGIGN 133 Query: 126 KKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMI 185 E +K+ L VG+ P+ +YP+Q+SGGQ+QR+ IAR ILRP +++ DEPTS + Sbjct: 134 AAERNRQVKDILDLVGM-PERTHAQYPNQLSGGQRQRVAIARALILRPDILICDEPTSAL 192 Query: 186 DASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLE 245 D S + I+ LL +L+ E G + +FI+HDLG+ ++ D + VM G IVE +++ E Sbjct: 193 DVSVQAQILNLLLDLKAEFGLTYLFISHDLGVVEHLVDRVAVMNQGSIVELQSREQLFSE 252 Query: 246 PTHEYTKLLVGS 257 P H YT++L+ S Sbjct: 253 PQHLYTRMLLAS 264 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: 280 Length adjustment: 25 Effective length of query: 243 Effective length of database: 255 Effective search space: 61965 Effective search space used: 61965 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 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