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_011386731.1 AMB_RS22185 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_000009985.1:WP_011386731.1 Length = 533 Score = 156 bits (394), Expect = 1e-42 Identities = 90/235 (38%), Positives = 139/235 (59%), Gaps = 5/235 (2%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82 ++AV +S ++K + +VGESGSGKTT +LRLL + GEI F G I + Sbjct: 297 VKAVDGISLDLKRGHTIGVVGESGSGKTTLGLALLRLLD-SDGEISFGGTRI--ESMSAG 353 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGI 142 +L RR++ VFQDP+ S +P V + + + + + E + E LI +L VG+ Sbjct: 354 TLRPLRRQMQMVFQDPYGSLSPRMSVGQIVGEGLEVHE-PAMHAAERDRLIAAALEEVGL 412 Query: 143 DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELRE 202 DP +YPH+ SGGQ+QRI IAR +L+P IV DEPTS +D S + I+ LL +L+ Sbjct: 413 DPA-TRDRYPHEFSGGQRQRIAIARALVLKPKFIVLDEPTSALDVSVQAQIVDLLRDLQA 471 Query: 203 EQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGS 257 + +FI+HDL + ++D++ VMK+G++VE G D++ P YT+ L+ + Sbjct: 472 RHALAYLFISHDLRVVRALADDLLVMKDGKVVEAGRADELFKAPRTAYTRALMAA 526 Score = 150 bits (379), Expect = 6e-41 Identities = 94/245 (38%), Positives = 144/245 (58%), Gaps = 11/245 (4%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP-----PTSGEIYFEGKDIWKD 77 ++AVK VSF + + E ++LVGESGSGK+ TA IL+LLP G I +G ++ Sbjct: 20 VQAVKGVSFTLAKGETLALVGESGSGKSVTALSILQLLPYPRATHPRGSIRLDGAELVGA 79 Query: 78 IKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISL-LENKPSNKKEALELIKES 136 + V R + VFQ+P S NP + +E + + + L L + S ++ + E Sbjct: 80 PEPALRKVRGGR-IAMVFQEPMTSLNPLHSIEAQVGEVLELHLGLRGSTLRDR---VVEL 135 Query: 137 LFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIK 195 L VGI +P+ LG PH++SGGQ+QR+MIA P +++ADEPT+ +D + + I+ Sbjct: 136 LSLVGIPEPEKRLGALPHELSGGQRQRVMIAMALAGEPDILIADEPTTALDVTIQAQILA 195 Query: 196 LLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLV 255 LL+ L+ G +++FITHDLG+ ++D + VM GEIVE G +V P H YT+ L+ Sbjct: 196 LLKGLQARLGMALLFITHDLGIVRKMADRVCVMNAGEIVESGPLPQVFDAPAHPYTQRLL 255 Query: 256 GSIPK 260 + PK Sbjct: 256 AAEPK 260 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: 382 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 268 Length of database: 533 Length adjustment: 30 Effective length of query: 238 Effective length of database: 503 Effective search space: 119714 Effective search space used: 119714 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: 50 (23.9 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