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 SMc02829 SMc02829 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Smeli:SMc02829 Length = 542 Score = 179 bits (454), Expect = 1e-49 Identities = 101/242 (41%), Positives = 149/242 (61%), Gaps = 9/242 (3%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP-----PTSGEIYFEGKDIWKDIK 79 AV +SF++K E V+LVGESGSGK+ +A IL+LLP SGEI F GKD+ K Sbjct: 24 AVDRISFDIKRGETVALVGESGSGKSVSANSILKLLPYPAASHPSGEILFNGKDLLKASD 83 Query: 80 DRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFR 139 D V V +FQ+P S NP + +E+ + + + + ++ A L E L + Sbjct: 84 DELRHVR-GNDVTMIFQEPMTSLNPLHTIEQQIGEILEIHQDLKGAAARARTL--ELLEQ 140 Query: 140 VGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLE 198 VGI + + LG YPHQ+SGGQ+QR+MIA RP L++ADEPT+ +D + + I++LL+ Sbjct: 141 VGIREAEKRLGAYPHQLSGGQRQRVMIAMALANRPELLIADEPTTALDVTVQAQILELLK 200 Query: 199 ELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSI 258 L++E G S++FITHDLG+ ++D + VM G+IVE G ++ P H YT+ L+ S Sbjct: 201 SLKDEHGMSMLFITHDLGIVRKIADRVCVMTKGKIVETGPTAEIFANPQHAYTRHLLASE 260 Query: 259 PK 260 P+ Sbjct: 261 PR 262 Score = 147 bits (372), Expect = 4e-40 Identities = 79/235 (33%), Positives = 137/235 (58%), Gaps = 5/235 (2%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82 ++AV + ++ + + +VGESGSGKTT + RL+ + G I F G+DI D Sbjct: 299 VKAVDGIDLTLRAGQTLGVVGESGSGKTTLGLALTRLIS-SKGRIAFVGEDI--DAYSFR 355 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGI 142 + R ++ VFQDP+ S +P + + + + + E K E + + +L VG+ Sbjct: 356 EMRPLRNRMQVVFQDPYGSLSPRMSIADIIGEGLKIHE-KALTDGERDQRVAAALEEVGL 414 Query: 143 DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELRE 202 DP +YPH+ SGGQ+QRI IAR +L+P ++ DEPTS +D S + ++ LL +L+ Sbjct: 415 DPA-TRWRYPHEFSGGQRQRIAIARAMVLKPQFVMLDEPTSALDMSVQAQVVDLLRDLQR 473 Query: 203 EQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGS 257 + + +FI+HDL + +++ + VM+ G++VE+G +++ PT +YTK L+ + Sbjct: 474 KHNLAYLFISHDLRVVRALANEVIVMRLGKVVEQGPAERIFEAPTEDYTKALMAA 528 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: 404 Number of extensions: 25 Number of successful extensions: 7 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: 542 Length adjustment: 30 Effective length of query: 238 Effective length of database: 512 Effective search space: 121856 Effective search space used: 121856 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