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 3609625 Dshi_3008 ABC transporter related (RefSeq)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Dino:3609625 Length = 576 Score = 197 bits (502), Expect = 3e-55 Identities = 102/240 (42%), Positives = 163/240 (67%), Gaps = 7/240 (2%) Query: 23 IEAVKNVSFEV--KEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWK-DIK 79 + A+ +SF + + +I+S+VG+SGSGK+T ++L PP++G++ FEG+DI K Sbjct: 298 VTALHPMSFALDGETPKIISIVGQSGSGKSTMGSLMLGFNPPSTGQVLFEGEDIAKHSAA 357 Query: 80 DRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFR 139 DR +EFR+ V AVFQDP+A +NPFY V+ L L S+ + +++ E+ Sbjct: 358 DR---LEFRKNVQAVFQDPYACFNPFYRVDHALKFPYKRLGLGTSDDEIEAKML-EACEA 413 Query: 140 VGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199 VG+D +L ++PH++SGGQ+QR+++AR +L P L++ADEP SM+DAS R I+K + + Sbjct: 414 VGLDGALILRRFPHELSGGQRQRLIVARALMLSPKLLIADEPVSMVDASLRATILKNIYD 473 Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIP 259 L++ G SI++ITHDL AY+VSD + V+ +G +VE G P +V+ +P H YT++L+ +IP Sbjct: 474 LKDRYGISILYITHDLATAYHVSDYVMVLYHGHVVEAGPPKQVIGDPQHPYTRMLIEAIP 533 Score = 126 bits (316), Expect = 1e-33 Identities = 84/244 (34%), Positives = 127/244 (52%), Gaps = 13/244 (5%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTS----GEIYFEGKDIWKDI 78 + AV +S ++ V +GESGSGKTTTA ++R+L + G I DI Sbjct: 22 VHAVTKLSLNIRPGIRVGFIGESGSGKTTTALSVMRMLGGSGRVAEGAIRLGETDILALS 81 Query: 79 KDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKES-- 136 ++ L R V + Q S NP +E +W I E K +A L S Sbjct: 82 EEEMRLTRLSR-VSYIPQGAMNSLNPIMRIENQIWDGIVAHEGKT----DAATLKARSNA 136 Query: 137 -LFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIK 195 L VG+ P YPH++SGG KQR+ IA L P LI+ADEPTS +D ++ +++ Sbjct: 137 CLESVGL-PARTGRLYPHELSGGMKQRVCIALGVSLNPELIIADEPTSALDVVTQRHVMQ 195 Query: 196 LLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLV 255 L++++ G+ +I I HD+GL D + V+K+G +VE G +++ P H YT+ L+ Sbjct: 196 TLKDVQARIGSGLILIGHDMGLMAQSVDELAVLKDGVLVEHGTVKQILEAPKHPYTRQLI 255 Query: 256 GSIP 259 S+P Sbjct: 256 SSVP 259 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: 420 Number of extensions: 18 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: 576 Length adjustment: 31 Effective length of query: 237 Effective length of database: 545 Effective search space: 129165 Effective search space used: 129165 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