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 Dsui_2799 Dsui_2799 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__PS:Dsui_2799 Length = 670 Score = 175 bits (444), Expect = 2e-48 Identities = 100/240 (41%), Positives = 151/240 (62%), Gaps = 9/240 (3%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82 ++AV VS E++ ++LVGESG GKTT K +LRLLP T G + +G+++ + +RE Sbjct: 375 VKAVDGVSLELQRGRTLALVGESGCGKTTAGKAVLRLLPAT-GSVRLDGRELL-GLPERE 432 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSN--KKEALELIKESLFRV 140 L RR++ VFQDPFAS NP V + + ++ L S ++ AL + ES V Sbjct: 433 -LKPLRRRMQMVFQDPFASLNPRLTVGEIIEEGMTALRVAASRDERRAALAALLES---V 488 Query: 141 GIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEEL 200 G+ P + LG+YPH+ SGGQ+QRI IAR ++P L+V DEPTS +D S + I+ LL L Sbjct: 489 GL-PAEALGRYPHEFSGGQRQRIAIARALAVQPELLVCDEPTSALDVSVQAQILNLLRRL 547 Query: 201 REEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIPK 260 +EE G + +FITH+ + Y++ ++ VM G IVE+G +V+ P H YT+ L+ ++P+ Sbjct: 548 QEELGLAYLFITHNFAVVEYLAHDVAVMYLGRIVEQGPVQQVLAAPCHPYTRALLSAVPE 607 Score = 141 bits (355), Expect = 4e-38 Identities = 100/267 (37%), Positives = 143/267 (53%), Gaps = 19/267 (7%) Query: 4 LVVKNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPT 63 L V+NL F G R + AV VSF V E +L+GESG GK+ TA +LRLLP Sbjct: 5 LSVRNLKAGFLAG---GRVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPNA 61 Query: 64 S----GEIYFEGKDIWKDIKDRESLVEFRRKVHA--VFQDPFASYNPFYPVERTLWQAIS 117 GE++ EG++I + E+ + RR A +FQ+P S NP + R + +++ Sbjct: 62 GRIQGGEVWLEGEEI---LALPEAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLE 118 Query: 118 LLENKPSN--KKEALELIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPL 174 ++EAL L L VGI DP+ L +YP Q+SGG KQR MIA P Sbjct: 119 RHRGMKGEAARREALAL----LTAVGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPR 174 Query: 175 LIVADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIV 234 L++ADEPT+ +D + + I+ LL L+ E+ ++ ITHDLG+ + + VM GEIV Sbjct: 175 LLIADEPTTALDVTIQAQILDLLARLQAERAMGMLLITHDLGVVARSAHRVGVMYAGEIV 234 Query: 235 ERGHPDKVVLEPTHEYTKLLVGSIPKL 261 E + P H YT+ L ++P L Sbjct: 235 ETAPRQEFFASPRHPYTQKLFAALPDL 261 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: 435 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: 670 Length adjustment: 32 Effective length of query: 236 Effective length of database: 638 Effective search space: 150568 Effective search space used: 150568 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