Align TM0028, 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 N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Dyella79:N515DRAFT_1821 Length = 238 Score = 88.2 bits (217), Expect = 2e-22 Identities = 74/238 (31%), Positives = 118/238 (49%), Gaps = 17/238 (7%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPL- 63 +LK ++ Y+ E V A+ + ++ E E + V G SG GKTT F+ + L Sbjct: 1 MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTT-----FLTIAGLLE 55 Query: 64 TLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLA 123 T G+ L + VE+S++ D + K ++I I QA L+P + + V Sbjct: 56 TFTGGEYHL----DGVEVSNLN-DNARSKIRNEKIGFIFQAFN--LIPDLNVYDNVEVPL 108 Query: 124 ESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADE 183 G+ E + E VGL K YP ELSGG +QR IA A +P LL+ADE Sbjct: 109 RYRGMKALERKQRIMDALERVGLASR-AKHYPAELSGGQQQRVAIARALAGSPRLLLADE 167 Query: 184 PTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFA 241 PT LD + ++++L ++ R+G +I+ +THD + A R + + G++V+ A Sbjct: 168 PTGNLDTQMARGVMELLEEIHREG--ATIVMVTHDPELATR-AQRNVHVIDGQVVDLA 222 Lambda K H 0.321 0.138 0.405 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: 150 Number of extensions: 7 Number of successful extensions: 2 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: 330 Length of database: 238 Length adjustment: 26 Effective length of query: 304 Effective length of database: 212 Effective search space: 64448 Effective search space used: 64448 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 (21.8 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