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 HSERO_RS07880 HSERO_RS07880 peptide ABC transporter substrate-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__HerbieS:HSERO_RS07880 Length = 330 Score = 177 bits (448), Expect = 4e-49 Identities = 114/328 (34%), Positives = 178/328 (54%), Gaps = 16/328 (4%) Query: 1 MKEILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMV 60 M + L+ N+R ++ + + AVD +S + ++G+VGESG GK+ I + Sbjct: 1 MSALTLEVRNLRTHFFTPEGVLPAVDDVSLSVGRGRILGLVGESGSGKSVTGFSILGMVD 60 Query: 61 KPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVR 120 P +V G+I + +L M + + R+ G I +I Q M L P +++E + Sbjct: 61 APGRIVGGEILFQGR----DLVRMDKTSL-RELQGNRIAMIFQDPMMTLNPVLKVEAQMV 115 Query: 121 HLAESHG-IDEEELLDKARRRFEEVGL--DPLWIKRYPFELSGGMRQRAVIAIATILNPS 177 +H + ++ + AR +G+ ++ YP +LSGGMRQR IAIA + P Sbjct: 116 DAVLAHSKVSRQQARELARDTLGMMGIASPEERLQAYPHQLSGGMRQRVAIAIAMLHKPD 175 Query: 178 LLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237 L+IADEPT+ALDV Q +L + ++ RQ ++I+ITHD++ V +AD + +MYAG+I Sbjct: 176 LIIADEPTTALDVTIQAQILSEVQKLARQHGT-ALIWITHDLSVVAGLADEVAVMYAGRI 234 Query: 238 VEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRG--ITTIPGAPPNLINPPSGCRFHP 295 VE V+++L+ PLHPYTQGL S+ P +RG + IPG PNL++ P C F Sbjct: 235 VEQGSVDAVLDAPLHPYTQGLIGSL----PSNNRRGARLRQIPGMTPNLLHLPPTCAFAA 290 Query: 296 RCPHAMDVCKEKEPPLTEIEPGRRVACW 323 RC C P ++E P RV C+ Sbjct: 291 RCERLSQQCL-VAPAISEPLPAHRVRCY 317 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: 245 Number of extensions: 6 Number of successful extensions: 4 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: 330 Length adjustment: 28 Effective length of query: 302 Effective length of database: 302 Effective search space: 91204 Effective search space used: 91204 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: 49 (23.5 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