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 7025499 Shewana3_2653 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__ANA3:7025499 Length = 335 Score = 127 bits (319), Expect = 4e-34 Identities = 97/328 (29%), Positives = 167/328 (50%), Gaps = 20/328 (6%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64 LL N+ V+A++ +S + E+ G+VGESG G++ L+ I T Sbjct: 3 LLDVRNLTIELDTPHGRVRALEKVSLTLNAGEIHGLVGESGSGRSLLARAILGIPGPNWT 62 Query: 65 LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIR-----MEKYV 119 + ++ N L +MT E +R G ++ +I Q +L P+ M+ Sbjct: 63 ITADRMMWDGNN----LMAMTSKE-RRNLMGSDMAMIFQDPSGSLDPSQTVGSQLMQAMP 117 Query: 120 RHLAESHGIDEEELLDKARRRFEEVGL-DPLWIK-RYPFELSGGMRQRAVIAIATILNPS 177 ++ + A++ +VG+ +P + Y +ELS G Q+ +IA+A P Sbjct: 118 KNPKAYFWQKHKHAKLTAQKWLHKVGIKNPQKVMLSYAWELSEGECQKVMIAMAIANQPR 177 Query: 178 LLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237 LLIADEPT+++++ Q + ++L Q+ + V SI+ I+H++ T+ Q D + ++Y G++ Sbjct: 178 LLIADEPTNSMELSTQAQIFRLLSQLNQLQNV-SILIISHELETLAQWCDHLSVLYCGQV 236 Query: 238 VEFAPVESLLEKPLHPYTQGLFNSVLTPE---PEVKKRGITTIPGAPPNLINPPSGCRFH 294 +E P E L+ +P HPYT+ L +++ P+ E K + T+PG+ P L + P GCR Sbjct: 237 MESGPTEELINQPYHPYTKALLDNM--PDYSGIEAHKAIMPTLPGSAPALQHLPIGCRLG 294 Query: 295 PRCPHAMDVCKEKEPPLTEIEPGRRVAC 322 PRCP A C +P L+ + R AC Sbjct: 295 PRCPEAQKKC-VNQPSLSHLR-DRYFAC 320 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: 260 Number of extensions: 17 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: 335 Length adjustment: 28 Effective length of query: 302 Effective length of database: 307 Effective search space: 92714 Effective search space used: 92714 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