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 WP_106709178.1 CU102_RS01465 ATP-binding cassette domain-containing protein
Query= TCDB::Q9WXN5 (330 letters) >NCBI__GCF_003010955.1:WP_106709178.1 Length = 329 Score = 183 bits (464), Expect = 6e-51 Identities = 108/296 (36%), Positives = 171/296 (57%), Gaps = 20/296 (6%) Query: 19 KVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEF 78 K + AV+G+ + + EV+G+VGESGCGK+TL+ ++ + ++ P + +R +G Sbjct: 24 KRKLHAVNGIDLTLEKGEVLGIVGESGCGKSTLARIL-LGLLPPTSGT-----IRFDGRD 77 Query: 79 VELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEE-ELLDKA 137 + +KR+ +++ + Q ++L P + V + HGI + +A Sbjct: 78 LRT-------LKRRDLARQVQPVFQDPYSSLNPRRTIASIVAFPLDVHGIGSSADRRREA 130 Query: 138 RRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLL 197 + + VGL + R+P ELSGG RQR IA A I+ P +++ DEPTSALDV Q +L Sbjct: 131 LKIMDLVGLPARFADRHPRELSGGQRQRVAIARALIMKPEIIVCDEPTSALDVSVQSQIL 190 Query: 198 KVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQG 257 +L++++ + + +FI+H++ V IA R+ +MY G++VE A ++ P HPYT+ Sbjct: 191 NLLLELRNE-FGLTYVFISHNLGVVEHIATRVAVMYLGRVVELAETSAMFANPRHPYTRA 249 Query: 258 LFNSVLTPEPEVKKRGI--TTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPL 311 L +S+LTP P + GI T + A P+ +NPPSGC FHPRCP A D CK EP L Sbjct: 250 LLSSILTPVPGL---GIPETGLGLAFPDPLNPPSGCVFHPRCPSAFDACKCVEPQL 302 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: 307 Number of extensions: 16 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: 329 Length adjustment: 28 Effective length of query: 302 Effective length of database: 301 Effective search space: 90902 Effective search space used: 90902 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 24 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