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 CA265_RS02090 CA265_RS02090 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Pedo557:CA265_RS02090 Length = 208 Score = 63.9 bits (154), Expect = 3e-15 Identities = 63/191 (32%), Positives = 100/191 (52%), Gaps = 19/191 (9%) Query: 30 FEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNG-EFVELSSMTRDE 88 +EI + E ++G SG GK+TL N+I +++P G++ VNG + L + RD Sbjct: 22 WEIADMEQWLLLGASGSGKSTLLNII-SGLLEP---TQGEVL--VNGTDLYTLPARGRD- 74 Query: 89 VKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFEEVGLDP 148 +F G+ I II Q L+ ++ + + A G+ + ++ E+G+ Sbjct: 75 ---RFRGRHIGIIFQRPH--LIRSLDVLDNLELAAVMAGVPVDH--ERNLSLLHELGIAG 127 Query: 149 LWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVL-MQMKRQG 207 L K YP +LS G QR +A A + P LLIADEPTS+LD N +++++L Q K G Sbjct: 128 L-AKNYPDQLSEGQLQRVSVARALVNKPDLLIADEPTSSLDDENASLVIQMLTTQAKDNG 186 Query: 208 IVKSIIFITHD 218 ++I THD Sbjct: 187 --AALIIATHD 195 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: 142 Number of extensions: 8 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: 208 Length adjustment: 25 Effective length of query: 305 Effective length of database: 183 Effective search space: 55815 Effective search space used: 55815 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