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 BWI76_RS07535 BWI76_RS07535 dipeptide/oligopeptide/nickel ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Koxy:BWI76_RS07535 Length = 347 Score = 200 bits (508), Expect = 5e-56 Identities = 119/326 (36%), Positives = 190/326 (58%), Gaps = 24/326 (7%) Query: 5 LLKAENVRAYY-----KLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNM 59 LLK N+ ++ K +V V+AVD +SF +++ E +GVVGESGCGK+T + ++ M + Sbjct: 16 LLKVNNLLKHFPAGGGKAREV-VQAVDDVSFAVIKGETLGVVGESGCGKSTTARLL-MQL 73 Query: 60 VKPLTLVDGKIFLRVNGEFV-ELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKY 118 +K + +GE + + + + K + +++ ++ Q + +L P + ME+ Sbjct: 74 LK-----------QDSGELIFDGLEVGSSRLPMKAYRRQVQMVFQDSYASLNPRMTMEES 122 Query: 119 VRHLAESHGIDEEELLDKARRRFEEVGLDP-LWIKRYPFELSGGMRQRAVIAIATILNPS 177 + HG+ +E + AR VGL+P + RYP LSGG RQR IA A + P Sbjct: 123 IAFGQRVHGVSAKEASEYARYLLAHVGLEPERFAHRYPHALSGGQRQRVNIARALAMKPR 182 Query: 178 LLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237 L+I DE SALD + +L++L ++KR + + +FI+HD+ VR ++DR+++MY G++ Sbjct: 183 LVILDEAVSALDKSVEAQVLQLLQELKRT-LALTYVFISHDLHVVRWLSDRILVMYLGEV 241 Query: 238 VEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITT-IPGAPPNLINPPSGCRFHPR 296 VE P E L HPYT+ L +S+ + +P R +T+ + G PP+ I+PPSGCRFH R Sbjct: 242 VEIGPAEQLFTASAHPYTRALLSSMPSMDPH--NRTLTSALNGDPPSPISPPSGCRFHTR 299 Query: 297 CPHAMDVCKEKEPPLTEIEPGRRVAC 322 CPHA VC E +P L + G + AC Sbjct: 300 CPHARAVCAEVKPTLQSVGEGHQSAC 325 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: 276 Number of extensions: 18 Number of successful extensions: 5 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: 347 Length adjustment: 28 Effective length of query: 302 Effective length of database: 319 Effective search space: 96338 Effective search space used: 96338 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