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 1936449 b1246 oligopeptide transporter ATP-binding component (NCBI)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Keio:1936449 Length = 337 Score = 202 bits (515), Expect = 7e-57 Identities = 119/329 (36%), Positives = 188/329 (57%), Gaps = 13/329 (3%) Query: 3 EILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKP 62 + LL +++R + V AV+ L+F + E +G+VGESG GK+ + + Sbjct: 17 DALLNVKDLRVTFSTPDGDVTAVNDLNFSLRAGETLGIVGESGSGKSQTAFALM-----G 71 Query: 63 LTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHL 122 L +G+I E+ ++ E+ K ++I++I Q M +L P +R+ + + + Sbjct: 72 LLAANGRIGGSATFNGREILNLPEHELN-KLRAEQISMIFQDPMTSLNPYMRVGEQLMEV 130 Query: 123 AESH-GIDEEELLDKARRRFEEVGLDPLW--IKRYPFELSGGMRQRAVIAIATILNPSLL 179 H + + E +++ R + V + +K YP E SGGMRQR +IA+A + P LL Sbjct: 131 LMLHKNMSKAEAFEESVRMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLL 190 Query: 180 IADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVE 239 IADEPT+ALDV Q ++ +L ++KR+ +II ITHD+ V I D++++MYAG+ +E Sbjct: 191 IADEPTTALDVTVQAQIMTLLNELKRE-FNTAIIMITHDLVVVAGICDKVLVMYAGRTME 249 Query: 240 FAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPH 299 + + +P+HPY+ GL N+V P + + + TIPG PPNL+ P GC F PRCPH Sbjct: 250 YGNARDVFYQPVHPYSIGLLNAV--PRLDAEGETMLTIPGNPPNLLRLPKGCPFQPRCPH 307 Query: 300 AMDVCKEKEPPLTEIEPGRRVACWLYMEE 328 AM++C PPL E PGR AC+ +EE Sbjct: 308 AMEIC-SSAPPLEEFTPGRLRACFKPVEE 335 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: 289 Number of extensions: 13 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: 337 Length adjustment: 28 Effective length of query: 302 Effective length of database: 309 Effective search space: 93318 Effective search space used: 93318 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