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 GFF204 HP15_203 oligopeptide/dipeptide ABC transporter, ATPase subunit
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Marino:GFF204 Length = 332 Score = 184 bits (468), Expect = 2e-51 Identities = 111/308 (36%), Positives = 178/308 (57%), Gaps = 11/308 (3%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64 LL+ +++ + + + A+ G+SF + + E +G+VGESG GK+ + I + KP Sbjct: 3 LLEVKDLDVRFAVRGGDLTALRGISFSLDKGERLGLVGESGAGKSVAAFSILNLIAKPGY 62 Query: 65 LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRM-EKYVRHLA 123 + G+I E +L++M+ E++R G I +I Q M L P + + + V + Sbjct: 63 IAGGQILF----EGRDLAAMSERELRR-IRGNRIAMIFQDPMMTLNPVLTIGTQMVEAIL 117 Query: 124 ESHGIDEEELLDKARRRFEEVGLDP--LWIKRYPFELSGGMRQRAVIAIATILNPSLLIA 181 I ++E A R ++V + + +YP ELSGGMRQR +IAIA +L+P ++IA Sbjct: 118 AHRKISKKEARAIALDRLQKVQIPSPEKRLDQYPHELSGGMRQRVIIAIALLLDPEIIIA 177 Query: 182 DEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFA 241 DEPT+ALDV Q ++ +L+ + Q V +++ ITHD+ V Q+ RM++MY+G+I+E Sbjct: 178 DEPTTALDVTIQAEIMDLLLNLCEQENV-ALMLITHDLGVVSQVTQRMLVMYSGRIIEQG 236 Query: 242 PVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAM 301 P ++ HPYTQGL N++ P+ + IPG+ P+L N PSGC FHPRC A Sbjct: 237 PTREIINDAQHPYTQGLINAL--PQMGEPGERLFQIPGSMPSLKNVPSGCPFHPRCNFAT 294 Query: 302 DVCKEKEP 309 + CK+ P Sbjct: 295 EQCKQAMP 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: 269 Number of extensions: 8 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: 332 Length adjustment: 28 Effective length of query: 302 Effective length of database: 304 Effective search space: 91808 Effective search space used: 91808 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