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_RS17225 BWI76_RS17225 oligopeptide ABC transporter ATP-binding protein OppD
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Koxy:BWI76_RS17225 Length = 337 Score = 197 bits (501), Expect = 3e-55 Identities = 115/323 (35%), Positives = 184/323 (56%), Gaps = 13/323 (4%) Query: 4 ILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPL 63 +LL +++R + V AV+ L+F + E +G+VGESG GK+ + + L Sbjct: 18 LLLDVKDLRVTFGTPDGDVTAVNDLNFNLRAGETLGIVGESGSGKSQTAFALM-----GL 72 Query: 64 TLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLA 123 +G+I ++ ++ E+ K ++I++I Q M +L P +R+ + + + Sbjct: 73 LAANGRIGGSATFNGKQILNLPERELN-KLRAEQISMIFQDPMTSLNPYMRVGEQLMEVL 131 Query: 124 ESH-GIDEEELLDKARRRFEEVGLDPLW--IKRYPFELSGGMRQRAVIAIATILNPSLLI 180 H + + E +++ + + V + +K YP E SGGMRQR +IA+A + P LLI Sbjct: 132 MLHKALSKAEAFEESVKMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLLI 191 Query: 181 ADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEF 240 ADEPT+ALDV Q ++ +L ++KR+ +II ITHD+ V I D++++MYAG+ +E+ Sbjct: 192 ADEPTTALDVTVQAQIMTLLNELKRE-FNTAIIMITHDLGVVAGICDKVLVMYAGRTMEY 250 Query: 241 APVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHA 300 + +P HPY+ GL N+V P + + + TIPG PPNL+ P GC F PRCPHA Sbjct: 251 GQARDVFYQPSHPYSIGLLNAV--PRLDAEGDALLTIPGNPPNLLRLPKGCPFQPRCPHA 308 Query: 301 MDVCKEKEPPLTEIEPGRRVACW 323 M++C PPL E PGR AC+ Sbjct: 309 MEIC-NSAPPLEEFAPGRLRACF 330 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: 275 Number of extensions: 14 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