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 Pf1N1B4_1127 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1127 Length = 326 Score = 202 bits (514), Expect = 9e-57 Identities = 121/328 (36%), Positives = 193/328 (58%), Gaps = 24/328 (7%) Query: 4 ILLKAENVRAYYKLEK------VSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFM 57 ++L A N+ +Y++ + +V+A++G+SFE+ + + VVGESGCGK+TL+ Sbjct: 3 VVLTARNLTRHYEVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLA----- 57 Query: 58 NMVKPLTLVD--GKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRM 115 + LTL++ L++ G+ V + D+ +RK K++ ++ Q+ +L P ++ Sbjct: 58 ---RALTLIEEPSSGSLKIAGQEVAGA----DKAQRKQLRKDVQMVFQSPYASLNPRQKV 110 Query: 116 -EKYVRHLAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATIL 174 ++ L + + E +K + ++VGL P +RYP SGG RQR +A A +L Sbjct: 111 GDQLAEPLLINTNLSASERREKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMML 170 Query: 175 NPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYA 234 P +L+ADEPTSALDV Q +L + M + +Q + +FI+H++A VR +AD +++MY Sbjct: 171 QPKVLVADEPTSALDVSIQAQVLNLFMDL-QQEFNTAYVFISHNLAVVRHVADHVMVMYL 229 Query: 235 GKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFH 294 G+ VE P E + +PLHPYTQ L ++ T P+ K I I G PN +NPPSGC FH Sbjct: 230 GRPVEMGPKEDIYTRPLHPYTQALLSATPTIHPDPTKPKI-KIVGELPNPLNPPSGCAFH 288 Query: 295 PRCPHAMDVCKEKEPPLTEIEPGRRVAC 322 RCP+A D C +EP L ++ R+VAC Sbjct: 289 KRCPYATDRCTTEEPLLRLVDT-RQVAC 315 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: 293 Number of extensions: 10 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: 326 Length adjustment: 28 Effective length of query: 302 Effective length of database: 298 Effective search space: 89996 Effective search space used: 89996 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 Apr 09 2024. 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