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 H281DRAFT_05806 H281DRAFT_05806 dipeptide transport system ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Burk376:H281DRAFT_05806 Length = 339 Score = 181 bits (460), Expect = 2e-50 Identities = 115/327 (35%), Positives = 183/327 (55%), Gaps = 25/327 (7%) Query: 5 LLKAENVRAYYKLEKV-----SVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNM 59 +L A+ + YY +++ +VKA++G+SF + + + VVGESGCGK+TL+ Sbjct: 18 VLVADKLARYYTVKRGMFATGTVKALNGVSFALERGKTLAVVGESGCGKSTLA------- 70 Query: 60 VKPLTLVDGKIF--LRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEK 117 + LT+++ L ++GE V + D K + + ++ Q +L P +E+ Sbjct: 71 -RQLTMIEAPSAGRLLIDGEDVAGA----DHAKIAALRRRVQMVFQNPFASLNPRKTVEQ 125 Query: 118 YVRH-LAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNP 176 + LA + + E ++ + VGL P KRYP SGG RQR IA A IL+P Sbjct: 126 TLGEPLAINSQLSVTERAERIAQMMRTVGLRPEHAKRYPHMFSGGQRQRVAIARAMILDP 185 Query: 177 SLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGK 236 +++ADEP SALDV Q +L + M + +Q S +FI+H+++ V IAD +++MY G Sbjct: 186 QIVVADEPVSALDVSIQAQILNLFMDL-QQEFKTSYVFISHNLSVVEHIADDVMVMYFGG 244 Query: 237 IVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGI-TTIPGAPPNLINPPSGCRFHP 295 + E + + KP HPYT+ L ++ TP R I + G P+ +NPPSGC FH Sbjct: 245 VAELGDKKRIFSKPRHPYTRALMSA--TPSIFEADRTIKIKLQGEMPSPLNPPSGCTFHQ 302 Query: 296 RCPHAMDVCKEKEPPLTEIEPGRRVAC 322 RCP+ +D C+ +EP L E++ GR+V+C Sbjct: 303 RCPYVIDRCRSEEPKLREVD-GRQVSC 328 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: 285 Number of extensions: 7 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: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 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