Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 119 bits (297), Expect = 2e-31 Identities = 82/235 (34%), Positives = 129/235 (54%), Gaps = 9/235 (3%) Query: 63 IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122 I A+ S + GE+ GIIG SG+GK+TLI I RP G G ++ +G ++ ++ Sbjct: 18 IPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSG----GSILIDGTEMTALG 73 Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVG 182 D + + I + Q N L+ I + ++ GE D ++ R ELL+ VG Sbjct: 74 -DAALRAQRRRIGMIFQHF-NLLSSQTVADNIAFPLRLA-GETDAGKIKARVDELLRRVG 130 Query: 183 LDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNIN 242 L+ A K YP QLSGG KQRV IA +L P ++L DE TSALD +L+L+ IN Sbjct: 131 LE-AHASK-YPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEIN 188 Query: 243 QEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVS 297 +E+ +TIV +TH++ + ++ +R+ V+ G ++E G ++ P +P T V+ Sbjct: 189 RELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFVN 243 Lambda K H 0.319 0.138 0.391 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: 238 Number of extensions: 10 Number of successful extensions: 3 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: 362 Length of database: 336 Length adjustment: 29 Effective length of query: 333 Effective length of database: 307 Effective search space: 102231 Effective search space used: 102231 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