Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BPHYT_RS31200 BPHYT_RS31200 peptide ABC transporter substrate-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__BFirm:BPHYT_RS31200 Length = 325 Score = 195 bits (495), Expect = 2e-54 Identities = 116/303 (38%), Positives = 176/303 (58%), Gaps = 6/303 (1%) Query: 46 LEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGK 105 L V NL + G + + KAV+D SF V GEI+G++GESGSGK+ ++L I PG+ Sbjct: 6 LSVQNLRTHFFTG-AGVAKAVDDTSFDVAPGEIVGLVGESGSGKSITGFSVLGLIDAPGR 64 Query: 106 IISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEA 165 I++G+V+F G D+ ++T + R+L I+ + Q LNPVL I +H Sbjct: 65 IVAGRVLFKGEDLTTLTPEALRRLRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVQAHTRV 124 Query: 166 DKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTS 224 K +RA + L VG+ P L+ YP QLSGGM+QRV IA++LL +P+LI+ DEPT+ Sbjct: 125 SKHAARQRARDALASVGIPSPDERLRAYPHQLSGGMRQRVAIAIALLHDPELIIADEPTT 184 Query: 225 ALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEII 284 ALD+ Q +L ++ + +V+V+HD+ +A +A+R+ VMY G V+E G +EI+ Sbjct: 185 ALDVTIQAQILAEMQKLCARSHTAMVWVSHDLAVVAGLADRICVMYAGRVVETGSVDEIL 244 Query: 285 KSPLNPYTSLLVSSIP--SLKGEVKVINVPLDEPLVSK-EKGCPFLARCSKAFGRCKEEL 341 + P +PYT L+ S+P + +GE + +P P K GC F RC A C+ Sbjct: 245 ERPRHPYTIGLIDSLPEKARRGE-SLTQIPGMAPSALKLPVGCAFAPRCVYATSLCRSAE 303 Query: 342 PEI 344 P + Sbjct: 304 PPV 306 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: 237 Number of extensions: 5 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: 325 Length adjustment: 29 Effective length of query: 333 Effective length of database: 296 Effective search space: 98568 Effective search space used: 98568 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