Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate HSERO_RS15940 HSERO_RS15940 peptide ABC transporter substrate-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__HerbieS:HSERO_RS15940 Length = 334 Score = 175 bits (444), Expect = 1e-48 Identities = 101/302 (33%), Positives = 167/302 (55%), Gaps = 6/302 (1%) Query: 44 MILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPP 103 ++L+V NL V N ++ AV + F V +GE+L ++GESG GK+ A++ + Sbjct: 3 VLLDVKNLKVDLPTENG-MLHAVRGIDFQVRRGEMLCLVGESGCGKSMTSLALMGLLPRK 61 Query: 104 GKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163 + + ++F+G+D+ M + +L K ++ + Q +LNP + + Sbjct: 62 AQCSADHILFDGVDLHGMPDKQLMQLRGKRMAMIFQEPMTSLNPSYTLGNQLCEAMLQQP 121 Query: 164 EADKKRVIERASELLKLVGLDPARV-LKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 + ERA LL G+ A L+ YP QLSGG++QRVMIA+SL+ NP LI+ DEP Sbjct: 122 GVSRAEARERALYLLHRTGISNAEDRLRQYPHQLSGGLRQRVMIAMSLMCNPDLIIADEP 181 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD+ Q +L++I+ + QE G ++++THD+ +++IA+R+ VMY G V+E + Sbjct: 182 TTALDVTIQAQILRMIRELQQEFGAAVIFITHDLGVVSRIADRVAVMYAGQVVETTDVAQ 241 Query: 283 IIKSPLNPYTSLLVSSIP----SLKGEVKVINVPLDEPLVSKEKGCPFLARCSKAFGRCK 338 + P +PYT L++ IP +L G + LV + GC F RC+KA C+ Sbjct: 242 LFAQPRHPYTQGLLNCIPVRGKTLPGSHLQAIPGVVPSLVGQVSGCAFRNRCAKADSGCE 301 Query: 339 EE 340 + Sbjct: 302 RD 303 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: 245 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: 334 Length adjustment: 29 Effective length of query: 333 Effective length of database: 305 Effective search space: 101565 Effective search space used: 101565 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