Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Pf6N2E2_1812 peptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1812 Length = 338 Score = 192 bits (488), Expect = 1e-53 Identities = 107/310 (34%), Positives = 187/310 (60%), Gaps = 11/310 (3%) Query: 45 ILEVHNLNVIYDEGNSR----IIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAI 100 +L V NL V GNS ++ AV + F VE+GE+L I+GESG GK+ A++ + Sbjct: 3 LLHVENLRVDIPMGNSPTPDDMLHAVRGLDFEVERGEMLCIVGESGCGKSLTSLALMDLL 62 Query: 101 RPPGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAI 160 + + ++ +G+D+ + L ++ + Q +LNP I + Sbjct: 63 PRKARRTASRLTLDGIDMLGQSERRMCDLRGNRLAMIFQEPMTSLNPAYSIGDQLSEVLT 122 Query: 161 SHGEADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILM 219 H + +K + RA+++L+ VG+ + A L+ YP QLSGG++QRV+IA++L+ P LI+ Sbjct: 123 QHRKVSRKDALARAAQMLEKVGISNAAERLRQYPHQLSGGLRQRVIIAMALMCEPDLIIA 182 Query: 220 DEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGK 279 DEPT+ALD+ Q +L+LI++I +E+G+ ++++THD+ +A+IA+R+ VMY G ++E Sbjct: 183 DEPTTALDVTIQAQILRLIRDIQKELGLAVIFITHDLGLVARIADRVAVMYAGEIVETAP 242 Query: 280 TEEIIKSPLNPYTSLLVSSIPSLKGEVK----VINVP-LDEPLVSKEKGCPFLARCSKAF 334 ++ ++P +PYT L++SIP + G K + ++P L LV +++GC F RC++A Sbjct: 243 ARQLFENPQHPYTRGLLASIP-IPGRTKPGEALGSIPGLVPSLVGEQQGCAFRNRCAQAI 301 Query: 335 GRCKEELPEI 344 C +++PEI Sbjct: 302 TACAQDIPEI 311 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: 219 Number of extensions: 8 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: 338 Length adjustment: 29 Effective length of query: 333 Effective length of database: 309 Effective search space: 102897 Effective search space used: 102897 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