Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate RR42_RS11230 RR42_RS11230 peptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Cup4G11:RR42_RS11230 Length = 347 Score = 203 bits (516), Expect = 6e-57 Identities = 115/314 (36%), Positives = 186/314 (59%), Gaps = 5/314 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LEV +L+ +D ++VN VS+ V G+ LG++GESG GK+ +I+R + P Sbjct: 16 LLEVDDLHTHFDTLTGPA-RSVNGVSYTVRAGQTLGVVGESGCGKSVTALSIMRLLPTPP 74 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 + G V G+D+ ++ E R++ +S + Q +LNPVL I H Sbjct: 75 ARMRGAVRLRGIDLLQLSEREMRRIRGNRVSMIFQEPMTSLNPVLTIGRQIAETVQLHQG 134 Query: 165 ADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 A + ++RA+E+L+LV + +P R + YP QLSGGM+QRVMIAL+L NP++++ DEPT Sbjct: 135 ASRADALKRAAEMLRLVQIPEPERRVNEYPHQLSGGMRQRVMIALALACNPEVLIADEPT 194 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q +L LI+ + +E+G+ +V +THD+ +A+ +R++VMY G +EE ++ Sbjct: 195 TALDVTIQAQILDLIRRLQKELGMGVVMITHDLGVVAECCDRVIVMYAGRKVEEASVIDL 254 Query: 284 IKSPLNPYTSLLVSSIPSLK-GEVKVINVPLDEPLVSK-EKGCPFLARCSKAFGRCKEEL 341 PL+PYT L++S+PS+ ++ +P P + +GC F ARC A RC E+ Sbjct: 255 FDRPLHPYTRALMASMPSMNTSSQRLAEIPGLVPSPQQARRGCAFAARCPHADTRCAREI 314 Query: 342 PEI-RLVYDRKVRC 354 P++ R D V C Sbjct: 315 PQLTRHGADHAVAC 328 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: 270 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: 347 Length adjustment: 29 Effective length of query: 333 Effective length of database: 318 Effective search space: 105894 Effective search space used: 105894 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