Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate CCNA_02173 CCNA_02173 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Caulo:CCNA_02173 Length = 249 Score = 97.8 bits (242), Expect = 3e-25 Identities = 74/248 (29%), Positives = 125/248 (50%), Gaps = 17/248 (6%) Query: 46 LEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGK 105 LE L + G S I+ + + F + G++ ++G SGSGK+TL++A+ ++P Sbjct: 14 LEARGLVKRFKTGRS-YIEVLKGIDFDAKHGDVTMVMGPSGSGKSTLVAALSGLLKPD-- 70 Query: 106 IISGKV-IFNGMDIFSMTIDEFRKLLWKDISYVPQASQ--NALNPVLPISEIFYHEAISH 162 GKV D++S+ + K ++ Q AL + ++ S Sbjct: 71 --EGKVSALEAKDLWSLPTGKIDKFRLDHCGFIFQGFNLFPALTAKQQVMTALKYQGASP 128 Query: 163 GEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 GE + RA L+ VGL P + P +LSGG KQRV IA +L NP LI DEP Sbjct: 129 GEQAR-----RAQAALESVGLGPR--VNQRPSELSGGEKQRVAIARALAKNPNLIFADEP 181 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE-GKTE 281 TSALD N +++++L++ G ++ VTHD + A+R++ + G ++++ +T Sbjct: 182 TSALDGENGQIVIRLLREAASVRGAAVICVTHD-PRLEAYADRVIHIEDGRILDDVRRTP 240 Query: 282 EIIKSPLN 289 + +PL+ Sbjct: 241 DANPAPLS 248 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: 163 Number of extensions: 5 Number of successful extensions: 2 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: 249 Length adjustment: 27 Effective length of query: 335 Effective length of database: 222 Effective search space: 74370 Effective search space used: 74370 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: 48 (23.1 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