Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Korea:Ga0059261_2703 Length = 313 Score = 100 bits (249), Expect = 5e-26 Identities = 81/278 (29%), Positives = 140/278 (50%), Gaps = 34/278 (12%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 IL V ++ Y G+ KA+ V + KGEI ++G +G+GKTTLIS I + P Sbjct: 4 ILSVRGVSKTYASGH----KALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPS- 58 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 SG ++ +G D S P+A++ + V + E + Sbjct: 59 ---SGTIVVDGHDAISE----------------PRAARMKIGLVPQELSVDMFETVQATT 99 Query: 165 ADKKRVIERAS------ELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLIL 218 +R+ R + ++LK + L R K+ +LSGGMK+RV+IA +L P ++ Sbjct: 100 RYSRRLFGRPANDAYIDQVLKDLSLYDKRNSKV--MELSGGMKRRVLIAKALAHEPDILF 157 Query: 219 MDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKG-YVMEE 277 +DEPT+ +D+ + + KLI ++ +E G TI+ TH I ++A+R+ V+ KG ++ E Sbjct: 158 LDEPTAGVDVSLRRDMWKLIGSL-RERGTTIILTTHYIEEAEEMADRVGVINKGELLLVE 216 Query: 278 GKTEEIIKSPLNPYTSLLVSSIPSLKGEVKVINVPLDE 315 GK E + K LV + ++ GE++ ++ L++ Sbjct: 217 GKAELMKKLGKREMDIALVEPMTAIPGELEEWHLALED 254 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: 231 Number of extensions: 9 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: 313 Length adjustment: 28 Effective length of query: 334 Effective length of database: 285 Effective search space: 95190 Effective search space used: 95190 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