Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 114 bits (284), Expect = 3e-30 Identities = 77/233 (33%), Positives = 124/233 (53%), Gaps = 13/233 (5%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 IL + N++ IY G SR + + D++ V+ G+ + I+G SGSGKTTL+ Sbjct: 3 ILSIENVSKIYQSG-SRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGL----D 57 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 SG V NG + ++ D+ + ++I ++ Q Q +LP + + Sbjct: 58 SASSGSVALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQ-----LLPTLTALENVMVPLEL 112 Query: 165 ADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTS 224 +K ++A+ELL+ VGL + YP QLSGG +QRV IA + PK++ DEPT Sbjct: 113 KKRKDAKQKATELLQQVGLGDR--MTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTG 170 Query: 225 ALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277 LD EL+ LI ++N+ +G T++ VTHD ++A NR++ + G + EE Sbjct: 171 NLDTETGELIETLIFDLNKALGTTLILVTHD-TDLAAKTNRIIHIKGGKIQEE 222 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: 144 Number of extensions: 6 Number of successful extensions: 1 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: 225 Length adjustment: 26 Effective length of query: 336 Effective length of database: 199 Effective search space: 66864 Effective search space used: 66864 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: 47 (22.7 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