GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Echinicola vietnamensis KMM 6221, DSM 17526

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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