GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Gallaecimonas xiamenensis 3-C-1

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_008484720.1 B3C1_RS10465 cell division ATP-binding protein FtsE

Query= TCDB::Q97VF4
         (324 letters)



>NCBI__GCF_000299915.1:WP_008484720.1
          Length = 225

 Score =  103 bits (256), Expect = 5e-27
 Identities = 71/199 (35%), Positives = 116/199 (58%), Gaps = 8/199 (4%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86
           AL++VS  + +G++  + G SGAGK+TL R+I   ++P++G+V  +G++I + +      
Sbjct: 17  ALQNVSFHLGKGEMAFLTGHSGAGKSTLLRLITLQERPSAGKVSINGHDISRLRSAQIPL 76

Query: 87  YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146
            R+D+ +I QD    L  +KTV E +  P++        E+RKR+   L  V L+     
Sbjct: 77  VRRDIGIIFQD--HRLLMDKTVFENVALPLI-VVGFTAGEIRKRVQTALGWVGLSDKAHC 133

Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206
              YP QLSGG++QR+ IAR++   P +++ADEP   +D  L + IL  L E  N L ++
Sbjct: 134 ---YPIQLSGGEQQRVGIARAVVNKPPLLLADEPTGNLDPKLSMDILR-LFEDLNSLGIS 189

Query: 207 MVFITHDIP-IARYFYHLF 224
           ++  THD+  IAR  +H F
Sbjct: 190 VLVATHDLGLIARMRHHTF 208


Lambda     K      H
   0.321    0.141    0.410 

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: 194
Number of extensions: 11
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: 324
Length of database: 225
Length adjustment: 25
Effective length of query: 299
Effective length of database: 200
Effective search space:    59800
Effective search space used:    59800
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 24 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