GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Caulobacter crescentus NA1000

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  162 bits (409), Expect = 2e-44
 Identities = 88/242 (36%), Positives = 142/242 (58%), Gaps = 2/242 (0%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           I  +++SK + +G     A+  VS+++ +G  FGV+G SG GK+T +RLI GLE P++G 
Sbjct: 2   ITFQDVSKTYAQGGHP--ALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQ 59

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           +  D + V++     +   +R + M+FQ++ L    TV  N+AFPLKLA  P  +++ + 
Sbjct: 60  VIVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKART 119

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
            E+ E +GLS    +YP +LSGGQ QR  IARAL  +PKVLL DE  S LD +  E    
Sbjct: 120 AELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILD 179

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243
           L+  + RE  LT ++++H+   +  + ++  V+  G+  + G   E++ +PA+D   R  
Sbjct: 180 LIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV 239

Query: 244 GE 245
            E
Sbjct: 240 RE 241


Lambda     K      H
   0.317    0.136    0.374 

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: 260
Number of extensions: 7
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: 371
Length of database: 332
Length adjustment: 29
Effective length of query: 342
Effective length of database: 303
Effective search space:   103626
Effective search space used:   103626
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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