GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutV in Caulobacter crescentus NA1000

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02751 CCNA_02751 ABC transporter
           ATP-binding protein
          Length = 332

 Score =  185 bits (469), Expect = 1e-51
 Identities = 100/223 (44%), Positives = 144/223 (64%), Gaps = 1/223 (0%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           L+ VSL + AG++F ++G SG+GKSTL+R IN L  P++G+V+ DGD++  LG   LRA 
Sbjct: 19  LSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDGDDVAALGVAGLRAL 78

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPH 162
           R RRV M+FQ F L+  +TV QNV +  ++ G    + +    + ++ VGLS +  K+P 
Sbjct: 79  R-RRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAELLERVGLSAHAGKYPA 137

Query: 163 QLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITH 222
           QLSGG KQRVG+ARALA +  V+L DEA SALDP     + D +  L R L  TIV ITH
Sbjct: 138 QLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLIAGLNRELGLTIVLITH 197

Query: 223 DLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQ 265
           ++D   R+   +A+L  G+VV+ G   ++  +PA+D   RFV+
Sbjct: 198 EMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFVR 240


Lambda     K      H
   0.323    0.139    0.397 

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: 272
Number of extensions: 17
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: 275
Length of database: 332
Length adjustment: 27
Effective length of query: 248
Effective length of database: 305
Effective search space:    75640
Effective search space used:    75640
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 (21.9 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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