GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Caulobacter crescentus NA1000

Align ATPase (characterized, see rationale)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  187 bits (474), Expect = 3e-52
 Identities = 105/242 (43%), Positives = 154/242 (63%), Gaps = 4/242 (1%)

Query: 21  MIYAEGVEKWYGNQ-FQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEI 79
           MI  + V K Y      AL GVSL+V+ GEV  ++G SG+GKST +R +N LE+   G++
Sbjct: 1   MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60

Query: 80  WIEGHRLSH-DRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATA 138
            ++G  ++      +  +R+ VGM+FQ FNL    TV QN+   P+++   P A+ +A  
Sbjct: 61  IVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAF-PLKLAGRPAAEVKART 119

Query: 139 RQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLD 198
            +LLERV ++  A KYP QLSGGQ+QRV IARALA  P++LL DE TSALDPE   ++LD
Sbjct: 120 AELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILD 179

Query: 199 VMRDLASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFL 257
           ++  L  E G+T+++ THE+   R V DRV ++  G++VEE   +  F  P SD A++F+
Sbjct: 180 LIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFV 239

Query: 258 AQ 259
            +
Sbjct: 240 RE 241


Lambda     K      H
   0.321    0.134    0.387 

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: 207
Number of extensions: 11
Number of successful extensions: 4
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: 261
Length of database: 332
Length adjustment: 26
Effective length of query: 235
Effective length of database: 306
Effective search space:    71910
Effective search space used:    71910
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 (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