GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Nocardioides daejeonensis MJ31

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_110206230.1 DNK54_RS07055 ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_2050
         (263 letters)



>NCBI__GCF_003194585.1:WP_110206230.1
          Length = 231

 Score =  150 bits (378), Expect = 3e-41
 Identities = 91/235 (38%), Positives = 140/235 (59%), Gaps = 18/235 (7%)

Query: 12  PLLDIRGLRKQY----GPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQG 67
           P+L+++G+RK Y    G +E ++G+D  +  G  V ++G SGSGK+TL+  +  L+    
Sbjct: 4   PVLELQGVRKTYSTGAGAVEAVRGIDAVVVAGEYVAVVGPSGSGKSTLMHILGCLDVPTS 63

Query: 68  GQIMLDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLK- 126
           G+ ++ G+ +   D         +    R+R + G  FQQF+L P LTAL+NV L L+  
Sbjct: 64  GRQLVRGQDVAAMD-------EAQLAAVRNREI-GFVFQQFHLLPGLTALRNVELPLIYA 115

Query: 127 -VKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEV 185
            V  L +     +A   L RVGL +R DH PG+LSGGQQQRVAIARA+  +P+L+L DE 
Sbjct: 116 GVTALERRRRATVA---LTRVGLGDRADHRPGELSGGQQQRVAIARALVTDPALVLADEP 172

Query: 186 TSALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQG 240
           T  LD     +VL + + L + G T++L+THE   A E +D+++ +  G +E+ G
Sbjct: 173 TGNLDSRATADVLALFRELHDQGRTIVLITHEQEVAAE-ADRVLTLRDGLLEDAG 226


Lambda     K      H
   0.320    0.138    0.392 

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: 130
Number of extensions: 5
Number of successful extensions: 3
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: 263
Length of database: 231
Length adjustment: 24
Effective length of query: 239
Effective length of database: 207
Effective search space:    49473
Effective search space used:    49473
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: 46 (22.3 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