GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Nocardioides daejeonensis MJ31

Align ATPase (characterized, see rationale)
to candidate WP_110207539.1 DNK54_RS13505 ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_003194585.1:WP_110207539.1
          Length = 330

 Score =  149 bits (375), Expect = 1e-40
 Identities = 90/222 (40%), Positives = 132/222 (59%), Gaps = 6/222 (2%)

Query: 37  ALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRLSHDRRDIATI 96
           A+ GVSL V+RGE++ ++GPSG GKST LR +  LE    G +  +G  L+     + T 
Sbjct: 16  AVDGVSLRVERGEILAVLGPSGCGKSTLLRAVAGLEPPAAGCVRADGEDLAR----VPTH 71

Query: 97  RQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPG 156
           R+   ++FQ   LF   TV  N+   P+++RR P A+      +LLE V ++  A++ P 
Sbjct: 72  RRGFALMFQDGQLFNQKTVAGNVGY-PLRIRRRPRAEVRDRVAELLELVGLSAYAERRPD 130

Query: 157 QLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRD-LASEGMTMLVATH 215
            LSGG++QRVA+ARALA++PR+LL DEP SALD  +   +   +R+ L + G T L+ TH
Sbjct: 131 SLSGGERQRVALARALAVEPRLLLLDEPLSALDAALRDRLAGELREILTAAGTTALLVTH 190

Query: 216 EVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFL 257
           +   A  VADR+ LM  G++V+   P   + AP    A  FL
Sbjct: 191 DHEEAFAVADRMALMRAGRVVQSGTPADVWAAPVDAEAADFL 232


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: 237
Number of extensions: 13
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: 261
Length of database: 330
Length adjustment: 26
Effective length of query: 235
Effective length of database: 304
Effective search space:    71440
Effective search space used:    71440
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 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