GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Nocardioides daejeonensis MJ31

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_110206230.1 DNK54_RS07055 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>NCBI__GCF_003194585.1:WP_110206230.1
          Length = 231

 Score = 96.3 bits (238), Expect = 5e-25
 Identities = 75/229 (32%), Positives = 114/229 (49%), Gaps = 16/229 (6%)

Query: 3   MSQPLIRMQGIEKHF----GSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHK 58
           MS P++ +QG+ K +    G+V A+ G+   V  GE   ++G +G+GKST +  +  +  
Sbjct: 1   MSTPVLELQGVRKTYSTGAGAVEAVRGIDAVVVAGEYVAVVGPSGSGKSTLMHILGCLDV 60

Query: 59  PTKGDILFEGQPLHFADPRDAIAAG---IATVHQHLAMIPLMSVSRNFFMGNEPIRKIGP 115
           PT G  L  GQ +   D     A     I  V Q   ++P ++  RN  +   P+   G 
Sbjct: 61  PTSGRQLVRGQDVAAMDEAQLAAVRNREIGFVFQQFHLLPGLTALRNVEL---PLIYAGV 117

Query: 116 LKLFDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEP 175
             L   +   R T+  + ++G+  R  D   G LSGG++Q VAIARA+     +++ DEP
Sbjct: 118 TAL---ERRRRATVA-LTRVGLGDRA-DHRPGELSGGQQQRVAIARALVTDPALVLADEP 172

Query: 176 TSALGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRG 224
           T  L  R TA+VLA   ++  QG  +V ITH  +   A  DR   L  G
Sbjct: 173 TGNLDSRATADVLALFRELHDQGRTIVLITHE-QEVAAEADRVLTLRDG 220


Lambda     K      H
   0.321    0.137    0.395 

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: 145
Number of extensions: 11
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: 261
Length of database: 231
Length adjustment: 24
Effective length of query: 237
Effective length of database: 207
Effective search space:    49059
Effective search space used:    49059
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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