GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ady2 in Methanospirillum stamsii Pt1

Align Accumulation of dyads protein 2; Ammonia transport outward protein 1 (characterized)
to candidate WP_109939208.1 DLD82_RS00825 hypothetical protein

Query= SwissProt::P25613
         (283 letters)



>NCBI__GCF_003173335.1:WP_109939208.1
          Length = 196

 Score =  108 bits (271), Expect = 7e-29
 Identities = 65/168 (38%), Positives = 87/168 (51%), Gaps = 9/168 (5%)

Query: 88  ANPAPLGLSAFALTTFVLSMFNARAQGITVPNVVVGCAMFYGGLVQLIAGIWEIALENTF 147
           ANPAPLGL AF +TT +LS+ NA       P  +   AMFYGG+ Q+IAGI+E    NTF
Sbjct: 19  ANPAPLGLCAFGMTTILLSLHNAGLTAAGSP--IFSMAMFYGGIAQIIAGIFEWKKNNTF 76

Query: 148 GGTALCSYGGFWLSFAAI-YIPWFGILEAYEDNESDLNNALGFYLLGWAIFTFGLTVCTM 206
           G     S+G FW+SFA I ++P  G+           N  L  +L  W +F  GL VCT 
Sbjct: 77  GMVTFGSFGFFWISFAFIGFLPKLGL------TAPPTNLELAAFLSVWGLFAMGLFVCTF 130

Query: 207 KSTVMFFLLFFLLALTFLLLSIGHFANRLGVTRAGGVLGVVVAFIAWY 254
           K   +  +  F + L  + L +G        +  GGV G+V   +A Y
Sbjct: 131 KMHRVLQVTLFTVVLLVVFLVVGEITEIGLFSNLGGVTGIVAGLLALY 178


Lambda     K      H
   0.323    0.140    0.436 

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: 197
Number of extensions: 12
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: 283
Length of database: 196
Length adjustment: 23
Effective length of query: 260
Effective length of database: 173
Effective search space:    44980
Effective search space used:    44980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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