GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Methanospirillum lacunae Ki8-1

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_109969118.1 DK846_RS11600 carbon-nitrogen hydrolase family protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_2504
         (264 letters)



>NCBI__GCF_003173355.1:WP_109969118.1
          Length = 261

 Score = 81.3 bits (199), Expect = 2e-20
 Identities = 69/232 (29%), Positives = 104/232 (44%), Gaps = 5/232 (2%)

Query: 32  ADLLVLPEMFLTGYNIGIDAVSVLAEVHNGESAQQIARIAKTTGIAILYGYPERTEDGQI 91
           A  +  PE  +TG++  +D  + + +  + E    +   A    I IL  Y E+ +    
Sbjct: 34  ASFISFPEQVITGWD-PLDGKNFV-QTESDEIVSVLCEYACDFSIGILGSYREKYQPHPR 91

Query: 92  YNAVQLIDANGERLCNYRKTHLFGD-LDHSMFSPGPDEFPLVELNGWKLGFLICYDLEFP 150
             A+  I  +G  L  Y K HLF    +   + PG +E  L   +G + G  ICYDL F 
Sbjct: 92  NTAIA-IAPDGRILGRYSKMHLFSPGHEDQAYCPG-EEIALFSYDGCRCGIAICYDLRFA 149

Query: 151 ENARRLALAGAELILVPTANMIPYDFIADVTVRARAFENQCYVAYANYCGHEGEIQYCGQ 210
           +  R    A  +L++VP+A         ++   ARA E Q YVA  N  G      Y G 
Sbjct: 150 DLFRLYRDADVDLVMVPSAWPASRMRYFELFATARAAEFQMYVAGINTVGRTPVDLYSGG 209

Query: 211 SSIAAPDGSRIAQAGLDEALIVGELDRQLMIDSRAANRYFLDRRPELYGELN 262
           S IA PDG+ I +    E L+  ++   L+   R +     DRR E+Y  L+
Sbjct: 210 SLIAGPDGAVICRGSEVEELLFSDICPDLVAGIRESFPVHSDRRSEVYQNLS 261


Lambda     K      H
   0.322    0.140    0.420 

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: 203
Number of extensions: 14
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: 264
Length of database: 261
Length adjustment: 25
Effective length of query: 239
Effective length of database: 236
Effective search space:    56404
Effective search space used:    56404
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: 47 (22.7 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