GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Nocardioides daejeonensis MJ31

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_110207698.1 DNK54_RS14440 carbon-nitrogen hydrolase family protein

Query= reanno::pseudo3_N2E3:AO353_07425
         (264 letters)



>NCBI__GCF_003194585.1:WP_110207698.1
          Length = 272

 Score =  107 bits (266), Expect = 3e-28
 Identities = 90/267 (33%), Positives = 126/267 (47%), Gaps = 22/267 (8%)

Query: 1   MRVALYQCPPLPLDVAGNLQRLQKLATE--AKGADLLVFPEMFLTGYNIGAEAVGALAEA 58
           +RVAL Q     LD A N   +  LA E  A  ADL+V PE     +    + +   AE+
Sbjct: 11  LRVALAQLAS-GLDPAENRAAIAGLAEEPSAMTADLVVLPEAIARDFGSPRDDLAPYAES 69

Query: 59  QDGTCAQYIASIAKASGIAIVYGYPERAEDGQIYNAVQLIDSRGQRLANYRKTHL---FG 115
             G  AQ I ++A  S   +V G  E    G  +N + +   RG R A+YRK HL   FG
Sbjct: 70  TSGPFAQAITALA-GSDRTVVAGMFEAYPGGHPFNTLVM---RGARSADYRKIHLYDSFG 125

Query: 116 ELDHSMFSVGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVP---TANMI 172
             +    + GP E   V+L G++LG + CYDL FPE AR L   GA++++VP    A   
Sbjct: 126 YRESERLTAGPWEPVTVDLAGFRLGLMTCYDLRFPELARDLVDRGADVLVVPAAWVAGRT 185

Query: 173 PYDFIADV-----TVRSRAFENQCYVAYANYCGHEGEIHYCGQSSIAAPDGSRIAQAGLD 227
           P +    V      VR+RA EN  YV        +    Y G S +  P G  + +AG  
Sbjct: 186 PEEHALKVEHWRTLVRARAIENVAYVVAVG----QPSPRYTGHSMVVDPTGRVLVEAGDA 241

Query: 228 EALIVGTLDRQLMVDSRAANRYFLDRR 254
             ++  TL+   +  +R AN    +RR
Sbjct: 242 TEVLCATLEASTLRAAREANPSLDNRR 268


Lambda     K      H
   0.322    0.139    0.414 

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: 198
Number of extensions: 12
Number of successful extensions: 4
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: 272
Length adjustment: 25
Effective length of query: 239
Effective length of database: 247
Effective search space:    59033
Effective search space used:    59033
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.

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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