GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Dyella japonica UNC79MFTsu3.2

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate N515DRAFT_1536 N515DRAFT_1536 N-carbamoylputrescine amidase

Query= reanno::pseudo5_N2C3_1:AO356_14225
         (264 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1536
          Length = 296

 Score =  101 bits (252), Expect = 2e-26
 Identities = 81/258 (31%), Positives = 124/258 (48%), Gaps = 23/258 (8%)

Query: 29  ARGADVLVLPEMFMTGYNIGVDAVNVL--AEVYNGEWAQQIGRIAKAANLAIVYGYPERG 86
           A GA++++L E+    Y    ++V     AE   G   ++IG++A+   L +V    E+ 
Sbjct: 35  AAGAELVLLQELHNGPYFCQHESVGEFDHAETIPGPGTERIGKLAEELKLVVVASLFEKR 94

Query: 87  EDGQIYNAVQLIDAQGERLANYRKSHLFGD---LDHAMFSAGDSALPIVELNGWKLGLLI 143
             G  +N   + D   +    YRK H+  D    +   F+ GD     ++    +LG+L+
Sbjct: 95  ATGLYHNTAVVFDRSAKIAGKYRKMHIPDDPAFYEKFYFTPGDLGFDPIDTAVGRLGVLV 154

Query: 144 CYDLEFPENARRLALAGAELILVPTA-NMQPYEFIAD--------VTV-RARAIENQCFV 193
           C+D  +PE AR +ALAGAEL+L PTA    P +  A+        VTV R  A+ N   +
Sbjct: 155 CWDQWYPEAARLMALAGAELLLYPTAIGWDPNDEQAEKDRQREAWVTVQRGHAVANGLPL 214

Query: 194 AYANYCGHE-------AELQYCGQSSIAAPNGSRPALAGLD-EALIVGELDRQLLDDSRA 245
              N  G+E       A +Q+ G S +A P G     AG D   L+V E+D    +  R 
Sbjct: 215 LACNRTGYEPDPSGVGAGIQFWGTSFVAGPQGEFLGQAGTDGRQLLVVEIDMARSEHVRR 274

Query: 246 AYNYLHDRRPELYDDLHK 263
            + +L DRR + Y DL K
Sbjct: 275 IWPFLRDRRIDAYGDLLK 292


Lambda     K      H
   0.321    0.139    0.419 

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: 202
Number of extensions: 11
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 264
Length of database: 296
Length adjustment: 26
Effective length of query: 238
Effective length of database: 270
Effective search space:    64260
Effective search space used:    64260
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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