GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Pseudomonas fluorescens GW456-L13

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate PfGW456L13_2675 5-aminopentanamidase (EC 3.5.1.30)

Query= reanno::pseudo6_N2E2:Pf6N2E2_4777
         (264 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2675
          Length = 279

 Score =  120 bits (301), Expect = 3e-32
 Identities = 92/243 (37%), Positives = 132/243 (54%), Gaps = 20/243 (8%)

Query: 30  RGADVLVLPEMFMTGYNIG--VDAVNVLAEVYNGEWAQQIARIAKAAGLAIVYGYPERGE 87
           +GA V+VLPE+  +GY      +A+  LAE  +G   Q    +A+   L IV G+ ER  
Sbjct: 38  QGAQVVVLPELVQSGYLFADRFEALG-LAETVDGPTLQLWQTLARELNLVIVGGFCERLP 96

Query: 88  DGQIYNAVQLIDAQGERLANYRKSHLFGDLDHAMFSAGDAALPIVELNGWKLGLLICYDL 147
             ++ N+  +IDA G R A YRK+HL+ D +  +F+AGDA  P+VE    +LG+LICYDL
Sbjct: 97  ADELANSAAMIDANGLR-AVYRKAHLW-DAEKDIFTAGDAPPPVVETLHGRLGMLICYDL 154

Query: 148 EFPENARRLALAGAELILVPT--------ANMQPYEFIADVTVRARAIENQCFVAYANYC 199
           EFPE  R  ALAGAEL+  P            +P E +    V+A A  N+ F+A  +  
Sbjct: 155 EFPEWVRLAALAGAELLCAPVNWPDGPRPQTERPAEVL---RVQANASVNRMFIAACDRY 211

Query: 200 GHEGELQYCGQSSIAAPNG---SRPALAGLDEALIVAELDRQLMDDSRAAYNYLH-DRRP 255
           GHE  + +   S I   +G   + PA  G ++ L+      +  +   +A N LH DRRP
Sbjct: 212 GHERGVGWVQGSVIVDADGYPLAGPAEQGGEQMLLATLNLAEARNKRISARNDLHQDRRP 271

Query: 256 ELY 258
           +LY
Sbjct: 272 QLY 274


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: 211
Number of extensions: 11
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: 264
Length of database: 279
Length adjustment: 25
Effective length of query: 239
Effective length of database: 254
Effective search space:    60706
Effective search space used:    60706
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 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