TABLE 3.
BLAST analysis of Delaware estuary pufMa
| Library | Top BLASTX hit | Accession no. | Phylogenetic groupb | % of clones | Avg % identityc |
|---|---|---|---|---|---|
| December 2001 river | DelRiverFos06H03 | AAX48200 | Beta | 88 | 99 |
| Roseateles depolymerans | BAB19668 | Beta | 4 | 94 | |
| Lake Fryxell c1 | AAO62372 | Alpha-1 | 3 | 96 | |
| Lake Fryxell c7 | AAO62378 | Alpha-3 | 1 | 100 | |
| Rhodobacter blasticus | BAA22642 | Alpha-3 | 1 | 93 | |
| Thiocapsa roseopersicina | CAD66535 | Gamma | 1 | 93 | |
| Thiocystis gelatinosa | BAA22650 | Gamma | 1 | 90 | |
| August 2002 river | Congregibacter litoralis KT71 | ZP_01104362 | Gamma | 51 | 92 |
| DelRiverFos06H03 | AAX48200 | Beta | 16 | 98 | |
| Lake Fryxell c1 | AAO62372 | Alpha-1 | 15 | 93 | |
| Lake Fryxell c8 | AAO62379 | Alpha-1 | 8 | 89 | |
| Blastomonas sp. strain NT12 | BAA25728 | Alpha-4 | 7 | 95 | |
| Rhodobacter blasticus | BAA22642 | Alpha-3 | 2 | 95 | |
| DelRiverFos13D03 | AAX48162 | Alpha-3 | 1 | 98 | |
| August 2002 river cDNA | DelRiverFos06H03 | AAX48200 | Beta | 30 | 94 |
| Lake Fryxell c1 | AAO62372 | Alpha-1 | 19 | 94 | |
| Blastomonas natatoria | BAA25728 | Alpha-4 | 14 | 90 | |
| Congregibacter litoralis KT71 | ZP_01104362 | Gamma | 14 | 92 | |
| Roseiflexus sp. strain RS-1 | ZP_01355478 | Green non-sulfur | 7 | 72 | |
| DelRiverFos13D03 | AAX48162 | Alpha-3 | 4 | 98 | |
| Jannaschia sp. strain CCS1 | YP_508114 | Alpha-3 | 4 | 94 | |
| Roseococcus thiosulfatophilus | AAL57746 | Alpha-1 | 3 | 86 | |
| Porphyrobacter neustonensis | BAA25904 | Alpha-4 | 3 | 93 | |
| Lake Fryxell c8 | AAO62379 | Alpha-1 | 1 | 92 | |
| Rhodobacter veldkampii | BAC54030 | Alpha-3 | 1 | 92 | |
| August 2002 bay | EBAC000-29C02 | AAM48603 | Gamma | 37 | 95 |
| Congregibacter litoralis KT71 | ZP_01626201 | Gamma | 32 | 95 | |
| Rhodobacter blasticus | BAA22642 | Alpha-3 | 21 | 89 | |
| Roseobacter sp. strain SYOP2 | AAT79391 | Alpha-3 | 3 | 98 | |
| Porphyrobacter sanguineus | BAA25723 | Alpha-4 | 3 | 87 | |
| Jannaschia sp. strain CCS1 | YP_508114 | Alpha-3 | 2 | 95 | |
| Blastomonas sp. strain NT12 | BAA77030 | Alpha-4 | 1 | 90 | |
| Hawaii envhot3 | AAL02391 | Gamma | 1 | 95 |
a
All pufM genes were compared to database sequences (January 2007) using BLASTX. Sequences similar to those boldfaced in the table were targeted by qPCR in this study.
b
Phylogenetic group assignment of each top BLAST hit was based on 16S rRNA for cultured bacteria and on pufM for uncultured bacteria. Alpha, beta, and gamma refer to subclasses of the Proteobacteria. Lake Fryxell clone 1 and 7 pufM phylogenetic affiliations were assigned to the alpha-1 and alpha-3 subclasses of Proteobacteria (19). The pufM gene in clone EBAC000-29C02 was assigned to the Gammaproteobacteria (15).
c
Average pufM product percent amino acid identity to the top BLASTX hit for all clones in each library is noted.