T0087 relatives include sequences related to the RecJ family.
Suggest: build HMM from an alignment of the 5/7 motifs
indicated below and use this HMM (i) to search PDB and (ii)
generate T0087 family alignment.

Rajman LA; Lovett ST.
     A thermostable single-strand DNase from Methanococcus jannaschii related
     to the RecJ recombination and repair exonuclease from Escherichia coli.
   Journal of Bacteriology, 2000 Feb, 182(3):607-12.
       (UI:  20100748)

Abstract: The RecJ protein of Escherichia coli plays an important role in a
    number of DNA repair and recombination pathways. RecJ catalyzes processive
    degradation of single-stranded DNA in a 5'-to-3' direction. Sequences
    highly related to those encoding RecJ can be found in most of the
    eubacterial genomes sequenced to date. From alignment of these sequences,
    seven conserved motifs are apparent. At least five of these motifs are
    shared among a large family of proteins in eubacteria, eukaryotes, and
    archaea, including the PPX1 polyphosphatase of yeast and Drosophila Prune.
    Archaeal genomes are particularly rich in such sequences, but it has not
    been clear whether any of the encoded proteins play a functional role
    similar to that of RecJ exonuclease. We have investigated three such
    proteins from Methanococcus jannaschii with the strongest overall sequence
    similarity to E. coli RecJ. Two of the genes, MJ0977 and MJ0831, partially
    complement a recJ mutant phenotype in E. coli. The expression of MJ0977 in
    E. coli resulted in high levels of a thermostable single-stranded DNase
    activity with properties similar to those of RecJ exonuclease. Despite
    overall weak sequence similarity between the MJ0977 product and RecJ, these
    nucleases are likely to have similar biological functions.

PSI-BLAST: T0087 query

>pir||A70485 single-strand-DNA-specific exonuclease RecJ - Aquifex aeolicus
 gb|AAC07869.1| (AE000775) single-strand-DNA-specific exonuclease RecJ [Aquifex
           aeolicus]
          Length = 538

 Score = 32.2 bits (72), Expect = 6.1
 Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 13/92 (14%)

Query: 3   KILVFGHQNPDSDAIGSSMAYAYLKRQLGVDAQAVAL-----GNPNEETAFVLDYFGIQA 57
           +I+++G  + D D I  +     + + LG     V          N+E   + + +G   
Sbjct: 79  RIIIYG--DYDVDGITGTAILYRVLKLLGAKVYPVLPNRQTGYGLNKELMSIFEKYGDFL 136
                     ^ ^
                     active site?? metal ion coordination

Query: 58  PPVV------KSAQAEGAKQVILTDHNEFQQS 83
             V       +       + V++  HN   + 
Sbjct: 137 ITVDNGTSAVEEIDQSSLETVVIDHHNVPPRI 168
                                  ^ 
                                  active site? metal ion coordination


PSI-BLAST: RecJ/A70485 query yields match to a PDB entry.

>pdb|1QHG|B Chain B, Structure Of Dna Helicase Mutant With Adpnp
 pdb|1QHH|B Chain B, Structure Of Dna Helicase With Adpnp
          Length = 273

 Score = 40.0 bits (92), Expect = 0.056
 Identities = 22/118 (18%), Positives = 43/118 (35%), Gaps = 9/118 (7%)

Query: 48  NPKLSHIPTYRELEGIEEA---IERIKEAVLKKKRXXXXXXXXXXXXXXXAILYRVLKLL 104
           NP+   I  Y  +   +EA     RI+EAV + +R                ++  +L  L
Sbjct: 148 NPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEML--L 205

Query: 105 GAKVYPVLPNRQTGYGLNKELMSIFEKYGDFLITVDNGTSAVEEID--QSSLETVVID 160
            A +   +      Y  +++ +     Y   +   D+  S +  I+  +  +    ID
Sbjct: 206 KANIPYQIVGGLKFY--DRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTID 261

>pdb|2PJR|F Chain F, Helicase Product Complex
          Length = 544

 Score = 40.0 bits (92), Expect = 0.056
 Identities = 22/118 (18%), Positives = 43/118 (35%), Gaps = 9/118 (7%)

Query: 48  NPKLSHIPTYRELEGIEEA---IERIKEAVLKKKRXXXXXXXXXXXXXXXAILYRVLKLL 104
           NP+   I  Y  +   +EA     RI+EAV + +R                ++  +L  L
Sbjct: 312 NPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEML--L 369

Query: 105 GAKVYPVLPNRQTGYGLNKELMSIFEKYGDFLITVDNGTSAVEEID--QSSLETVVID 160
            A +   +      Y  +++ +     Y   +   D+  S +  I+  +  +    ID
Sbjct: 370 KANIPYQIVGGLKFY--DRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTID 425