RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780796|ref|YP_003065209.1| ribonuclease H [Candidatus
Liberibacter asiaticus str. psy62]
         (152 letters)



>gnl|CDD|30676 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
           repair].
          Length = 154

 Score =  170 bits (431), Expect = 2e-43
 Identities = 84/146 (57%), Positives = 105/146 (71%), Gaps = 3/146 (2%)

Query: 7   REVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKY- 65
           ++V  +TDGAC GNPGPGGWG +LRY   EK +SGGE  TTNNR EL A I+AL ALK  
Sbjct: 2   KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKEL 61

Query: 66  -PCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQH-KVDLY 123
             C+V LYTDS YV +G ++WI KW++NGWKT+DKK VKN DLW +  E   +H  V   
Sbjct: 62  GACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWE 121

Query: 124 WIKGHAGNQENEKVDRIARNAAVSFK 149
           W+KGHAG+ ENE+ D++AR AA + K
Sbjct: 122 WVKGHAGHPENERADQLAREAARAAK 147


>gnl|CDD|119393 cd06222, RnaseH, RNase H (RNase HI) is an endonuclease that cleaves
           the RNA strand of an RNA/DNA hybrid in a not
           sequence-specific manner. One of the important functions
           of RNase H is to remove Okazaki fragments during DNA
           replication.  RNase H knockout mice lack mitochondrial
           DNA replication and die as embryos. The retroviral
           reverse transcriptase contains an RNase H domain that
           plays an important role in converting a single stranded
           retroviral genomic RNA into a dsDNA for integration into
           host chromosomes. RNase H inhibitors have been explored
           as an anti-HIV drug target because RNase H inactivation
           inhibits reverse transcription..
          Length = 130

 Score =  132 bits (333), Expect = 6e-32
 Identities = 60/141 (42%), Positives = 79/141 (56%), Gaps = 16/141 (11%)

Query: 10  HAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGE--KETTNNRMELMAAIKALTALKY-- 65
             YTDG+C GNPGP G GV+LR  G E ++SGG     TTNNR EL+A I+AL       
Sbjct: 1   VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELG 60

Query: 66  PCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQ-HKVDLYW 124
             KV +YTDS YV    + W +            K VKN+DLW + +    + HKV   W
Sbjct: 61  GKKVNIYTDSQYVINALTGWYE-----------GKPVKNVDLWQRLLALLKRFHKVRFEW 109

Query: 125 IKGHAGNQENEKVDRIARNAA 145
           + GH+G + NE+ D +A+ AA
Sbjct: 110 VPGHSGIEGNERADALAKEAA 130


>gnl|CDD|143857 pfam00075, RnaseH, RNase H.  RNase H digests the RNA strand of an
           RNA/DNA hybrid. Important enzyme in retroviral
           replication cycle, and often found as a domain
           associated with reverse transcriptases. Structure is a
           mixed alpha+beta fold with three a/b/a layers.
          Length = 126

 Score =  119 bits (300), Expect = 3e-28
 Identities = 52/134 (38%), Positives = 72/134 (53%), Gaps = 15/134 (11%)

Query: 12  YTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCKVLL 71
           YTDG+C+GNPG GG G +    GK++        TTN R EL+A I+AL AL    KV +
Sbjct: 7   YTDGSCNGNPGTGGAGYVT-DGGKQRSKPLPG--TTNQRAELLALIEALEALS-GQKVNI 62

Query: 72  YTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGHAGN 131
           YTDS YV  G    +  W       S+ K +KN ++W        +H V + W+ GH+G 
Sbjct: 63  YTDSQYVIGGI---LNGWP----TKSESKPIKN-EIWE---LLLKKHAVYIQWVPGHSGI 111

Query: 132 QENEKVDRIARNAA 145
             NE  D++A+  A
Sbjct: 112 PGNELADKLAKQGA 125


>gnl|CDD|38956 KOG3752, KOG3752, KOG3752, Ribonuclease H [Replication,
           recombination and repair].
          Length = 371

 Score = 75.5 bits (185), Expect = 5e-15
 Identities = 55/155 (35%), Positives = 76/155 (49%), Gaps = 16/155 (10%)

Query: 12  YTDGACSGNPGPG---GWGVLLRYKGKEKIISG--GEKETTNNRMELMAAIKAL-TALKY 65
           YTDG+ SGN       G+GV     G E  +SG       TNNR EL+AAI+AL  A   
Sbjct: 216 YTDGSSSGNGRKSSRAGYGVYWG-PGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK 274

Query: 66  PC-KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKT-----VKNIDLWMKFVEASAQH- 118
              KV++ TDS Y     + W++ W++NGWKTS+        VKN D + +  E   +  
Sbjct: 275 NINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEIS 334

Query: 119 --KVDLYWIKGHAGNQENEKVDRIARNAAVSFKNK 151
             KV   ++ GH+G   NE  D +AR  +      
Sbjct: 335 NKKVQQEYVGGHSGILGNEMADALARKGSTLASRS 369


>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This CD
           represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 468

 Score = 27.7 bits (62), Expect = 1.5
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 24  GGWGVLLRYKGKEKIISGGEKE----TTNNRMELMAAIKALTALKYPCKVLLYTDSSYVH 79
                  R    E++ +   ++        R EL+  I+ L A + P   L Y     VH
Sbjct: 402 SNTKKSARGYDNEELNALLRQQLQEMDPEKRKELVFEIQELYAEELPMIPLYYPTMYTVH 461

Query: 80  KG 81
           +G
Sbjct: 462 RG 463


>gnl|CDD|145449 pfam02301, HORMA, HORMA domain.  The HORMA (for Hop1p, Rev7p and
           MAD2) domain has been suggested to recognize chromatin
           states that result from DNA adducts, double stranded
           breaks or non-attachment to the spindle and acts as an
           adaptor that recruits other proteins. MAD2 is a spindle
           checkpoint protein which prevents progression of the
           cell cycle upon detection of a defect in mitotic spindle
           integrity.
          Length = 189

 Score = 26.5 bits (59), Expect = 3.3
 Identities = 19/85 (22%), Positives = 26/85 (30%), Gaps = 11/85 (12%)

Query: 30  LRYKGKEKIISGGEKETTNNRMELMAAIKALTAL---------KYPC--KVLLYTDSSYV 78
             Y       S  EK     R E+ A ++ L AL            C  K+L YT   Y 
Sbjct: 96  FSYFPSGGNSSDSEKTEDETRQEIRALLRQLIALVTFLPPLPEDRTCTFKLLYYTPPDYE 155

Query: 79  HKGFSQWIKKWQQNGWKTSDKKTVK 103
             GF            +  + + V 
Sbjct: 156 PPGFKWADSDSDVKLIENGEPEEVS 180


>gnl|CDD|31961 COG1775, HgdB, Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA
           dehydratase subunit, BcrC/BadD/HgdB [Amino acid
           transport and metabolism].
          Length = 379

 Score = 26.0 bits (57), Expect = 4.6
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 45  ETTNNRM----ELMAAIKALTALKYPCKVLLYTDSSYVHKGFSQWIKKWQQ-NGWKTSDK 99
           E T N      E+MA IK +  +  P          Y H    ++ +  ++  G + +++
Sbjct: 104 ENTCNGKKKMYEVMARIKPVHVMDLPFHRKDEPSVKYWHNELDKFKELLEELTGNEITEE 163

Query: 100 KTVKNIDLWMKFVEA 114
           K    I  + +  EA
Sbjct: 164 KLRDAIARYNRLREA 178


>gnl|CDD|31521 COG1330, RecC, Exonuclease V gamma subunit [DNA replication,
           recombination, and repair].
          Length = 1078

 Score = 25.7 bits (56), Expect = 5.8
 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 4/46 (8%)

Query: 82  FSQWIKKWQQNGWKTSDKKTVKNIDLWMKFV----EASAQHKVDLY 123
              WI  W+   +           +LW   V    E S  H+ +L+
Sbjct: 142 RPDWIAAWEDGLFLGLGDNEKWQAELWRALVADTTELSQPHRANLH 187


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.315    0.131    0.408 

Gapped
Lambda     K      H
   0.267   0.0773    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,821,792
Number of extensions: 83078
Number of successful extensions: 202
Number of sequences better than 10.0: 1
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 13
Length of query: 152
Length of database: 6,263,737
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,426,972
Effective search space: 296607124
Effective search space used: 296607124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)