RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

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



>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
          Length = 150

 Score =  252 bits (647), Expect = 2e-68
 Identities = 87/146 (59%), Positives = 111/146 (76%)

Query: 6   LREVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKY 65
           +++V  YTDGAC GNPGPGGWG +LRYKG EK +SGGE  TTNNRMELMAAI+AL ALK 
Sbjct: 1   MKQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE 60

Query: 66  PCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWI 125
           PC+V LYTDS YV +G ++WI  W++NGWKT+DKK VKN+DLW +   A  +H++  +W+
Sbjct: 61  PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWV 120

Query: 126 KGHAGNQENEKVDRIARNAAVSFKNK 151
           KGHAG+ ENE+ D +AR  A     +
Sbjct: 121 KGHAGHPENERCDELARAGAEEATLE 146


>gnl|CDD|169558 PRK08719, PRK08719, ribonuclease H; Reviewed.
          Length = 147

 Score = 84.9 bits (210), Expect = 8e-18
 Identities = 39/101 (38%), Positives = 61/101 (60%), Gaps = 2/101 (1%)

Query: 46  TTNNRMELMAAIKALTALKYPCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNI 105
           T N  +EL+A I+AL   +     ++Y+DS Y  +GF++W+  W+Q GW+ SDKK V N 
Sbjct: 48  TDNAELELLALIEALEYARD--GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANR 105

Query: 106 DLWMKFVEASAQHKVDLYWIKGHAGNQENEKVDRIARNAAV 146
           DLW +  E  A+  V++  +  H+G + NE  D +A+ AA 
Sbjct: 106 DLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146


>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
          Length = 161

 Score = 77.5 bits (190), Expect = 1e-15
 Identities = 46/145 (31%), Positives = 72/145 (49%), Gaps = 4/145 (2%)

Query: 8   EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67
           E+ A TDG+   NPGP GW     Y  +    SGG    TNN  EL A  + L A ++  
Sbjct: 5   EIIAATDGSSLANPGPSGWA---WYVDENTWDSGGWDIATNNIAELTAVRELLIATRHTD 61

Query: 68  K-VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIK 126
           + +L+ +DS YV    ++W+  W+   W+ +D K V N ++  +         + + W+ 
Sbjct: 62  RPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVN 121

Query: 127 GHAGNQENEKVDRIARNAAVSFKNK 151
            H G+  NE  D +AR AA +F  +
Sbjct: 122 AHTGHPLNEAADSLARQAANNFSTR 146


>gnl|CDD|139967 PRK13907, rnhA, ribonuclease H; Provisional.
          Length = 128

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 41/143 (28%), Positives = 61/143 (42%), Gaps = 27/143 (18%)

Query: 9   VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCK 68
           +  Y DGA  GNPGP G GV ++       +S      +N+  E  A    L ALKY  +
Sbjct: 2   IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHA---LLAALKYCTE 58

Query: 69  -----VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQH--KVD 121
                V   TDS  V +                 +K+  KN  ++   +E + Q+    D
Sbjct: 59  HNYNIVSFRTDSQLVERAV---------------EKEYAKN-KMFAPLLEEALQYIKSFD 102

Query: 122 LYWIKGHAGNQENEKVDRIARNA 144
           L++IK    +Q N+  D +AR A
Sbjct: 103 LFFIKWIPSSQ-NKVADELARKA 124


>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase;
           Provisional.
          Length = 372

 Score = 33.4 bits (77), Expect = 0.021
 Identities = 42/154 (27%), Positives = 61/154 (39%), Gaps = 39/154 (25%)

Query: 14  DGACSGNPGPGGWGVLLRYKGKEKIISGGE-----KETTNNRME---LMAAIKALTALKY 65
           DG   GNPGP G+G ++    + +++   E        TNN  E   L+A ++A   L  
Sbjct: 8   DGGSRGNPGPAGYGAVVWDADRGEVL--AERAEAIGRATNNVAEYRGLIAGLEAAAELG- 64

Query: 66  PCKVLLYTDSSYVHKGFSQWIKKWQQNG-WKTSDKKTVKNIDLWMKFVEASAQH------ 118
             +V +  DS  V +         Q +G WK      VK+ D  MK + A A+       
Sbjct: 65  ATEVEVRMDSKLVVE---------QMSGRWK------VKHPD--MKPLAAQARELASQFG 107

Query: 119 KVDLYWI----KGHAGNQENEKVDRIARNAAVSF 148
           +V   WI      HA    NE +D  A       
Sbjct: 108 RVTYTWIPRARNAHADRLANEAMDAAAGGEPWGP 141


>gnl|CDD|131706 TIGR02658, TTQ_MADH_Hv, methylamine dehydrogenase heavy chain.
           This family consists of the heavy chain of methylamine
           dehydrogenase light chain, a periplasmic enzyme. The
           enzyme contains a tryptophan tryptophylquinone (TTQ)
           prothetic group derived from two Trp residues in the
           light subunity. The enzyme forms a complex with the type
           I blue copper protein amicyanin and a cytochrome.
           Electron transfer procedes from TQQ to the copper and
           then to the heme group of the cytochrome.
          Length = 352

 Score = 26.7 bits (59), Expect = 2.7
 Identities = 10/37 (27%), Positives = 21/37 (56%)

Query: 2   DSKHLREVHAYTDGACSGNPGPGGWGVLLRYKGKEKI 38
           D+K L  + A+T+   +    PGGW  +  ++ +++I
Sbjct: 226 DAKFLPAIEAFTEAEKADGWRPGGWQQVAYHRARDRI 262


>gnl|CDD|152347 pfam11912, DUF3430, Protein of unknown function (DUF3430).  This
          family of proteins are functionally uncharacterized.
          This protein is found in eukaryotes. Proteins in this
          family are typically between 209 to 265 amino acids in
          length.
          Length = 204

 Score = 26.7 bits (59), Expect = 2.7
 Identities = 8/16 (50%), Positives = 8/16 (50%)

Query: 12 YTDGACSGNPGPGGWG 27
          Y DG CSG     G G
Sbjct: 29 YQDGDCSGEGSSSGIG 44


>gnl|CDD|178087 PLN02468, PLN02468, putative pectinesterase/pectinesterase
          inhibitor.
          Length = 565

 Score = 25.6 bits (56), Expect = 5.8
 Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 6/38 (15%)

Query: 40 SGGEKETTNNRMELMAAIKALTALKYPCKVLLYTDSSY 77
          SG  ++T NN   +  ++KA+      C V LY DS Y
Sbjct: 50 SGNSEKTGNNGKSISTSVKAV------CDVTLYKDSCY 81


>gnl|CDD|184795 PRK14698, PRK14698, V-type ATP synthase subunit A; Provisional.
          Length = 1017

 Score = 25.4 bits (55), Expect = 6.2
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 14/83 (16%)

Query: 15  GACSGNPGPGGWGV--------------LLRYKGKEKIISGGEKETTNNRMELMAAIKAL 60
           G  +  PGP G G               L++ K   +I+ G  K+T     E     + +
Sbjct: 227 GGTAAIPGPFGSGKCVDGDTLILTKEFGLIKIKDLYEILDGKGKKTVEGNEEWTELEEPI 286

Query: 61  TALKYPCKVLLYTDSSYVHKGFS 83
           T   Y    ++   +++V+KG S
Sbjct: 287 TLYGYKDGKIVEIKATHVYKGAS 309


>gnl|CDD|148573 pfam07037, DUF1323, Putative transcription regulator (DUF1323).
           This family consists of several hypothetical
           Enterobacterial proteins of around 120 residues in
           length. This family appears to have an HTH domain and is
           therefore likely to act as a transcriptional regulator.
          Length = 122

 Score = 25.5 bits (56), Expect = 6.3
 Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 1/21 (4%)

Query: 84  QWIKKW-QQNGWKTSDKKTVK 103
           Q I +W ++ GWKTS K  VK
Sbjct: 15  QTINRWVRKEGWKTSPKPGVK 35


>gnl|CDD|162390 TIGR01496, DHPS, dihydropteroate synthase.  This model represents
           dihydropteroate synthase, the enzyme that catalyzes the
           second to last step in folic acid biosynthesis. The gene
           is usually designated folP (folic acid biosynthsis) or
           sul (sulfanilamide resistance). This model represents
           one branch of the family of pterin-binding enzymes
           (pfam00809) and of a cluster of dihydropteroate synthase
           and related enzymes (COG0294). Other members of
           pfam00809 and COG0294 are represented by TIGR00284.
          Length = 257

 Score = 25.3 bits (56), Expect = 6.6
 Identities = 7/21 (33%), Positives = 12/21 (57%)

Query: 46  TTNNRMELMAAIKALTALKYP 66
           T  + +EL+  ++   AL YP
Sbjct: 178 TPEHNLELLKHLEEFVALGYP 198


>gnl|CDD|178740 PLN03199, PLN03199, delta6-acyl-lipid desaturase-like protein;
           Provisional.
          Length = 485

 Score = 25.0 bits (54), Expect = 7.6
 Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 1/33 (3%)

Query: 67  CKVLLYTDSSYVHKGFSQWIKK-WQQNGWKTSD 98
           C ++ Y+D   +H   +  +   +QQ GW   D
Sbjct: 149 CALVFYSDRFAMHIASALLLGLFFQQCGWLAHD 181


>gnl|CDD|165130 PHA02765, PHA02765, hypothetical protein; Provisional.
          Length = 117

 Score = 25.0 bits (54), Expect = 8.3
 Identities = 16/74 (21%), Positives = 32/74 (43%)

Query: 72  YTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGHAGN 131
           Y D+  + K F Q+I    +N    S K+T KN +     +      K+D   +  H   
Sbjct: 25  YGDTEKIFKKFRQYIYNHDKNSHVFSIKETTKNSNGLHYHILVFTNKKLDYSRVHKHMPP 84

Query: 132 QENEKVDRIARNAA 145
             + +++ + +N +
Sbjct: 85  HSDIRIELVPKNIS 98


>gnl|CDD|115110 pfam06433, Me-amine-dh_H, Methylamine dehydrogenase heavy chain
           (MADH).  Methylamine dehydrogenase (EC:1.4.99.3) a
           periplasmic quinoprotein found in several methyltrophic
           bacteria. Induced when grown on methylamine as a carbon
           source MADH catalyses the oxidative deamination of
           amines to there corresponding aldehydes. MADH is a
           hetero- tetramer, comprised of two heavy chains (H) and
           two light chains (L). The H-chain forms a beta-propeller
           like structure.
          Length = 342

 Score = 24.8 bits (54), Expect = 8.9
 Identities = 9/37 (24%), Positives = 21/37 (56%)

Query: 2   DSKHLREVHAYTDGACSGNPGPGGWGVLLRYKGKEKI 38
            +K L+ + A+T+   +    PGGW  +  ++ +++I
Sbjct: 216 GAKFLKPIEAFTEAEKADGWRPGGWQQVAYHRARDRI 252


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.315    0.131    0.408 

Gapped
Lambda     K      H
   0.267   0.0616    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,402,943
Number of extensions: 132247
Number of successful extensions: 252
Number of sequences better than 10.0: 1
Number of HSP's gapped: 249
Number of HSP's successfully gapped: 17
Length of query: 152
Length of database: 5,994,473
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,157,793
Effective search space: 278572131
Effective search space used: 278572131
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 (24.4 bits)