RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780661|ref|YP_003065074.1| exonuclease I [Candidatus
Liberibacter asiaticus str. psy62]
         (471 letters)



>gnl|CDD|183310 PRK11779, sbcB, exonuclease I; Provisional.
          Length = 476

 Score =  723 bits (1868), Expect = 0.0
 Identities = 265/467 (56%), Positives = 339/467 (72%), Gaps = 2/467 (0%)

Query: 1   MTNHFVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFI 60
           M   F+ +DYETFG + ALDRPAQFAG+R D     I    VF+CKPADDYLP PEAV I
Sbjct: 4   MQPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLI 63

Query: 61  TGITPQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRW 120
           TGITPQ+AL  G+ EAEF+ RIH  FS P TCI+GYNNIRFDD  +R IFYRNFYD Y  
Sbjct: 64  TGITPQEALEKGLPEAEFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAR 123

Query: 121 SWDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKAD 180
            W NGNSRWDLLDV+RA YA  P+GI WP  +DG  SFKL+ L  ANGIEH NAHDA +D
Sbjct: 124 EWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEHENAHDAMSD 183

Query: 181 VYATLALVWLIREKKPKLFEYLYDYRNKNQLRKLIDIQNMTPLVHVSGMFGASRSNTALI 240
           VYAT+A+  LI++K+PKLF+YL+  RNK ++  LID+  M PLVHVSGMFGA R  T+ +
Sbjct: 184 VYATIAMAKLIKQKQPKLFDYLFQLRNKRKVAALIDVPAMKPLVHVSGMFGAERGCTSWV 243

Query: 241 APVAWHPRYKDSVIGCNLSGDMRVFQDLDSVQLAKRLFTSHDELK-GLVPVPIKEVHLNK 299
           AP+AWHP  K++VI C+L+GD     +LD+  L +RL+T   +L  G +PVP+K VHLNK
Sbjct: 244 APLAWHPTNKNAVIVCDLAGDPSPLLELDADTLRERLYTRRADLAEGELPVPLKLVHLNK 303

Query: 300 CPILMPIDYCKKEHFERWGIDHKRCLENLTLLRQQTNLRDRFKAIYNKPYT-SSSQDVDS 358
           CP+L P    + E  ER GID ++CL+NL LLRQ  +LR++  A++ +    + S DVD+
Sbjct: 304 CPVLAPAKTLRPEDAERLGIDRQQCLDNLALLRQNPDLREKVVAVFAEAEPFAPSDDVDA 363

Query: 359 QLYDGFFADVDRQIMDRILRTAPEQLSTLNLPFSDRRLPELFFRYRARNFPHTLSEKEKQ 418
           QLYDGFF+D DR++M+ I  T PE L+ L+L F D RL EL FRYRARNFP TL ++E+Q
Sbjct: 364 QLYDGFFSDADRRLMEIIRETEPENLAALDLTFDDPRLEELLFRYRARNFPETLDDEEQQ 423

Query: 419 DWLEHRKKMLTRSRIEEYKNKLQSLSGEYKGDEGKEGLINALYEYLQ 465
            WLEHR++ LT  R+++Y  +L+ L+ EY+ DE K+ L+ ALY+Y +
Sbjct: 424 RWLEHRRQRLTPERLQQYAAELEQLAQEYEDDEEKQALLKALYDYAE 470


>gnl|CDD|149465 pfam08411, Exonuc_X-T_C, Exonuclease C-terminal.  This bacterial
           domain is found at the C-terminus of
           Exodeoxyribonuclease I/Exonuclease I (pfam00929), which
           is a single-strand specific DNA nuclease affecting
           recombination and expression pathways. The exonuclease I
           protein in E. coli is associated with DNA
           deoxyribophosphodiesterase (dRPase).
          Length = 268

 Score =  328 bits (844), Expect = 1e-90
 Identities = 132/268 (49%), Positives = 183/268 (68%), Gaps = 10/268 (3%)

Query: 206 RNKNQLRKLIDIQNMTPLVHVSGMFGASRSNTALIAPVAWHPRYKDSVIGCNLSGDMRVF 265
           R+K  + KLID+  M PLVHVSGMFGA R  T+ + P+AWHP  K++VI C+L+ D    
Sbjct: 1   RSKKAVAKLIDLVAMKPLVHVSGMFGAERGCTSWVLPLAWHPTNKNAVIVCDLAQDPSPL 60

Query: 266 QDLDSVQLAKRLFTSHDEL-KGLVPVPIKEVHLNKCPILMPIDYCKKEHFERWGIDHKRC 324
            DL + +L +RL+T  ++L +G + VP+K VHLNKCPIL P    + E  ER GID ++C
Sbjct: 61  LDLSAEELRQRLYTKREDLAEGELRVPLKLVHLNKCPILAPAKTLRPEDAERLGIDREQC 120

Query: 325 LENLTLLRQQTNLRDRFKAIYN--KPYTSSSQDVDSQLYDGFFADVDRQIMDRILRTAPE 382
           L+NL LLRQ   LR++ K ++   + +  S+ DVD QLYDGFF+D D+++M+ I  T+PE
Sbjct: 121 LKNLALLRQNPELREKLKEVFEEEREFPPST-DVDQQLYDGFFSDADKRLMEIIRETSPE 179

Query: 383 QLSTLNLPFSDRRLPELFFRYRARNFPHTLSEKEKQDWLEHRKKMLTRSR-----IEEYK 437
           QL+ L L F D+RLPEL FRYRARNFP TLSE+E+Q W E+ ++ L         +E+Y+
Sbjct: 180 QLAELELNFDDKRLPELLFRYRARNFPETLSEEEQQRWQEYCQQRLLDPAGGALTLEDYE 239

Query: 438 NKLQSLSGEYKGDEGKEGLINALYEYLQ 465
            KL+ L+ EY  DE K+ L+ ALY+Y Q
Sbjct: 240 QKLEQLAAEYSDDE-KQALLQALYDYAQ 266


>gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
           putative.  This model represents a family of proteins in
           Gram-positive bacteria. The N-terminal region of about
           200 amino acids resembles the epsilon subunit of E. coli
           DNA polymerase III and the homologous region of the
           Gram-positive type DNA polymerase III alpha subunit. The
           epsilon subunit contains an exonuclease domain. The
           remainder of this protein family resembles a predicted
           ATP-dependent helicase, the DNA damage-inducible protein
           DinG of E. coli.
          Length = 850

 Score = 53.7 bits (129), Expect = 9e-08
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 33/197 (16%)

Query: 5   FVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLP-DPEAVFITGI 63
           + + D ET G  ++ D+  Q  G+ V    E +++    F    +   P  P    +TGI
Sbjct: 2   YAVVDLETTGTQLSFDKIIQI-GIVVVEDGEIVDT----FHTDVNPNEPIPPFIQELTGI 56

Query: 64  TPQKALRDGVVEA-EFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYD-SYRWS 121
           +        + +A  FS+   + + +    I   +N+ FD     N   +   D  Y   
Sbjct: 57  SDNM-----LQQAPYFSQVAQEIYDLLEDGIFVAHNVHFD----LNFLAKALKDCGYEP- 106

Query: 122 WDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKADV 181
                 R D +++ +  +         P+ +    S++L +L+ A G+ H N H A +D 
Sbjct: 107 --LPKPRIDTVELAQIFF---------PTEE----SYQLSELSEALGLTHENPHRADSDA 151

Query: 182 YATLALVWLIREKKPKL 198
            AT  L+ L+ EK  KL
Sbjct: 152 QATAELLLLLFEKMEKL 168


>gnl|CDD|128755 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
           epsilon chain, ribonuclease T and other exonucleases. 
          Length = 169

 Score = 44.2 bits (105), Expect = 7e-05
 Identities = 47/194 (24%), Positives = 68/194 (35%), Gaps = 27/194 (13%)

Query: 5   FVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGIT 64
            V+ D ET G D   D   + A V VD    +I      + KP  D      A  I GIT
Sbjct: 2   LVVIDCETTGLDPGKDEIIEIAAVDVDG--GRIIVVFDTYVKP--DRPITDYATEIHGIT 57

Query: 65  PQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWSWDN 124
           P+  L D     E    + +F       ++  N + FD       F +  +         
Sbjct: 58  PEM-LDDAPTFEEVLEELLEFLK--GKILVAGNALNFD--LR---FLKLEHPRLGIKDPP 109

Query: 125 GNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHV-NAHDAKADVYA 183
            N   D L + RA+                   + L+ LA   G+E +  AH A  D  A
Sbjct: 110 KNPVIDTLKLARALN--------------PGRKYSLKKLAERLGLEVIGRAHRALDDARA 155

Query: 184 TLALVWLIREKKPK 197
           T  L   + E+  +
Sbjct: 156 TAKLFKKLVERLLE 169


>gnl|CDD|162340 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
           Gram-positive type.  The N-terminal region of about 200
           amino acids is rich in low-complexity sequence, poorly
           alignable, and not included n this model.
          Length = 1213

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 45/192 (23%), Positives = 73/192 (38%), Gaps = 33/192 (17%)

Query: 5   FVIYDYETFGRDVALDRPAQFAGVRV--DRQWEKIESTEVFFCKPADDYLPDPEAVF-IT 61
           +V++D ET G     D   +F  V+V   R  +K +    FF KP +   P    V  +T
Sbjct: 192 YVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQ----FFIKPHE---PLSAFVTELT 244

Query: 62  GITPQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWS 121
           GIT Q  L +     E   +  +FF      I+  +N  FD  +    F +         
Sbjct: 245 GIT-QDMLENAPEIEEVLEKFKEFF---KDSILVAHNASFDIGFLNTNFEK--VGLEPLE 298

Query: 122 WDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKADV 181
               N   D L++ RA+                  S +L ++    G++  + H A  D 
Sbjct: 299 ----NPVIDTLELARALNP-------------EYKSHRLGNICKKLGVDLDDHHRADYDA 341

Query: 182 YATLALVWLIRE 193
            AT  +  ++ E
Sbjct: 342 EATAKVFKVMVE 353


>gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon;
           Provisional.
          Length = 232

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 20/100 (20%)

Query: 8   YDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDP------EAVFIT 61
           +D ET G D    R    A V VD   E +ES E         +L DP      EA  + 
Sbjct: 11  FDLETTGVDPETARIVTAALVVVDADGEVVESRE---------WLADPGVEIPEEASAVH 61

Query: 62  GITPQKALRDG----VVEAEFSRRIHQFFSVPNTCIIGYN 97
           GIT + A   G     V AE +  + + ++     ++ +N
Sbjct: 62  GITTEYARAHGRPAAEVLAEIADALREAWA-RGVPVVVFN 100



 Score = 34.6 bits (80), Expect = 0.050
 Identities = 13/40 (32%), Positives = 19/40 (47%)

Query: 159 KLQDLALANGIEHVNAHDAKADVYATLALVWLIREKKPKL 198
            L  L    G+   NAH+A AD  A   + W +  + P+L
Sbjct: 144 TLTALCEHYGVRLDNAHEATADALAAARVAWALARRFPEL 183


>gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
           polymerase III subunit epsilon; Validated.
          Length = 928

 Score = 33.4 bits (77), Expect = 0.13
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 154 GATSFKLQDLALANGIEHVNAHDAKADVYAT 184
            A S+KL+DL+   G+EH   H A +D   T
Sbjct: 128 TAESYKLRDLSEELGLEHDQPHRADSDAEVT 158


>gnl|CDD|162758 TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase.
            This family consists of examples of
           ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
           involved in biosynthesis of the inner core of
           lipopolysaccharide (LPS) for Gram-negative bacteria.
           This enzyme is homologous to UDP-glucose 4-epimerase
           (TIGR01179) and belongs to the NAD dependent
           epimerase/dehydratase family (pfam01370).
          Length = 314

 Score = 28.0 bits (63), Expect = 4.8
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 190 LIREKKPKLFEYLYDYRNKNQLRKLIDIQ-----NMTPLVH-VSGMF----GASRSNTAL 239
           +      KLF+    +++  QLR  + ++     N+  L + VSG+F    G +RS   L
Sbjct: 192 IKAGGNVKLFKSSEGFKDGEQLRDFVYVKDVVDVNLWLLENGVSGIFNLGTGRARSFNDL 251

Query: 240 IAPV 243
              V
Sbjct: 252 ADAV 255


>gnl|CDD|162870 TIGR02468, sucrsPsyn_pln, sucrose phosphate synthase/possible
           sucrose phosphate phosphatase, plant.  Members of this
           family are sucrose-phosphate synthases of plants. This
           enzyme is known to exist in multigene families in
           several species of both monocots and dicots. The
           N-terminal domain is the glucosyltransferase domain.
           Members of this family also have a variable linker
           region and a C-terminal domain that resembles sucrose
           phosphate phosphatase (SPP) (EC 3.1.3.24) (see
           TIGR01485), the next and final enzyme of sucrose
           biosynthesis. The SPP-like domain likely serves a
           binding and not a catalytic function, as the reported
           SPP is always encoded by a distinct protein.
          Length = 1050

 Score = 28.2 bits (63), Expect = 4.8
 Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 2/31 (6%)

Query: 350 TSSSQDVDSQ--LYDGFFADVDRQIMDRILR 378
           TS+ Q+++ Q  LYDGF   ++R++  R  R
Sbjct: 387 TSTRQEIEEQWGLYDGFDVILERKLRARARR 417


>gnl|CDD|130365 TIGR01298, RNaseT, ribonuclease T.  in gamma-subdivision
          Proteobacteria such as Escherichia coli and Xylella
          fastidiosa. Ribonuclease T is homologous to the DNA
          polymerase III alpha chain. It can liberate AMP from
          the common C-C-A terminus of uncharged tRNA. It appears
          also to be involved in RNA maturation. It also acts as
          a 3' to 5' single-strand DNA-specific exonuclease; it
          is distinctive for its ability to remove residues near
          a double-stranded stem. Ribonuclease T is a high copy
          suppressor in E. coli of a uv-repair defect caused by
          deletion of three other single-stranded DNA
          exonucleases.
          Length = 200

 Score = 27.9 bits (62), Expect = 5.8
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 6  VIYDYETFGRDVALDRPAQFAGVRV---DRQWEKIESTEVFFCKPADDYLPDPEAVFITG 62
          V+ D ET G +   D   + A + +   ++ W   ++T  F  +P +     PEA+  TG
Sbjct: 11 VVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTG 70

Query: 63 ITPQKALRDGVVEAEFSRRIHQFFSV 88
          I     LR  V E E    +H+ F V
Sbjct: 71 IDLDHPLRGAVSEYE---ALHEIFKV 93


>gnl|CDD|151027 pfam10453, NUFIP1, Nuclear fragile X mental retardation-interacting
           protein 1 (NUFIP1).  Proteins in this family have been
           implicated in the assembly of the large subunit of the
           ribosome and in telomere maintenance. Some proteins in
           this family contain a CCCH zinc finger. This family
           contains a protein called human fragile X mental
           retardation-interacting protein 1, which is known to
           bind RNA and is phosphorylated upon DNA damage.
          Length = 57

 Score = 27.3 bits (61), Expect = 9.7
 Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 1/27 (3%)

Query: 413 SEKEKQDWLEHRKKM-LTRSRIEEYKN 438
           + +E   W+E RKK   T++ IE+ K 
Sbjct: 20  TPEEIAKWIEERKKNYPTKANIEKKKK 46


>gnl|CDD|182476 PRK10458, PRK10458, DNA cytosine methylase; Provisional.
          Length = 467

 Score = 27.3 bits (61), Expect = 9.7
 Identities = 8/17 (47%), Positives = 12/17 (70%)

Query: 196 PKLFEYLYDYRNKNQLR 212
           P L++YLY Y  K+Q +
Sbjct: 328 PVLWKYLYRYAKKHQAK 344


  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
   0.322    0.139    0.431 

Gapped
Lambda     K      H
   0.267   0.0734    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 8,184,521
Number of extensions: 545276
Number of successful extensions: 1123
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1115
Number of HSP's successfully gapped: 27
Length of query: 471
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 374
Effective length of database: 3,898,497
Effective search space: 1458037878
Effective search space used: 1458037878
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: 59 (26.5 bits)