RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780288|ref|YP_003064701.1| exodeoxyribonuclease III
protein [Candidatus Liberibacter asiaticus str. psy62]
         (281 letters)



>gnl|CDD|161757 TIGR00195, exoDNase_III, exodeoxyribonuclease III.  The model
           brings in reverse transcriptases at scores below 50,
           model also contains eukaryotic apurinic/apyrimidinic
           endonucleases which group in the same family.
          Length = 254

 Score =  226 bits (578), Expect = 5e-60
 Identities = 89/256 (34%), Positives = 135/256 (52%), Gaps = 4/256 (1%)

Query: 6   VATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSY 65
           + +WNVN +RAR+H   AW+KEN PD++CLQETK +D+ FP E      YH+   GQK Y
Sbjct: 3   IISWNVNGLRARLHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGY 62

Query: 66  NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYD 125
           +GVAI SK +P+ +      ++ D + R I A F     +  + N Y P+G+   S K  
Sbjct: 63  SGVAIFSKEEPLSVRRGFGVEEEDAEGRIIMAEF----DSFLVINGYFPNGSRDDSEKLP 118

Query: 126 DKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQK 185
            K+ W++    +  + ++ ++P++  GD NI P   D ++P    N   F  E R+   +
Sbjct: 119 YKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHSPDENRNHTGFLPEEREWLDR 178

Query: 186 LQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKP 245
           L   G  D  R  +     YS+WDY   +  +N+G RID+ ++S           ID   
Sbjct: 179 LLEAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDI 238

Query: 246 RGWTKPSDHTPVIVSL 261
           RG  KPSDH PV++  
Sbjct: 239 RGSEKPSDHCPVVLEF 254


>gnl|CDD|161970 TIGR00633, xth, exodeoxyribonuclease III (xth).  This family is
           based on the phylogenomic analysis of JA Eisen (1999,
           Ph.D. Thesis, Stanford University).
          Length = 255

 Score =  221 bits (565), Expect = 2e-58
 Identities = 89/261 (34%), Positives = 142/261 (54%), Gaps = 12/261 (4%)

Query: 6   VATWNVNSIRARIHNLA-AWIKENNPDIICLQETKTEDKNFPFETLQSLNYH--IETCGQ 62
           + +WNVN +RAR+H L   W+KE  PD++CLQETK  D+ FP E  + L YH        
Sbjct: 3   IISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAKS 62

Query: 63  KSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITST 122
           K Y+GVAILSK +P+++     G++ D + R I A F        + N+Y+P+G      
Sbjct: 63  KGYSGVAILSKVEPLDVRYGFGGEEHDEEGRVITAEFDG----FTVVNVYVPNGGSRGLE 118

Query: 123 KYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQS 182
           + + K+ +     ++  + L+  +P+I  GD N+     D  NP   + +A FT E R+ 
Sbjct: 119 RLEYKLQFWDALFQYYEKELDAGKPVIICGDMNVAHTEIDLGNPKENKGNAGFTPEEREW 178

Query: 183 FQKLQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARI 241
           F +L   G  D  R  + DT   Y++WDY + +  +N+G RID+ ++S      +  + I
Sbjct: 179 FDELLEAGLVDTFRHFNPDTEGAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYI 238

Query: 242 DTKPRGWTKPSDHTPVIVSLD 262
           D++ RG    SDH P+++ LD
Sbjct: 239 DSEIRG----SDHCPIVLELD 255


>gnl|CDD|183300 PRK11756, PRK11756, exonuclease III; Provisional.
          Length = 268

 Score =  192 bits (490), Expect = 8e-50
 Identities = 90/266 (33%), Positives = 130/266 (48%), Gaps = 16/266 (6%)

Query: 10  NVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVA 69
           N+N +RAR H L A I+++ PD+I LQETK  D+ FP E +++L YH+   GQK + GVA
Sbjct: 7   NINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVA 66

Query: 70  ILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPIT-STKYDDKI 128
           +LSK  PI +    P DD + Q R I AT       L + N Y P G      TK+  K 
Sbjct: 67  LLSKQTPIAVRKGFPTDDEEAQRRIIMATIPTPNGNLTVINGYFPQGESRDHPTKFPAKR 126

Query: 129 SWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPI-IWENDA---------CFTLE 178
            + +    +    L  + PL+  GD NI P   D    I I E +           F  E
Sbjct: 127 QFYQDLQNYLETELSPDNPLLIMGDMNISPTDLD----IGIGEENRKRWLRTGKCSFLPE 182

Query: 179 VRQSFQKLQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLH 237
            R+   +L + G  D  R  + D +  +S++DY +  +  N+G+RID I+ +        
Sbjct: 183 EREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCV 242

Query: 238 SARIDTKPRGWTKPSDHTPVIVSLDI 263
              ID   RG  KPSDH P+  +  +
Sbjct: 243 ETGIDYDIRGMEKPSDHAPIWATFKL 268


>gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional.
          Length = 250

 Score =  102 bits (255), Expect = 1e-22
 Identities = 74/257 (28%), Positives = 121/257 (47%), Gaps = 15/257 (5%)

Query: 8   TWNVNSIRA-RIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCG-QKSY 65
           +WNVN +RA        +    + D+ C+QE+K + +   FE     ++    C  +K Y
Sbjct: 5   SWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFW--NCAIKKGY 62

Query: 66  NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYD 125
           +GV   +K +P+ +   +  ++ D + R I   F    ++  + N+Y P+     S +  
Sbjct: 63  SGVVTFTKKEPLSVSYGINIEEHDKEGRVITCEF----ESFYLVNVYTPNSQQALS-RLS 117

Query: 126 DKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQK 185
            ++SW   F +F  + LEL++P+I  GD N+     D  NP     +A F+ E R  F +
Sbjct: 118 YRMSWEVEFKKFL-KALELKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSE 176

Query: 186 LQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTK 244
           L N GF D  R  + +    Y++W Y   +  KN G RID+ + S    + L  A I   
Sbjct: 177 LLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKD 236

Query: 245 PRGWTKPSDHTPVIVSL 261
             G    SDH PV + L
Sbjct: 237 ILG----SDHCPVGLEL 249


>gnl|CDD|180068 PRK05421, PRK05421, hypothetical protein; Provisional.
          Length = 263

 Score = 31.8 bits (73), Expect = 0.19
 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 24/90 (26%)

Query: 6   VATWNVNSIRARIH--NLAAWIKE-----NNPDIICLQETKT--EDKNFP----FETLQS 52
           +  WN       I+    A W+        + D++ LQE +T  E   F         Q+
Sbjct: 46  LLVWN-------IYKQQRAGWLSVLKNLGKDADLVLLQEAQTTPELVQFATANYLAADQA 98

Query: 53  LNYHIETCGQKSYNGVAILSKYQPIEIVTH 82
             + +     +  +GV  LSK  P+     
Sbjct: 99  PAFVLP----QHPSGVMTLSKAHPVYCCPL 124


>gnl|CDD|147983 pfam06113, BRE, Brain and reproductive organ-expressed protein
           (BRE).  This family consists of several eukaryotic brain
           and reproductive organ-expressed (BRE) proteins. BRE is
           a putative stress-modulating gene, found able to
           down-regulate TNF-alpha-induced-NF-kappaB activation
           upon over expression. A total of six isoforms are
           produced by alternative splicing predominantly at either
           end of the gene.Compared to normal cells, immortalized
           human cell lines uniformly express higher levels of BRE.
           Peripheral blood monocytes respond to LPS by
           down-regulating the expression of all the BRE
           isoforms.It is thought that the function of BRE and its
           isoforms is to regulate peroxisomal activities.
          Length = 238

 Score = 29.7 bits (66), Expect = 0.93
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 137 FASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWE--NDACFTLEVRQSFQKLQN 188
           F +Q  EL    IF  D + +P P   ++   W+  N  C  L V++  Q+  N
Sbjct: 73  FNAQYPELPPDFIFGEDADFLPDPSALHHLAQWDAGNPECLLLLVKELIQQYHN 126


>gnl|CDD|162065 TIGR00844, c_cpa1, na(+)/h(+) antiporter.  This model is specific
           for the fungal members of this family.
          Length = 810

 Score = 28.0 bits (62), Expect = 2.8
 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 137 FASQRLELEEPLIFAGDYNIIPQPH--DCYNPIIWENDACFTLEVRQSFQKLQ 187
           F  ++L + E ++ A  + +I  PH  + +NP+ W N    TLE+ +    LQ
Sbjct: 31  FVKEKLYIGESMV-ASIFGLIVGPHCLNWFNPLSWGNTDSITLEISRILLCLQ 82


>gnl|CDD|182963 PRK11101, glpA, sn-glycerol-3-phosphate dehydrogenase subunit A;
           Provisional.
          Length = 546

 Score = 27.7 bits (62), Expect = 3.3
 Identities = 10/15 (66%), Positives = 10/15 (66%)

Query: 83  LPGDDLDVQARFIEA 97
           LP DDL  QA FI A
Sbjct: 94  LPEDDLAFQATFIRA 108


>gnl|CDD|128433 smart00128, IPPc, Inositol polyphosphate phosphatase, catalytic
          domain homologues.  Mg(2+)-dependent/Li(+)-sensitive
          enzymes.
          Length = 310

 Score = 27.7 bits (62), Expect = 3.5
 Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 10/45 (22%)

Query: 4  VTVATWNVNSIRARIHN-LAAWIK-------ENNPDIIC--LQET 38
          V V TWNV  ++A     + +W+           PDI    LQE 
Sbjct: 5  VLVGTWNVGGLKADPKVDVTSWLFQKIDVKQSEKPDIYVIGLQEV 49


>gnl|CDD|129656 TIGR00565, trpE_proteo, anthranilate synthase component I,
           proteobacterial subset.  This enzyme resembles some
           other chorismate-binding enzymes, including
           para-aminobenzoate synthase (pabB) and isochorismate
           synthase. There is a fairly deep split between two sets,
           seen in the pattern of gaps as well as in amino acid
           sequence differences. This group includes proteobacteria
           such as E. coli and Helicobacter pylori but also the
           gram-positive organism Corynebacterium glutamicum. The
           second group includes eukaryotes, archaea, and most
           other bacterial lineages; sequences from the second
           group may resemble pabB more closely than other trpE
           from this group.
          Length = 498

 Score = 27.5 bits (61), Expect = 4.2
 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 6/81 (7%)

Query: 182 SFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSW----SKNKGIRIDHIMLSPEATSLLH 237
           S+  +        ++A ++    + F  Y A++      + K  RI     +        
Sbjct: 134 SYDLVAGFEDLPHLKAKNNNCPDFCF--YLAETLIVIDHQKKSTRIQASCFAERFEKQRL 191

Query: 238 SARIDTKPRGWTKPSDHTPVI 258
            AR+D   +  T  +D  PV 
Sbjct: 192 QARLDLLEQQKTIKADPVPVK 212


>gnl|CDD|180586 PRK06483, PRK06483, dihydromonapterin reductase; Provisional.
          Length = 236

 Score = 27.2 bits (61), Expect = 5.0
 Identities = 7/22 (31%), Positives = 12/22 (54%)

Query: 10 NVNSIRARIHNLAAWIKENNPD 31
          + + +RA IHN + W+ E    
Sbjct: 71 HTDGLRAIIHNASDWLAEKPGA 92


>gnl|CDD|181356 PRK08290, PRK08290, enoyl-CoA hydratase; Provisional.
          Length = 288

 Score = 26.8 bits (60), Expect = 5.7
 Identities = 9/21 (42%), Positives = 10/21 (47%)

Query: 184 QKLQNMGFTDAIRATHDTHHL 204
           Q L   GF  A+ A  D H L
Sbjct: 235 QTLDAQGFRAALDAVFDLHQL 255


>gnl|CDD|184801 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
          Length = 1627

 Score = 26.3 bits (58), Expect = 7.8
 Identities = 6/35 (17%), Positives = 13/35 (37%)

Query: 45  FPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEI 79
              E L+ L  + E   +   N +  ++     E+
Sbjct: 581 TDLENLKDLVQNWEEKAKPFKNVIHFINLLSRFEL 615


  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
   0.319    0.134    0.419 

Gapped
Lambda     K      H
   0.267   0.0719    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,648,157
Number of extensions: 286039
Number of successful extensions: 545
Number of sequences better than 10.0: 1
Number of HSP's gapped: 533
Number of HSP's successfully gapped: 15
Length of query: 281
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 189
Effective length of database: 4,006,537
Effective search space: 757235493
Effective search space used: 757235493
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 (21.8 bits)
S2: 56 (25.4 bits)