RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

Query= gi|254780791|ref|YP_003065204.1| exodeoxyribonuclease VII large
subunit [Candidatus Liberibacter asiaticus str. psy62]
         (529 letters)



>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
           translation termination, ATP-binding, cytoplasm,
           hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
           (A:1-326)
          Length = 326

 Score = 39.0 bits (90), Expect = 0.001
 Identities = 27/205 (13%), Positives = 67/205 (32%), Gaps = 67/205 (32%)

Query: 236 IANSSIPIISAIGHETDWTLADYAADL--RAPTPTG--AAEMAVPVKEHLQSSLINLEAR 291
           I   ++P++          L++   ++  ++ + TG  AA  A+ +   + +S+   +A 
Sbjct: 145 IQEKALPLL----------LSNPPRNMIGQSQSGTGKTAA-FALTMLSRVDASVPKPQAI 193

Query: 292 LNNIIIRLIKYKINTLNSLLKALPNSDQTLSCSRYRLDRLPRELEHNLEIIIFRKYR--- 348
                  L +  ++ +  + K        +  +    D +P+  + + +I+I        
Sbjct: 194 CLAPSRELARQIMDVVTEMGKYTE-----VKTAFGIKDSVPKGAKIDAQIVIGTPGTVMD 248

Query: 349 ---------------------------HFNHIINRIKSDFLIHNIQKNRQHIL------E 375
                                             RI      H + +N Q +L      E
Sbjct: 249 LMKRRQLDARDIKVFVLDEADNMLDQQGLGDQSMRI-----KHLLPRNTQIVLFSATFSE 303

Query: 376 KQQHIEQIVKQHLR---YIFLEKKE 397
           +   +E+  ++       I L+ +E
Sbjct: 304 R---VEKYAERFAPNANEIRLKTEE 325


>1sg6_A Pentafunctional AROM polypeptide; shikimate pathway,
           aromatic amino acid biosynthesis, DHQS, open form, form
           J, domain movement, cyclase; HET: NAD; 1.70A {Emericella
           nidulans} (A:1-181)
          Length = 181

 Score = 34.4 bits (78), Expect = 0.033
 Identities = 20/161 (12%), Positives = 42/161 (26%), Gaps = 16/161 (9%)

Query: 91  KITTFPGSSKYQIIIESLIPSGSGTLLTALEKRKKKLLEEGLFSDQHKNPIPFIPKIIAV 150
             T      +  II +  +           +      +   L +D +             
Sbjct: 3   NPTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYV---LVTDTN------------- 46

Query: 151 ITSPTGAVIRDILQRISCRFPLRVIIFPVKVQGDECPKEIANAILQLNTLKEGRTCPRPD 210
           I S       +  ++ +        +        E  K         + +         D
Sbjct: 47  IGSIYTPSFEEAFRKRAAEITPSPRLLIYNRPPGEVSKSRQTKADIEDWMLSQNPPCGRD 106

Query: 211 IIILARGGGSIEDLWHFNDEMIVRAIANSSIPIISAIGHET 251
            +++A GGG I DL  F     +R +    +P       ++
Sbjct: 107 TVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDS 147


>2hpi_A DNA polymerase III alpha subunit; POL-beta-like
           nucleotidyltransferase fold; HET: DNA; 3.00A {Thermus
           aquaticus} PDB: 2hpm_A* 3e0d_A* (A:1024-1128)
          Length = 105

 Score = 32.1 bits (73), Expect = 0.19
 Identities = 15/100 (15%), Positives = 40/100 (40%), Gaps = 8/100 (8%)

Query: 14  EYSVSELSYHLKHIVESNLSHVCVRGEISGYRGIHS-SGH--AYFSLKDNHSRIDAIIWK 70
             ++ ELS  ++ +       V + G +       + SG   A F+L D    ++ +++ 
Sbjct: 3   SCTIEELSEFVRELPGK--PKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFG 60

Query: 71  GTLNKIEFLPEEGIEFLVIGKITTFPGSSKYQIIIESLIP 110
                +    +E I  LV+ ++         +++ +++  
Sbjct: 61  RAYEGVSPKLKEDIPLLVLAEVEKGEE---LRVLAQAVWT 97


>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
           {Thermotoga maritima} (A:160-248)
          Length = 89

 Score = 31.6 bits (72), Expect = 0.24
 Identities = 11/74 (14%), Positives = 21/74 (28%), Gaps = 2/74 (2%)

Query: 33  SHVCVRGEISGYRGIHSSGH--AYFSLKDNHSRIDAIIWKGTLNKIEFLPEEGIEFLVIG 90
             V  +G+I                 L D    +    +     +       G E  V G
Sbjct: 7   EKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQDYLQTYLKQLTGKEVFVTG 66

Query: 91  KITTFPGSSKYQII 104
            + +   + +Y+I 
Sbjct: 67  TVKSNAYTGQYEIH 80


>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase
           C; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB:
           3f2c_A* 3f2d_A* (A:1-110)
          Length = 110

 Score = 31.3 bits (71), Expect = 0.31
 Identities = 14/81 (17%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

Query: 35  VCVRGEISGYRGIHS-SGH--AYFSLKDNHSRIDAIIWKGTLNKIEFLP--EEGIEFLVI 89
           V V+G +         SG       + D  + I   ++       E +   ++G+   V 
Sbjct: 20  VVVQGYVFDAEVSELKSGRTLLTMKITDYTNSILVKMFSRDKEDAELMSGVKKGMWVKVR 79

Query: 90  GKITTFPGSSKYQIIIESLIP 110
           G +          II   L  
Sbjct: 80  GSVQNDTFVRDLVIIANDLNE 100


>2z7x_B TOLL-like receptor 1, variable lymphocyte receptor B; TLR2,
           TLR1, lipopeptide, innate immunity, glycoprotein, immune
           response, inflammatory response, leucine-rich repeat,
           membrane; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}
           (B:1-484)
          Length = 484

 Score = 31.1 bits (68), Expect = 0.33
 Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 4/54 (7%)

Query: 319 QTLSCSRYRLDRLPRELEHNLEIIIFRKYRHFNHIINRIKSDFLIHNIQKNRQH 372
             +  S+  L  +P++L     I+        N+I     SD L  +  +    
Sbjct: 3   FLVDRSKNGLIHVPKDLSQKTTILNI----SQNYISELWTSDILSLSKLRILII 52


>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET:
           NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A*
           3ciy_A* (A:)
          Length = 680

 Score = 30.0 bits (65), Expect = 0.67
 Identities = 7/69 (10%), Positives = 20/69 (28%), Gaps = 6/69 (8%)

Query: 319 QTLSCSRYRLDRLPRELEHNLEIIIFRKYRHFNHIINRIKSDFLIHNIQKNRQHILEKQQ 378
           +   CS  +L ++P +L  N+ ++        N +              +     +    
Sbjct: 7   EVADCSHLKLTQVPDDLPTNITVLNL----THNQLRRLP--AANFTRYSQLTSLDVGFNT 60

Query: 379 HIEQIVKQH 387
             +   +  
Sbjct: 61  ISKLEPELC 69


>2z63_A TOLL-like receptor 4, variable lymphocyte receptor B; TLR4,
           MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo
           sapiens} (A:1-534)
          Length = 534

 Score = 29.7 bits (64), Expect = 0.82
 Identities = 7/53 (13%), Positives = 16/53 (30%), Gaps = 4/53 (7%)

Query: 316 NSDQTLSCSRYRLDRLPRELEHNLEIIIFRKYRHFNHIINRIKSDFLIHNIQK 368
             + T  C      ++P  L  + + +       FN + +     F      +
Sbjct: 7   VPNITYQCMELNFYKIPDNLPFSTKNLDL----SFNPLRHLGSYSFFSFPELQ 55


>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-;
           fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
           reductase, beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae} (A:1221-1330,A:1541-1688)
          Length = 258

 Score = 29.5 bits (66), Expect = 1.0
 Identities = 15/115 (13%), Positives = 32/115 (27%), Gaps = 30/115 (26%)

Query: 321 LSCSRYRL--DRLPRELEHNLEIIIFRKYRHFNHIINRIKSDFLIHNIQKNRQHILE--- 375
           L+ +R      +        L +    KYR       + +       I+   ++ LE   
Sbjct: 7   LTTAREHHSSVKYASPN---LNM----KYR-------KRQLVTREAQIKDWVENELEALK 52

Query: 376 ------KQQHIEQIVKQHLRYIFLEKKEKIA-ILHMLREQTKNRIFYLHTHIKKL 423
                   +   + + +  R I  E + ++            N  +     I  L
Sbjct: 53  LEAEEIPSEDQNEFLLERTREIHNEAESQLRAAQQQW----GNDFYKRDPRIAPL 103



 Score = 26.8 bits (59), Expect = 7.3
 Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 9/79 (11%)

Query: 348 RHFNHIINRIKSDFLIHNIQKNRQHILEKQQHIEQIVKQHLRYIFLEKKEKIAILHMLRE 407
           R  +H   +  S  L  N++  ++ ++ ++  I+  V+  L  +    K +     +  E
Sbjct: 11  RE-HHSSVKYASPNL--NMKYRKRQLVTREAQIKDWVENELEAL----KLEAE--EIPSE 61

Query: 408 QTKNRIFYLHTHIKKLITR 426
                +      I      
Sbjct: 62  DQNEFLLERTREIHNEAES 80


>3clh_A 3-dehydroquinate synthase; shikimate pathway, aromatic amino
           acid biosynthesis, DHQS, amino-acid biosynthesis,
           cytoplasm, lyase, NAD; HET: NAD; 2.40A {Helicobacter
           pylori} (A:1-160)
          Length = 160

 Score = 29.7 bits (66), Expect = 1.0
 Identities = 22/109 (20%), Positives = 37/109 (33%), Gaps = 15/109 (13%)

Query: 148 IAVITSPT-----GAVIRDILQRISCRFPLRVIIFPVKVQGDECPKEIANAILQLNTLKE 202
             +I+           + + L+       +RV +        E  K   +    LN   E
Sbjct: 29  ALIISDSIVAGLHLPYLLERLKA----LEVRVCVIE----SGEKYKNFHSLERILNNAFE 80

Query: 203 GRTCPRPDIIILARGGGSIEDLWHFNDEMIVRAIANSSIPIISAIGHET 251
            +   R  ++I A GGG I D+  F   +  R I   +IP       + 
Sbjct: 81  MQ-LNRHSLMI-ALGGGVISDMVGFASSIYFRGIDFINIPTTLLAQVDA 127


>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte
           receptor B; TLR2, PAM3CSK4, lipopeptide, innate
           immunity, cytoplasmic vesicle; HET: NAG BMA MAN PCJ;
           1.80A {Mus musculus} PDB: 2z82_A* 2z7x_A* (A:1-513)
          Length = 513

 Score = 28.5 bits (61), Expect = 2.1
 Identities = 5/52 (9%), Positives = 12/52 (23%), Gaps = 12/52 (23%)

Query: 306 TLNSLLKALPNSDQTLSCSRYRLDRLPRELEHNLEIIIFRKYRHFNHIINRI 357
           + ++                     +P  L   ++ +       FN I    
Sbjct: 3   SCDAS--------GVCDGRSRSFTSIPSGLTAAMKSLDL----SFNKITYIG 42


>3g23_A Peptidase U61, LD-carboxypeptidase A; structural genomics,
           joint center for structural genomics, JCSG; HET: MSE;
           1.89A {Novosphingobium aromaticivorans DSM12444}
           (A:1-155,A:263-274)
          Length = 167

 Score = 28.3 bits (63), Expect = 2.2
 Identities = 14/93 (15%), Positives = 28/93 (30%), Gaps = 7/93 (7%)

Query: 148 IAVITSPTGAVIRDILQRISCRFPLRVIIFPVKVQGDECPKE---IANAILQ-LNTLKEG 203
           IA+  +P+    R+   R+            +    ++C       A +    L+   E 
Sbjct: 6   IAIC-APSTPFTREDSARVIALAAAEFPDLSLSF-HEQCFASEGHFAGSDALRLSAFLEC 63

Query: 204 RTCPRPDIIILARGG-GSIEDLWHFNDEMIVRA 235
                 + +   RGG G+          +   A
Sbjct: 64  ANDDAFEAVWFVRGGYGANRIAEDALARLGRAA 96


>1xah_A Sadhqs, 3-dehydroquinate synthase; shikimate pathway,
           aromatic amino acid biosynthesis, open form, form B,
           domain movement, cyclase; HET: NAD; 2.20A
           {Staphylococcus aureus} PDB: 1xag_A* 1xai_A* 1xaj_A*
           1xal_A* (A:1-165)
          Length = 165

 Score = 27.0 bits (59), Expect = 6.3
 Identities = 13/106 (12%), Positives = 28/106 (26%), Gaps = 5/106 (4%)

Query: 148 IAVITSPTGAVIRDILQRISCRFPLRVIIFPVKVQGDECPKEIANAILQLNTLKEGRTCP 207
             ++      V +    +         +   +   G++          +           
Sbjct: 34  SFLLIDEY--VNQYFANKFDDILSYENVHKVIIPAGEKTKTF--EQYQETLEYILSHHVT 89

Query: 208 RPDIIILARGGGSIEDLWHFNDEMIVRAIANSSIPIISAIGHETDW 253
           R   II A GGG+  D   F    ++R +    +P        +  
Sbjct: 90  RNTAII-AVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVG 134


>3l39_A Putative PHOU-like phosphate regulatory protein; BT4638,
           structural genomics, joint center for structural
           genomics, JCSG; 1.93A {Bacteroides thetaiotaomicron}
           (A:)
          Length = 227

 Score = 26.7 bits (58), Expect = 6.7
 Identities = 18/151 (11%), Positives = 43/151 (28%), Gaps = 1/151 (0%)

Query: 279 EHLQSSLINLEARLNNIIIRLIKYKINTLNSLLKALPNSDQTLSCSRY-RLDRLPRELEH 337
               S     E +   ++ +L      +   L++++ +   T     Y ++  + RE + 
Sbjct: 15  NSFFSKFTPKEPKFFPLLKQLSDVLSASSVLLVESMEHDLPTERADYYKQIKDMEREGDR 74

Query: 338 NLEIIIFRKYRHFNHIINRIKSDFLIHNIQKNRQHILEKQQHIEQIVKQHLRYIFLEKKE 397
              +I       F    +R     L   +      I    + I     + +     E   
Sbjct: 75  LTHLIFDELSTTFITPFDREDIHDLASCMDDVIDGINSSAKRIVIYNPRPISESGKELSR 134

Query: 398 KIAILHMLREQTKNRIFYLHTHIKKLITRIE 428
            I    +   +  + +     + K L     
Sbjct: 135 LIHEEAINIGKAMDELETFRKNPKPLRDYCT 165


>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific
           LRR-IG containing, ligand binding protein, membrane
           protein; HET: NAG MAN; 2.70A {Homo sapiens} (A:1-375)
          Length = 375

 Score = 26.7 bits (57), Expect = 6.8
 Identities = 6/35 (17%), Positives = 12/35 (34%), Gaps = 4/35 (11%)

Query: 319 QTLSCSRYRLDRLPRELEHNLEIIIFRKYRHFNHI 353
           + + C R R   +P  +     ++        N I
Sbjct: 14  RAVLCHRKRFVAVPEGIPTETRLLDL----GKNRI 44


>1pq4_A Periplasmic binding protein component of AN ABC type zinc
           uptake transporter; ZNUA, loop, metal-binding, metal
           binding protein; 1.90A {Synechocystis SP} (A:189-270)
          Length = 82

 Score = 26.6 bits (59), Expect = 8.9
 Identities = 5/39 (12%), Positives = 13/39 (33%)

Query: 380 IEQIVKQHLRYIFLEKKEKIAILHMLREQTKNRIFYLHT 418
           I+   + +L  +F E +        +  +    +  L  
Sbjct: 42  IDTAKENNLTMVFGETQFSTKSSEAIAAEIGAGVELLDP 80


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.321    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0504    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 3,991,772
Number of extensions: 188029
Number of successful extensions: 596
Number of sequences better than 10.0: 1
Number of HSP's gapped: 595
Number of HSP's successfully gapped: 43
Length of query: 529
Length of database: 4,956,049
Length adjustment: 93
Effective length of query: 436
Effective length of database: 1,812,184
Effective search space: 790112224
Effective search space used: 790112224
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: 57 (26.3 bits)