RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780125|ref|YP_003064538.1| prophage antirepressor
[Candidatus Liberibacter asiaticus str. psy62]
         (262 letters)



>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 36.8 bits (85), Expect = 0.005
 Identities = 51/376 (13%), Positives = 104/376 (27%), Gaps = 166/376 (44%)

Query: 8   EFES-----NKIRTIV-----DKDQNIWFVAKDV------ATALGYENSNEA-----INA 46
           EFE+     N I  +      + D  +    K++      A  +     ++        A
Sbjct: 90  EFENCYLEGNDIHALAAKLLQENDTTL-VKTKELIKNYITARIMAKRPFDKKSNSALFRA 148

Query: 47  HCKGVAKRYPL-----KTEGGIQKVRIISEPDVYRLLVK-------------STLP-SAQ 87
             +G A+   +      T+   +++R +     Y +LV                    A+
Sbjct: 149 VGEGNAQLVAIFGGQGNTDDYFEELRDLY--QTYHVLVGDLIKFSAETLSELIRTTLDAE 206

Query: 88  KF-------ERWVF-EEVLPTLRKTGSYSVEAP--------------------------K 113
           K          W+      P       Y +  P                          +
Sbjct: 207 KVFTQGLNILEWLENPSNTPDK----DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGE 262

Query: 114 LR-----------------ATSASTVLRVHKHLEELAKQA-------GLKDNQ------L 143
           LR                 A + +      +      ++A       G++  +      L
Sbjct: 263 LRSYLKGATGHSQGLVTAVAIAETDSW---ESFFVSVRKAITVLFFIGVRCYEAYPNTSL 319

Query: 144 ------------------LLKVNRGVTKITGVDQLEA-MDI--KHLPSSDNDEYLTITQI 182
                             +L +   +T+    +Q++  ++    HLP+    + + I+ +
Sbjct: 320 PPSILEDSLENNEGVPSPMLSI-SNLTQ----EQVQDYVNKTNSHLPA---GKQVEISLV 371

Query: 183 -GERLN-----PPQRARFLNKLLLK----RGLQVSKVSGGYRPTPKGEERGGKMCDVPM- 231
            G + N     PPQ    LN  L K     GL  S++    R   K   R      +P+ 
Sbjct: 372 NGAK-NLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK-LKFSNRF-----LPVA 424

Query: 232 -----QHVEGSTQQLK 242
                  +  ++  + 
Sbjct: 425 SPFHSHLLVPASDLIN 440


>1y8a_A Hypothetical protein AF1437; structural genomics, protein structure
           initiative, PSI, midwest center for structural genomics,
           MCSG; 1.40A {Archaeoglobus fulgidus dsm 4304} SCOP:
           c.108.1.24
          Length = 332

 Score = 28.1 bits (62), Expect = 2.0
 Identities = 8/105 (7%), Positives = 21/105 (20%), Gaps = 6/105 (5%)

Query: 99  PTLRKTGSYSVEAPKLRATSASTVLRVHKHLEELAKQAGLKDNQLLLKVNRGVTKITGVD 158
                   Y                   K L      AG+K+  +          +   +
Sbjct: 50  RFFSNLSEYDDYLAYEVRREGYEAGYTLKLLTPFLAAAGVKNRDVERIAELSAKFVPDAE 109

Query: 159 Q----LEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLL 199
           +    L+      + S+   +   + +    +             
Sbjct: 110 KAMATLQERWTPVVISTSYTQ--YLRRTASMIGVRGELHGTEVDF 152


>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix
           prnai nucleotide-binding domain; HET: MSE; 1.80A
           {Sulfolobus solfataricus}
          Length = 244

 Score = 27.0 bits (59), Expect = 4.2
 Identities = 7/50 (14%), Positives = 14/50 (28%), Gaps = 2/50 (4%)

Query: 174 DEYLTITQIGERLN-PPQRARFLNKLLLKRGL-QVSKVSGGYRPTPKGEE 221
            +   IT++ + L+   +        L K G+               G  
Sbjct: 164 TKGTGITELAKMLDKSEKTLINKIAELKKFGILTQKGKDRKVELNELGLN 213


>1lt8_A Betaine-homocysteine methyltransferase; homocysteine metabolism,
           homocysteinemia, zinc, thiol alkyl transfer; HET: CBH
           CIT; 2.05A {Homo sapiens} SCOP: c.1.26.1 PDB: 1lt7_A*
           1umy_A
          Length = 406

 Score = 27.1 bits (59), Expect = 4.6
 Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 3/76 (3%)

Query: 128 HLEELAKQAGLKDNQLLLKVNRGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLN 187
           H+  +A++   +   L     +  +  +G+D      ++     +  E L I   G   N
Sbjct: 306 HIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWVRARARKEYWENLRIA-SGRPYN 364

Query: 188 PPQRARFLNKLLLKRG 203
           P           + +G
Sbjct: 365 PSMSKPD--GWGVTKG 378


>2dk8_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural
           genomics, RNA_POL_RPC34 domain, RNA polymerase III C39
           subunit, NPPSFA; NMR {Mus musculus} SCOP: a.4.5.85
          Length = 81

 Score = 26.3 bits (58), Expect = 6.3
 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%)

Query: 186 LNPPQRARFLNKLLLKRGLQVSKVSGG--YR 214
           +   QRA  +N+LL    L + + + G  YR
Sbjct: 42  IEAQQRAVAINRLLSMGQLDLLRSNTGLLYR 72


>1tnr_A Tumor necrosis factor beta; complex(lymphokine/receptor); 2.85A
           {Homo sapiens} SCOP: b.22.1.1
          Length = 144

 Score = 26.5 bits (58), Expect = 6.6
 Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 3/28 (10%)

Query: 230 PMQHVEG---STQQLKWNSNLLVSFLQN 254
           P  H+ G       L W +N   +FLQ+
Sbjct: 2   PAAHLIGDPSKQNSLLWRANTDRAFLQD 29


>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
           termination, ATP-binding, cytoplasm, hydrolase,
           membrane; 2.80A {Schizosaccharomyces pombe}
          Length = 508

 Score = 26.2 bits (57), Expect = 8.1
 Identities = 30/139 (21%), Positives = 52/139 (37%), Gaps = 24/139 (17%)

Query: 79  VKSTLPSAQKF----ERWVFEEVLPTLRKTGSYSVEAPKLRATSASTVLRVHKHLEELAK 134
           V +++P  Q       R +  +++  + + G Y         T   T   +   + + AK
Sbjct: 183 VDASVPKPQAICLAPSRELARQIMDVVTEMGKY---------TEVKTAFGIKDSVPKGAK 233

Query: 135 QAGLKDNQLLLKVNRGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARF 194
                D Q+++     V  +    QL+A DIK     + D  L    +G+     Q  R 
Sbjct: 234 ----IDAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGD-----QSMRI 284

Query: 195 LNKLLLKRGLQVSKVSGGY 213
             K LL R  Q+   S  +
Sbjct: 285 --KHLLPRNTQIVLFSATF 301


>2tnf_A Protein (tumor necrosis factor alpha); lymphokine, cytokine,
           cytotoxin, transmembrane, glycoprotein, signal-anchor;
           1.40A {Mus musculus} SCOP: b.22.1.1 PDB: 1a8m_A 1tnf_A
           2tun_A 2az5_A* 4tsv_A 5tsw_A 2e7a_A 2zpx_A 2zjc_A
          Length = 156

 Score = 26.1 bits (57), Expect = 8.5
 Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 3/30 (10%)

Query: 228 DVPMQHVEG---STQQLKWNSNLLVSFLQN 254
           D P+ HV       +QL+W S    + L N
Sbjct: 10  DKPVAHVVANHQVEEQLEWLSQRANALLAN 39


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.315    0.132    0.378 

Gapped
Lambda     K      H
   0.267   0.0521    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,136,459
Number of extensions: 94895
Number of successful extensions: 248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 10
Length of query: 262
Length of database: 5,693,230
Length adjustment: 91
Effective length of query: 171
Effective length of database: 3,487,026
Effective search space: 596281446
Effective search space used: 596281446
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: 56 (25.8 bits)