RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780406|ref|YP_003064819.1| putative ribosomal large
subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus
str. psy62]
         (354 letters)



>3dh3_A Ribosomal large subunit pseudouridine synthase F;
           protein-RNA complex, S4 domain, alpha/beta protein,
           isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A
           {Escherichia coli} (A:64-290)
          Length = 227

 Score =  101 bits (252), Expect = 1e-22
 Identities = 45/234 (19%), Positives = 92/234 (39%), Gaps = 15/234 (6%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE   L   +KP+G+V+  ++   R  + D +     RV  +GRLD +++GL+ LTN G 
Sbjct: 1   AEDLVLIALNKPVGIVS-TTEDGERDNIVDFVNHSK-RVFPIGRLDKDSQGLIFLTNHGD 58

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     + ++ +  +  G+ I G      +     +K +    
Sbjct: 59  LVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCK----VKKEAPFVF 114

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
            + L +G NR+I+++ E F ++V +L R       L  +  G  R+++      L + + 
Sbjct: 115 RITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 174

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
               E        P              + ++     +  + +S     +   +
Sbjct: 175 NSSSEVKPKAKAKPKT------AGIKRPVVKMEKTAEKGGRPASNGKRFTSPGR 222


>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA,
           lyase; 2.00A {Escherichia coli} (A:59-234)
          Length = 176

 Score =  101 bits (251), Expect = 2e-22
 Identities = 40/176 (22%), Positives = 72/176 (40%), Gaps = 3/176 (1%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R +  +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L T+DG  
Sbjct: 3   HGPRYFXLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLXTDDGQW 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P     + Y V     V  D      KG+ +              +  +   V 
Sbjct: 63  SHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPA--VLEVITPTQVR 120

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
           + + EG+  ++K+ F      V  L R   G   L   L  G  R ++++ +   +
Sbjct: 121 LTISEGRYHQVKRXFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEIASVV 176


>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF,
           ribosome, RNA modifying enzyme, isomerase; 2.60A
           {Escherichia coli} (A:)
          Length = 237

 Score =  100 bits (248), Expect = 4e-22
 Identities = 42/244 (17%), Positives = 86/244 (35%), Gaps = 15/244 (6%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +              L   +KP+G+V+  ++   R  + D +     RV  +GRLD +++
Sbjct: 1   MGSSHHHHHHGSDLVLIALNKPVGIVS-TTEDGERDNIVDFVNHSK-RVFPIGRLDKDSQ 58

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+ LTN G L   +        + Y V     + ++      +G        G +    
Sbjct: 59  GLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEF----IRGXSAGVPILGTVTKKC 114

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK- 238
             +K +     + L +G NR+I++  E F ++V +L R       L  +  G  R+++  
Sbjct: 115 KVKKEAPFVFRITLVQGLNRQIRRXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDD 174

Query: 239 --KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               L + +     E        P              + +      +  + +S     +
Sbjct: 175 ELIDLFKLIENSSSEVKPKAKAKPKT------AGIKRPVVKXEKTAEKGGRPASNGKRFT 228

Query: 297 KQKK 300
              +
Sbjct: 229 SPGR 232


>1vio_A Ribosomal small subunit pseudouridine synthase A; structural
           genomics, lyase; 1.59A {Haemophilus influenzae}
           (A:58-243)
          Length = 186

 Score = 93.5 bits (231), Expect = 3e-20
 Identities = 43/173 (24%), Positives = 79/173 (45%), Gaps = 3/173 (1%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  + ++ +KP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  
Sbjct: 3   EEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQW 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P     + Y V     V+++      +GI+++G         L+     N  +T
Sbjct: 63  SHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNLT 122

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
             + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + 
Sbjct: 123 --ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIE 173


>1v9k_A Ribosomal large subunit pseudouridine synthase C;
           pseudouridine syntase, RNA binding, lyase; 2.00A
           {Escherichia coli} (A:)
          Length = 228

 Score = 93.1 bits (230), Expect = 5e-20
 Identities = 31/231 (13%), Positives = 60/231 (25%), Gaps = 33/231 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           E   + + +KP G             +            +  V RLD +T G+LL+    
Sbjct: 7   EDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKR 66

Query: 129 GLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGD 174
              R L     +    + Y     GQ      ++             +   V Q     +
Sbjct: 67  SALRSLHEQLREKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE 126

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +  ++ +      V      G+  +I+   ++    +    R     F      AG+  
Sbjct: 127 TRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGL 186

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                          L  A +    P         +   I +   +   R 
Sbjct: 187 N-----------RLFLHAAALKFTHPGT------GEVXRIEAPXDEGLKRC 220


>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA
           binding, lyase; 1.70A {Escherichia coli} (A:)
          Length = 325

 Score = 86.0 bits (211), Expect = 6e-18
 Identities = 48/315 (15%), Positives = 91/315 (28%), Gaps = 43/315 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           ++    V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + 
Sbjct: 4   VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQ 63

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + ++     +A             E   + + +KP  LV      +   TV + L   + 
Sbjct: 64  VAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYP 123

Query: 107 RVIS------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL 158
            +        V RLD +T GL+++         L     +    R Y     G +     
Sbjct: 124 PIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGT 183

Query: 159 NL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                           V            +      +  + + L  G+  +I+       
Sbjct: 184 VDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHIT 243

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
             +         P             +       +     L    + L  PI S   +  
Sbjct: 244 HPLVGDPVYGGRPRPPKGASEAFISTLR------KFDRQALHATMLRLYHPI-SGIEME- 295

Query: 270 DRPNIISEVPDDFTR 284
                 + +P D   
Sbjct: 296 ----WHAPIPQDMVE 306


>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated
           beta sheet, isomerase; 1.60A {Escherichia coli}
           (A:1-102,A:201-217)
          Length = 119

 Score = 82.7 bits (204), Expect = 7e-17
 Identities = 29/111 (26%), Positives = 48/111 (43%), Gaps = 10/111 (9%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ +      Q+              V              + + TR+ L++KP  ++  
Sbjct: 2   RQFIISENTMQKTSFRNHQ-------VKRFSSQRSTRRKP-ENQPTRVILFNKPYDVLPQ 53

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
            +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  P 
Sbjct: 54  FTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPG 102


>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated
           beta sheet, thrombin-cleaved, isomerase; 1.20A
           {Escherichia coli} (A:)
          Length = 189

 Score = 81.5 bits (200), Expect = 1e-16
 Identities = 50/182 (27%), Positives = 86/182 (47%), Gaps = 17/182 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P         GRLD ++EGLL+LTN+G L
Sbjct: 9   QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYA--AGRLDRDSEGLLVLTNNGAL 66

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------------- 176
              L  P  +  ++Y V+  G   QD L  L+ G+ +                       
Sbjct: 67  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 126

Query: 177 -VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 127 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 186

Query: 236 VS 237
           V+
Sbjct: 187 VT 188


>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA
           complex; HET: FOU; 2.05A {Escherichia coli} (A:)
          Length = 217

 Score = 76.9 bits (188), Expect = 4e-15
 Identities = 21/184 (11%), Positives = 51/184 (27%), Gaps = 16/184 (8%)

Query: 58  DHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLD 115
           ++       L    +   + + +KP GL++     +               +  SV RLD
Sbjct: 3   NYNPPQEPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQAESVHRLD 62

Query: 116 INTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
             T G++++       R L+      +  + Y  R  G     +  +    I        
Sbjct: 63  XATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPK 122

Query: 174 DMQVTLDTQK------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                   +              + A V +    G++ +++         +      +  
Sbjct: 123 QKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHXLALGHPILGDRFYASP 182

Query: 222 PFQL 225
             + 
Sbjct: 183 EARA 186


>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region;
           heat shock proteins, protein-RNA interactions, ribosome,
           structural genomics; 2.00A {Escherichia coli} (A:)
          Length = 133

 Score = 70.5 bits (172), Expect = 3e-13
 Identities = 15/131 (11%), Positives = 33/131 (25%), Gaps = 8/131 (6%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + ++     R+ K +  A    +R     MI   +V  NG   + + +  ++       G
Sbjct: 1   MKEKPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQG 60

Query: 65  VPLRKAERTRL-WLYHKPIGLVTTHSDPDGRS----TVFDNLPSIF-SRVISVGRLD-IN 117
              R      +             + +          +         +      R D   
Sbjct: 61  NDERTVIVKAITEQRRPASEAALLYEETAESVEKREKMALARKLNALTMPHPDRRPDKKE 120

Query: 118 TEGLLLLTNDG 128
              LL   +  
Sbjct: 121 RRDLLRFKHGD 131


>1vio_A Ribosomal small subunit pseudouridine synthase A;
          structural genomics, lyase; 1.59A {Haemophilus
          influenzae} (A:1-57)
          Length = 57

 Score = 57.3 bits (139), Expect = 3e-09
 Identities = 15/55 (27%), Positives = 26/55 (47%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L
Sbjct: 2  SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELL 56


>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA,
          lyase; 2.00A {Escherichia coli} (A:1-58)
          Length = 58

 Score = 56.1 bits (136), Expect = 7e-09
 Identities = 18/53 (33%), Positives = 26/53 (49%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL
Sbjct: 5  RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPL 57


>3dh3_A Ribosomal large subunit pseudouridine synthase F;
          protein-RNA complex, S4 domain, alpha/beta protein,
          isomerase, RNA-binding, rRNA processing; HET: FHU;
          3.00A {Escherichia coli} (A:1-63)
          Length = 63

 Score = 53.9 bits (130), Expect = 3e-08
 Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   E
Sbjct: 6  SVRLNKYISESGICSRREADRYIEQGNVFLNGKRA-TIGDQVKPGDVVKVNGQLIEPRE 63


>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding
          protein, E.coli, montreal-kingston bacterial structural
          genomics initiative, BSGI; NMR {Escherichia coli K12}
          (A:)
          Length = 79

 Score = 50.1 bits (120), Expect = 4e-07
 Identities = 10/64 (15%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
                    +  ++   G + S  + +  IA+ +VKV+G +  R    +++   +   G
Sbjct: 13 FSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG 72

Query: 65 VPLR 68
            ++
Sbjct: 73 HSVQ 76


>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis,
          aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine,
          RNA-binding, ATP-binding; 2.9A {Mycobacterium
          tuberculosis} (A:345-432)
          Length = 88

 Score = 48.2 bits (115), Expect = 2e-06
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          P  +  ++  +G++ S+    R I +  V VN I ++       S+D +    + LR+ +
Sbjct: 11 PDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDFLHGRWLVLRRGK 70

Query: 72 RTRLWLYHKPIGLVTTHSDPDGR 94
          R+           V         
Sbjct: 71 RS----IA----GVERIGLEHHH 85


>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated
           beta sheet, isomerase; 1.60A {Escherichia coli}
           (A:103-200)
          Length = 98

 Score = 45.4 bits (107), Expect = 1e-05
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 15/94 (15%)

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------------GSNA 187
           ++Y V+  G   QD L  L+ G+ +           L  +                   +
Sbjct: 5   KIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTS 64

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           W+ + L EG+NR+++++     +   RLIR + G
Sbjct: 65  WLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 98


>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2,
          protein structure initiative; HET: MSE; 1.53A
          {Streptococcus thermophilus lmg 18311} (A:1-65)
          Length = 65

 Score = 42.8 bits (101), Expect = 6e-05
 Identities = 11/63 (17%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 9  ENFTPQRVSKVIARAGIA-SRREVERMIAQQRV--KVNGILLERAAVNVMSTDHIEVDGV 65
               +RV  +  + G+  +R + +R +    V   +NG   ++    +     +++ G 
Sbjct: 2  NAXPKERVDVLAYKQGLFETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGTELKLKGE 61

Query: 66 PLR 68
           LR
Sbjct: 62 KLR 64


>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA
          synthetase; HET: TYB; 2.0A {Thermus thermophilus}
          (A:350-432)
          Length = 83

 Score = 35.8 bits (83), Expect = 0.008
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           V+++   AG+  S  E  R+I  + ++++G +L    + V  +    +
Sbjct: 21 WVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRIL 69


>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer;
           truncation, structure based inhibitor design, ligase;
           HET: 485; 2.20A {Staphylococcus aureus} (A:247-420)
          Length = 174

 Score = 34.6 bits (79), Expect = 0.022
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            KD   V  +     + +V+   GI+ S+R+    +    + +NG   +     +   D 
Sbjct: 94  FKDVPQVTLSNDTTNIVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDK 153

Query: 60  IEVDGVPLRK 69
           I+ +   +R+
Sbjct: 154 IDGEFTIIRR 163


>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A
           {Geobacillus stearothermophilus} (A:246-419)
          Length = 174

 Score = 33.8 bits (77), Expect = 0.032
 Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            KD            + +++  AGI+ S+R+    I    + VNG  L+     + +   
Sbjct: 94  FKDVPSFVHEGGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHR 153

Query: 60  IEVDGVPLRK 69
           +E     +R+
Sbjct: 154 LEGRFTVIRR 163


>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding,
          metal-binding, zinc-finger, translation; HET: TM2 PAR;
          2.5A {Thermus thermophilus} (D:100-193)
          Length = 94

 Score = 30.2 bits (68), Expect = 0.38
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  V+ R G A SRR+  +++    + VNG  ++  +  V   D I V
Sbjct: 1  RLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAV 49


>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3
          homolog; S4 domain, structural genomics, NPPSFA; NMR
          {Homo sapiens} (A:)
          Length = 71

 Score = 30.0 bits (68), Expect = 0.51
 Identities = 9/57 (15%), Positives = 21/57 (36%), Gaps = 3/57 (5%)

Query: 9  ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAA--VNVMSTDHIEV 62
             + +R+  V+ +  +A   +     + Q  V+V   ++   A  V     D +  
Sbjct: 3  SGSSGRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTW 59


>2k6p_A Uncharacterized protein HP_1423; alpha-L motif,
          RNA-binding, unknown function; NMR {Helicobacter
          pylori} (A:)
          Length = 92

 Score = 28.4 bits (63), Expect = 1.4
 Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 2/49 (4%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ K +   G+   R     M     V +NG    +A+  V + D I +
Sbjct: 2  RIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCA-KASKEVKAGDTISL 49


>1p9y_A Trigger factor, TF; alpha-beta protein, isomerase; 2.15A
           {Escherichia coli} (A:)
          Length = 121

 Score = 28.2 bits (63), Expect = 1.6
 Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 15/81 (18%)

Query: 174 DMQVTLDTQKGSNAWVTVGLREGK-NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            MQV+++T +G    VT+ +        +K         V + +RI     + G      
Sbjct: 3   HMQVSVETTQGLGRRVTITIAADSIETAVKSELV----NVAKKVRID--GLRKG------ 50

Query: 233 TREVSKKILREQLGPHLLEEA 253
             +V   I+ ++ G  + ++ 
Sbjct: 51  --KVPMNIVAQRYGASVRQDV 69


>3dhw_C Methionine import ATP-binding protein METN; ABC-transporter,
           methionine uptake transporter, membrane protein,
           amino-acid transport; 3.70A {Escherichia coli K12}
           (C:246-343)
          Length = 98

 Score = 26.7 bits (59), Expect = 4.6
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 6/82 (7%)

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             R+   P T  + + R+ F GQ     L     ++  V   I    M      + G   
Sbjct: 9   QERLQAEPFTDCVPMLRLEFTGQSVDAPLLSETARRFNVNNNIISAQMDYAGGVKFG--- 65

Query: 188 WVTVGLREGKNREIKKVFEFFN 209
            +   +  G  ++ +    +  
Sbjct: 66  IMLTEM-HGTQQDTQAAIAWLQ 86


>3e4v_A NADH:FMN oxidoreductase like protein; YP_544701.1,
          structural genomics, joint center for structural
          genomics, JCSG; HET: MSE FMN; 1.40A {Methylobacillus
          flagellatus KT} (A:)
          Length = 186

 Score = 26.1 bits (57), Expect = 7.4
 Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 7/34 (20%)

Query: 61 EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
          E+      +       L   PI LV+T    DGR
Sbjct: 5  ELPPENAYRI------LESGPIVLVSTR-GADGR 31


  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
   0.318    0.134    0.385 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,602,391
Number of extensions: 117932
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 31
Length of query: 354
Length of database: 4,956,049
Length adjustment: 89
Effective length of query: 265
Effective length of database: 1,947,404
Effective search space: 516062060
Effective search space used: 516062060
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 (21.7 bits)
S2: 55 (25.0 bits)