RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 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)



>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase;
           2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB:
           1ksl_A 1ksv_A*
          Length = 234

 Score =  161 bits (409), Expect = 2e-40
 Identities = 58/226 (25%), Positives = 100/226 (44%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 5   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 65  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +              +  +   V + + 
Sbjct: 125 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPA--VLEVITPTQVRLTIS 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   L  G  R ++++
Sbjct: 183 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 228


>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}
          Length = 290

 Score =  157 bits (398), Expect = 3e-39
 Identities = 58/234 (24%), Positives = 103/234 (44%), Gaps = 5/234 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   E
Sbjct: 5   SSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPRE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L 
Sbjct: 64  AEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     + ++ +  +  G+ I G      +V    +K +     +
Sbjct: 124 NKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKV----KKEAPFVFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +  
Sbjct: 180 TLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF 233


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

 Score =  125 bits (316), Expect = 1e-29
 Identities = 51/235 (21%), Positives = 101/235 (42%), Gaps = 19/235 (8%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
             +KP+G+V+T  D + R  + D +     RV  +GRLD +++GL+ LTN G L   +  
Sbjct: 18  ALNKPVGIVSTTEDGE-RDNIVDFVNH-SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR 75

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
                 + Y V     + ++ +  +  G+ I     G +      +K +     + L +G
Sbjct: 76  AGNDHEKEYLVTVDKPITEEFIRGMSAGVPI----LGTVTKKCKVKKEAPFVFRITLVQG 131

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256
            NR+I+++ E F ++V +L R       L  +  G  R+++   L +     L+E +   
Sbjct: 132 LNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFK--LIENS--- 186

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG--LSKQKKLATPVHRRN 309
                 SSE   + +    +          + +++K G   S  K+  +P  ++ 
Sbjct: 187 ------SSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 235


>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta
           sheet, isomerase; 1.60A {Escherichia coli}
          Length = 217

 Score =  124 bits (312), Expect = 3e-29
 Identities = 53/200 (26%), Positives = 90/200 (45%), Gaps = 18/200 (9%)

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            V              + + TR+ L++KP  ++   +D  GR T+ + +P     V + G
Sbjct: 20  QVKRFSSQRSTRRKP-ENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAG 76

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +     
Sbjct: 77  RLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPT 136

Query: 173 GDMQVTLDTQK---------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
                 L  +                   +W+ + L EG+NR+++++     +   RLIR
Sbjct: 137 LPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIR 196

Query: 218 ISYGPFQLGTLLAGSTREVS 237
            + G + L  L  G  REV+
Sbjct: 197 YAMGDYSLDNLANGEWREVT 216


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

 Score =  119 bits (300), Expect = 8e-28
 Identities = 52/184 (28%), Positives = 89/184 (48%), Gaps = 17/184 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G
Sbjct: 7   ENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNG 64

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----- 183
            L   L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +      
Sbjct: 65  ALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWP 124

Query: 184 ----------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                        +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  
Sbjct: 125 RNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEW 184

Query: 234 REVS 237
           REV+
Sbjct: 185 REVT 188


>1vio_A Ribosomal small subunit pseudouridine synthase A; structural
           genomics, lyase; 1.59A {Haemophilus influenzae} SCOP:
           d.265.1.3 d.66.1.5
          Length = 243

 Score =  116 bits (291), Expect = 6e-27
 Identities = 58/226 (25%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 4   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  +
Sbjct: 64  YFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRI 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V+++      +GI+++G         L+     N  +T+   
Sbjct: 124 TSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNLTI--S 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     KV  L R   G   L   L  G  R +++ 
Sbjct: 182 EGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQS 227


>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein,
          E.coli, montreal-kingston bacterial structural genomics
          initiative, BSGI; NMR {Escherichia coli K12} SCOP:
          d.66.1.6
          Length = 79

 Score = 52.8 bits (127), Expect = 1e-07
 Identities = 11/69 (15%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M   ++ +       +  ++   G + S  + +  IA+ +VKV+G +  R    +++   
Sbjct: 10 MATFSLGKHPHV--ELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQT 67

Query: 60 IEVDGVPLR 68
          +   G  ++
Sbjct: 68 VSFAGHSVQ 76


>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding,
           lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB:
           2ist_A 1qyu_A 1prz_A
          Length = 325

 Score = 47.7 bits (112), Expect = 4e-06
 Identities = 49/311 (15%), Positives = 92/311 (29%), Gaps = 43/311 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 9   TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 68

Query: 65  VPLRKAERT-------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
               +A                 + + +KP  LV      +   TV + L   +  +   
Sbjct: 69  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 128

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
                V RLD +T GL+++         L     +                    + + I
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 188

Query: 166 VIQGICYGDMQVT-----------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                    M V            +      +  + + L  G+  +I+         +  
Sbjct: 189 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV- 247

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
                YG        A      + +    Q     L    + L  PI S   +       
Sbjct: 248 -GDPVYGGRPRPPKGASEAFISTLRKFDRQ----ALHATMLRLYHPI-SGIEM-----EW 296

Query: 275 ISEVPDDFTRM 285
            + +P D   +
Sbjct: 297 HAPIPQDMVEL 307


>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 = 44.9 bits (106), Expect = 3e-05
 Identities = 38/243 (15%), Positives = 75/243 (30%), Gaps = 100/243 (41%)

Query: 56  STDHIEVDGVP-----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
           S ++ E  GVP     +    + ++      +    +H            LP+   + + 
Sbjct: 327 SLENNE--GVPSPMLSISNLTQEQV---QDYVNKTNSH------------LPA--GKQVE 367

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +  L +N    L+++   G  + L               +G      LNL          
Sbjct: 368 IS-L-VNGAKNLVVS---GPPQSL---------------YG------LNL---------- 391

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLG 226
                  TL   K  +     GL +  +R    E K  F       NR + ++  PF   
Sbjct: 392 -------TLRKAKAPS-----GLDQ--SRIPFSERKLKF------SNRFLPVA-SPFH-S 429

Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD-R---PNIISEVPDDF 282
            LL  ++      ++ + L  + +     ++  P+Y +     D R    +I     +  
Sbjct: 430 HLLVPAS-----DLINKDLVKNNVSFNAKDIQIPVYDTFD-GSDLRVLSGSIS----ERI 479

Query: 283 TRM 285
              
Sbjct: 480 VDC 482



 Score = 41.9 bits (98), Expect = 3e-04
 Identities = 24/92 (26%), Positives = 29/92 (31%), Gaps = 39/92 (42%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRKAERTRLWLYHKPIGL-VTT 87
             I +  VK      E       +T HI +D    G                  GL V T
Sbjct: 481 DCIIRLPVK-----WE-TTTQFKAT-HI-LDFGPGGAS----------------GLGVLT 516

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           H + DG             RVI  G LDIN +
Sbjct: 517 HRNKDGTGV----------RVIVAGTLDINPD 538



 Score = 32.6 bits (74), Expect = 0.14
 Identities = 24/140 (17%), Positives = 48/140 (34%), Gaps = 46/140 (32%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAP----IYSSETLVRDRPNIISEV---PDDF-- 282
           S   ++    +EQ+  ++    + N   P    +  S  LV    N++  V   P     
Sbjct: 340 SISNLT----QEQVQDYV---NKTNSHLPAGKQVEIS--LVNGAKNLV--VSGPPQSLYG 388

Query: 283 --TRMKKNSSQKNGLS------KQKKLATPVHRRNLASNVWMAKGI----HSSFLSDSGQ 330
               ++K  +   GL        ++KL      R L         +    HS  L  +  
Sbjct: 389 LNLTLRKAKAPS-GLDQSRIPFSERKLK--FSNRFLP--------VASPFHSHLLVPASD 437

Query: 331 R--EENHRRSPSFPSKRSLR 348
              ++  + + SF +K  ++
Sbjct: 438 LINKDLVKNNVSFNAK-DIQ 456


>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} SCOP:
           d.66.1.3 PDB: 3bbu_A
          Length = 133

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 16/112 (14%), Positives = 31/112 (27%), Gaps = 9/112 (8%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRK 69
              R+ K +  A    +R     MI   +V  NG    + +  V     + +  G   R 
Sbjct: 7   VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNG-QRSKPSKIVELNATLTLRQGNDERT 65

Query: 70  AERTRLWLYHKPIG----LVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLD 115
                +    +P      L    ++   +          +  +      R D
Sbjct: 66  VIVKAITEQRRPASEAALLYEETAESVEKREKMALARKLNALTMPHPDRRPD 117


>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2,
          protein structure initiative; HET: MSE; 1.53A
          {Streptococcus thermophilus lmg 18311}
          Length = 291

 Score = 36.8 bits (85), Expect = 0.008
 Identities = 12/62 (19%), Positives = 27/62 (43%), Gaps = 3/62 (4%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRV--KVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          +RV  +  + G+  +R + +R +    V   +NG   ++    +     +++ G  LR  
Sbjct: 7  ERVDVLAYKQGLFETREQAKRGVMAGLVVNVINGERYDKPGEKIDDGTELKLKGEKLRYV 66

Query: 71 ER 72
           R
Sbjct: 67 SR 68


>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation,
           structure based inhibitor design, ligase; HET: 485;
           2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB:
           1jij_A* 1jii_A* 1jik_A*
          Length = 420

 Score = 31.9 bits (72), Expect = 0.20
 Identities = 10/55 (18%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 16  VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + +V+   GI+ S+R+    +    + +NG   +     +   D I+ +   +R+
Sbjct: 355 IVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKIDGEFTIIRR 409


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

 Score = 31.3 bits (70), Expect = 0.36
 Identities = 13/62 (20%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 9   ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +  +P  +  ++  +G++ S+    R I +  V VN I ++       S+D +    + L
Sbjct: 351 KPGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDFLHGRWLVL 410

Query: 68  RK 69
           R+
Sbjct: 411 RR 412


>1eje_A FMN-binding protein; structural genomics, PSI, protein structure
          initiative, northeast structural genomics consortium,
          NESG; HET: FMN; 2.20A
          {Methanothermobacterthermautotrophicus} SCOP: b.45.1.2
          Length = 192

 Score = 30.7 bits (69), Expect = 0.52
 Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 4/36 (11%)

Query: 59 HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
           ++ +  P+  A R    L  +P  +VTT  D +G 
Sbjct: 9  SMDFEDFPVESAHR---ILTPRPTVMVTTV-DEEGN 40


>2vk9_A Alpha-toxin; glycosyltransferase; 2.85A {Clostridium novyi} SCOP:
           c.68.1.22
          Length = 551

 Score = 30.3 bits (68), Expect = 0.66
 Identities = 6/52 (11%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV---HRRNLASNVWMAKGIH 321
           + ++E+ D++     +S +   L   +           +N  ++   +K + 
Sbjct: 50  SKLNELVDNYQTKYPSSGRNLALENFRDSLYSELRELIKNSRTSTIASKNLS 101


>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}
          Length = 186

 Score = 30.1 bits (67), Expect = 0.71
 Identities = 12/30 (40%), Positives = 14/30 (46%), Gaps = 4/30 (13%)

Query: 65 VPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
          +P   A R    L   PI LV+T    DGR
Sbjct: 6  LPPENAYRI---LESGPIVLVSTR-GADGR 31


>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus
           stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E*
           1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A
          Length = 419

 Score = 29.7 bits (66), Expect = 1.0
 Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 16  VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + +++  AGI+ S+R+    I    + VNG  L+     + +   +E     +R+
Sbjct: 354 LVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRLEGRFTVIRR 408


>3hmz_A Flavin reductase domain protein, FMN-binding; YP_001049024.1,
          FMN-binding domain of flavin reductases-like enzyme,
          structural genomics; HET: MSE FMN; 1.50A {Shewanella
          baltica OS155}
          Length = 199

 Score = 29.3 bits (65), Expect = 1.5
 Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 3/30 (10%)

Query: 61 EVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
           +  V L KA R    L H P  LV+  S 
Sbjct: 13 NIAAVELAKAYRL---LNHGPTVLVSARSQ 39


>1rkd_A Ribokinase; carbohydrate kinase, ribose, nucleotide binding,
           transferase; HET: RIB ADP; 1.84A {Escherichia coli K12}
           SCOP: c.72.1.1 PDB: 1gqt_A* 1rka_A 1rk2_A* 1rks_A*
          Length = 309

 Score = 28.6 bits (62), Expect = 2.2
 Identities = 6/24 (25%), Positives = 14/24 (58%)

Query: 16  VSKVIARAGIASRREVERMIAQQR 39
           V++  A+  +  R E++  + +QR
Sbjct: 286 VTRKGAQPSVPWREEIDAFLDRQR 309


>3epu_A STM2138 virulence chaperone; TYPEIII secretion system, SRCA
           (SSRB-regulated chaperone A); 2.50A {Salmonella
           typhimurium}
          Length = 144

 Score = 28.3 bits (63), Expect = 2.7
 Identities = 8/51 (15%), Positives = 20/51 (39%)

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
            +  D L   FS  ++   +  +   L     D     +L   +++++ +Y
Sbjct: 2   YSRADRLLRQFSLKLNTDSIVFDENRLCSFIIDNRYRILLTSTNSEYIMIY 52


>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET:
           TYB; 2.0A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4
           PDB: 1h3e_A*
          Length = 432

 Score = 28.2 bits (62), Expect = 2.8
 Identities = 9/34 (26%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 16  VSKVIARAGIA-SRREVERMIAQQRVKVNGILLE 48
           V+++   AG+  S  E  R+I  + ++++G +L 
Sbjct: 371 VARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLT 404


>3cmw_A Protein RECA, recombinase A; homologous recombination,
            recombination/DNA complex; HET: DNA ADP; 2.80A
            {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*
          Length = 1706

 Score = 27.9 bits (62), Expect = 3.1
 Identities = 8/73 (10%), Positives = 21/73 (28%), Gaps = 5/73 (6%)

Query: 213  NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             +LI  +   +       G  +  +   L++   P   +E +  +   + S+        
Sbjct: 1304 EKLIEKAGAWYSYKGEKIGQGKANATAWLKDN--PETAKEIEKKVRELLLSN---PNSTT 1358

Query: 273  NIISEVPDDFTRM 285
                 +      M
Sbjct: 1359 GSTGSMSGRTGSM 1371


>1vjj_A Protein-glutamine glutamyltransferase E; transglutaminase 3, X-RAY
           crystallography, metalloenzyme, calcium ION; HET: GDP;
           1.90A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1
           d.3.1.4 PDB: 1sgx_A* 1l9m_A 1l9n_A* 1nud_A 1nuf_A 1nug_A
           1rle_A*
          Length = 692

 Score = 27.9 bits (62), Expect = 3.5
 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 8/63 (12%)

Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDA--------PIYSSETLVRDRPNIISEV 278
           +L      E   KI   Q   +L  +  + + A         +     ++ D P +  EV
Sbjct: 541 SLDPEEEAEHPIKISYAQYERYLKSDNMIRITAVCKVPDESEVVVERDIILDNPTLTLEV 600

Query: 279 PDD 281
            ++
Sbjct: 601 LNE 603


>2d5m_A Flavoredoxin; flavoprotein, FMN binding, electron transport; HET:
          FMN MES; 1.05A {Desulfovibrio vulgaris str}
          Length = 190

 Score = 27.1 bits (59), Expect = 5.7
 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)

Query: 67 LRKAERTRLWLYHKPIGLVTTHSDPDGR 94
          ++K+   R   Y  P+ LV T+ D D R
Sbjct: 1  MKKSLGARTLAYPTPLFLVGTY-DRDSR 27


>2jgs_A Circular permutant of avidin; biotin, D-biotin, beta-barrel,
           protein engineering, nanobiotechnology, biotin-binding
           protein, glycoprotein; HET: BTN; 1.9A {Gallus gallus}
          Length = 130

 Score = 27.2 bits (60), Expect = 6.3
 Identities = 10/34 (29%), Positives = 15/34 (44%)

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
             FTR++      +G S +K   T     +L SN
Sbjct: 76  MIFTRLRTQKEGGSGGSARKCSLTGKWTNDLGSN 109


>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase,
           ATP-binding cassette, ATPase, transport protein; 1.45A
           {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB:
           1oxs_C 1oxt_A 1oxu_A* 1oxv_A*
          Length = 353

 Score = 26.7 bits (59), Expect = 7.3
 Identities = 7/43 (16%), Positives = 15/43 (34%)

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
            +  D   +    +  +    + IG+V          T F+N+
Sbjct: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENI 103


  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
   0.318    0.134    0.385 

Gapped
Lambda     K      H
   0.267   0.0676    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,975,492
Number of extensions: 140609
Number of successful extensions: 382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 372
Number of HSP's successfully gapped: 35
Length of query: 354
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 261
Effective length of database: 3,438,538
Effective search space: 897458418
Effective search space used: 897458418
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: 57 (25.8 bits)