RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780479|ref|YP_003064892.1| A/G-specific adenine
glycosylase [Candidatus Liberibacter asiaticus str. psy62]
         (356 letters)



>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA
           glycosylase, transition state analog, DNA repair; HET:
           NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A*
           1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
          Length = 369

 Score =  270 bits (690), Expect = 5e-73
 Identities = 107/348 (30%), Positives = 166/348 (47%), Gaps = 16/348 (4%)

Query: 8   IQSKILDWYDTNHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQK 67
            Q  +LDW+    R LPWR            PYKVW+SE+MLQQT V+TV PYF++F+ +
Sbjct: 16  FQRDLLDWFARERRDLPWRKDR--------DPYKVWVSEVMLQQTRVETVIPYFEQFIDR 67

Query: 68  WPTIFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIG 127
           +PT+  L+ A ++E+L AW GLGYY+R RNL      +  +Y G  P   +   +L G+G
Sbjct: 68  FPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVG 127

Query: 128 DYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPLY--HKTIKNYARKITSTSRPG 185
            YT  A++++A+      VD N+ R++SR F +          K  +   R+I +   PG
Sbjct: 128 PYTVGAVLSLAYGVPEPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPG 187

Query: 186 DFVQAMMDLGALICTSNKPLCPLCPIQKNCLTFSEGKSHLLGINTIKKKRPMRTGAVFIA 245
            F +A+++LGAL+CT  +P C LCP+Q  C  F+EG +  L +   K        AV + 
Sbjct: 188 AFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVL 247

Query: 246 ITNDNRILLRKRTNTRLLEGMDELPGSAWSSTKDG----NIDTHSAPFTANWI-LCNTIT 300
             ++ R+L+RKR +T LL  + E P               +                +  
Sbjct: 248 ADDEGRVLIRKRDSTGLLANLWEFPSCETDGADGKEKLEQMVGEQYGLQVELTEPIVSFE 307

Query: 301 HTFTHFTLTLFVWKTIVPQIVIIPDST-WHDAQNLANAALPTVMKKAL 347
           H F+H    L V+   +     + +         L   A P   ++  
Sbjct: 308 HAFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVW 355


>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices,
           helix-hairpin-helix motif, iron-sulfur cluste hydrolase;
           2.30A {Homo sapiens}
          Length = 287

 Score =  253 bits (646), Expect = 5e-68
 Identities = 95/266 (35%), Positives = 135/266 (50%), Gaps = 5/266 (1%)

Query: 8   IQSKILDWYDTNHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQK 67
            +  +L WYD   R LPWR   + E       Y VW+SE+MLQQT V TV  Y+  +MQK
Sbjct: 18  FRGSLLSWYDQEKRDLPWRRRAEDEMDLDRRAYAVWVSEVMLQQTQVATVINYYTGWMQK 77

Query: 68  WPTIFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYEGNFPHK-VEILKKLPGI 126
           WPT+  L+SA  EE+   WAGLGYY+R R L++ A  +V++  G+ P     + + LPG+
Sbjct: 78  WPTLQDLASASLEEVNQLWAGLGYYSRGRRLQEGARKVVEELGGHMPRTAETLQQLLPGV 137

Query: 127 GDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKP--APLYHKTIKNYARKITSTSRP 184
           G YTA AI +IAF     VVD N+ R++ R   I     + L  + +   A+++   +RP
Sbjct: 138 GRYTAGAIASIAFGQATGVVDGNVARVLCRVRAIGADPSSTLVSQQLWGLAQQLVDPARP 197

Query: 185 GDFVQAMMDLGALICTSNKPLCPLCPIQKNCLTFSEGKSHLLGINTIKKKRPMRTGAVFI 244
           GDF QA M+LGA +CT  +PLC  CP++  C      +   L  +      P        
Sbjct: 198 GDFNQAAMELGATVCTPQRPLCSQCPVESLCRARQRVEQEQLLASGSLSGSPDVEECAP- 256

Query: 245 AITNDNRILLRKRTNTRLLEGMDELP 270
             T    + L          G+   P
Sbjct: 257 -NTGQCHLCLPPSEPWDQTLGVVNFP 281


>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A
           {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A
           1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A*
           1wef_A* 1kg7_A 1kqj_A
          Length = 225

 Score =  214 bits (545), Expect = 3e-56
 Identities = 87/231 (37%), Positives = 132/231 (57%), Gaps = 14/231 (6%)

Query: 8   IQSKILDWYDT-NHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQ 66
             +++LDWYD    + LPW+           +PYKVW+SE+MLQQT V TV PYF++FM 
Sbjct: 6   FSAQVLDWYDKYGRKTLPWQIDK--------TPYKVWLSEVMLQQTQVATVIPYFERFMA 57

Query: 67  KWPTIFCLSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYEGNFPHKVEILKKLPGI 126
           ++PT+  L++A  +E+L  W GLGYY RARNL K A  +   + G FP   E +  LPG+
Sbjct: 58  RFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGV 117

Query: 127 GDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPLYH--KTIKNYARKITSTSRP 184
           G  TA AI++++      ++D N++R+++R + +            + + + ++T     
Sbjct: 118 GRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSEQVTPAVGV 177

Query: 185 GDFVQAMMDLGALICTSNKPLCPLCPIQKNCLTFSEGKSHLLGINTIKKKR 235
             F QAMMDLGA+ICT +KP C LCP+Q  C+  +     L      KK +
Sbjct: 178 ERFNQAMMDLGAMICTRSKPKCSLCPLQNGCIAAANNSWALY---PGKKPK 225


>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase,
           DNA mismatch, methylation, base twisting, hydrolase;
           2.00A {Methanothermobacterthermautotrophicus} SCOP:
           a.96.1.2
          Length = 221

 Score =  201 bits (512), Expect = 2e-52
 Identities = 65/219 (29%), Positives = 105/219 (47%), Gaps = 10/219 (4%)

Query: 7   IIQSKILDWYDTNHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQ 66
           +  S IL +++T+ R  PWR +          PY + I+EI+L++TT   V+  + KF  
Sbjct: 11  VFVSTILTFWNTDRRDFPWRHTR--------DPYVILITEILLRRTTAGHVKKIYDKFFV 62

Query: 67  KWPTIFCLSSAKDEEILSAWAGLGYY-TRARNLKKCADIIVKKYEGNFPHKVEILKKLPG 125
           K+     +      EI      +G    RA  LK+ A +++  Y G  P   + +  LPG
Sbjct: 63  KYKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPG 122

Query: 126 IGDYTASAIVAIAFNHFAVVVDTNIERIISRYFDII-KPAPLYHKTIKNYARKITSTSRP 184
           +G YT +A++ +AF   A +VD N  R+I+RYF    +     HK +   A  +    + 
Sbjct: 123 VGKYTCAAVMCLAFGKKAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKC 182

Query: 185 GDFVQAMMDLGALICTSNKPLCPLCPIQKNCLTFSEGKS 223
            DF   +MD  A+IC   KP C  C + K C  + +  +
Sbjct: 183 RDFNLGLMDFSAIICAPRKPKCEKCGMSKLCSYYEKCST 221


>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster,
           iron-sulfur cluster, hydrolase/DNA complex; HET: PED;
           1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1
           PDB: 1orp_A* 1p59_A*
          Length = 226

 Score =  172 bits (437), Expect = 9e-44
 Identities = 51/214 (23%), Positives = 87/214 (40%), Gaps = 14/214 (6%)

Query: 6   HIIQSKILDWYDTNHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFM 65
                ++   +   H  L  R            P+++ I+ ++  Q T   V    K+  
Sbjct: 11  RYCLDEMAKMFPDAHCELVHRN-----------PFELLIAVVLSAQCTDALVNKVTKRLF 59

Query: 66  QKWPTIFCLSSAKDEEILSAWAGLGY-YTRARNLKKCADIIVKKYEGNFPHKVEILKKLP 124
           +K+ T     +   EE+      +G    +ARN++K   +++ KY G  P   + L KLP
Sbjct: 60  EKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLP 119

Query: 125 GIGDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPLYHKTIKNYARKITSTSRP 184
           G+G  TA+ +V++AF   A+ VDT++ER+  R              ++    KI      
Sbjct: 120 GVGRKTANVVVSVAFGVPAIAVDTHVERVSKRLGFC--RWDDSVLEVEKTLMKIIPKEEW 177

Query: 185 GDFVQAMMDLGALICTSNKPLCPLCPIQKNCLTF 218
                 M+  G   C +  P CP CP+   C   
Sbjct: 178 SITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREG 211


>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision
           repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori}
           SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*
          Length = 218

 Score =  140 bits (354), Expect = 4e-34
 Identities = 28/216 (12%), Positives = 59/216 (27%), Gaps = 25/216 (11%)

Query: 8   IQSKILDWYDTNHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVE-------PY 60
           I   +       +    W  +           ++  +  ++ Q T  + V          
Sbjct: 7   ILKALKSLDLLKNAPAWWWPNA--------LKFEALLGAVLTQNTKFEAVLKSLENLKNA 58

Query: 61  FKKFMQKWPTIFCLSSAKDEEILSAWAGLGYYTRA-RNLKKCADIIVKKYE----GNFPH 115
           F         +  ++  +  ++       G+Y +  + L   +  I+K ++         
Sbjct: 59  FILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEV 118

Query: 116 KVEILKKLPGIGDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKP-----APLYHKT 170
             E L    GIG  +A AI+  A     +VVD      + +    I+             
Sbjct: 119 TREWLLDQKGIGKESADAILCYACAKEVMVVDKYSYLFLKKLGIEIEDYDELQHFFEKGV 178

Query: 171 IKNYARKITSTSRPGDFVQAMMDLGALICTSNKPLC 206
            +N    +          Q        I   +K   
Sbjct: 179 QENLNSALALYENTISLAQLYARFHGKIVEFSKQKL 214


>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA,
           DNA binding protein; 2.10A {Mus musculus} SCOP: a.96.1.2
           PDB: 3iho_A
          Length = 155

 Score =  120 bits (302), Expect = 5e-28
 Identities = 29/147 (19%), Positives = 58/147 (39%), Gaps = 11/147 (7%)

Query: 21  RVLPWRTS-PKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKD 79
           +  P R+     ++     P+K+ I+ I L +T+ K   P   +F++K+P+     +A  
Sbjct: 12  KWTPPRSPFNLVQEILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADW 71

Query: 80  EEILSAWAGLGYY-TRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIA 138
            ++      LG Y  RA+ + K +D  + K             +L GIG Y   +     
Sbjct: 72  RDVSELLKPLGLYDLRAKTIIKFSDEYLTKQ-------WRYPIELHGIGKYGNDSYRIFC 124

Query: 139 FNHF--AVVVDTNIERIISRYFDIIKP 163
            N +      D  + +     ++  + 
Sbjct: 125 VNEWKQVHPEDHKLNKYHDWLWENHEK 151


>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
           coli} SCOP: a.96.1.1
          Length = 211

 Score =  114 bits (286), Expect = 3e-26
 Identities = 46/208 (22%), Positives = 85/208 (40%), Gaps = 8/208 (3%)

Query: 9   QSKILDWYDTNHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKW 68
           ++K L+         P  T+     S    P+++ I+ ++  Q T  +V     K     
Sbjct: 3   KAKRLEILTRLRENNPHPTTELNFSS----PFELLIAVLLSAQATDVSVNKATAKLYPVA 58

Query: 69  PTIFCLSSAKDEEILSAWAGLGYYT-RARNLKKCADIIVKKYEGNFPHKVEILKKLPGIG 127
            T   +     E + +    +G Y  +A N+ K   I+++++ G  P     L+ LPG+G
Sbjct: 59  NTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVG 118

Query: 128 DYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPLYHKTIKNYARKITSTSRPGDF 187
             TA+ ++  AF    + VDT+I R+ +R            + ++    K+       D 
Sbjct: 119 RKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGK---NVEQVEEKLLKVVPAEFKVDC 175

Query: 188 VQAMMDLGALICTSNKPLCPLCPIQKNC 215
              ++  G   C + KP C  C I+  C
Sbjct: 176 HHWLILHGRYTCIARKPRCGSCIIEDLC 203


>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix,
           8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
           glycosidase, hydrolase; 2.00A {Methanocaldococcus
           jannaschii}
          Length = 214

 Score =  110 bits (275), Expect = 7e-25
 Identities = 28/190 (14%), Positives = 57/190 (30%), Gaps = 17/190 (8%)

Query: 11  KILDWYDTNHRVLPWRTSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPT 70
            I+D      +    +++           +K     I+    T +      K+       
Sbjct: 24  DIIDKRIQEFKSFKNKSNE--------EWFKELCFCILTANFTAEGGIRIQKEIGDG--- 72

Query: 71  IFCLSSAKDEEILSAWAGLGYYTRARNLKKCADII-----VKKYEGNFPHKVEILKKLPG 125
              L   + EE L       Y  RA  +            V+ +E     +  +++ + G
Sbjct: 73  FLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKG 132

Query: 126 IGDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIK-PAPLYHKTIKNYARKITSTSRP 184
           IG   AS  +         ++D +I R +     I + P  L  +        +      
Sbjct: 133 IGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILRDIGEE 192

Query: 185 GDFVQAMMDL 194
            +   + +DL
Sbjct: 193 VNLKLSELDL 202


>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix,
           8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair,
           glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}
          Length = 207

 Score = 95.9 bits (238), Expect = 1e-20
 Identities = 26/172 (15%), Positives = 57/172 (33%), Gaps = 17/172 (9%)

Query: 37  PSPYKVWISE----IMLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKDEEILSAWAGLGYY 92
            S  +VW  E    ++   ++  +         QK   I+  +  +   IL +     Y 
Sbjct: 27  LSNEEVWFRELTLCLLTANSSFISAYQALNCLGQK---IYYANEEEIRNILKSCKYRFYN 83

Query: 93  TRARNLKKCADIIVKKYEG--------NFPHKVEILKKLPGIGDYTASAIVAIAFNHFAV 144
            +A+ +    + +  + +         +     E L  + GIG   AS  +         
Sbjct: 84  LKAKYIIMAREKVYGRLKEEIKPLADEDQQLARERLLNIKGIGMQEASHFLRNVGYFDLA 143

Query: 145 VVDTNIERIISRYFDI--IKPAPLYHKTIKNYARKITSTSRPGDFVQAMMDL 194
           ++D +I   + R   I       L      ++   + S +   +    ++DL
Sbjct: 144 IIDRHIIDFMRRIGAIGETNVKQLSKSLYISFENILKSIASNLNMSVGILDL 195


>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG,
           8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET:
           DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2
           PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A*
           1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A*
           2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A*
           ...
          Length = 317

 Score = 67.8 bits (165), Expect = 3e-12
 Identities = 29/173 (16%), Positives = 55/173 (31%), Gaps = 29/173 (16%)

Query: 37  PSPYKVWISEIMLQQTTVK---------------TVEPYFKKFMQKWPTIFCLSSAKDEE 81
             P +   S I      +                 +          +P++  L+  + E 
Sbjct: 127 QDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEA 186

Query: 82  ILSAWAGLGYYTRARNLKKCADIIVKKY----------EGNFPHKVEILKKLPGIGDYTA 131
            L     LG   RAR +   A  I+++           E ++    + L  LPG+G   A
Sbjct: 187 HLRK---LGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVA 243

Query: 132 SAIVAIAFNHF-AVVVDTNIERIISRYFDIIKPAPLYHKTIKNYARKITSTSR 183
             I  +A +   AV V+ ++  I  R +                 +++ +  R
Sbjct: 244 DCICLMALDKPQAVPVEVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFR 296


>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG,
           glycosylase, cytosine, hydrolase,lyase/DNA complex; HET:
           8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A*
           3f10_A* 3f0z_A
          Length = 290

 Score = 64.0 bits (155), Expect = 5e-11
 Identities = 26/160 (16%), Positives = 52/160 (32%), Gaps = 21/160 (13%)

Query: 37  PSPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKDEEILSA----------W 86
             P+++ +S I+     +  ++       +K                +           +
Sbjct: 113 QDPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEKDF 172

Query: 87  AGLGYYTRARNLKKCADIIVKK-------YEGNFPHKVEILKKLPGIGDYTASAIVAIAF 139
                  RA+ LK   D I             N     E LKK  G+G   A  I+  + 
Sbjct: 173 EECTAGFRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSM 232

Query: 140 NHF-AVVVDTNIERIISRYFDIIKPAPLYHKTIKNYARKI 178
             + A  VDT +++ +   +     +    K I+++ R+ 
Sbjct: 233 QKYSAFPVDTWVKKAMMSLYVAPDVSL---KKIRDFGREK 269


>1x51_A A/G-specific adenine DNA glycosylase; nudix domain, DNA repair,
           alpha-3 isoform, structural genomics, NPPSFA; NMR {Homo
           sapiens} SCOP: d.113.1.3
          Length = 155

 Score = 58.5 bits (140), Expect = 2e-09
 Identities = 29/135 (21%), Positives = 45/135 (33%), Gaps = 15/135 (11%)

Query: 230 TIKKKRPMRTGAVFI---AITNDNRILLRKRTNTRLLEGMDELPGSAWSSTKDGNIDTHS 286
             +K     + A  +         +ILL +R N+ LL G+ E P   W  ++        
Sbjct: 11  ASRKPPREESSATCVLEQPGALGAQILLVQRPNSGLLAGLWEFPSVTWEPSEQLQRKALL 70

Query: 287 APFTANWILCNTI--------THTFTHFTLTLFVWKTIV----PQIVIIPDSTWHDAQNL 334
                                 HTF+H  LT  V+   +    P   + P + W   +  
Sbjct: 71  QELQRWAGPLPATHLRHLGEVVHTFSHIKLTYQVYGLALEGQTPVTTVPPGARWLTQEEF 130

Query: 335 ANAALPTVMKKALSA 349
             AA+ T MKK    
Sbjct: 131 HTAAVSTAMKKVFRV 145


>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 = 42.6 bits (100), Expect = 1e-04
 Identities = 49/350 (14%), Positives = 81/350 (23%), Gaps = 113/350 (32%)

Query: 35  SLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKDEEILSA---WAG-LG 90
            L  P   +     LQ+   K +           PT      A D+E  +        LG
Sbjct: 19  VLLVPTASFFIASQLQEQFNKILPE---------PT---EGFAADDEPTTPAELVGKFLG 66

Query: 91  YYTRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNHF--AVVVDT 148
           Y          +               ++L                +    F    +   
Sbjct: 67  Y---------VSS---LVEPSKVGQFDQVLN---------------LCLTEFENCYLEGN 99

Query: 149 NIERIISRYFDIIKPAPLYHKT-IKNY--ARKITSTSRPGDFVQAMMDLGALICTSNKPL 205
           +I  + ++         +  K  IKNY  AR +                 AL     +  
Sbjct: 100 DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK------KSNSALFRAVGEGN 153

Query: 206 CPLCPI---QKN---CLTFSEGKSHLLGINTIKKKRPM------RTGAVF--IAITNDNR 251
             L  I   Q N      F E    L  +        +       +      +  T  + 
Sbjct: 154 AQLVAIFGGQGNTDDY--FEE----LRDLYQT--YHVLVGDLIKFSAETLSELIRTTLDA 205

Query: 252 ILLRKRTNTRLLEGMDELPGSAWSSTKDGNIDTH---SAPFTANWILCNTITHT-FTHFT 307
             +  +       G++ L    W        D     S P     I C  I      H+ 
Sbjct: 206 EKVFTQ-------GLNIL---EWLENPSNTPDKDYLLSIP-----ISCPLIGVIQLAHYV 250

Query: 308 LT-------------LFVWKT-----IVPQIVIIPDSTWHDAQNLANAAL 339
           +T                  T     +V  + I    +W         A+
Sbjct: 251 VTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI 300



 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 57/332 (17%), Positives = 94/332 (28%), Gaps = 152/332 (45%)

Query: 77  AKDEEILSAWAGLGYYTRARN-------------LKKCA-DIIVKKY-----EGNFPHKV 117
            K +E++       Y   AR              L +   +   +       +GN     
Sbjct: 117 VKTKELIKN-----YI-TARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF 170

Query: 118 EILKKL-----PGIGDYTASAIVAIAFNHFAVVVDTNIERIISRYFDIIKPAPLYHKTIK 172
           E L+ L       +GD    +  A   +        + E++ ++  +I+       + ++
Sbjct: 171 EELRDLYQTYHVLVGDLIKFS--AETLSELIRT-TLDAEKVFTQGLNIL-------EWLE 220

Query: 173 NYARKITSTSRPG-DFVQAMMDLGALICTSNKPL-CPL-CPIQ--KNCLTFSEGKSHLLG 227
           N       ++ P  D++     L         P+ CPL   IQ     +T       LLG
Sbjct: 221 N------PSNTPDKDYL-----LSI-------PISCPLIGVIQLAHYVVTA-----KLLG 257

Query: 228 INTIKKKRP--MR------TG-------AVFIAITNDNRILLRKRTNTRLLEGMDELPGS 272
                   P  +R      TG       AV IA T+                        
Sbjct: 258 FT------PGELRSYLKGATGHSQGLVTAVAIAETDS----------------------- 288

Query: 273 AWSSTKDGNIDTHSAPFTANWILCNTITHTFTHFTLTLFVWKTI-------VPQIVIIPD 325
            W S            F  +     T+          LF +  I        P    +P 
Sbjct: 289 -WES------------FFVSVRKAITV----------LF-F--IGVRCYEAYPNTS-LPP 321

Query: 326 STWHDAQNLANA-ALPTVMKKALSAGGIKVPQ 356
           S   D+  L N   +P+ M   LS   +   Q
Sbjct: 322 SILEDS--LENNEGVPSPM---LSISNLTQEQ 348


>1mut_A MUTT, nucleoside triphosphate pyrophosphohydrolase; DNA repair; NMR
           {Escherichia coli} SCOP: d.113.1.1 PDB: 1ppx_A* 1pun_A*
           1puq_A* 1pus_A* 1tum_A* 3a6s_A* 3a6t_A* 3a6u_A* 3a6v_A*
          Length = 129

 Score = 41.2 bits (96), Expect = 4e-04
 Identities = 21/127 (16%), Positives = 36/127 (28%), Gaps = 26/127 (20%)

Query: 241 AVFIAITNDNRILLRKRTNTRLLEGMDELPGSAWSSTKDGNIDTHSAPFTA--------- 291
           AV I    +N I + +R     +    E PG        G I+    P  A         
Sbjct: 7   AVGIIRNENNEIFITRRAADAHMANKLEFPG--------GKIEMGETPEQAVVRELQEEV 58

Query: 292 -----NWILCNTITHTFTHFTLTLFVWKTIVPQIVIIP----DSTWHDAQNLANAALPTV 342
                ++ L   + + F    +TL+ W     +            W     L     P  
Sbjct: 59  GITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPA 118

Query: 343 MKKALSA 349
            +  ++ 
Sbjct: 119 NEPVIAK 125


>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair,
           N1-methyladenine, N3-methylcytosine, hyperthermophiles,
           hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus}
           PDB: 2jhj_A
          Length = 295

 Score = 39.3 bits (91), Expect = 0.001
 Identities = 28/157 (17%), Positives = 50/157 (31%), Gaps = 20/157 (12%)

Query: 37  PSPYKVWISEIMLQQTTVKTVEPYFKKF--------------MQKWPTIFCLSSAKDEEI 82
            S ++     I+ QQ +    E    K                  +PT   +  A  E +
Sbjct: 116 MSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGL 175

Query: 83  LSAWAGLGYY-TRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNH 141
                GL              + + +  E       E L    GIG +TA  +++IA   
Sbjct: 176 --RECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALGK 233

Query: 142 FA-VVVDTNIERIISRYFDIIKPAPLYHKTIKNYARK 177
                 D  + R +SR +   +      + ++  AR+
Sbjct: 234 NVFPADDLGVRRAVSRLYFNGEIQS--AEKVREIARE 268


>3hhj_A Mutator MUTT protein; niaid, ssgcid, decode, UW, SBRI, infectious
           diseases, hydrolase, structural genomics; 2.10A
           {Bartonella henselae str}
          Length = 158

 Score = 36.8 bits (84), Expect = 0.009
 Identities = 23/135 (17%), Positives = 43/135 (31%), Gaps = 12/135 (8%)

Query: 227 GINTIKKKRPMRTGAVFIAITNDNRILLRKRTNTRLLEGMDELPGSAW--------SSTK 278
           G  ++  K  +        +  DNR+LL +R   + L G+ E PG           S  +
Sbjct: 18  GPGSMPIKSSLLIVVACALLDQDNRVLLTQRPEGKSLAGLWEFPGGKVEQGETPEASLIR 77

Query: 279 DGNIDTHSAPFTANWILCNTITHTFTHFTLTLFVWKTIVPQIVIIPDST----WHDAQNL 334
           +   +        N       +H +  F L + ++     + V          W    +L
Sbjct: 78  ELEEELGVHVQADNLFPLTFASHGYETFHLLMPLYFCSHYKGVAQGREGQNLKWIFINDL 137

Query: 335 ANAALPTVMKKALSA 349
               +P   K  +  
Sbjct: 138 DKYPMPEADKPLVQV 152


>3oga_A Nucleoside triphosphatase NUDI; salmonella enterica subsp. enterica
           serovar typhimurium STR. unknown function; HET: PO4;
           1.75A {Salmonella enterica subsp} PDB: 3n77_A
          Length = 165

 Score = 33.4 bits (76), Expect = 0.083
 Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 2/41 (4%)

Query: 233 KKRPMRTGAVFIA-ITNDNRILLRKRT-NTRLLEGMDELPG 271
           +   MR   +    I ND   LL K   N  +  G   L G
Sbjct: 21  QSNAMRQRTIVCPLIQNDGCYLLCKMADNRGVFPGQWALSG 61


>3ees_A Probable pyrophosphohydrolase; nudix, RNA pyrophosphohydrolase;
           1.90A {Bdellovibrio bacteriovorus} PDB: 3eeu_A 3ef5_A*
           3ffu_A*
          Length = 153

 Score = 33.0 bits (74), Expect = 0.10
 Identities = 20/137 (14%), Positives = 41/137 (29%), Gaps = 14/137 (10%)

Query: 227 GINTIKKKRPMRTG----AVFIAITNDNRILLRKRTNTRLLEGMDELPGSAWSSTKD--- 279
            + + +KK  +R G     V   +  D +IL+ +R     L G  E PG    + +    
Sbjct: 6   AVESKQKKSKIRKGHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEE 65

Query: 280 -------GNIDTHSAPFTANWILCNTITHTFTHFTLTLFVWKTIVPQIVIIPDSTWHDAQ 332
                    +   +          ++             ++    P+        W   +
Sbjct: 66  ALARELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMMLEWIHPE 125

Query: 333 NLANAALPTVMKKALSA 349
            L +  +P   +K L  
Sbjct: 126 ELKHRNIPEANRKILHK 142


>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base
           excision, methylation, hydrolase; 1.80A {Escherichia
           coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A*
           3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A*
           3d4v_A*
          Length = 282

 Score = 32.3 bits (73), Expect = 0.16
 Identities = 21/137 (15%), Positives = 44/137 (32%), Gaps = 17/137 (12%)

Query: 37  PSPYKVWISEIMLQQTTVKTVEPYFKKFMQKW-------------PTIFCLSSAKDEEIL 83
              ++  +  I+ Q  +V        +  Q +             PT   L++A  + + 
Sbjct: 111 VDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALK 170

Query: 84  SAWAGLGYYTRARNLKK--CADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNH 141
           +    L       +L        +     G+    ++ L+  PGIG +TA+      +  
Sbjct: 171 ALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQA 230

Query: 142 FAV--VVDTNIERIISR 156
             V    D  I++    
Sbjct: 231 KDVFLPDDYLIKQRFPG 247


>1vct_A Hypothetical protein PH0236; helix rich, structural genomics, riken
           structural genomics/proteomics initiative, RSGI, NPPSFA;
           1.85A {Pyrococcus horikoshii} SCOP: a.7.12.1 d.286.1.1
           PDB: 2bkn_A 2bko_A 2bkp_A
          Length = 205

 Score = 31.7 bits (71), Expect = 0.23
 Identities = 11/124 (8%), Positives = 33/124 (26%), Gaps = 3/124 (2%)

Query: 148 TNIERIISRYFDIIKPAPLYHKTIKNYARKITSTSRPGDFVQAMMDLGALICTSNKPLCP 207
             +   +  +  +        + +    +   +     +    +  +       +  +  
Sbjct: 55  DLLNYQLMMHSVLAARNVKEAEQVITILQIANAIEDISNAAGDLAKMVLEGVELHPVIKE 114

Query: 208 L--CPIQKNCLTFSEGKSHLLGINTIKKKRPMRTGAVFIAITNDNRILLRKRTNTRLLEG 265
                 +         +S ++G    +      TG   IA+    R +     N ++  G
Sbjct: 115 TILEGEEIIGKIQVYPESVIVGKTLGELDLATNTGVWIIAVRRGKRWIFGPNENFKIRAG 174

Query: 266 MDEL 269
            D L
Sbjct: 175 -DVL 177


>2b06_A MUTT/nudix family protein; structural genomics, PSI, protein
           structure initiative, midwest center for structural
           genomics, MCSG; 1.40A {Streptococcus pneumoniae} SCOP:
           d.113.1.1
          Length = 155

 Score = 31.6 bits (71), Expect = 0.31
 Identities = 6/40 (15%), Positives = 13/40 (32%)

Query: 232 KKKRPMRTGAVFIAITNDNRILLRKRTNTRLLEGMDELPG 271
           + +  + T    I      R++++ R            PG
Sbjct: 3   RSQLTILTNICLIEDLETQRVVMQYRAPENNRWSGYAFPG 42


>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus
           musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB:
           1kdh_A* 1kej_A*
          Length = 381

 Score = 29.7 bits (66), Expect = 0.95
 Identities = 19/114 (16%), Positives = 39/114 (34%), Gaps = 21/114 (18%)

Query: 27  TSPKTEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKWPTIFCLSSAKDEEILSAW 86
            SP     ++P+P    IS+   Q+ T  T+  Y + F      +      ++ E     
Sbjct: 4   PSPVPGSQNVPAPAVKKISQYACQRRT--TLNNYNQLFTDALDILAENDELRENEG---- 57

Query: 87  AGLGYYTRARNLKKCADIIVKKYEGNFPHKV---EILKKLPGIGDYTASAIVAI 137
                        + + ++      + P  +   +  + +P +GD   S I  I
Sbjct: 58  -------SCLAFMRASSVL-----KSLPFPITSMKDTEGIPCLGDKVKSIIEGI 99


>3gwy_A Putative CTP pyrophosphohydrolase; structural genomics, PSI-2,
           protein structure initiative; 2.00A {Bacteroides
           fragilis nctc 9343}
          Length = 140

 Score = 29.8 bits (66), Expect = 0.96
 Identities = 16/119 (13%), Positives = 34/119 (28%), Gaps = 17/119 (14%)

Query: 237 MRTGAVFIA-ITNDNRILLRKRTNTR--LLEGMDELPGSAWSSTKDGNIDTHSAPFTAN- 292
           +++  V  A I    + L  +R  T+        E PG      +  ++           
Sbjct: 3   LKSIEVVAAVIRLGEKYLCVQRGQTKFSYTSFRYEFPGGKV--EEGESLQEALQREIMEE 60

Query: 293 -------WILCNTITHTFTHFTLTLFVWKTIVPQIVIIP----DSTWHDAQNLANAALP 340
                       T+ HT+  F +T+  +         +      + W   + +A     
Sbjct: 61  MDYVIEVGEKLLTVHHTYPDFEITMHAFLCHPVGQRYVLKEHIAAQWLSTREMAILDWA 119


>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport
           photosystem, membrane complex, transmembrane
           alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG
           LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U*
           3bz2_U* 3a0b_U* 3a0h_U*
          Length = 104

 Score = 29.4 bits (66), Expect = 1.1
 Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 3/48 (6%)

Query: 117 VEILKKLPGIGDYTASAIVAIAFNHFAVVVD-TNIERIISRYFDIIKP 163
           +    +  G+    A  I  +    +  V D  NI  +  R   I++ 
Sbjct: 32  IAAFIQYRGLYPTLAKLI--VKNAPYESVEDVLNIPGLTERQKQILRE 77


>2duy_A Competence protein comea-related protein; helix-hairpin-helix,
           structural genomics, NPPSFA; 1.75A {Thermus thermophilus
           HB8} SCOP: a.60.2.7
          Length = 75

 Score = 29.3 bits (66), Expect = 1.5
 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 117 VEILKKLPGIGDYTASAIVAIAFNHFAVVVD-TNIERIISRYFDIIKP 163
           +E L  LPGIG   A  IV      +A V D   ++ I     + ++P
Sbjct: 26  LEELMALPGIGPVLARRIV--EGRPYARVEDLLKVKGIGPATLERLRP 71


>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis,
           mutation, deletion, streisinger, slippage, transferase,
           lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP:
           a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A*
           2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A*
           1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A*
           1rzt_A* 3hx0_A* 1nzp_A*
          Length = 335

 Score = 29.0 bits (64), Expect = 1.7
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 2/60 (3%)

Query: 94  RARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNHFAVVVDTNIERI 153
           RA    K  + + K +        +    +PGIG   A  I+ I  +     +D   E +
Sbjct: 35  RALGYAKAINAL-KSFHKPV-TSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESV 92


>2yvp_A NDX2, MUTT/nudix family protein; nudix protein, ADP-ribose, FAD,
           hydrolase, structural genomics, NPPSFA; HET: RBY; 1.66A
           {Thermus thermophilus HB8} PDB: 2yvn_A 2yvm_A* 2yvo_A*
          Length = 182

 Score = 29.0 bits (64), Expect = 1.9
 Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 235 RPMRTGAVFI-AITNDNRILLRKRTNTRLLEGMDELPGSAW 274
           RP    A F+  +T     LL ++      + + E+P    
Sbjct: 37  RPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKV 77


>2w4e_A MUTT/nudix family protein; ADP-ribose pyrophosphatase, hydrolase;
           2.00A {Deinococcus radiodurans}
          Length = 145

 Score = 28.6 bits (63), Expect = 2.2
 Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 235 RPMRTGAVFI-AITNDNRILLRKRTNTRLLEGMDELPGSAW 274
           RP    AVFI  +T     +L ++    L   + E+     
Sbjct: 1   RPRGPRAVFILPVTAQGEAVLIRQFRYPLRATITEIVAGGV 41


>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA
           complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP:
           a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A*
           1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A*
           1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A*
           1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...
          Length = 335

 Score = 28.6 bits (63), Expect = 2.5
 Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 10/92 (10%)

Query: 94  RARNLKKCADIIVKKYEGNFPHKV---EILKKLPGIGDYTASAIVAIAFNHFAVVVDTNI 150
           +    +K A +I       +PHK+      KKLPG+G   A  I           ++   
Sbjct: 35  KYNAYRKAASVI-----AKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIR 89

Query: 151 ERIISRYFDIIKPAP-LYHKTIKN-YARKITS 180
           +   S   + +     +     +      I +
Sbjct: 90  QDDTSSSINFLTRVSGIGPSAARKFVDEGIKT 121


>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function;
           2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A
          Length = 126

 Score = 28.4 bits (63), Expect = 2.5
 Identities = 8/61 (13%), Positives = 20/61 (32%)

Query: 149 NIERIISRYFDIIKPAPLYHKTIKNYARKITSTSRPGDFVQAMMDLGALICTSNKPLCPL 208
           ++ +   ++        +   T   YA  +  T    D  + ++ L  L+   +K     
Sbjct: 16  DLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRD 75

Query: 209 C 209
            
Sbjct: 76  Y 76


>3grn_A MUTT related protein; structural genomics, hydrolase, PSI-2,
           protein structure initiative; 1.70A {Methanosarcina
           mazei}
          Length = 153

 Score = 28.2 bits (62), Expect = 2.8
 Identities = 13/126 (10%), Positives = 32/126 (25%), Gaps = 12/126 (9%)

Query: 234 KRPMRTGAVFIAITNDNRILLRKRT-NTRLLEGMDELPGSAWSSTKDGNIDTHSAPFT-- 290
           ++P       +        LL +R+ N+R   G  +LPG   +  +          +   
Sbjct: 4   EKPYIISVYALIRNEKGEFLLLRRSENSRTNAGKWDLPGGKVNPDESLKEGVAREVWEET 63

Query: 291 ----ANWILCNTITHTFTHFTLTLFVWKTIVPQIVIIPDS-----TWHDAQNLANAALPT 341
                   +   +    T   +   V+        +         +W   + +       
Sbjct: 64  GITMVPGDIAGQVNFELTEKKVIAIVFDGGYVVADVKLSYEHIEYSWVSLEKILGMETLP 123

Query: 342 VMKKAL 347
              +  
Sbjct: 124 AYFRDF 129


>1v8y_A ADP-ribose pyrophosphatase; nudix motif, loop-helix-loop, MUTT
           family, riken structural genomics/proteomics initiative,
           RSGI; HET: APR; 1.65A {Thermus thermophilus} SCOP:
           d.113.1.1 PDB: 1v8v_A* 1v8n_A 1v8l_A* 1v8m_A* 1v8i_A
           1v8r_A* 1v8s_A* 1v8t_A* 1v8w_A 1v8u_A
          Length = 170

 Score = 28.1 bits (62), Expect = 2.8
 Identities = 6/37 (16%), Positives = 13/37 (35%)

Query: 238 RTGAVFIAITNDNRILLRKRTNTRLLEGMDELPGSAW 274
              AV +    + R+L  ++    +     E+P    
Sbjct: 33  HKPAVAVIALREGRMLFVRQMRPAVGLAPLEIPAGLI 69


>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis,
           oxygen-evolving, tetra- manganese, membrane; HET: CL1
           PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus
           elongatus}
          Length = 134

 Score = 28.0 bits (62), Expect = 2.9
 Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 3/48 (6%)

Query: 117 VEILKKLPGIGDYTASAIVAIAFNHFAVVVD-TNIERIISRYFDIIKP 163
           +    +  G+    A  IV      +  V D  NI  +  R   I++ 
Sbjct: 62  IAAFIQYRGLYPTLAKLIV--KNAPYESVEDVLNIPGLTERQKQILRE 107


>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural
           genomics, PSI-2, protein structure initiative; 2.55A
           {Bacillus halodurans}
          Length = 233

 Score = 27.9 bits (61), Expect = 3.7
 Identities = 23/151 (15%), Positives = 49/151 (32%), Gaps = 12/151 (7%)

Query: 37  PSPYKVWISEIMLQQTTVKTVEPYFKKFMQ------KWPTIFCLSSAKDEEILSAWAGLG 90
           P+P++  +S I+ QQ ++K     + +  Q      + P      S +            
Sbjct: 49  PNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKI 108

Query: 91  YYTR--ARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNH--FAVVV 146
            Y R    +++       +         +E L  + GIG +TA   +  +        V 
Sbjct: 109 EYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVG 168

Query: 147 DTNIERIISRYFDIIKPAPLYHKTIKNYARK 177
           D  ++R     +          K +  + + 
Sbjct: 169 DVGLQRGAKWLYGN--GEGDGKKLLIYHGKA 197


>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
           2.46A {Deinococcus radiodurans}
          Length = 578

 Score = 27.9 bits (62), Expect = 3.9
 Identities = 5/49 (10%), Positives = 14/49 (28%), Gaps = 10/49 (20%)

Query: 94  RARNLKKCADIIVKKYEGNFPHKVEI-----LKKLPGIGDYTASAIVAI 137
           ++R  +  A  +          +           +P +G   A+ +   
Sbjct: 33  KSRAYRSAARSL-----EELNEETPELLAREFTGIPKVGKGIAAELSDF 76


>3o8s_A Nudix hydrolase, ADP-ribose pyrophosphatase; structural genomics,
           joint center for structural genomics, J protein
           structure initiative, PSI; 2.27A {Streptococcus suis}
          Length = 206

 Score = 27.6 bits (61), Expect = 4.1
 Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 5/31 (16%)

Query: 241 AVFIAITNDNRILLRKRTNTRLLEGMDELPG 271
               AI  +++ILL +  +     G+  LPG
Sbjct: 72  DTRAAIFQEDKILLVQEND-----GLWSLPG 97


>2v82_A 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; lyase, kdpgal;
           HET: KDP; 2.1A {Escherichia coli} PDB: 2v81_A*
          Length = 212

 Score = 27.7 bits (61), Expect = 4.1
 Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 9/42 (21%)

Query: 313 WKTIVPQIVIIPDSTWHDAQNLANAALPTVMKKALSAGGIKV 354
           W+T +P I I+   T  +A              A+   G   
Sbjct: 3   WQTKLPLIAILRGITPDEALAHV---------GAVIDAGFDA 35


>1y9i_A Low temperature requirement C protein; structural genomics, protein
           structure initiative, PSI; 1.80A {Listeria
           monocytogenes} SCOP: a.195.1.1
          Length = 178

 Score = 27.8 bits (62), Expect = 4.2
 Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 17/64 (26%)

Query: 107 KKYEGNFPHKVEILKKLPGIGDYTASAIV----AIAFNHFAVVVDTNIERIISRYFDIIK 162
            +      + +   + L G+ +  A +IV    +I F ++              Y D +K
Sbjct: 78  GELVQPLQNIISADEGLYGVDEILALSIVNVYGSIGFTNY-------------GYIDKVK 124

Query: 163 PAPL 166
           P  L
Sbjct: 125 PGIL 128


>3id9_A MUTT/nudix family protein; hydrolase, protein structure initiative
           II(PSI II), NYSGXRC, structural genomics; 2.55A
           {Bacillus thuringiensis str}
          Length = 171

 Score = 27.7 bits (61), Expect = 4.3
 Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 4/41 (9%)

Query: 231 IKKKRPMRTGAVFIAITNDNRILLRKRTNTRLLEGMDELPG 271
           +  +  M+     I +  D ++LL K+   ++      LPG
Sbjct: 16  LYIENIMQVRVTGI-LIEDEKVLLVKQ---KVANRDWSLPG 52


>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix
           turn helix motif, structural genomics, NPPSFA; NMR {Homo
           sapiens} SCOP: a.60.2.7
          Length = 98

 Score = 27.5 bits (61), Expect = 4.9
 Identities = 7/20 (35%), Positives = 8/20 (40%)

Query: 117 VEILKKLPGIGDYTASAIVA 136
              L+ L  IG   A  IV 
Sbjct: 39  ARDLRSLQRIGPKKAQLIVG 58



 Score = 27.1 bits (60), Expect = 5.6
 Identities = 10/57 (17%), Positives = 24/57 (42%), Gaps = 7/57 (12%)

Query: 79  DEEILSAWAGLGYYTRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIV 135
               L +   +G   +A+ +     +  ++  G F  +VE L+++ GI      + +
Sbjct: 38  SARDLRSLQRIGP-KKAQLI-----VGWRELHGPF-SQVEDLERVEGITGKQMESFL 87


>3b4w_A Aldehyde dehydrogenase; RV0223C-NAD complex, structural genomics,
           PSI-2, protein structure initiative; HET: NAD GOL; 1.80A
           {Mycobacterium tuberculosis H37RV}
          Length = 495

 Score = 27.0 bits (59), Expect = 5.9
 Identities = 4/37 (10%), Positives = 15/37 (40%)

Query: 74  LSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYE 110
           +++A+       W     + RA  +     ++ ++ +
Sbjct: 52  VAAARAAFDNGPWPSTPPHERAAVIAAAVKMLAERKD 88


>2o2p_A Formyltetrahydrofolate dehydrogenase; aldehyde dehydrogenase, FDH,
           oxidoreductase; 1.70A {Rattus norvegicus} PDB: 2o2q_A*
           2o2r_A*
          Length = 517

 Score = 27.3 bits (60), Expect = 6.0
 Identities = 9/37 (24%), Positives = 18/37 (48%)

Query: 74  LSSAKDEEILSAWAGLGYYTRARNLKKCADIIVKKYE 110
           +++AK+      W  +    R R L + AD++ +  E
Sbjct: 80  VAAAKEAFENGLWGKINARDRGRLLYRLADVMEQHQE 116


>3oru_A DUF1989 family protein; structural genomics, joint center for
           structural genomics, J protein structure initiative,
           PSI, metal binding protein; HET: MSE; 1.11A {Ruegeria
           SP}
          Length = 234

 Score = 27.3 bits (60), Expect = 6.2
 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 7/30 (23%)

Query: 180 STSRPGDFV--QAMMDLGALICTSNKPLCP 207
             SR GD V  +A +D+  ++  S    CP
Sbjct: 185 PVSRRGDHVLFRAELDV--VVVISC---CP 209


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 26.9 bits (58), Expect = 6.9
 Identities = 7/24 (29%), Positives = 12/24 (50%), Gaps = 4/24 (16%)

Query: 170 TIKNYARKITSTSRPGDFVQAMMD 193
           ++K YA      S P   ++A M+
Sbjct: 28  SLKLYA----DDSAPALAIKATME 47


>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA
           complex; HET: DNA D3T; 2.40A {Mus musculus}
          Length = 360

 Score = 27.0 bits (59), Expect = 7.3
 Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 8/47 (17%)

Query: 94  RARNLKKCADIIVKKYEGNFPHKVEI---LKKLPGIGDYTASAIVAI 137
           R  +  + A ++      + P  V     L  LP  G+++   I  +
Sbjct: 39  RLLSFSRAASVL-----KSLPCPVASLSQLHGLPYFGEHSTRVIQEL 80


>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger,
           toprim, walker B ATP binding motif; 2.50A {Deinococcus
           radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
          Length = 228

 Score = 26.8 bits (59), Expect = 7.6
 Identities = 9/28 (32%), Positives = 14/28 (50%)

Query: 108 KYEGNFPHKVEILKKLPGIGDYTASAIV 135
           KY  +    +  L +LPGIG  +A  + 
Sbjct: 2   KYPPSLVSLIRELSRLPGIGPKSAQRLA 29


>3gg6_A Nudix motif 18, nucleoside diphosphate-linked moiety X motif 18;
           NUDT18, NXR1, nucleotide hydrolase, hydrolase,
           structural genomics; 2.10A {Homo sapiens}
          Length = 156

 Score = 26.6 bits (58), Expect = 7.8
 Identities = 6/41 (14%), Positives = 18/41 (43%), Gaps = 1/41 (2%)

Query: 231 IKKKRPMRTGAVFIAITNDNRILLRKRTNTRLLEGMDELPG 271
           ++ ++ +    + + ++  + +LL +    R   G   LP 
Sbjct: 13  VRLRKNVCYVVLAVFLSEQDEVLLIQEAK-RECRGSWYLPA 52


>2w8n_A Succinate-semialdehyde dehydrogenase, mitochondrial; mitochondrion,
           oxidoreductase, transit peptide, disease mutation, SSA,
           NAD, ssadh; 2.00A {Homo sapiens} PDB: 2w8o_A 2w8p_A
           2w8q_A 2w8r_A*
          Length = 487

 Score = 26.6 bits (58), Expect = 8.1
 Identities = 4/26 (15%), Positives = 13/26 (50%)

Query: 85  AWAGLGYYTRARNLKKCADIIVKKYE 110
            W  +    R+  L+K  +++++  +
Sbjct: 63  RWREVSAKERSSLLRKWYNLMIQNKD 88


>3iwj_A Putative aminoaldehyde dehydrogenase; rossmann fold, dimer, betaine
           aldehyde dehydrogenase, NAD, oxidoreductase; HET: NAD;
           2.15A {Pisum sativum} PDB: 3iwk_A*
          Length = 503

 Score = 26.5 bits (58), Expect = 8.3
 Identities = 9/34 (26%), Positives = 13/34 (38%)

Query: 77  AKDEEILSAWAGLGYYTRARNLKKCADIIVKKYE 110
           A      + WA      RAR L+  A  + +K  
Sbjct: 57  ALTRNKGADWATASGAVRARYLRAIAAKVTEKKP 90


>3ek1_A Aldehyde dehydrogenase; ssgcid, oxidoreductase, structural
           genomics; HET: MES; 2.10A {Brucella melitensis biovar
           ABORTUS2308}
          Length = 504

 Score = 26.9 bits (59), Expect = 8.4
 Identities = 8/26 (30%), Positives = 12/26 (46%)

Query: 85  AWAGLGYYTRARNLKKCADIIVKKYE 110
            WA      RA  L+K  D+I+   +
Sbjct: 85  GWAAKTAKERAGILRKWFDLIIANAD 110


>3i44_A Aldehyde dehydrogenase; oxidoreductase, structural genomics,
           seattle structural genomics center for infectious
           disease, ssgcid; 2.00A {Bartonella henselae}
          Length = 497

 Score = 26.8 bits (59), Expect = 8.5
 Identities = 5/26 (19%), Positives = 10/26 (38%)

Query: 85  AWAGLGYYTRARNLKKCADIIVKKYE 110
            W     + R   ++K  +I  K+  
Sbjct: 78  TWKTTSPHERLGFVEKILEIYEKRSS 103


>1o04_A Aldehyde dehydrogenase, mitochondrial precursor; ALDH, NAD, NADH,
           isomerization, oxidoreductase; HET: NAD; 1.42A {Homo
           sapiens} SCOP: c.82.1.1 PDB: 1nzw_A* 3inl_A* 3inj_A*
           1nzz_A* 1o00_A* 1nzx_A* 1o01_A* 1o05_A 1of7_A* 1o02_A*
           1zum_A 2onm_A* 2onp_A* 2onn_A 2ono_A* 2vle_A* 1cw3_A*
           1ag8_A 1a4z_A
          Length = 500

 Score = 26.5 bits (58), Expect = 9.3
 Identities = 8/30 (26%), Positives = 14/30 (46%)

Query: 81  EILSAWAGLGYYTRARNLKKCADIIVKKYE 110
           ++ S W  +    R R L + AD+I +   
Sbjct: 71  QLGSPWRRMDASHRGRLLNRLADLIERDRT 100


>2j6l_A Aldehyde dehydrogenase family 7 member A1; NAD, reductase,
           oxidoreductase, lysine catabolism; HET: NAI; 1.3A {Homo
           sapiens} PDB: 2jg7_A*
          Length = 500

 Score = 26.4 bits (57), Expect = 9.4
 Identities = 5/26 (19%), Positives = 12/26 (46%)

Query: 85  AWAGLGYYTRARNLKKCADIIVKKYE 110
            WA +    R   +++  D + +K +
Sbjct: 74  IWADIPAPKRGEIVRQIGDALREKIQ 99


>1wnd_A Putative betaine aldehyde dehydrogenase; NADH, fluorescence,
           kinetics, oxidoreductase; 2.10A {Escherichia coli K12}
           SCOP: c.82.1.1 PDB: 1wnb_A
          Length = 495

 Score = 26.3 bits (57), Expect = 9.6
 Identities = 8/26 (30%), Positives = 11/26 (42%)

Query: 85  AWAGLGYYTRARNLKKCADIIVKKYE 110
            W       RA  L K AD+I +  +
Sbjct: 75  EWGQTTPKVRAECLLKLADVIEENGQ 100


>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
          RRM, transcription termination, NUC phosphoprotein; NMR
          {Saccharomyces cerevisiae}
          Length = 96

 Score = 26.6 bits (59), Expect = 9.6
 Identities = 6/38 (15%), Positives = 17/38 (44%)

Query: 31 TEKSSLPSPYKVWISEIMLQQTTVKTVEPYFKKFMQKW 68
          TE  ++P   +++I  + L+  + + +   F  +    
Sbjct: 2  TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM 39


>1euh_A NADP dependent non phosphorylating glyceraldehyde-3-phosphate
           dehydrogenase; oxidoreductase; 1.82A {Streptococcus
           mutans} SCOP: c.82.1.1 PDB: 1qi6_A 2euh_A* 2id2_A*
           2qe0_A* 2esd_A* 1qi1_A*
          Length = 475

 Score = 26.3 bits (57), Expect = 10.0
 Identities = 12/26 (46%), Positives = 15/26 (57%)

Query: 85  AWAGLGYYTRARNLKKCADIIVKKYE 110
           AW  L Y  RA  L K ADI+++  E
Sbjct: 55  AWRALSYIERAAYLHKVADILMRDKE 80


  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
   0.321    0.135    0.421 

Gapped
Lambda     K      H
   0.267   0.0556    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,215,341
Number of extensions: 149574
Number of successful extensions: 491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 71
Length of query: 356
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 263
Effective length of database: 3,438,538
Effective search space: 904335494
Effective search space used: 904335494
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 (26.1 bits)