RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781170|ref|YP_003065583.1| deoxyribodipyrimidine
photolyase [Candidatus Liberibacter asiaticus str. psy62]
         (483 letters)



>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein,
           flavoprotein, FAD, mitochondrion, plastid, chromophore,
           chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana}
           PDB: 2vtb_A* 2ijg_X* 2vtb_B* (A:317-525)
          Length = 209

 Score =  209 bits (533), Expect = 6e-55
 Identities = 65/208 (31%), Positives = 108/208 (51%), Gaps = 4/208 (1%)

Query: 276 SGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPI 335
           +  +  L ELIWR+++R L     +        P   + +W++D  L ++W+   TG+P+
Sbjct: 1   NSTYWVLFELIWRDYFRFLSIKCGNSLF-HLGGPRNVQGKWSQDQKLFESWRDAKTGYPL 59

Query: 336 IDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWA 395
           IDA M++L+T G+M NR R I  SFLV+D+ +DWR+G E+F + LLD D  SN G W + 
Sbjct: 60  IDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYG 119

Query: 396 ASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLN 455
           A  GND     R F+   Q + +DP+G ++  WL +L  +P +  H P   +  + +   
Sbjct: 120 AGVGNDP-REDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPL 178

Query: 456 --YPLPIVDHKKACHHTLNQYYAAKKQS 481
                P+    K+       +   + + 
Sbjct: 179 KHGNGPMAGGSKSGGGFRGSHSGRRSRH 206


>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation
           energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A
           {Escherichia coli} (A:264-426)
          Length = 163

 Score =  201 bits (512), Expect = 2e-52
 Identities = 113/161 (70%), Positives = 136/161 (84%)

Query: 276 SGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPI 335
                WLNELIWREFYRHL+ ++PS+C  +PFI WT++++W  +   LQAW++G TG+PI
Sbjct: 3   GAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPI 62

Query: 336 IDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWA 395
           +DAAMRQLN+ GWMHNRLRMITASFLVKDLL+DWR GE YFMSQL+DGDLA+NNGGWQWA
Sbjct: 63  VDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWA 122

Query: 396 ASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVP 436
           ASTG D+ PYFRIFNPT QG++FD +G FIR WLPEL +VP
Sbjct: 123 ASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVP 163


>2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding
           protein, flavoprotein, nucleotide- binding, antenna
           chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus}
           (A:222-395)
          Length = 174

 Score =  199 bits (507), Expect = 7e-52
 Identities = 77/181 (42%), Positives = 106/181 (58%), Gaps = 8/181 (4%)

Query: 255 SPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKI 314
           SPR      +        +   GA  W+ EL+WR+F  HL+  +P +   +P  P  +  
Sbjct: 1   SPRLAAWEAER-------RGGEGARKWVAELLWRDFSYHLLYHFPWMAE-RPLDPRFQAF 52

Query: 315 EWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEE 374
            W +D  L QAW +G TG P++DAAMR+L+  G++ NR RM  A F VK LL+ W+  EE
Sbjct: 53  PWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWKRCEE 112

Query: 375 YFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNN 434
            F   LLDGD A N  GWQWA   G D+ PYFR+FNP +QG+R DP+G +++ W PE  +
Sbjct: 113 AFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPS 172

Query: 435 V 435
            
Sbjct: 173 Y 173


>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling
           protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana}
           (A:318-446)
          Length = 129

 Score =  164 bits (416), Expect = 2e-41
 Identities = 58/127 (45%), Positives = 83/127 (65%)

Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370
            +   W  D +  +AW+QG TG+P++DA MR+L   GW+H+R+R++ +SF VK L + WR
Sbjct: 2   LKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWR 61

Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430
            G +YF   LLD DL S+  GWQ+   T  DS  + RI NP  +G +FDP G ++R WLP
Sbjct: 62  WGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEGYKFDPNGEYVRRWLP 121

Query: 431 ELNNVPT 437
           EL+ +PT
Sbjct: 122 ELSRLPT 128


>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling
           protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana}
           (A:1-259)
          Length = 259

 Score =  161 bits (408), Expect = 2e-40
 Identities = 57/260 (21%), Positives = 98/260 (37%), Gaps = 11/260 (4%)

Query: 1   MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHF 60
           +    +    +VW R DLR+ DN AL AA       VIA+F+  PE+   +        +
Sbjct: 5   VSGCGSGGCSIVWFRRDLRVEDNPALAAAVRA--GPVIALFVWAPEEEGHYHPGRVSRWW 62

Query: 61  IYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRD 120
           +  SL Q+  SL   G      +     DS+  L         +++F+N  Y+   + RD
Sbjct: 63  LKNSLAQLDSSLRSLGTCLITKRS---TDSVASLLDVVKSTGASQIFFNHLYDPLSLVRD 119

Query: 121 KLLEKRLQHRVI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPV 179
              +  L  + I  +SF+  +L  P  + +   + + ++  F +  +      +   LP 
Sbjct: 120 HRAKDVLTAQGIAVRSFNADLLYEPWEVTDELGRPFSMFAAFWERCLSMPYDPESPLLPP 179

Query: 180 PAIRLTGPVTPSNIPRFFDYPFQA-----IDPMFPIGEQNALHILRKFCKEKVYYYVEQR 234
             I           P  F+   +      +   +  G  N    L  F    +  Y + R
Sbjct: 180 KKIISGDVSKCVADPLVFEDDSEKGSNALLARAWSPGWSNGDKALTTFINGPLLEYSKNR 239

Query: 235 DIPAIQGTSQLSPYLSIGVL 254
                  TS LSP+L  G +
Sbjct: 240 RKADSATTSFLSPHLHFGEV 259


>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair,
           flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A
           {Synechococcus elongatus pcc 6301} (A:308-448)
          Length = 141

 Score =  161 bits (408), Expect = 2e-40
 Identities = 73/135 (54%), Positives = 92/135 (68%), Gaps = 1/135 (0%)

Query: 312 EKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRI 371
           ++  W     L  AW Q  TG+PI+DAAMRQL   GWMHNR RMI ASFL KDL++DWR 
Sbjct: 3   QQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRR 62

Query: 372 GEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPE 431
           GE++FM  L+DGDLA+NNGGWQW+AS+G D     RIFNP  Q K+FD   T+I+ WLPE
Sbjct: 63  GEQFFMQHLVDGDLAANNGGWQWSASSGMDP-KPLRIFNPASQAKKFDATATYIKRWLPE 121

Query: 432 LNNVPTQYIHAPHSW 446
           L +V  + + +    
Sbjct: 122 LRHVHPKDLISGEIT 136


>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD;
           1.90A {Synechocystis SP} (A:314-441)
          Length = 128

 Score =  159 bits (403), Expect = 7e-40
 Identities = 61/127 (48%), Positives = 83/127 (65%), Gaps = 1/127 (0%)

Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370
            +   W +D    + W+ G TG+P++DA MR+LN  G+M NR R   ASFL K+L +DWR
Sbjct: 2   NKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCKNLGIDWR 61

Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430
            G E+F S L+D D+ SN G W + A  GND+   FR FN   Q +++DPQGT++RHWLP
Sbjct: 62  WGAEWFESCLIDYDVCSNWGNWNYTAGIGNDA-RDFRYFNIPKQSQQYDPQGTYLRHWLP 120

Query: 431 ELNNVPT 437
           EL N+P 
Sbjct: 121 ELKNLPG 127


>2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase;
           FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii
           str} (A:268-406)
          Length = 139

 Score =  158 bits (401), Expect = 1e-39
 Identities = 68/136 (50%), Positives = 91/136 (66%), Gaps = 2/136 (1%)

Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370
            + I W  +    +AWK+G TG+PIIDA MR LN+ G+++ R+RM+ A FLVK L VDWR
Sbjct: 2   YDNISWENNESYFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKVLFVDWR 61

Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430
            GE YF ++L+D D A NNG WQW ASTG D    FR+FNP  Q ++FDP+  FI+ W+ 
Sbjct: 62  WGERYFATKLVDYDPAINNGNWQWIASTGVD--YMFRVFNPWKQQEKFDPEAKFIKEWVE 119

Query: 431 ELNNVPTQYIHAPHSW 446
           EL +VP   IH+ +  
Sbjct: 120 ELKDVPPSIIHSIYKT 135


>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase;
           HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB:
           2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*
           (A:347-475)
          Length = 129

 Score =  153 bits (388), Expect = 4e-38
 Identities = 53/129 (41%), Positives = 74/129 (57%), Gaps = 2/129 (1%)

Query: 310 WTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVK-DLLVD 368
           +  +I W +    L+AW  G TG+P IDA MRQL   GW+H+  R   A FL + DL + 
Sbjct: 1   YCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWIS 60

Query: 369 WRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHW 428
           W  G+  F   LLD D A N G W W +++      YFR+++P   GK+ DPQG +IR +
Sbjct: 61  WEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFH-QYFRVYSPVAFGKKTDPQGHYIRKY 119

Query: 429 LPELNNVPT 437
           +PEL+  P 
Sbjct: 120 VPELSKYPA 128


>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES
           FAD; 2.70A {Arabidopsis thaliana} (A:323-451)
          Length = 129

 Score =  153 bits (387), Expect = 6e-38
 Identities = 54/129 (41%), Positives = 76/129 (58%), Gaps = 2/129 (1%)

Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLL-VDW 369
            ++I WN+D  +L AW+ G TG+P IDA M QL   GWMH+  R   A FL +  L + W
Sbjct: 2   CKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGDLFIHW 61

Query: 370 RIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWL 429
             G + F   L+D D A NNG W W + +      + RI++P   GK++DP G +IRH+L
Sbjct: 62  EQGRDVFERLLIDSDWAINNGNWMWLSCSSFFY-QFNRIYSPISFGKKYDPDGKYIRHFL 120

Query: 430 PELNNVPTQ 438
           P L ++P Q
Sbjct: 121 PVLKDMPKQ 129


>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation
           energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A
           {Escherichia coli} (A:1-140)
          Length = 140

 Score =  133 bits (337), Expect = 4e-32
 Identities = 68/141 (48%), Positives = 97/141 (68%), Gaps = 1/141 (0%)

Query: 8   SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQ 67
           + HLVW R DLR+ DN AL AAC NS A+V+A++IATP QW  H +S RQ+  I A L  
Sbjct: 1   TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNG 60

Query: 68  VQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL 127
           +Q +L++KGI   + +  +F  S+E +   C +  VT LFYN QYE+NE  RD  +E+ L
Sbjct: 61  LQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERAL 120

Query: 128 QHRVICKSFDDSVLLPPGSIL 148
           ++ V+C+ FDDSV+LPPG+++
Sbjct: 121 RN-VVCEGFDDSVILPPGAVM 140


>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair,
           flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A
           {Synechococcus elongatus pcc 6301} (A:1-196)
          Length = 196

 Score =  124 bits (311), Expect = 4e-29
 Identities = 42/196 (21%), Positives = 72/196 (36%), Gaps = 9/196 (4%)

Query: 7   MS-VHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASL 65
           M+   L W R DLR++DN  L AA   S  ++I +F   P+  +   ++  +  ++   L
Sbjct: 1   MAAPILFWHRRDLRLSDNIGLAAARAQSA-QLIGLFCLDPQILQSADMAPARVAYLQGCL 59

Query: 66  LQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEK 125
            ++Q+   Q G      Q     D    +     Q +   +++N+  E     RD  +  
Sbjct: 60  QELQQRYQQAGSRLLLLQG----DPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAA 115

Query: 126 RLQHRVI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRL 184
            L+   I      D +L  P  IL+ +   Y VY PF K          +       +  
Sbjct: 116 ALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVA--TPTELVD 173

Query: 185 TGPVTPSNIPRFFDYP 200
             P   + I       
Sbjct: 174 LSPEQLTAIAPLLLSE 189


>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD;
           1.90A {Synechocystis SP} (A:147-313)
          Length = 167

 Score =  120 bits (303), Expect = 3e-28
 Identities = 34/162 (20%), Positives = 62/162 (38%), Gaps = 12/162 (7%)

Query: 153 QMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPR-----FFDYPFQAIDP- 206
            +  ++T FRK + +  +         P+  L  P     +       F    F      
Sbjct: 6   DLPDLFTKFRKDIEKKKISI-RPCFFAPSQLLPSPNIKLELTAPPPEFFPQINFDHRSVL 64

Query: 207 MFPIGEQNALHILRKFCKEK--VYYYVEQRD-IPAIQGTSQLSPYLSIGVLSPRQCWNRL 263
            F  GE   L  L+ +      +  Y E R+ +     +S+ SP+L++G LSPR  +  +
Sbjct: 65  AFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSKFSPWLALGCLSPRFIYQEV 124

Query: 264 KEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGK 305
           K    +            + EL+WR+F+R +   Y +    +
Sbjct: 125 KRYEQE--RVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNR 164


>2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding
           protein, flavoprotein, nucleotide- binding, antenna
           chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus}
           (A:1-149)
          Length = 149

 Score =  113 bits (283), Expect = 6e-26
 Identities = 28/164 (17%), Positives = 57/164 (34%), Gaps = 16/164 (9%)

Query: 7   MSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLL 66
           M   LVW R DLR+ D+ AL  A       V+ + +  P   +      R+  +   ++ 
Sbjct: 1   MGPLLVWHRGDLRLHDHPALLEALAR--GPVVGLVVLDPNNLKTT---PRRRAWFLENVR 55

Query: 67  QVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKR 126
            ++++   +G      +        E +     + +   ++    +      RD  + + 
Sbjct: 56  ALREAYRARGGALWVLEG----LPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREA 111

Query: 127 LQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLV 170
           L            +L  P  +     + Y+VYTPF +       
Sbjct: 112 L-------PVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAP 148


>2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase;
           FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii
           str} (A:133-267)
          Length = 135

 Score =  112 bits (282), Expect = 9e-26
 Identities = 33/151 (21%), Positives = 59/151 (39%), Gaps = 25/151 (16%)

Query: 153 QMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDP-MFPIG 211
             ++ +T F   + +  V+      P            S++   F   F+ I+  +F  G
Sbjct: 3   FHHRNFTSFYNEVSKVKVRE-----PETMEGSFDVT-DSSMNVDFLLTFKKIESPLFRGG 56

Query: 212 EQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLL 271
            +  L++L +           +RD PA     +LSP+L  G +S R+ +   K       
Sbjct: 57  RREGLYLLHRNV------DFRRRDYPAENNNYRLSPHLKFGTISMREAYYTQK------- 103

Query: 272 IKPKSGAFSWLNELIWREFYRHLMAFYPSVC 302
                G   ++ EL WR+F+  L  + P V 
Sbjct: 104 -----GKEEFVRELYWRDFFTLLAYYNPHVF 129


>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD;
           1.90A {Synechocystis SP} (A:1-146)
          Length = 146

 Score =  111 bits (279), Expect = 2e-25
 Identities = 35/153 (22%), Positives = 63/153 (41%), Gaps = 13/153 (8%)

Query: 1   MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG-----ISA 55
           MK        LVW RNDLR+ D++ L+ A  +    + AV+   P Q+ Q          
Sbjct: 1   MKHVPP--TVLVWFRNDLRLHDHEPLHRALKSGL-AITAVYCYDPRQFAQTHQGFAKTGP 57

Query: 56  RQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEIN 115
            +S+F+  S+  + +SL + G               + +     Q     ++Y+R+    
Sbjct: 58  WRSNFLQQSVQNLAESLQKVGNKLLVTTG----LPEQVIPQIAKQINAKTIYYHREVTQE 113

Query: 116 EVRRDKLLEKRL-QHRVICKSFDDSVLLPPGSI 147
           E+  ++ L K+L    +  K +  S L  P  +
Sbjct: 114 ELDVERNLVKQLTILGIEAKGYWGSTLCHPEDL 146


>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein,
           flavoprotein, FAD, mitochondrion, plastid, chromophore,
           chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana}
           PDB: 2vtb_A* 2ijg_X* 2vtb_B* (A:34-183)
          Length = 150

 Score =  110 bits (275), Expect = 5e-25
 Identities = 32/154 (20%), Positives = 61/154 (39%), Gaps = 14/154 (9%)

Query: 3   ATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQH------GISAR 56
                 V ++W RNDLR+ DN ALY A  +SD  ++ V+   P  +            A 
Sbjct: 2   KRKGKGVTILWFRNDLRVLDNDALYKAWSSSD-TILPVYCLDPRLFHTTHFFNFPKTGAL 60

Query: 57  QSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINE 116
           +  F+   L+ ++K+L ++G+              E L S         +F +++    E
Sbjct: 61  RGGFLMECLVDLRKNLMKRGLNLLIRSG----KPEEILPSLAKDFGARTVFAHKETCSEE 116

Query: 117 VRRDKLLEKRLQHR---VICKSFDDSVLLPPGSI 147
           V  ++L+ + L+        +    S +     +
Sbjct: 117 VDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDL 150


>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase;
           HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB:
           2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*
           (A:1-163)
          Length = 163

 Score =  106 bits (266), Expect = 5e-24
 Identities = 27/146 (18%), Positives = 47/146 (32%), Gaps = 10/146 (6%)

Query: 1   MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAK-----VIAVFIATPEQWRQHGISA 55
               +  S  + W R  LR+ DN AL      ++A      V  +FI  P       + A
Sbjct: 22  GLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGA 81

Query: 56  RQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEIN 115
            +  F+  +L  +   L +        +        E         RV  L +    E  
Sbjct: 82  NRWRFLQQTLEDLDNQLRKLNSRLFVVRG----KPAEVFPRIFKSWRVEMLTFETDIEPY 137

Query: 116 EVRRDKLLEKRLQHRVI-CKSFDDSV 140
            V RD  ++K  +   +  ++     
Sbjct: 138 SVTRDAAVQKLAKAEGVRVETHCSHT 163


>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair,
           flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A
           {Synechococcus elongatus pcc 6301} (A:197-307)
          Length = 111

 Score =  104 bits (262), Expect = 2e-23
 Identities = 33/97 (34%), Positives = 46/97 (47%), Gaps = 1/97 (1%)

Query: 208 FPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEF 267
              GE  A+  L++FC   +  Y  QR+ PA  GTS LSP L  G +  RQ W       
Sbjct: 10  VEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQAASAAH 69

Query: 268 VD-LLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCM 303
                 + ++    W  EL WREFY+H +  +PS+  
Sbjct: 70  ALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLAD 106


>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES
           FAD; 2.70A {Arabidopsis thaliana} (A:1-142)
          Length = 142

 Score =  101 bits (254), Expect = 1e-22
 Identities = 27/142 (19%), Positives = 46/142 (32%), Gaps = 15/142 (10%)

Query: 8   SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG---------ISARQS 58
           S  L+W R  LR+ DN AL  A   S+  +  VF+  P                    + 
Sbjct: 5   SGSLIWFRKGLRVHDNPALEYASKGSE-FMYPVFVIDPHYMESDPSAFSPGSSRAGVNRI 63

Query: 59  HFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVR 118
            F+  SL  +  SL + G      +     +  E L     + +V +L +    +     
Sbjct: 64  RFLLESLKDLDSSLKKLGSRLLVFKG----EPGEVLVRCLQEWKVKRLCFEYDTDPYYQA 119

Query: 119 RDKLLEKRLQHRVI-CKSFDDS 139
            D  ++       +   S    
Sbjct: 120 LDVKVKDYASSTGVEVFSPVSH 141


>2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase;
           FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii
           str} (A:1-132)
          Length = 132

 Score =  101 bits (252), Expect = 3e-22
 Identities = 35/136 (25%), Positives = 61/136 (44%), Gaps = 9/136 (6%)

Query: 10  HLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQH-GISARQSHFIYASLLQV 68
            +   R DLR+ DN  L  A    D +VI VFIA P Q   +   S     F+  SLL++
Sbjct: 3   CIFIFRRDLRLEDNTGLNYALSECD-RVIPVFIADPRQLINNPYKSEFAVSFMINSLLEL 61

Query: 69  QKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL- 127
              L +KG            ++ + +  +    +V  ++ N  Y    + RD+ + K   
Sbjct: 62  DDELRKKGSRLNVFFG----EAEKVVSRFF--NKVDAIYVNEDYTPFSISRDEKIRKVCE 115

Query: 128 QHRVICKSFDDSVLLP 143
           ++ +  K+++D +L P
Sbjct: 116 ENGIEFKAYEDYLLTP 131


>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein,
           flavoprotein, FAD, mitochondrion, plastid, chromophore,
           chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana}
           PDB: 2vtb_A* 2ijg_X* 2vtb_B* (A:1-33,A:184-316)
          Length = 166

 Score = 98.3 bits (244), Expect = 2e-21
 Identities = 23/133 (17%), Positives = 46/133 (34%), Gaps = 7/133 (5%)

Query: 142 LPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPF 201
           LP  S       +  VYT FRK++           +P+            ++P       
Sbjct: 28  LPSSSSPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGV 87

Query: 202 ----QAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRD---IPAIQGTSQLSPYLSIGVL 254
                     F  GE   +  + ++  +K    V +     +     +++ SP+L+ G +
Sbjct: 88  EPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCI 147

Query: 255 SPRQCWNRLKEEF 267
           SPR  +  ++   
Sbjct: 148 SPRFIYEEVQRYE 160


>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation
           energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A
           {Escherichia coli} (A:184-263)
          Length = 80

 Score = 74.9 bits (184), Expect = 2e-14
 Identities = 34/72 (47%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 197 FDYPFQAIDP-MFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLS 255
            +YP Q+ D   FP+ E+ A+  LR+FC+     Y +QRD PA++GTS+LS  L+ G LS
Sbjct: 5   LNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLS 64

Query: 256 PRQCWNRLKEEF 267
           PRQC +RL  E 
Sbjct: 65  PRQCLHRLLAEQ 76


>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES
           FAD; 2.70A {Arabidopsis thaliana} (A:196-290)
          Length = 95

 Score = 73.8 bits (181), Expect = 4e-14
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 7/89 (7%)

Query: 184 LTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEK--VYYYVEQRDIPAI-- 239
           ++   +   +   +    QA    F  GE  AL  L K   +K  V  + + +  P+   
Sbjct: 1   ISEVPSLEELG--YKDDEQADWTPFRGGESEALKRLTKSISDKAWVANFEKPKGDPSAFL 58

Query: 240 -QGTSQLSPYLSIGVLSPRQCWNRLKEEF 267
              T+ +SPYL  G LS R  +  L+  +
Sbjct: 59  KPATTVMSPYLKFGCLSSRYFYQCLQNIY 87


>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase;
           HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB:
           2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*
           (A:220-313)
          Length = 94

 Score = 68.8 bits (168), Expect = 1e-12
 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 190 PSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEK--VYYYVEQRDIPAI--QGTSQL 245
           P+          +     FP GE  AL  + +  K++  V  + +    P      T+ L
Sbjct: 7   PTMKQLVKRPE-ELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVL 65

Query: 246 SPYLSIGVLSPRQCWNRLKEEF 267
           SPYL  G LS R    +LKE  
Sbjct: 66  SPYLKFGCLSARLFNQKLKEII 87


>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES
           FAD; 2.70A {Arabidopsis thaliana} (A:452-537)
          Length = 86

 Score = 42.7 bits (100), Expect = 1e-04
 Identities = 10/49 (20%), Positives = 17/49 (34%), Gaps = 6/49 (12%)

Query: 439 YIHAPHSWLDKN------DLSLNYPLPIVDHKKACHHTLNQYYAAKKQS 481
           YI+ P +            +  +YP P+V H  A      +   A   +
Sbjct: 1   YIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALN 49


>1aua_A Phosphatidylinositol transfer protein SEC14P;
           phospholipid-binding protein, peripheral golgi membrane
           protein, phospholipid exchange; HET: BOG; 2.50A
           {Saccharomyces cerevisiae} (A:94-296)
          Length = 203

 Score = 30.3 bits (67), Expect = 0.55
 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 6/82 (7%)

Query: 192 NIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSI 251
           N P  F   F+   P       + + IL    ++++   +   ++P   G          
Sbjct: 120 NAPFGFSTAFRLFKPFLDPVTVSKIFILGSSYQKELLKQIPAENLPVKFGGKSEVDESKG 179

Query: 252 GVLSPRQCWNRLKEEFVDLLIK 273
           G       +      + D    
Sbjct: 180 G------LYLSDIGPWRDPKYI 195


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

 Score = 29.7 bits (66), Expect = 0.81
 Identities = 7/100 (7%), Positives = 19/100 (19%), Gaps = 28/100 (28%)

Query: 40  VFIATPEQWRQHGISARQSHFIYA---SLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDS 96
           + I TP               +         ++  +                D    +  
Sbjct: 238 IVIGTPG---------TVMDLMKRRQLDARDIKVFVLD--EADNMLDQQGLGDQSMRIKH 286

Query: 97  YCLQQRVTKLF--------------YNRQYEINEVRRDKL 122
              +     LF              +        ++ ++L
Sbjct: 287 LLPRNTQIVLFSATFSERVEKYAERFAPNANEIRLKTEEL 326


>1r31_A 3-hydroxy-3-methylglutaryl-coenzyme A reductase; 4-electron
           oxido-reductase, oxidoreductase; HET: COA MEV; 2.10A
           {Pseudomonas mevalonii} (A:56-109,A:219-428)
          Length = 264

 Score = 29.8 bits (67), Expect = 0.87
 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 9/82 (10%)

Query: 4   TTAMSVHLVWLRNDLRITDNKALYAACHNSDAK--VIAVFIATPEQWRQ-----HGISAR 56
           +    +  +         D        HN      +  + +AT   WR      H  + R
Sbjct: 76  SGEAVIEGILDAYAFAAVDPYRAAT--HNKGIMNGIDPLIVATGNDWRAVEAGAHAYACR 133

Query: 57  QSHFIYASLLQVQKSLSQKGIV 78
             H+   +  +   +    G +
Sbjct: 134 SGHYGSLTTWEKDNNGHLVGTL 155


>1xsz_A Guanine nucleotide exchange protein; ARF guanine nucleotide
           exchange factor, signaling protein; 1.41A {Legionella
           pneumophila} (A:198-356)
          Length = 159

 Score = 29.6 bits (66), Expect = 1.0
 Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 6/65 (9%)

Query: 385 LASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPH 444
               + G++  ++T N     F+  +  +     +    F     P + +     +  P 
Sbjct: 1   FVKTSPGYELTSTTLNKD-STFKKLDSFLHSTDVNINTVF-----PGIGDNVKTTVDQPK 54

Query: 445 SWLDK 449
           SWL  
Sbjct: 55  SWLSF 59


>3b7n_A Uncharacterized protein YKL091C; SEC14, golgi, phospholipid,
           phosphatidylinositol, signaling protein; HET: B7N; 1.86A
           {Saccharomyces cerevisiae} PDB: 3b74_A* 3b7q_A* 3b7z_A*
           (A:95-320)
          Length = 226

 Score = 28.7 bits (63), Expect = 1.6
 Identities = 11/86 (12%), Positives = 27/86 (31%), Gaps = 6/86 (6%)

Query: 192 NIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSI 251
           + P  F   F+ + P       + + IL    K+++   +   ++P   G + +      
Sbjct: 134 HSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHN--- 190

Query: 252 GVLSPRQCWNRLKEEFVDLLIKPKSG 277
                 + +      + D       G
Sbjct: 191 ---PNDKFYYSDIGPWRDPRYIGPEG 213


>3cwv_A DNA gyrase, B subunit, truncated; structural genomics,
           unknown function, ATP-binding, isomerase,
           nucleotide-binding, topoisomerase; HET: DNA; 1.95A
           {Myxococcus xanthus dk 1622} (A:1-206)
          Length = 206

 Score = 27.8 bits (61), Expect = 3.0
 Identities = 13/102 (12%), Positives = 28/102 (27%), Gaps = 12/102 (11%)

Query: 279 FSWLNELIWREFYRHLMAFYPSVCMGKPFIPWT-EKIEWNKDSHLLQAWKQGYTGFPIID 337
            S     IW +  +  +        G+       E +  + +  +   +    T F ++ 
Sbjct: 109 SSRYQVDIWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEVLA 168

Query: 338 AAMRQLNTIGWMHNRLRMITASFLVKDL---LVDWRIGEEYF 376
                      +  R   +  + L   L     D + GE   
Sbjct: 169 FDRA------RLSRRCNEL--AALAPGLRVSFADLQRGERTL 202


>2ix5_A Acyl-coenzyme A oxidase 4, peroxisomal; FAD, ACX4, flavin,
           peroxisome, glyoxysome, fatty acid metabolism, lipid
           metabolism; HET: CAA FAD; 2.7A {Arabidopsis thaliana}
           PDB: 2ix6_A* (A:1-164,A:273-436)
          Length = 328

 Score = 27.1 bits (59), Expect = 5.2
 Identities = 8/74 (10%), Positives = 25/74 (33%)

Query: 162 RKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRK 221
           R +  + +  +     P+         TP++        +   + +    EQ     +R+
Sbjct: 9   RASNEKKVKSSYFDLPPMEMSVAFPQATPASTFPPCTSDYYHFNDLLTPEEQAIRKKVRE 68

Query: 222 FCKEKVYYYVEQRD 235
             +++V   + +  
Sbjct: 69  CMEKEVAPIMTEYW 82


>2qe8_A Uncharacterized protein; YP_324691.1, structural genomics,
           joint center for structural genomics, JCSG; HET: MSE UNL
           PG4; 1.35A {Anabaena variabilis atcc 29413}
           (A:117-167,A:195-289)
          Length = 146

 Score = 26.9 bits (59), Expect = 5.3
 Identities = 9/99 (9%), Positives = 22/99 (22%), Gaps = 15/99 (15%)

Query: 336 IDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDG--DLASNNGGWQ 393
           +DA    L            I ++ L    L D  +G +            ++ +     
Sbjct: 59  LDAENEWLYLSPXHSTSXYRIKSADLSNLQLTDAELGSKIERYSEKPICDGISIDKDHNI 118

Query: 394 WAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHW-LPE 431
           +     + ++                      +     E
Sbjct: 119 YVGDLAHSAI------------GVITSADRAYKLLVTDE 145


>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone
           receptors superfamily; nuclear receptor, ligand binding
           domain, dafachronic acid, nematode, DNA-binding,
           metal-binding, nucleus, receptor; HET: DL4; 2.40A
           {Strongyloides stercoralis} PDB: 3gyu_A* (A:)
          Length = 244

 Score = 27.0 bits (58), Expect = 5.3
 Identities = 5/145 (3%), Positives = 28/145 (19%), Gaps = 8/145 (5%)

Query: 159 TPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHI 218
           +      + ++  +                         D        +  + +     +
Sbjct: 6   SEKDLKELDSIRDSFQCMNEPLDNDQQASTLAKKEHNPTD--------ILNVMDITMRRL 57

Query: 219 LRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGA 278
           ++   +   +  + +    ++     +      GV          +           +  
Sbjct: 58  VKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMF 117

Query: 279 FSWLNELIWREFYRHLMAFYPSVCM 303
                ++   +    L  F      
Sbjct: 118 DKLRPDIKDTQKKGFLHFFNLLHSD 142


  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
   0.324    0.138    0.444 

Gapped
Lambda     K      H
   0.267   0.0480    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 4,048,323
Number of extensions: 192019
Number of successful extensions: 761
Number of sequences better than 10.0: 1
Number of HSP's gapped: 717
Number of HSP's successfully gapped: 44
Length of query: 483
Length of database: 4,956,049
Length adjustment: 92
Effective length of query: 391
Effective length of database: 1,845,989
Effective search space: 721781699
Effective search space used: 721781699
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 56 (26.0 bits)