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)