RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781170|ref|YP_003065583.1| deoxyribodipyrimidine
photolyase [Candidatus Liberibacter asiaticus str. psy62]
(483 letters)
>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*
Length = 543
Score = 386 bits (993), Expect = e-108
Identities = 131/510 (25%), Positives = 206/510 (40%), Gaps = 38/510 (7%)
Query: 1 MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAK-----VIAVFIATPEQWRQHGISA 55
M + + VH W R LR+ DN AL ++A V +FI P + A
Sbjct: 24 MDSQRSTLVH--WFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGA 81
Query: 56 RQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEIN 115
+ F+ +L + L + + E RV L + E
Sbjct: 82 NRWRFLQQTLEDLDNQLRKLNSRLFVVRG----KPAEVFPRIFKSWRVEMLTFETDIEPY 137
Query: 116 EVRRDKLLEKRL-QHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADL 174
V RD ++K V ++ + P ++ L + +++ L +
Sbjct: 138 SVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKV 197
Query: 175 RSLPVPAIRLTGP------------VTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKF 222
+P + P + + P + FP GE AL + +
Sbjct: 198 LGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEES 257
Query: 223 CKEKVYYYVEQRDIPAI----QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGA 278
K++++ ++ A T+ LSPYL G LS R +LKE + K
Sbjct: 258 LKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKE-IIKRQPKHSQPP 316
Query: 279 FSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDA 338
S + +L+WREFY + A P+ + +I W + L+AW G TG+P IDA
Sbjct: 317 VSLIGQLMWREFYYTVAAAEPN-FDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDA 375
Query: 339 AMRQLNTIGWMHNRLRMITASFLVK-DLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAAS 397
MRQL GW+H+ R A FL + DL + W G+ F LLD D A N G W W ++
Sbjct: 376 IMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSA 435
Query: 398 TGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKN------D 451
+ YFR+++P GK+ DPQG +IR ++PEL+ P I+ P +
Sbjct: 436 SAFFH-QYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCV 494
Query: 452 LSLNYPLPIVDHKKACHHTLNQYYAAKKQS 481
L +YP IV H+ + + AA K +
Sbjct: 495 LGTDYPHRIVKHEVVHKENIKRMGAAYKVN 524
>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin
enzyme, photoreactivating enzyme; HET: FAD; 1.80A
{Synechococcus elongatus pcc 6301} SCOP: a.99.1.1
c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A*
1tez_A*
Length = 484
Score = 354 bits (910), Expect = 2e-98
Identities = 156/479 (32%), Positives = 222/479 (46%), Gaps = 19/479 (3%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70
L W R DLR++DN L AA S ++I +F P+ + ++ + ++ L ++Q+
Sbjct: 6 LFWHRRDLRLSDNIGLAAARAQSA-QLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQ 64
Query: 71 SLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHR 130
Q G Q D + Q + +++N+ E RD + L+
Sbjct: 65 RYQQAGSRLLLLQG----DPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTA 120
Query: 131 -VICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVT 189
+ D +L P IL+ + Y VY PF K + + +T
Sbjct: 121 GIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLT 180
Query: 190 PSNIPRFFDYPFQAIDPM-------FPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGT 242
+ P GE A+ L++FC + Y QR+ PA GT
Sbjct: 181 AIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGT 240
Query: 243 SQLSPYLSIGVLSPRQCWNRLKEEF-VDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSV 301
S LSP L G + RQ W + + ++ W EL WREFY+H + +PS+
Sbjct: 241 SGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSL 300
Query: 302 CMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFL 361
P+ ++ W L AW Q TG+PI+DAAMRQL GWMHNR RMI ASFL
Sbjct: 301 AD-GPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFL 359
Query: 362 VKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQ 421
KDL++DWR GE++FM L+DGDLA+NNGGWQW+AS+G D P RIFNP Q K+FD
Sbjct: 360 TKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKP-LRIFNPASQAKKFDAT 418
Query: 422 GTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQ 480
T+I+ WLPEL +V + + + YP PIV+H Y K
Sbjct: 419 ATYIKRWLPELRHVHPKDLISGEIT---PIERRGYPAPIVNHNLRQKQFKALYNQLKAA 474
>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy
transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A
{Escherichia coli} SCOP: a.99.1.1 c.28.1.1
Length = 471
Score = 342 bits (877), Expect = 1e-94
Identities = 243/472 (51%), Positives = 324/472 (68%), Gaps = 3/472 (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 QHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGP 187
++ +C+ FDDSV+LPPG+++ +MYKV+TPF+ A ++ L + + P +R +G
Sbjct: 121 RNV-VCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGS 179
Query: 188 VTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSP 247
+ PS FP+ E+ A+ LR+FC+ Y +QRD PA++GTS+LS
Sbjct: 180 IEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSA 239
Query: 248 YLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPF 307
L+ G LSPRQC +RL E WLNELIWREFYRHL+ ++PS+C +PF
Sbjct: 240 SLATGGLSPRQCLHRLLAEQPQ--ALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPF 297
Query: 308 IPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLV 367
I WT++++W + LQAW++G TG+PI+DAAMRQLN+ GWMHNRLRMITASFLVKDLL+
Sbjct: 298 IAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLI 357
Query: 368 DWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRH 427
DWR GE YFMSQL+DGDLA+NNGGWQWAASTG D+ PYFRIFNPT QG++FD +G FIR
Sbjct: 358 DWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQ 417
Query: 428 WLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKK 479
WLPEL +VP + +H P W K ++L+YP PIV+HK+A TL Y AA+K
Sbjct: 418 WLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARK 469
>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A
{Synechocystis SP} SCOP: a.99.1.1 c.28.1.1
Length = 489
Score = 336 bits (861), Expect = 8e-93
Identities = 136/479 (28%), Positives = 225/479 (46%), Gaps = 31/479 (6%)
Query: 9 VHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQH-----GISARQSHFIYA 63
LVW RNDLR+ D++ L+ A + + AV+ P Q+ Q +S+F+
Sbjct: 7 TVLVWFRNDLRLHDHEPLHRALKSGL-AITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQ 65
Query: 64 SLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLL 123
S+ + +SL + G + + Q ++Y+R+ E+ ++ L
Sbjct: 66 SVQNLAESLQKVGNKLLVTT----GLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNL 121
Query: 124 EKRLQ-HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQ------ADLRS 176
K+L + K + S L P + + ++T FRK + + + A +
Sbjct: 122 VKQLTILGIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQL 181
Query: 177 LPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKV---YYYVEQ 233
LP P I+L P ++ +++ F GE L L+ + Y +
Sbjct: 182 LPSPNIKLELTAPPPEFFPQINFDHRSVLA-FQGGETAGLARLQDYFWHGDRLKDYKETR 240
Query: 234 RDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRH 293
+ +S+ SP+L++G LSPR + +K + + + + EL+WR+F+R
Sbjct: 241 NGMVGADYSSKFSPWLALGCLSPRFIYQEVKRYEQERVSNDSTHWLIF--ELLWRDFFRF 298
Query: 294 LMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRL 353
+ Y + + + W +D + W+ G TG+P++DA MR+LN G+M NR
Sbjct: 299 VAQKYGNKLFNRGG-LLNKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRG 357
Query: 354 RMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTI 413
R ASFL K+L +DWR G E+F S L+D D+ SN G W + A GND+ FR FN
Sbjct: 358 RQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGNDARD-FRYFNIPK 416
Query: 414 QGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKN------DLSLNYPLPIVDHKKA 466
Q +++DPQGT++RHWLPEL N+P IH P L ++YP P V+ ++
Sbjct: 417 QSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQS 475
>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*
Length = 525
Score = 274 bits (702), Expect = 2e-74
Identities = 118/491 (24%), Positives = 217/491 (44%), Gaps = 27/491 (5%)
Query: 8 SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG------ISARQSHFI 61
V ++W RNDLR+ DN ALY A +SD ++ V+ P + A + F+
Sbjct: 40 GVTILWFRNDLRVLDNDALYKAWSSSD-TILPVYCLDPRLFHTTHFFNFPKTGALRGGFL 98
Query: 62 YASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDK 121
L+ ++K+L ++G+ E L S +F +++ EV ++
Sbjct: 99 MECLVDLRKNLMKRGLNLLIRSG----KPEEILPSLAKDFGARTVFAHKETCSEEVDVER 154
Query: 122 LLEKRLQ---HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLP 178
L+ + L+ + + S + + + VYT FRK++ +P
Sbjct: 155 LVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIP 214
Query: 179 VPAIRLTGPVTPSNIPRFFDYPFQAIDP----MFPIGEQNALHILRKFCKEK---VYYYV 231
+ ++P + + F GE + + ++ +K Y
Sbjct: 215 LSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKE 274
Query: 232 EQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFY 291
+ + +++ SP+L+ G +SPR + ++ + + + L ELIWR+++
Sbjct: 275 TRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKE--RVANNSTYWVLFELIWRDYF 332
Query: 292 RHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHN 351
R L + P + +W++D L ++W+ TG+P+IDA M++L+T G+M N
Sbjct: 333 RFLSIKCGNSLF-HLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSN 391
Query: 352 RLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNP 411
R R I SFLV+D+ +DWR+G E+F + LLD D SN G W + A GND R F+
Sbjct: 392 RGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPRED-RYFSI 450
Query: 412 TIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPH--SWLDKNDLSLNYPLPIVDHKKACHH 469
Q + +DP+G ++ WL +L +P + H P ++D + P+ K+
Sbjct: 451 PKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKHGNGPMAGGSKSGGG 510
Query: 470 TLNQYYAAKKQ 480
+ + +
Sbjct: 511 FRGSHSGRRSR 521
>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein;
HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP:
a.99.1.1 c.28.1.1 PDB: 1u3c_A*
Length = 509
Score = 256 bits (653), Expect = 1e-68
Identities = 136/490 (27%), Positives = 222/490 (45%), Gaps = 22/490 (4%)
Query: 6 AMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASL 65
+ +VW R DLR+ DN AL AA VIA+F+ PE+ + ++ SL
Sbjct: 10 SGGCSIVWFRRDLRVEDNPALAAAVRAG--PVIALFVWAPEEEGHYHPGRVSRWWLKNSL 67
Query: 66 LQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEK 125
Q+ SL G + + DS+ L +++F+N Y+ + RD +
Sbjct: 68 AQLDSSLRSLGTCLITKRST---DSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKD 124
Query: 126 RLQHRVI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRL 184
L + I +SF+ +L P + + + + ++ F + + + LP I
Sbjct: 125 VLTAQGIAVRSFNADLLYEPWEVTDELGRPFSMFAAFWERCLSMPYDPESPLLPPKKIIS 184
Query: 185 TGPVTPSNIPRFFDYPFQ-----AIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAI 239
P F+ + + + G N L F + Y + R
Sbjct: 185 GDVSKCVADPLVFEDDSEKGSNALLARAWSPGWSNGDKALTTFINGPLLEYSKNRRKADS 244
Query: 240 QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLN----ELIWREFYRHLM 295
TS LSP+L G +S R+ ++ ++ + V + +N + RE+ R++
Sbjct: 245 ATTSFLSPHLHFGEVSVRKVFHLVRIKQVAWANEGNEAGEESVNLFLKSIGLREYSRYIS 304
Query: 296 AFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRM 355
F +P + + W D + +AW+QG TG+P++DA MR+L GW+H+R+R+
Sbjct: 305 -FNHPYSHERPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRV 363
Query: 356 ITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQG 415
+ +SF VK L + WR G +YF LLD DL S+ GWQ+ T DS + RI NP +G
Sbjct: 364 VVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEG 423
Query: 416 KRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKN------DLSLNYPLPIVDHKKACHH 469
+FDP G ++R WLPEL+ +PT +IH P + + +L NYPLPIV +A
Sbjct: 424 YKFDPNGEYVRRWLPELSRLPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKAR 483
Query: 470 TLNQYYAAKK 479
+
Sbjct: 484 LHEALSQMWQ 493
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA
repair; HET: FAD; 2.80A {Sulfolobus tokodaii str}
Length = 440
Score = 255 bits (651), Expect = 2e-68
Identities = 140/473 (29%), Positives = 221/473 (46%), Gaps = 44/473 (9%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGI-SARQSHFIYASLLQVQ 69
+ R DLR+ DN L A D +VI VFIA P Q + S F+ SLL++
Sbjct: 4 IFIFRRDLRLEDNTGLNYALSECD-RVIPVFIADPRQLINNPYKSEFAVSFMINSLLELD 62
Query: 70 KSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH 129
L +KG F ++ + + + + + R +K+ + ++
Sbjct: 63 DELRKKGSRLNVF----FGEAEKVVSRFF-NKVDAIYVNEDYTPFSISRDEKIRKVCEEN 117
Query: 130 RVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVT 189
+ K+++D +L P +L ++ +T F + + V+ P
Sbjct: 118 GIEFKAYEDYLLTP------KSLFHHRNFTSFYNEVSKVKVRE-----PETMEGSFDVTD 166
Query: 190 PSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYL 249
S F + P+F G + L++L + + +RD PA +LSP+L
Sbjct: 167 SSMNVDFLLTFKKIESPLFRGGRREGLYLLHRNVDFR------RRDYPAENNNYRLSPHL 220
Query: 250 SIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIP 309
G +S R+ + + G ++ EL WR+F+ L + P V +
Sbjct: 221 KFGTISMREAYYT------------QKGKEEFVRELYWRDFFTLLAYYNPHVFG-HCYRR 267
Query: 310 WTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDW 369
+ I W + +AWK+G TG+PIIDA MR LN+ G+++ R+RM+ A FLVK L VDW
Sbjct: 268 EYDNISWENNESYFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKVLFVDW 327
Query: 370 RIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWL 429
R GE YF ++L+D D A NNG WQW ASTG D FR+FNP Q ++FDP+ FI+ W+
Sbjct: 328 RWGERYFATKLVDYDPAINNGNWQWIASTGVD--YMFRVFNPWKQQEKFDPEAKFIKEWV 385
Query: 430 PELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSL 482
EL +VP IH+ + YP PIV+ + ++ ++Y K L
Sbjct: 386 EELKDVPPSIIHSIYKTKVP-----GYPSPIVNWLERVNYVKSEYKNVKAVLL 433
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A
{Arabidopsis thaliana}
Length = 537
Score = 245 bits (626), Expect = 1e-65
Identities = 131/504 (25%), Positives = 202/504 (40%), Gaps = 41/504 (8%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG---------ISARQSHFI 61
L+W R LR+ DN AL A S+ + VF+ P + F+
Sbjct: 8 LIWFRKGLRVHDNPALEYASKGSE-FMYPVFVIDPHYMESDPSAFSPGSSRAGVNRIRFL 66
Query: 62 YASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDK 121
SL + SL + G + + E L + +V +L + + D
Sbjct: 67 LESLKDLDSSLKKLGSRLLVFKG----EPGEVLVRCLQEWKVKRLCFEYDTDPYYQALDV 122
Query: 122 LLEKRLQHRVICKSFDDSVLLPPGS--ILNHALQMYKVYTPFRKALIQNLVQADLRSLPV 179
++ + S L + I + + Y F K + +
Sbjct: 123 KVKDYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQSFLKVAGEPSCAKSELVMSY 182
Query: 180 PAIRLTGPVTPSNIPR-------FFDYPFQAIDPMFPIGEQNALHILRKFCK--EKVYYY 230
++ G + I + QA F GE AL L K V +
Sbjct: 183 SSLPPIGDIGNLGISEVPSLEELGYKDDEQADWTPFRGGESEALKRLTKSISDKAWVANF 242
Query: 231 VEQRDIPAI---QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIW 287
+ + P+ T+ +SPYL G LS R + L+ + D+ S L +L+W
Sbjct: 243 EKPKGDPSAFLKPATTVMSPYLKFGCLSSRYFYQCLQNIYKDVKKHTSP-PVSLLGQLLW 301
Query: 288 REFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIG 347
REF+ P ++I WN+D +L AW+ G TG+P IDA M QL G
Sbjct: 302 REFFYTTAFGTP-NFDKMKGNRICKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQLLKWG 360
Query: 348 WMHNRLRMITASFLVK-DLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYF 406
WMH+ R A FL + DL + W G + F L+D D A NNG W W + + +
Sbjct: 361 WMHHLARHCVACFLTRGDLFIHWEQGRDVFERLLIDSDWAINNGNWMWLSCSSFFY-QFN 419
Query: 407 RIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLD------KNDLSLNYPLPI 460
RI++P GK++DP G +IRH+LP L ++P QYI+ P + + +YP P+
Sbjct: 420 RIYSPISFGKKYDPDGKYIRHFLPVLKDMPKQYIYEPWTAPLSVQTKANCIVGKDYPKPM 479
Query: 461 VDHKKA---CHHTLNQYYAAKKQS 481
V H A C + + YA K+
Sbjct: 480 VLHDSASKECKRKMGEAYALNKKM 503
>2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding
protein, flavoprotein, nucleotide- binding, antenna
chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus}
SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A*
2j09_A*
Length = 420
Score = 229 bits (585), Expect = 8e-61
Identities = 128/469 (27%), Positives = 198/469 (42%), Gaps = 54/469 (11%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70
LVW R DLR+ D+ AL A V+ + + P + + R+ + ++ +++
Sbjct: 5 LVWHRGDLRLHDHPALLEALAR--GPVVGLVVLDPNNLKT---TPRRRAWFLENVRALRE 59
Query: 71 SLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHR 130
+ +G + ++ + + V L + Y R + H
Sbjct: 60 AYRARGGALWVLEGLPWEK-VPEAARRLKAKAVYALTSHTPYGRYRDGRVREALPVPLHL 118
Query: 131 VICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTP 190
+ + + Y+VYTPF +
Sbjct: 119 LPAPHL----------LPPDLPRAYRVYTPFSRLYRGAAPPLPPPEALPKGPEE------ 162
Query: 191 SNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLS 250
P+ GE+ AL LR F + K+ Y E+RD +G S+LSPY +
Sbjct: 163 -----GEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEERDRLDGEGGSRLSPYFA 217
Query: 251 IGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPW 310
+GVLSPR + + GA W+ EL+WR+F H + ++ +P P
Sbjct: 218 LGVLSPRLAAWEAERRGGE-------GARKWVAELLWRDFSYH-LLYHFPWMAERPLDPR 269
Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370
+ W +D L QAW +G TG P++DAAMR+L+ G++ NR RM A F VK LL+ W+
Sbjct: 270 FQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWK 329
Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430
EE F LLDGD A N GWQWA G D+ PYFR+FNP +QG+R DP+G +++ W P
Sbjct: 330 RCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAP 389
Query: 431 ELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKK 479
E + P+VD ++A L +
Sbjct: 390 EYPSYA-------------------PKDPVVDLEEARRRYLRLARDLAR 419
>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 = 56.1 bits (135), Expect = 2e-08
Identities = 92/560 (16%), Positives = 145/560 (25%), Gaps = 253/560 (45%)
Query: 50 QHGISARQSHFIYASLLQVQ--KSLSQK--GIVFQYHQCSNFDDSIE-WLD--SYCLQQ- 101
+H + + F AS LQ Q K L + G + E Y
Sbjct: 17 EHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTT----PAELVGKFLGYVSSLV 72
Query: 102 ---------RVTKLFYN---RQY----EINEV------RRDKLLEKRLQHRVI------C 133
+V L Y +I+ + D L K +I
Sbjct: 73 EPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKT--KELIKNYITAR 130
Query: 134 KSFDDSVLLPPGSIL------NHA------------------LQ-MYKVYTPFRKALIQN 168
S L +A L+ +Y+ Y LI+
Sbjct: 131 IMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIK- 189
Query: 169 LVQADLRSL---PVPAIR-----------LTGP-VTPSNIPRFFDYPFQAIDPM-FP-IG 211
L L + A + L P TP DY P+ P IG
Sbjct: 190 FSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK-----DYLLSI--PISCPLIG 242
Query: 212 EQNALHILRKFCKEKVYYYV----------EQRDIPAIQGT---SQLSPYLSIGV----- 253
+ + +Y V E R ++G SQ G+
Sbjct: 243 -------VIQLA----HYVVTAKLLGFTPGELRS--YLKGATGHSQ-------GLVTAVA 282
Query: 254 LSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFY---RHLMAFYPSVCMGKPFIPW 310
++ W E F + K A + L F+ R A YP+ +P
Sbjct: 283 IAETDSW----ESFFVSVRK----AITVL-------FFIGVRCYEA-YPNT-----SLP- 320
Query: 311 TEKIEWNKDSHLLQAWKQGYTGFP-----IIDAAMRQLNT-IGWMHNRL---RMITASFL 361
S L + + G P I + Q+ + ++ L + + S
Sbjct: 321 --------PSILEDSLENN-EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEIS-- 369
Query: 362 VKDLLVDWRIGEEYFM-----SQL--LDGDLASNNGGWQWAASTGNDS--VPY----FRI 408
LV+ G + + L L+ L A +G D +P+ +
Sbjct: 370 ----LVN---GAKNLVVSGPPQSLYGLNLTLRKAK------APSGLDQSRIPFSERKLKF 416
Query: 409 FNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAP-HS-WLD------KNDL-------- 452
N RF LP + +P HS L DL
Sbjct: 417 SN------RF----------LP---------VASPFHSHLLVPASDLINKDLVKNNVSFN 451
Query: 453 --SLNYPLPIVDHKKACHHT 470
+ P+ + T
Sbjct: 452 AKDIQIPV---------YDT 462
Score = 48.8 bits (116), Expect = 3e-06
Identities = 58/320 (18%), Positives = 98/320 (30%), Gaps = 150/320 (46%)
Query: 28 AACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQY----HQ 83
A H S V AV IA + W F + +K+++ ++F ++
Sbjct: 270 ATGH-SQGLVTAVAIAETDSW---------ESFFVSV----RKAIT---VLFFIGVRCYE 312
Query: 84 C--------SNFDDSI---EWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL----Q 128
S +DS+ E + S L I+ + +++ ++ +
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPMLS-------------ISNLTQEQ-VQDYVNKTNS 358
Query: 129 H----RVICKSF---DDSVLL--PPGSI--LNHALQMYKVYT-------PF--RKALIQN 168
H + + S ++++ PP S+ LN L+ K + PF RK N
Sbjct: 359 HLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN 418
Query: 169 -------------------LVQADL--RSLPVPAIRLTGPV----TPSN--------IPR 195
L+ DL ++ A + PV S+ R
Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER 478
Query: 196 FFDYPFQAI--DPM-------FPIGEQNALHILRKFCKEKVYYYVEQRDI-PAIQGTSQL 245
D I P+ F A HIL D P G S
Sbjct: 479 IVD----CIIRLPVKWETTTQFK-----ATHIL---------------DFGPG--GAS-- 510
Query: 246 SPYLSIGVLSPRQCWNRLKE 265
+GVL+ +R K+
Sbjct: 511 ----GLGVLT-----HRNKD 521
Score = 41.1 bits (96), Expect = 5e-04
Identities = 83/480 (17%), Positives = 136/480 (28%), Gaps = 219/480 (45%)
Query: 25 ALYAACHNSDAKVIAVFIATPEQWRQHGISA-----RQSHFIYASLLQ--VQKS------ 71
AL+ A +A+++A+F Q R + Y L+ ++ S
Sbjct: 144 ALFRAVGEGNAQLVAIFGG------QGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSE 197
Query: 72 LSQKGIVFQYHQCSNFDDSIEWLD--------SY-----------CLQQRVTKLFYNRQY 112
L + + + + +EWL+ Y + Q Y
Sbjct: 198 LIRTTLDAEKVFTQGL-NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA-------HY 249
Query: 113 EINEVRRDKLLEKRLQHRVICKSFDDSVL-LPPGSILNH---------------ALQMYK 156
V K +L PG + ++ A+
Sbjct: 250 -----------------VVTAK-----LLGFTPGELRSYLKGATGHSQGLVTAVAIAETD 287
Query: 157 VYTPF----RKAL-----I----QNLVQADLR-SLPVPAIRLT----GPVTPSNIPRFFD 198
+ F RKA+ I +A SLP P+I PS
Sbjct: 288 SWESFFVSVRKAITVLFFIGVRCY---EAYPNTSLP-PSILEDSLENNEGVPS------- 336
Query: 199 YPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQ--RDIPAIQGTSQLSPYLSIGVLSP 256
PM L I +E+V YV + +PA Q+ +S+ V
Sbjct: 337 -------PM--------LSI-SNLTQEQVQDYVNKTNSHLPA---GKQVE--ISL-VNGA 374
Query: 257 RQCWNRLKEEFV------DLL--------IKPKSGA------FSWLNELIWR--EF-YRH 293
+ V L K SG FS E R +F R
Sbjct: 375 KN--------LVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS---E---RKLKFSNR- 419
Query: 294 LMAFYPSVCMGKPF-----IPWTEKIEWNKD---SHLLQAWKQGYTGFPIID----AAMR 341
F P + PF +P ++ I KD +++ ++ P+ D + +R
Sbjct: 420 ---FLP---VASPFHSHLLVPASDLIN--KDLVKNNV--SFNAKDIQIPVYDTFDGSDLR 469
Query: 342 QL--NTIGWMHNRL-RMITASFLVKDLLVDWRIGEEYFMSQLLD---------GDLASNN 389
L + R+ I L V W ++ + +LD G L N
Sbjct: 470 VLSGSISE----RIVDCIIR------LPVKWETTTQFKATHILDFGPGGASGLGVLTHRN 519
>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 = 34.6 bits (78), Expect = 0.047
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 162 RKALIQNLVQADLR-----SLPVPAIRLT 185
++AL + L QA L+ S P AI+ T
Sbjct: 19 KQAL-KKL-QASLKLYADDSAPALAIKAT 45
>2bas_A YKUI protein; EAL domain, structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 2.61A {Bacillus subtilis} SCOP: c.1.33.1
d.110.6.2 PDB: 2w27_A*
Length = 431
Score = 28.9 bits (64), Expect = 2.6
Identities = 5/41 (12%), Positives = 14/41 (34%), Gaps = 3/41 (7%)
Query: 24 KALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI 61
++ A ++ I Q ++G Q +++
Sbjct: 217 YSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQGYYL 257
>3gfz_A Klebsiella pneumoniae BLRP1; TIM-barrel, EAL domain, BLUF domain,
hydrolase, signaling protein; HET: C2E FMN; 2.05A
{Klebsiella pneumoniae subsp} PDB: 3gfy_A* 3gfx_A*
3gg0_A* 3gg1_A* 2kb2_A*
Length = 413
Score = 28.4 bits (63), Expect = 3.5
Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 24 KALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI 61
++ C + V+A + T E+W + GI Q
Sbjct: 351 ASVVRCCEDLGITVVAEGVETLEEWCWLQSVGIRLFQGFLF 391
>2ov8_A STAL; sulfotransferase, structural genomics, montreal-kingston
bacterial structural genomics initiative, BSGI, unknown
function; 2.58A {Streptomyces toyocaensis} PDB: 2ovb_A
2ovf_A*
Length = 288
Score = 28.4 bits (62), Expect = 3.8
Identities = 17/149 (11%), Positives = 41/149 (27%), Gaps = 5/149 (3%)
Query: 274 PKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPF----IPWTEKIEWNKDSHLLQAWKQG 329
PK+G WL ++ + +P + G P + E + D +L A
Sbjct: 29 PKAGG-HWLRCMLTSYVTGEPVETWPGIQAGVPHLEGLLRDGEAPSADPDEQVLLATHFT 87
Query: 330 YTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNN 389
+ + + N + + +K + + + + S+
Sbjct: 88 ADRPVLRFYRESTAKVVCLIRNPRDAMLSLMRMKGIPPEDVEACRKIAETFIADEGFSSV 147
Query: 390 GGWQWAASTGNDSVPYFRIFNPTIQGKRF 418
W S + + + +
Sbjct: 148 RIWAGEGSWPENIRSWTDSVHESFPNAAV 176
>2r6o_A Putative diguanylate cyclase/phosphodiesterase (ggdef & EAL
domains); ggdef and EAL domains, structural genomics,
PSI-2; 1.80A {Thiobacillus denitrificans atcc 25259}
PDB: 3ii8_A*
Length = 294
Score = 28.1 bits (61), Expect = 4.8
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 11/74 (14%)
Query: 13 WLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI-------- 61
+ + A +V+A I T +Q+ R G Q + +
Sbjct: 212 IPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNLMSTPQAADA 271
Query: 62 YASLLQVQKSLSQK 75
+ASLL QK+ Q+
Sbjct: 272 FASLLDRQKASGQR 285
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 27.5 bits (60), Expect = 6.4
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 146 SILNHA------LQMYKVYTPFRKALIQN-LVQADLRSLPVPAIRLTG 186
SIL H+ +++ Y P +K +IQ +V+ DL P A + T
Sbjct: 897 SILEHSGIRLIEPELFNGYNPEKKEMIQEVIVEEDLE--PFEASKETA 942
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
0.324 0.138 0.444
Gapped
Lambda K H
0.267 0.0529 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 4,551,054
Number of extensions: 216635
Number of successful extensions: 975
Number of sequences better than 10.0: 1
Number of HSP's gapped: 913
Number of HSP's successfully gapped: 33
Length of query: 483
Length of database: 5,693,230
Length adjustment: 96
Effective length of query: 387
Effective length of database: 3,365,806
Effective search space: 1302566922
Effective search space used: 1302566922
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: 59 (27.0 bits)