RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781170|ref|YP_003065583.1| deoxyribodipyrimidine
photolyase [Candidatus Liberibacter asiaticus str. psy62]
(483 letters)
>gnl|CDD|182638 PRK10674, PRK10674, deoxyribodipyrimidine photolyase; Provisional.
Length = 472
Score = 766 bits (1980), Expect = 0.0
Identities = 267/476 (56%), Positives = 345/476 (72%), Gaps = 5/476 (1%)
Query: 7 MSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLL 66
M+ HLVW RNDLR+ DN AL AAC + A+V+A+FIATP QW H ++ RQ+ FI A L
Sbjct: 1 MTTHLVWFRNDLRLHDNLALAAACRDPSARVLALFIATPAQWAAHDMAPRQAAFINAQLN 60
Query: 67 QVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKR 126
+Q +L++KGI +H+ +F S+EWL +C Q +VT LFYN QYE+NE +RD +E+
Sbjct: 61 ALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQQHQVTHLFYNYQYEVNERQRDAAVERA 120
Query: 127 LQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTG 186
L++ V+C+ FDDSVLLPPGS++ +MYKV+TPF+ A ++ L + D +P P +R +G
Sbjct: 121 LRN-VVCQGFDDSVLLPPGSVMTGNHEMYKVFTPFKNAFLKRLREGDPECVPAPKVRSSG 179
Query: 187 PVTPSNIPRFFDYPFQAIDP-MFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQL 245
+ P F +YP Q+ D +FP+GE+ A+ LR+FC++ Y +QRD PA+ GTS+L
Sbjct: 180 AIEPLPPIPF-NYPQQSFDTALFPVGEKAAIAQLRQFCQQGAGEYEQQRDFPAVDGTSRL 238
Query: 246 SPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGK 305
S YL+ GVLSPRQC +RL E L WLNELIWREFYRHLM YPS+C +
Sbjct: 239 SAYLATGVLSPRQCLHRLLAEQPQALDGGAGSV--WLNELIWREFYRHLMVAYPSLCKHR 296
Query: 306 PFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDL 365
PFI WT++++W + LQAW+QG TG+PI+DAAMRQLN+ GWMHNRLRMITASFLVKDL
Sbjct: 297 PFIAWTDRVQWQSNPAHLQAWQQGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDL 356
Query: 366 LVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFI 425
L+DWR GE YFMSQL+DGDLA+NNGGWQWAASTG D+ PYFRIFNPT QG+RFD G FI
Sbjct: 357 LIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGERFDRDGEFI 416
Query: 426 RHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQS 481
R WLPEL +VP + IH P W +K ++L+YP PIVDHK+A TL Y AA+K +
Sbjct: 417 RRWLPELRDVPGKAIHQPWRWAEKAGVTLDYPQPIVDHKQARLATLAAYEAARKGA 472
>gnl|CDD|132595 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo-lyase,
8-HDF type. This model describes a narrow clade of
cyanobacterial deoxyribodipyrimidine photo-lyase. This
group, in contrast to several closely related proteins,
uses a chromophore that, in other lineages is modified
further to become coenzyme F420. This chromophore is
called 8-HDF in most articles on the DNA photolyase and
FO in most literature on coenzyme F420.
Length = 471
Score = 316 bits (810), Expect = 1e-86
Identities = 169/474 (35%), Positives = 244/474 (51%), Gaps = 37/474 (7%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70
L W R DLR++DN L AA S AKV+ +F P + ++ + ++ L ++Q+
Sbjct: 4 LFWHRRDLRLSDNIGLAAARQQS-AKVVGLFCLDPNILQADDMAPARVAYLIGCLQELQQ 62
Query: 71 SLSQKG---IVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL 127
Q G ++ Q D ++ + Q +++N E +RD+ + L
Sbjct: 63 RYQQAGSQLLILQ-------GDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAAL 115
Query: 128 QHRVI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIR--- 183
+ I + D +L P IL + Y VYTPF K + + PV
Sbjct: 116 KEAGIAVVTLWDQLLHSPDEILTGSGNPYTVYTPFWKNW-----SSLPKPTPVATPTELE 170
Query: 184 --------LTGPVTPSNIPRFFDYPFQAIDPMFPI--GEQNALHILRKFCKEKVYYYVEQ 233
P+ +P D F D + GE A L +FC + Y EQ
Sbjct: 171 GLTEAELEAAAPLGVIALPTAKDLGFDW-DGDLILEPGETAAQARLEEFCDRAIADYQEQ 229
Query: 234 RDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAF-SWLNELIWREFYR 292
R+ PA+ GTSQLSP L GV+ R W +E + + + +W EL WREFY+
Sbjct: 230 RNFPALDGTSQLSPALKFGVIGIRTVWQATQEAHENSRSEEARNSIRTWQQELAWREFYQ 289
Query: 293 HLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNR 352
H + +P + G + W + QAW +G TG+PI+DAAMRQLN GWMHNR
Sbjct: 290 HALYHFPELADGPYRSLFQN-FPWENNEAHFQAWCEGRTGYPIVDAAMRQLNETGWMHNR 348
Query: 353 LRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPT 412
RMI ASFL KDL+++W+ GE+YFM +L+DGDLA+NNGGWQW+AS+G D P RIFNP
Sbjct: 349 CRMIVASFLTKDLIINWQWGEKYFMQKLIDGDLAANNGGWQWSASSGMDPKP-LRIFNPA 407
Query: 413 IQGKRFDPQGTFIRHWLPELNNVPTQY-IHAPHSWLDKNDLSLNYPLPIVDHKK 465
Q ++FDP+ +IR WLPEL +V T+ + + L++ ++ YPLPIVDH +
Sbjct: 408 SQAQKFDPEAEYIRRWLPELRSVDTKDLVTGKITPLERR--AVGYPLPIVDHNQ 459
>gnl|CDD|163007 TIGR02765, crypto_DASH, cryptochrome, DASH family. Photolyases and
cryptochromes are related flavoproteins. Photolyases
harness the energy of blue light to repair DNA damage by
removing pyrimidine dimers. Cryptochromes do not repair
DNA and are presumed to act instead in some other
(possibly unknown) process such as entraining circadian
rhythms. This model describes the cryptochrome DASH
subfamily, one of at least five major subfamilies, which
is found in plants, animals, marine bacteria, etc.
Members of this family bind both folate and FAD. They
may show weak photolyase activity in vitro but have not
been shown to affect DNA repair in vivo. Rather, DASH
family cryptochromes have been shown to bind RNA (Vibrio
cholerae VC1814), or DNA, and seem likely to act in
light-responsive regulatory processes.
Length = 429
Score = 220 bits (563), Expect = 6e-58
Identities = 136/455 (29%), Positives = 215/455 (47%), Gaps = 62/455 (13%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGI-------SARQSHFIYA 63
L W RNDLR+ DN ALY A +SD +I ++ P Q++ AR F+
Sbjct: 4 LYWFRNDLRVHDNPALYKASSSSD-TLIPLYCFDPRQFKLTHFFGFPKTGPARGK-FLLE 61
Query: 64 SLLQVQKSLSQKG---IVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRD 120
SL ++ SL + G +V + +D + L + V +F +++ E +
Sbjct: 62 SLKDLRTSLRKLGSDLLV----RSGKPEDVLPELIK---ELGVRTVFLHQEVGSEEKSVE 114
Query: 121 KLLEKRLQHRVICKSFDDSVLLPPGSILNHALQ-------MYKVYTPFRKAL-----IQN 168
+LL++ L I V GS L H + V+T FRK + I+
Sbjct: 115 RLLQQALARLGI------HVEQHWGSTLYHEDDLPFDLEDLPDVFTQFRKQVEAKCSIRP 168
Query: 169 LVQADLRSLPVPAIRLTGPV-TPSNIPRFFDYPFQAIDPMFPIGEQNAL-HILRKFCKEK 226
+ A + P+P++ G + T ++ + F GE L + F +
Sbjct: 169 PLPAPEKLPPLPSVDDPGWIPTLEDLG--EESSEVDRGLPFVGGETAGLARLKEYFWSKD 226
Query: 227 VYYYVEQRDIPAIQG---TSQLSPYLSIGVLSPRQCWNRLK---EEFVDLLIKPKSGAFS 280
+ Y E R+ + G +++ SP+L++G +SPRQ + L+ E +
Sbjct: 227 LKSYKETRN--GMLGPDYSTKFSPWLALGCVSPRQIYEELQRYETERGA-----NDSTYW 279
Query: 281 WLNELIWREFYRHLMAFYPSVCMGKPFI---PWTEKIEWNKDSHLLQAWKQGYTGFPIID 337
+ EL+WR+++R FY + F + +W+ D+ + WK G TG+P++D
Sbjct: 280 VIFELLWRDYFR----FYALKYGNRLFRFGGLRGKHPKWSFDAKRFEQWKTGTTGYPLVD 335
Query: 338 AAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAAS 397
A MR+LN G+M NR R ASFLVKDL +DWR G E+F +QL+D D+ SN G WQ+ A
Sbjct: 336 ANMRELNATGFMSNRGRQNVASFLVKDLGLDWRYGAEWFETQLVDYDVCSNWGNWQYLAG 395
Query: 398 TGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPEL 432
GND R FN Q + +DP G ++ W+PEL
Sbjct: 396 VGNDPRG-SRQFNIEKQAQDYDPDGEYVATWVPEL 429
>gnl|CDD|131813 TIGR02766, crypt_chrom_pln, cryptochrome, plant family. At least
five major families of cryptochomes and photolyases
share FAD cofactor binding, sequence homology, and the
ability to react to short wavelengths of visible light.
Photolysases are responsible for light-dependent DNA
repair by removal of two types of uv-induced DNA
dimerizations. Cryptochromes have other functions, often
regulatory and often largely unknown, which may include
circadian clock entrainment and control of development.
Members of this subfamily are known so far only in
plants; they may show some photolyase activity in vitro
but appear mostly to be regulatory proteins that respond
to blue light.
Length = 475
Score = 209 bits (534), Expect = 1e-54
Identities = 141/478 (29%), Positives = 220/478 (46%), Gaps = 42/478 (8%)
Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70
+VW R DLR+ DN AL AA VI VF+ PE+ Q+ ++ SL + +
Sbjct: 1 IVWFRRDLRVEDNPALAAAAR--AGPVIPVFVWAPEEEGQYYPGRVSRWWLKQSLAHLDQ 58
Query: 71 SLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYE-INEVRRDKLLEKRLQH 129
SL G + + D++ L T+LF+N Y+ ++ VR + E
Sbjct: 59 SLRSLGTCLVTIRST---DTVAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKEVLTAQ 115
Query: 130 RVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTG--- 186
+ +SF+ +L P + + + + ++ F + + + LP I
Sbjct: 116 GISVQSFNADLLYEPWEVYDELGRPFTMFAAFWERCLSMPYDPESPLLPPKKIISGDVSK 175
Query: 187 -PVTPSNIPRFFDYPFQAI-DPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQ 244
+ A+ + G NA L +F + Y + R TS
Sbjct: 176 CSADDLGFEDDSEKGSNALLARAWSPGWSNADKALTEFINGPLLEYSKNRKKADSATTSL 235
Query: 245 LSPYLSIGVLSPRQCW--------------NRLKEEFVDLLIKPKSGAFSWLNELIWREF 290
LSPYL G +S R+ + N EE V+L ++ + RE+
Sbjct: 236 LSPYLHFGEVSVRKVFHLVRMKQIAWANEGNSAGEESVNLFLR----------SIGLREY 285
Query: 291 YRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMH 350
R++ +P KP + + W D + +AW+QG TG+P++DA MR+L GW+H
Sbjct: 286 SRYISFNHP-FSHEKPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLH 344
Query: 351 NRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFN 410
+R+R++ +SF VK L + WR G +YF LLD DL S+ GWQ+ + + D RI N
Sbjct: 345 DRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYISGSLPDGRELDRIDN 404
Query: 411 PTIQGKRFDPQGTFIRHWLPELNNVPTQYIH----APHSWLDKN--DLSLNYPLPIVD 462
P ++G +FDP G ++R WLPEL +PT++IH AP S L +L NYPLPIV
Sbjct: 405 PQLEGYKFDPNGEYVRRWLPELARLPTEWIHHPWDAPESVLQAAGVELGSNYPLPIVG 462
>gnl|CDD|129679 TIGR00591, phr2, photolyase PhrII. All proteins in this family for
which functions are known are DNA-photolyases used for
the direct repair of UV irradiation induced DNA damage.
Some repair 6-4 photoproducts while others repair
cyclobutane pyrimidine dimers. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 454
Score = 33.6 bits (77), Expect = 0.12
Identities = 38/155 (24%), Positives = 64/155 (41%), Gaps = 17/155 (10%)
Query: 211 GEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDL 270
G L +L F ++++ ++ +R+ P S LSP+L G LS ++ +
Sbjct: 225 GTTAGLIMLESFIEKRLCFFRTRRNDPNNDALSMLSPWLHFGQLSAQRA---ARAVERAR 281
Query: 271 LIKPKSGAFSWLNELIWRE----FYRHLMAFYPSVCMGKPFIPWTEKI--EWNKDS---- 320
+S F + EL+ R + +Y S+C W + KD
Sbjct: 282 GNAGESVEF-FEEELVVRRELADNFCFYNPYYDSLCGAY---WWARTTLDDHAKDKREHL 337
Query: 321 HLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRM 355
+ L+ ++ T + +AA QL T G MH LRM
Sbjct: 338 YSLEQLEKSTTHDYLWNAAQEQLVTEGKMHGFLRM 372
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 30.4 bits (69), Expect = 1.1
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 113 EINEVRRDKLLEKRLQHRVICKSFDDS 139
E+N+ RR++L EKR + R + FD++
Sbjct: 620 ELNDERRERLAEKRERKRELEAEFDEA 646
>gnl|CDD|128716 smart00439, BAH, Bromo adjacent homology domain.
Length = 120
Score = 30.3 bits (69), Expect = 1.2
Identities = 20/77 (25%), Positives = 26/77 (33%), Gaps = 8/77 (10%)
Query: 211 GEQNALHILRKFCKEKVYYYVEQRDIPA--IQGT---SQLSPYLSIGVLSPRQCWNRLKE 265
E+ L F K +V+ E +P I G S Y L P
Sbjct: 46 PEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKCNVLSKSDYPG---LRPEGKIGEPDV 102
Query: 266 EFVDLLIKPKSGAFSWL 282
F + L P+ GAF L
Sbjct: 103 FFCESLYDPEKGAFKKL 119
>gnl|CDD|184766 PRK14610, PRK14610, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 283
Score = 28.9 bits (65), Expect = 3.2
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 70 KSLSQKGIVFQYHQCSNFDDSIEWLD 95
K LS + VF ++C F + I+ L
Sbjct: 173 KFLSTRK-VFNKYECKAFSEPIDNLP 197
>gnl|CDD|162451 TIGR01622, SF-CC1, splicing factor, CC1-like family. A homologous
gene from Plasmodium falciparum was identified in the
course of the analysis of that genome at TIGR and was
included in the model.
Length = 457
Score = 28.3 bits (63), Expect = 4.3
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 330 YTGFPIIDAAMRQLNTIGWMHNRL---RMITASFLVKDL 365
Y F +DAA L ++ R +MITA+F+V D+
Sbjct: 414 YLKFSSVDAA---LAAFQALNGRYFGGKMITAAFVVNDV 449
>gnl|CDD|182935 PRK11059, PRK11059, regulatory protein CsrD; Provisional.
Length = 640
Score = 27.5 bits (62), Expect = 7.3
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 26 LYAACHNSDAKVIAVFIATPEQWR---QHGISARQSHFIYAS 64
L AC ++ +V A + + E+W+ + G+S Q F S
Sbjct: 595 LVGACAGTETQVFATGVESREEWQTLQELGVSGGQGDFFAES 636
>gnl|CDD|178995 PRK00389, gcvT, glycine cleavage system aminomethyltransferase T;
Reviewed.
Length = 359
Score = 27.0 bits (61), Expect = 9.8
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 16 NDL-RITDNKALYAACHNSDAKVI 38
ND+ ++ KA Y N D VI
Sbjct: 72 NDVSKLKPGKAQYTCMLNEDGGVI 95
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.324 0.138 0.444
Gapped
Lambda K H
0.267 0.0624 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 8,289,346
Number of extensions: 545001
Number of successful extensions: 1236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1218
Number of HSP's successfully gapped: 20
Length of query: 483
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 386
Effective length of database: 3,898,497
Effective search space: 1504819842
Effective search space used: 1504819842
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 (26.7 bits)