RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9352
(146 letters)
>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 140 bits (355), Expect = 1e-43
Identities = 51/135 (37%), Positives = 74/135 (54%), Gaps = 6/135 (4%)
Query: 8 AVHWIRKGMRLHDNPALLSAINYKNEKGQNILLKPLYILDPHFRKFMRVGPNRWRFLQQS 67
+ W R+ +RLHDNPAL +A E G ++ P++ILDP ++G R FL +S
Sbjct: 1 VLVWFRRDLRLHDNPALAAAA----ESGAPVI--PVFILDPAQLGSHKLGAARRWFLLES 54
Query: 68 LADLDQKFRALGSRLYVVQGKPEEVFPDIFKTWNIKLLTWEYDIEPYAKKRDGLVEDMAK 127
LADLD+ LG RL V +G P EV P++ K + W D EPY ++RD V++ +
Sbjct: 55 LADLDESLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWNRDYEPYERQRDAAVKEALR 114
Query: 128 EYKVKVEQHVSHTLY 142
E ++V H L
Sbjct: 115 EAGIEVHSFDDHLLV 129
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 88.5 bits (220), Expect = 2e-21
Identities = 38/117 (32%), Positives = 59/117 (50%), Gaps = 9/117 (7%)
Query: 9 VHWIRKGMRLHDNPALLSAINYKNEKGQNILLKPLYILDPHFRKFMR-VGPNRWRFLQQS 67
+ W R+ +RL DN AL +A + GQ +++ ++ILDP + + P FL QS
Sbjct: 5 LVWFRRDLRLTDNAALAAAC----QSGQPVII-AVFILDP---EQLGHASPRHAAFLLQS 56
Query: 68 LADLDQKFRALGSRLYVVQGKPEEVFPDIFKTWNIKLLTWEYDIEPYAKKRDGLVED 124
L L Q LG L V +G PE+V P++ K + W D E + ++RD +
Sbjct: 57 LQALQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEWERQRDAALAQ 113
>gnl|CDD|234002 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 [Cellular
processes, Adaptations to atypical conditions,
Regulatory functions, DNA interactions].
Length = 429
Score = 86.3 bits (214), Expect = 1e-20
Identities = 50/140 (35%), Positives = 71/140 (50%), Gaps = 12/140 (8%)
Query: 9 VHWIRKGMRLHDNPALLSAINYKNEKGQNILLKPLYILDP------HFRKFMRVGPNRWR 62
++W R +R+HDNPAL A + + L PLY DP HF F + GP R +
Sbjct: 4 LYWFRNDLRVHDNPALYKASSSSDT------LIPLYCFDPRQFKLTHFFGFPKTGPARGK 57
Query: 63 FLQQSLADLDQKFRALGSRLYVVQGKPEEVFPDIFKTWNIKLLTWEYDIEPYAKKRDGLV 122
FL +SL DL R LGS L V GKPE+V P++ K ++ + ++ K + L+
Sbjct: 58 FLLESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEKSVERLL 117
Query: 123 EDMAKEYKVKVEQHVSHTLY 142
+ + VEQH TLY
Sbjct: 118 QQALARLGIHVEQHWGSTLY 137
>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 [DNA metabolism,
DNA replication, recombination, and repair].
Length = 471
Score = 79.9 bits (197), Expect = 2e-18
Identities = 38/126 (30%), Positives = 65/126 (51%), Gaps = 6/126 (4%)
Query: 11 WIRKGMRLHDNPALLSAINYKNEKGQNILLKPLYILDPHFRKFMRVGPNRWRFLQQSLAD 70
W R+ +RL DN L +A ++ ++ L+ LDP+ + + P R +L L +
Sbjct: 6 WHRRDLRLSDNIGLAAA----RQQSAKVV--GLFCLDPNILQADDMAPARVAYLIGCLQE 59
Query: 71 LDQKFRALGSRLYVVQGKPEEVFPDIFKTWNIKLLTWEYDIEPYAKKRDGLVEDMAKEYK 130
L Q+++ GS+L ++QG P ++ P + + K + W D+EPY +KRD V KE
Sbjct: 60 LQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAG 119
Query: 131 VKVEQH 136
+ V
Sbjct: 120 IAVVTL 125
>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 = 42.5 bits (100), Expect = 2e-05
Identities = 36/136 (26%), Positives = 63/136 (46%), Gaps = 10/136 (7%)
Query: 9 VHWIRKGMRLHDNPALLSAINYKNEKGQNILLKPLYILDPHFRKFMRVG-PNRWRFLQQS 67
+ W R+ +R+ DNPAL +A G I P+++ P G +RW +L+QS
Sbjct: 1 IVWFRRDLRVEDNPALAAAA----RAGPVI---PVFVWAPEEEGQYYPGRVSRW-WLKQS 52
Query: 68 LADLDQKFRALGSRLYVVQGKPE-EVFPDIFKTWNIKLLTWEYDIEPYAKKRDGLVEDMA 126
LA LDQ R+LG+ L ++ D ++ L + + +P + RD +++
Sbjct: 53 LAHLDQSLRSLGTCLVTIRSTDTVAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKEVL 112
Query: 127 KEYKVKVEQHVSHTLY 142
+ V+ + LY
Sbjct: 113 TAQGISVQSFNADLLY 128
>gnl|CDD|236734 PRK10674, PRK10674, deoxyribodipyrimidine photolyase;
Provisional.
Length = 472
Score = 29.2 bits (66), Expect = 0.69
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 5/76 (6%)
Query: 11 WIRKGMRLHDNPALLSAINYKNEKGQNILLKPLYILDPHFRKFMRVGPNRWRFLQQSLAD 70
W R +RLHDN AL +A ++ + + L+I P + P + F+ L
Sbjct: 7 WFRNDLRLHDNLALAAAC--RDPSARVL---ALFIATPAQWAAHDMAPRQAAFINAQLNA 61
Query: 71 LDQKFRALGSRLYVVQ 86
L G L +
Sbjct: 62 LQIALAEKGIPLLFHE 77
>gnl|CDD|236932 PRK11564, PRK11564, stationary phase inducible protein CsiE;
Provisional.
Length = 426
Score = 29.2 bits (66), Expect = 0.82
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 17/76 (22%)
Query: 7 CAVHWIRKGMRL-------HDNPALLSAINYKNEKGQNILLKPLYILDPHFRKFMRVGPN 59
C +HW+R+G+RL PAL K+E Q + + LY D + + + +
Sbjct: 86 CLLHWLRRGLRLCPSFITQQFTPAL------KSELKQRGIARNLYD-DTNLQALINLCS- 137
Query: 60 RWRFLQQSLADLDQKF 75
R L + + D++F
Sbjct: 138 --RRLNRQFEERDRQF 151
>gnl|CDD|235786 PRK06369, nac, nascent polypeptide-associated complex protein;
Reviewed.
Length = 115
Score = 27.1 bits (61), Expect = 2.1
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 73 QKFRALGSRLYVVQGKPEEVFPDIFKTWNIKLLTWEYDIEPYAKKRDGLVEDMAKE 128
A G + Y + G+PEEV + K I E DIE A ++ G+ E+ A++
Sbjct: 46 TVMDAQGQKTYQIVGEPEEVEKEAEKEVEIP----EEDIELVA-EQTGVSEEEARK 96
>gnl|CDD|235692 PRK06076, PRK06076, NADH:ubiquinone oxidoreductase subunit H;
Provisional.
Length = 322
Score = 27.5 bits (62), Expect = 2.8
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 2/20 (10%)
Query: 54 MRVGPNR--WRFLQQSLADL 71
+R GPNR L Q +AD
Sbjct: 43 LRYGPNRVGPFGLLQLVADG 62
>gnl|CDD|241151 cd12707, RRM_LARP4, RNA recognition motif in vertebrate
La-related protein 4 (LARP4). This subgroup
corresponds to the RRM of LARP4, a cytoplasmic factor
that can bind poly(A) RNA and interact with poly(A)
binding protein (PABP). It may play a role in promoting
translation by stabilizing mRNA. LARP4 is structurally
related to the La autoantigen. Like other La-related
proteins (LARPs) family members, LARP4 contains a La
motif (LAM) and an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 77
Score = 25.8 bits (56), Expect = 4.3
Identities = 13/31 (41%), Positives = 14/31 (45%)
Query: 59 NRWRFLQQSLADLDQKFRALGSRLYVVQGKP 89
N W QS D Q FR L + QGKP
Sbjct: 38 NNWYITFQSDTDAQQAFRYLREEVKTFQGKP 68
>gnl|CDD|152339 pfam11903, DUF3423, Protein of unknown function (DUF3423). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 73 to 118 amino acids in
length. This protein appears to be related to
ribbon-helix-helix DNA-binding domains, suggesting
these proteins may also bind DNA.
Length = 73
Score = 25.0 bits (55), Expect = 7.2
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 10 HWIRKGMRLHDNPAL 24
HW R G NP L
Sbjct: 31 HWARIGRLAELNPDL 45
>gnl|CDD|237524 PRK13826, PRK13826, Dtr system oriT relaxase; Provisional.
Length = 1102
Score = 26.3 bits (58), Expect = 7.2
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 60 RWRFLQ-QSLADLDQKFRALGSRLYVVQG 87
W Q Q LADL + RA+G RL + Q
Sbjct: 797 DWTLRQKQKLADLGARLRAIGERLGLAQS 825
>gnl|CDD|185623 PTZ00444, PTZ00444, hypothetical protein; Provisional.
Length = 184
Score = 25.9 bits (57), Expect = 7.9
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 97 FKTWNIKLLTWEYDIEPYAKKRDGLVEDMAKEYKVKVEQ 135
F N + + A+ + GL++D+AKE K+ E
Sbjct: 14 FSYINFSACLLPWTKKRKAENQMGLIKDIAKELKLASET 52
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.139 0.438
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,758,572
Number of extensions: 715052
Number of successful extensions: 692
Number of sequences better than 10.0: 1
Number of HSP's gapped: 686
Number of HSP's successfully gapped: 22
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.6 bits)