RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6305
(52 letters)
>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 55.3 bits (134), Expect = 9e-12
Identities = 18/34 (52%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 13 AVHWFRHGLRLHDNPALFEASLNSV-LYPVFIFD 45
+ WFR LRLHDNPAL A+ + + PVFI D
Sbjct: 1 VLVWFRRDLRLHDNPALAAAAESGAPVIPVFILD 34
>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 = 41.2 bits (97), Expect = 3e-06
Identities = 18/35 (51%), Positives = 27/35 (77%), Gaps = 1/35 (2%)
Query: 12 VAVHWFRHGLRLHDNPALFEAS-LNSVLYPVFIFD 45
V ++WFR+ LR+HDNPAL++AS + L P++ FD
Sbjct: 2 VVLYWFRNDLRVHDNPALYKASSSSDTLIPLYCFD 36
>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 = 37.5 bits (87), Expect = 7e-05
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 14 VHWFRHGLRLHDNPALFEASLNSVLYPVFIFDGETAGLF 52
+ WFR LR+ DNPAL A+ + PVF++ E G +
Sbjct: 1 IVWFRRDLRVEDNPALAAAARAGPVIPVFVWAPEEEGQY 39
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 37.3 bits (87), Expect = 8e-05
Identities = 18/37 (48%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 14 VHWFRHGLRLHDNPALFEA--SLNSVLYPVFIFDGET 48
+ WFR LRL DN AL A S V+ VFI D E
Sbjct: 5 LVWFRRDLRLTDNAALAAACQSGQPVIIAVFILDPEQ 41
>gnl|CDD|236734 PRK10674, PRK10674, deoxyribodipyrimidine photolyase;
Provisional.
Length = 472
Score = 34.2 bits (79), Expect = 9e-04
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 16 WFRHGLRLHDNPALFEA 32
WFR+ LRLHDN AL A
Sbjct: 7 WFRNDLRLHDNLALAAA 23
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving
DNA bubble structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this
group also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 26.0 bits (58), Expect = 0.83
Identities = 7/13 (53%), Positives = 8/13 (61%)
Query: 39 YPVFIFDGETAGL 51
PVF+FDG L
Sbjct: 71 KPVFVFDGGAPEL 83
>gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA;
Provisional.
Length = 196
Score = 25.3 bits (55), Expect = 1.2
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 21 LRLHDNPALFEASLNS 36
L +HD+PAL E +LN+
Sbjct: 78 LSVHDSPALVEQALNA 93
>gnl|CDD|192517 pfam10290, DUF2403, Glycine-rich protein domain (DUF2403). This
domain is found in the N-terminal region of members of
DUF2401 pfam10287. The function of this glycine-rich
region is unknown.
Length = 65
Score = 24.2 bits (53), Expect = 1.9
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 4 PNSPNNKEVAVHWFRHGLRLHD 25
+P N+E++VH FR L L
Sbjct: 38 ALAPLNEELSVH-FRGPLELKQ 58
>gnl|CDD|219580 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 24.5 bits (54), Expect = 2.3
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 18 RHGLRLHDNPALFEASLNSVL 38
R RL D+ LF+ +L +V+
Sbjct: 705 RGRARLLDDGLLFDRALEAVI 725
>gnl|CDD|203028 pfam04494, TFIID_90kDa, WD40 associated region in TFIID subunit.
This region, possibly a domain is found in subunits of
transcription factor TFIID. The function of this region
is unknown.
Length = 141
Score = 24.1 bits (53), Expect = 3.1
Identities = 6/21 (28%), Positives = 15/21 (71%)
Query: 23 LHDNPALFEASLNSVLYPVFI 43
+ D+ +++ L+ +LYP+F+
Sbjct: 25 IEDSLDIYKPELSRLLYPLFV 45
>gnl|CDD|220557 pfam10086, DUF2324, Putative membrane peptidase family (DUF2324).
This domain, found in various hypothetical bacterial
proteins, has no known function. This family appears to
be related to the prenyl protease 2 family pfam02517,
suggesting this family may be peptidases.
Length = 222
Score = 24.2 bits (53), Expect = 3.6
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 19 HGLRLHDNPALFEASLNSVLYPVFIFDGETAGLF 52
H L N A+ + +LY ++ TAG+F
Sbjct: 43 HLYLLQQNADGLIATSHPLLY--ALYGALTAGIF 74
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 0.447
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,660,214
Number of extensions: 168179
Number of successful extensions: 196
Number of sequences better than 10.0: 1
Number of HSP's gapped: 195
Number of HSP's successfully gapped: 11
Length of query: 52
Length of database: 10,937,602
Length adjustment: 24
Effective length of query: 28
Effective length of database: 9,873,106
Effective search space: 276446968
Effective search space used: 276446968
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: 53 (24.2 bits)