RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6650
(156 letters)
>gnl|CDD|216167 pfam00875, DNA_photolyase, DNA photolyase. This domain binds a
light harvesting cofactor.
Length = 164
Score = 153 bits (389), Expect = 2e-48
Identities = 53/138 (38%), Positives = 75/138 (54%)
Query: 17 MVHWFRKGLRMHDNPSLREGLKGCTTFRCVFILDPWFAGSSNVGINKWRFLLQCLEDLDI 76
++ WFR+ LR+HDNP+L + VFILDP GS +G + FLL+ L DLD
Sbjct: 1 VLVWFRRDLRLHDNPALAAAAESGAPVIPVFILDPAQLGSHKLGAARRWFLLESLADLDE 60
Query: 77 NLRKLNSRLFVIRGQPADILPKLFKEWKTTCLTFEEDPEPFGKVRDQNIMTLCRELNIEV 136
+L KL RL V RG PA++LP+L KE + + + D EP+ + RD + RE IEV
Sbjct: 61 SLAKLGIRLVVRRGDPAEVLPELAKELGASAVYWNRDYEPYERQRDAAVKEALREAGIEV 120
Query: 137 IARVSHTLYDLDQLKPDS 154
+ H L ++
Sbjct: 121 HSFDDHLLVPPGEVLTKK 138
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 84.7 bits (210), Expect = 5e-20
Identities = 41/141 (29%), Positives = 65/141 (46%), Gaps = 3/141 (2%)
Query: 15 KHMVHWFRKGLRMHDNPSLREGLKGCTTFR-CVFILDPWFAGSSNVGINKWRFLLQCLED 73
++ WFR+ LR+ DN +L + VFILDP G FLLQ L+
Sbjct: 2 STVLVWFRRDLRLTDNAALAAACQSGQPVIIAVFILDPEQLGH--ASPRHAAFLLQSLQA 59
Query: 74 LDINLRKLNSRLFVIRGQPADILPKLFKEWKTTCLTFEEDPEPFGKVRDQNIMTLCRELN 133
L +L +L L V G P +LP+L K+ T + + D E + + RD + E+
Sbjct: 60 LQQSLAELGIPLLVREGDPEQVLPELAKQLAATTVFWNRDYEEWERQRDAALAQPLTEVG 119
Query: 134 IEVIARVSHTLYDLDQLKPDS 154
I V + L++ +++ S
Sbjct: 120 IAVHSFWDALLHEPGEVRTGS 140
>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 = 77.8 bits (192), Expect = 1e-17
Identities = 46/139 (33%), Positives = 67/139 (48%), Gaps = 6/139 (4%)
Query: 18 VHWFRKGLRMHDNPSLREGLKGCTTFRCVFILDP-WFAGSSNVGINKW-----RFLLQCL 71
++WFR LR+HDNP+L + T ++ DP F + G K +FLL+ L
Sbjct: 4 LYWFRNDLRVHDNPALYKASSSSDTLIPLYCFDPRQFKLTHFFGFPKTGPARGKFLLESL 63
Query: 72 EDLDINLRKLNSRLFVIRGQPADILPKLFKEWKTTCLTFEEDPEPFGKVRDQNIMTLCRE 131
+DL +LRKL S L V G+P D+LP+L KE + ++ K ++ +
Sbjct: 64 KDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEKSVERLLQQALAR 123
Query: 132 LNIEVIARVSHTLYDLDQL 150
L I V TLY D L
Sbjct: 124 LGIHVEQHWGSTLYHEDDL 142
>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 = 66.4 bits (162), Expect = 2e-13
Identities = 30/117 (25%), Positives = 60/117 (51%)
Query: 20 WFRKGLRMHDNPSLREGLKGCTTFRCVFILDPWFAGSSNVGINKWRFLLQCLEDLDINLR 79
W R+ LR+ DN L + +F LDP + ++ + +L+ CL++L +
Sbjct: 6 WHRRDLRLSDNIGLAAARQQSAKVVGLFCLDPNILQADDMAPARVAYLIGCLQELQQRYQ 65
Query: 80 KLNSRLFVIRGQPADILPKLFKEWKTTCLTFEEDPEPFGKVRDQNIMTLCRELNIEV 136
+ S+L +++G P ++P+L ++ + + D EP+G+ RD+ + +E I V
Sbjct: 66 QAGSQLLILQGDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAV 122
>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 = 43.3 bits (102), Expect = 2e-05
Identities = 38/131 (29%), Positives = 56/131 (42%), Gaps = 4/131 (3%)
Query: 18 VHWFRKGLRMHDNPSLREGLKGCTTFRCVFILDPWFAGSSNVG-INKWRFLLQCLEDLDI 76
+ WFR+ LR+ DNP+L + VF+ P G G +++W +L Q L LD
Sbjct: 1 IVWFRRDLRVEDNPALAAAARAGPVIP-VFVWAPEEEGQYYPGRVSRW-WLKQSLAHLDQ 58
Query: 77 NLRKLNSRLFVIRGQPA-DILPKLFKEWKTTCLTFEEDPEPFGKVRDQNIMTLCRELNIE 135
+LR L + L IR L + T L F +P VRD + I
Sbjct: 59 SLRSLGTCLVTIRSTDTVAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKEVLTAQGIS 118
Query: 136 VIARVSHTLYD 146
V + + LY+
Sbjct: 119 VQSFNADLLYE 129
>gnl|CDD|236734 PRK10674, PRK10674, deoxyribodipyrimidine photolyase;
Provisional.
Length = 472
Score = 28.4 bits (64), Expect = 1.7
Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 16 HMVHWFRKGLRMHDNPSL 33
H+V WFR LR+HDN +L
Sbjct: 4 HLV-WFRNDLRLHDNLAL 20
>gnl|CDD|153152 cd04880, ACT_AAAH-PDT-like, ACT domain of the nonheme
iron-dependent, aromatic amino acid hydroxylases
(AAAH). ACT domain of the nonheme iron-dependent,
aromatic amino acid hydroxylases (AAAH): Phenylalanine
hydroxylases (PAH), tyrosine hydroxylases (TH) and
tryptophan hydroxylases (TPH), both peripheral (TPH1)
and neuronal (TPH2) enzymes. This family of enzymes
shares a common catalytic mechanism, in which dioxygen
is used by an active site containing a single, reduced
iron atom to hydroxylate an unactivated aromatic
substrate, concomitant with a two-electron oxidation of
tetrahydropterin (BH4) cofactor to its quinonoid
dihydropterin form. Eukaryotic AAAHs have an N-terminal
ACT (regulatory) domain, a middle catalytic domain and
a C-terminal domain which is responsible for the
oligomeric state of the enzyme forming a domain-swapped
tetrameric coiled-coil. The PAH, TH, and TPH enzymes
contain highly conserved catalytic domains but distinct
N-terminal ACT domains and differ in their mechanisms
of regulation. One commonality is that all three
eukaryotic enzymes appear to be regulated, in part, by
the phosphorylation of serine residues N-terminal of
the ACT domain. Also included in this CD are the
C-terminal ACT domains of the bifunctional chorismate
mutase-prephenate dehydratase (CM-PDT) enzyme and the
prephenate dehydratase (PDT) enzyme found in plants,
fungi, bacteria, and archaea. The P-protein of
Escherichia coli (CM-PDT) catalyzes the conversion of
chorismate to prephenate and then the decarboxylation
and dehydration to form phenylpyruvate. These are the
first two steps in the biosynthesis of L-Phe and L-Tyr
via the shikimate pathway in microorganisms and plants.
The E. coli P-protein (CM-PDT) has three domains with
an N-terminal domain with chorismate mutase activity, a
middle domain with prephenate dehydratase activity, and
an ACT regulatory C-terminal domain. The prephenate
dehydratase enzyme has a PDT and ACT domain. The ACT
domain is essential to bring about the negative
allosteric regulation by L-Phe binding. L-Phe binds
with positive cooperativity; with this binding, there
is a shift in the protein to less active tetrameric and
higher oligomeric forms from a more active dimeric
form. Members of this CD belong to the superfamily of
ACT regulatory domains.
Length = 75
Score = 26.7 bits (60), Expect = 2.0
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 67 LLQCLEDLDINLRKLNSR 84
L+ + INL K+ SR
Sbjct: 16 ALKVFAERGINLTKIESR 33
>gnl|CDD|153177 cd04905, ACT_CM-PDT, C-terminal ACT domain of the bifunctional
chorismate mutase-prephenate dehydratase (CM-PDT)
enzyme and the prephenate dehydratase (PDT) enzyme.
The C-terminal ACT domain of the bifunctional
chorismate mutase-prephenate dehydratase (CM-PDT)
enzyme and the prephenate dehydratase (PDT) enzyme,
found in plants, fungi, bacteria, and archaea. The
P-protein of E. coli (CM-PDT, PheA) catalyzes the
conversion of chorismate to prephenate and then the
decarboxylation and dehydration to form phenylpyruvate.
These are the first two steps in the biosynthesis of
L-Phe and L-Tyr via the shikimate pathway in
microorganisms and plants. The E. coli P-protein
(CM-PDT) has three domains with an N-terminal domain
with chorismate mutase activity, a middle domain with
prephenate dehydratase activity, and an ACT regulatory
C-terminal domain. The prephenate dehydratase enzyme
has a PDT and ACT domain. The ACT domain is essential
to bring about the negative allosteric regulation by
L-Phe binding. L-Phe binds with positive cooperativity;
with this binding, there is a shift in the protein to
less active tetrameric and higher oligomeric forms from
a more active dimeric form. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 80
Score = 26.7 bits (60), Expect = 2.1
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 67 LLQCLEDLDINLRKLNSR 84
+L + INL K+ SR
Sbjct: 18 VLGVFAERGINLTKIESR 35
>gnl|CDD|179567 PRK03355, PRK03355, glycerol-3-phosphate acyltransferase;
Validated.
Length = 783
Score = 27.4 bits (61), Expect = 3.4
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 78 LRKLNSRLFVIRGQPADILPKLFKEWKTTCLTFEEDPEPFGK-VRDQNIMTLCR-ELNI 134
LR+ R V+ G+PA + +L + W+ T T E+ F + VR + + L R E I
Sbjct: 118 LRRDPRRARVLAGEPAK-VSELRQRWRDT--TVGENSRDFARFVRRRAALALERAERRI 173
>gnl|CDD|241366 cd13212, PH-GRAM_MTMR10-like, Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain. MTMR10,
MTMR11, and MTMR12 are catalytically inactive
phosphatases that play a role as an adapter for the
phosphatase myotubularin to regulate
myotubularintracellular location. They contains a Glu
residue instead of a conserved Cys residue in the
dsPTPase catalytic loop which renders it catalytically
inactive as a phosphatase. They contains an N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, an inactive PTP domain, a SET interaction
domain, and a C-terminal coiled-coil domain.
Myotubularin-related proteins are a subfamily of
protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs
5, 9-13) contain naturally occurring substitutions of
residues required for catalysis by PTP family enzymes.
Although these proteins are predicted to be
enzymatically inactive, they are thought to function as
antagonists of endogenous phosphatase activity or
interaction modules. Most MTMRs contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, a PTP domain (which may be active or inactive),
a SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is
part of a larger motif with a pleckstrin homology (PH)
domain fold.
Length = 110
Score = 26.3 bits (58), Expect = 4.2
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 40 CTTFRCVFILDPWFAGSSNVGINKWRFLLQCLEDLD 75
CT FR F D W N +++ F L + L+
Sbjct: 20 CTNFRVTFQPDGWQRLQKNPLSSEYDFALHNIGRLE 55
>gnl|CDD|190856 pfam04078, Rcd1, Cell differentiation family, Rcd1-like. Two of
the members in this family have been characterized as
being involved in regulation of Ste11 regulated sex
genes. Mammalian Rcd1 is a novel transcriptional
cofactor that mediates retinoic acid-induced cell
differentiation.
Length = 262
Score = 26.8 bits (60), Expect = 5.5
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 15 KHMVHWFRKGLRMHDNPSLREGLKGCTTFRCVFILDPWFAGSSNVGINKWRFLLQCLEDL 74
KH++ + LR+ DNP RE L+ C + D F+ R+LLQ L++L
Sbjct: 207 KHVIRCY---LRLSDNPRAREALRKCLPEE---LRDGTFSQLLKEDPATKRWLLQLLQNL 260
>gnl|CDD|188564 TIGR04049, AIR_rel_sll0787, AIR synthase-related protein, sll0787
family. Members of this family include sll0787 from
Synechocystis sp. PCC 6803 and resemble the C-terminal
region of MSMEG_0567 from Mycobacterium smegmatis,
where the N-terminal is a GNAT family
N-acetyltransferase. The conserved cluster is found
broadly (Cyanobacteria, Proteobacteria, Actinobacteria)
in about 8 percent of genomes and appears to be
biosynthetic. The product is unkown [Unknown function,
Enzymes of unknown specificity].
Length = 316
Score = 26.1 bits (58), Expect = 8.2
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 50 DPWFAGSSNVGIN 62
DPWFAG S V +N
Sbjct: 71 DPWFAGWSGVMVN 83
>gnl|CDD|173023 PRK14558, pyrH, uridylate kinase; Provisional.
Length = 231
Score = 25.8 bits (57), Expect = 8.8
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 97 PKLFKEW-KTTCLTFEEDPEPFGKVRDQNIMTLCRELNIEVI 137
PK F + K LTF E + KV D ++C++ I ++
Sbjct: 164 PKKFPDAKKIDHLTFSEAIKMGLKVMDTEAFSICKKYGITIL 205
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
0.323 0.140 0.451
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,148,892
Number of extensions: 734140
Number of successful extensions: 586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 20
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.9 bits)