RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11729
(281 letters)
>gnl|CDD|187726 cd00540, AAG, Alkyladenine DNA glycosylase catalyzes the first step
in base excision repair. Alkyladenine DNA glycosylase
(AAG), also known as 3-methyladenine DNA glycosylase,
catalyzes the first step in base excision repair (BER)
by cleaving damaged DNA bases within double-stranded DNA
to produce an abasic site. AAG bends DNA by
intercalating between the base pairs, causing the
damaged base to flip out of the double helix and into
the enzyme active site for cleavage. Although AAG
represents one of six DNA glycosylase classes, it lacks
the helix-hairpin-helix active site motif associated
with other BER glycosylases and is structurally distinct
from them.
Length = 187
Score = 243 bits (622), Expect = 2e-81
Identities = 92/249 (36%), Positives = 119/249 (47%), Gaps = 64/249 (25%)
Query: 22 FFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPM 81
FFD+ +++A LLGK LVRRL G +L G+IVETE+YLG +D ASH+Y R T R E M
Sbjct: 1 FFDRDALEVARELLGKVLVRRLP-GGVLSGRIVETEAYLGPDDPASHAYRGRTT-RREAM 58
Query: 82 YMKPGTIYVYFTYGMYHCFNLSSQESG--GAVLIRSLEPVHGLDIMNRLRNQFNENQNKS 139
+ PGT YVY YGM+HC N+ + G AVLIR+LEP+ GLD+M R R +
Sbjct: 59 FGPPGTAYVYLIYGMHHCLNVVTGPEGEPAAVLIRALEPLEGLDLMRRRRGK-------- 110
Query: 140 KRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNKKSKLQDRDLCNGP 199
KR L N GP
Sbjct: 111 KRGRELTN--------------------------------------------------GP 120
Query: 200 SKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKAKLLRF 259
KLC ++ I LN + + +W++D IV + RIGI D+A E K RF
Sbjct: 121 GKLCQALGIDKS-LNGLDLTDPSGLWIEDGGERPPEEIVATPRIGI-DYAGEAADKPWRF 178
Query: 260 YILGNKCVS 268
Y+ GN VS
Sbjct: 179 YVKGNPFVS 187
>gnl|CDD|216945 pfam02245, Pur_DNA_glyco, Methylpurine-DNA glycosylase (MPG).
Methylpurine-DNA glycosylase is a base excision-repair
protein. It is responsible for the hydrolysis of the
deoxyribose N-glycosidic bond, excising 3-methyladenine
and 3-methylguanine from damaged DNA.
Length = 185
Score = 207 bits (529), Expect = 2e-67
Identities = 87/249 (34%), Positives = 112/249 (44%), Gaps = 67/249 (26%)
Query: 20 QAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNE 79
+ FF + +++A LLGK LVRRL GTL G+IVETE+YLG +D ASH+Y R TPRN
Sbjct: 2 REFFARDTLEVARDLLGKVLVRRLPGGTL-SGRIVETEAYLGPDDPASHAYRGR-TPRNA 59
Query: 80 PMYMKPGTIYVYFTYGMYHCFNLSSQESG--GAVLIRSLEPVHGLDIMNRLRNQFNENQN 137
M+ PG YVY YGM+HC N+ ++ G AVLIR++EP+ GLD+M R R
Sbjct: 60 VMFGPPGHAYVYLIYGMHHCLNVVTEPEGVPAAVLIRAIEPLEGLDLMRRRRG------G 113
Query: 138 KSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNKKSKLQDRDLCN 197
K +R+ L N P K LC
Sbjct: 114 KRERD--LT--------------NGPGK-----------------------------LC- 127
Query: 198 GPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKAKLL 257
L I N R + +W++D IV + RIGI E
Sbjct: 128 --QALGIDRS-----HNGRDLTGPPPLWLEDDGVPPE-EIVTTPRIGIS---GEAADLPW 176
Query: 258 RFYILGNKC 266
RFYI GN
Sbjct: 177 RFYIAGNPF 185
>gnl|CDD|129658 TIGR00567, 3mg, DNA-3-methyladenine glycosylase (3mg). This
families are based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University). All
proteins in this family for which the function is known
are involved in the base excision repair of alkylation
damage to DNA. The exact specificty of the type of
alkylation damage repaired by each of these varies
somewhat between species. Substrates include 3-methyl
adenine, 7-methyl-guanaine, and 3-methyl-guanine [DNA
metabolism, DNA replication, recombination, and repair].
Length = 192
Score = 184 bits (469), Expect = 2e-58
Identities = 84/254 (33%), Positives = 120/254 (47%), Gaps = 65/254 (25%)
Query: 18 LDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPR 77
+ FF Q + LA LLG+ LVRRL GT + G+IVETE+Y+G ED A+HS R+TPR
Sbjct: 1 MPPEFFQQDAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMGPEDSAAHSRGGRQTPR 60
Query: 78 NEPMYMKPGTIYVYFTYGMYHCFNLSSQESGG--AVLIRSLEPVHGLDIMNRLRNQFNEN 135
M+ PG +YVY YGM++ N+ + G AVLIR+LE
Sbjct: 61 TRGMFGPPGRLYVYIIYGMHYMLNVVAAPEGVPAAVLIRALE------------------ 102
Query: 136 QNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNKKSKLQDRDL 195
P + +L++ ++ S L+DR+L
Sbjct: 103 ---------------------------PLEGLELMRERRGRS------------LKDREL 123
Query: 196 CNGPSKLCISMDITIEYLNKRHICESEEMWVQD-LDCESNITIVESSRIGIGDFAKEWKA 254
NGP KLC ++ IT+ + N R + + +W++ S R+GI D+A EW
Sbjct: 124 TNGPGKLCQALGITMSF-NGRDLIQPSALWLERGPLEHSAPA---GPRVGI-DYAGEWDI 178
Query: 255 KLLRFYILGNKCVS 268
K RFY+ GN VS
Sbjct: 179 KPWRFYVTGNPWVS 192
>gnl|CDD|234840 PRK00802, PRK00802, 3-methyladenine DNA glycosylase; Reviewed.
Length = 188
Score = 176 bits (448), Expect = 4e-55
Identities = 79/253 (31%), Positives = 108/253 (42%), Gaps = 71/253 (28%)
Query: 18 LDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPR 77
L + FF + +++A LLGK LV G+IVETE+Y+G +D ASHSY R TPR
Sbjct: 5 LPREFFARDALEVARDLLGKVLVHEGGVS----GRIVETEAYIGADDPASHSYRGR-TPR 59
Query: 78 NEPMYMKPGTIYVYFTYGMYHCFNLSSQESG--GAVLIRSLEPVHGLDIMNRLRNQFNEN 135
E M+ PG YVYF YGM+HC N+ G AVLIR+LEP+ G+ +M R R
Sbjct: 60 TEVMFGPPGHAYVYFIYGMHHCLNVVCGPEGTGAAVLIRALEPLEGIALMRRRRG----- 114
Query: 136 QNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNKKSKLQDRDL 195
K N N P K L
Sbjct: 115 -GKRPEKNLC---------------NGPGK-----------------------------L 129
Query: 196 CNGPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKAK 255
C L I++ N + ++ ++++D IV RIGI A++
Sbjct: 130 C---KALGITLA-----DNGADLFDASPLYIEDGKEPPE--IVAGPRIGI-SKARD---L 175
Query: 256 LLRFYILGNKCVS 268
RF+I G+ VS
Sbjct: 176 PWRFWIPGSPFVS 188
>gnl|CDD|225005 COG2094, Mpg, 3-methyladenine DNA glycosylase [DNA replication,
recombination, and repair].
Length = 200
Score = 165 bits (420), Expect = 7e-51
Identities = 81/265 (30%), Positives = 114/265 (43%), Gaps = 68/265 (25%)
Query: 14 QANCLDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNR 73
+ L ++FF + + +A LLGK LVRR+ G G+IVETE+YLG +D A H+Y R
Sbjct: 2 KLMPLPRSFFARDTLVVARELLGKTLVRRIG-GLTTSGRIVETEAYLGPDDPACHAYRGR 60
Query: 74 RTPRNEPMYMKPGTIYVYFTYGMYHCFNLSSQESG--GAVLIRSLEPVHGLDIMNRLRNQ 131
T RN M+ PG YVY YGM++C N+ + G AVLIR++EP G++ M + R
Sbjct: 61 -TKRNRAMFGPPGHAYVYRIYGMHYCLNVVTGPEGIPAAVLIRAIEPEEGIEPMRQRRGV 119
Query: 132 FNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNKKSKLQ 191
+ L N
Sbjct: 120 --------RVLRLLTN-------------------------------------------- 127
Query: 192 DRDLCNGPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKE 251
GP KLC ++ IT E I SE +W++ ++ I +RIGI A +
Sbjct: 128 ------GPGKLCKALGITREDNGADLINPSEPLWLELG--KTPFAISAGARIGI-SKATD 178
Query: 252 WKAKLLRFYILGNKCVSKTDKKMES 276
K RFYI GN VS+ +
Sbjct: 179 ---KPWRFYITGNPFVSRRRRSQRG 200
>gnl|CDD|215248 PLN02451, PLN02451, homoserine kinase.
Length = 370
Score = 32.1 bits (73), Expect = 0.31
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 97 YHCFNLSSQESGGAVLIRSLEPVH 120
YH N++ GG VLIRS EP+H
Sbjct: 190 YHADNIAPALMGGFVLIRSYEPLH 213
>gnl|CDD|240339 PTZ00265, PTZ00265, multidrug resistance protein (mdr1);
Provisional.
Length = 1466
Score = 30.0 bits (67), Expect = 1.5
Identities = 28/116 (24%), Positives = 44/116 (37%), Gaps = 15/116 (12%)
Query: 100 FNLSSQESGGAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEE------ 153
F LS++E G V + + D N+ N N + + NN+ N NN
Sbjct: 650 FVLSNRERGSTVDVDIIGEDPTKD--NKENNNKNNKDDNNNNNNNNNNKINNAGSYIIEQ 707
Query: 154 -THSQSNRNSPA------KKQKLIKSKQTLSSNDWDQPNKKSKLQDRDLCNGPSKL 202
TH +N QK+ K + + ND D K S +D + P ++
Sbjct: 708 GTHDALMKNKNGIYYTMINNQKVSSKKSSNNDNDKDSDMKSSAYKDSERGYDPDEM 763
>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein. Rotavirus particles
consist of three concentric proteinaceous capsid layers.
The innermost capsid (core) is made of VP2. The genomic
RNA and the two minor proteins VP1 and VP3 are
encapsidated within this layer. The N-terminus of
rotavirus VP2 is necessary for the encapsidation of VP1
and VP3.
Length = 887
Score = 29.9 bits (67), Expect = 1.6
Identities = 11/57 (19%), Positives = 29/57 (50%)
Query: 136 QNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQPNKKSKLQD 192
+N+ + N + + ++ Q +N K+K++ K+ + +++ D P K+ Q+
Sbjct: 4 RNRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQE 60
>gnl|CDD|115805 pfam07175, Osteoregulin, Osteoregulin. This family represents a
conserved region approximately 180 residues long within
osteoregulin, a bone-remodelling protein expressed
highly in osteocytes within trabecular and cortical
bone. A conserved RGD motif is found towards the
C-terminal end of this region, and this is potentially
involved in integrin recognition.
Length = 163
Score = 28.8 bits (64), Expect = 2.2
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 102 LSSQESGGAVLIRSL-EPVHGLDIMNRLRNQFNENQNKSKRN--NHLPNSQNNEETHSQS 158
L QE GA L+R++ +PV L L + EN+ K+ ++ + +P N + HS+
Sbjct: 43 LHDQERYGAALLRNITQPVKSLVTGIELLGE--ENKEKTPQSVLSVIPADVNYAKAHSKD 100
Query: 159 NRNSPAKKQ---KLIKSKQT 175
+N +KSK T
Sbjct: 101 KKNQQRDLLAQKSPVKSKHT 120
>gnl|CDD|220976 pfam11091, T4_tail_cap, Tail-tube assembly protein. This tail tube
protein is also referred to as Gp48. It is required for
the assembly and length regulation of the tail tube of
bacteriophage T4.
Length = 348
Score = 28.7 bits (64), Expect = 3.8
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 59 YLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTYGMYHCFNLSSQESGGAVLIRSL 116
Y G ++R + ++ + TPR+ + IY F Y LS +GG+ L
Sbjct: 187 YKGADNR-TKTFTWQLTPRSLEDLKEIIKIYETFLY-------LSYGSTGGSTTANEL 236
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 28.8 bits (64), Expect = 4.1
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 124 IMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSNDWDQ 183
I++R N N + + +NHL +++ + S SP KKQ K +N +++
Sbjct: 315 IIHRNNGSSNSNNDDTSSSNHLGSNRISNRNPS-----SPYKKQTTTKHTNNTKNNKYNK 369
Query: 184 PNKKSK 189
K
Sbjct: 370 TKTTQK 375
>gnl|CDD|173635 cd05054, PTKc_VEGFR, Catalytic domain of the Protein Tyrosine
Kinases, Vascular Endothelial Growth Factor Receptors.
Protein Tyrosine Kinase (PTK) family; Vascular
Endothelial Growth Factor Receptor (VEGFR) subfamily;
catalytic (c) domain. The VEGFR subfamily consists of
VEGFR1 (Flt1), VEGFR2 (Flk1), VEGFR3 (Flt4), and similar
proteins. The PTKc family is part of a larger
superfamily that includes the catalytic domains of other
kinases such as protein serine/threonine kinases, RIO
kinases, and phosphoinositide 3-kinase (PI3K). PTKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to tyrosine (tyr) residues in protein substrates.
VEGFR subfamily members are receptor tyr kinases (RTKs)
containing an extracellular ligand-binding region with
seven immunoglobulin (Ig)-like domains, a transmembrane
segment, and an intracellular catalytic domain. In
VEGFR3, the fifth Ig-like domain is replaced by a
disulfide bridge. The binding of VEGFRs to their
ligands, the VEGFs, leads to receptor dimerization,
activation, and intracellular signaling. There are five
VEGF ligands in mammals, which bind, in an overlapping
pattern to the three VEGFRs, which can form homo or
heterodimers. VEGFRs regulate the cardiovascular system.
They are critical for vascular development during
embryogenesis and blood vessel formation in adults. They
induce cellular functions common to other growth factor
receptors such as cell migration, survival, and
proliferation. VEGFR1 binds VEGFA, VEGFB, and placenta
growth factor (PLGF). It regulates monocyte and
macrophage migration, vascular permeability,
haematopoiesis, and the recruitment of haematopietic
progenitor cells from the bone marrow.
Length = 337
Score = 28.3 bits (63), Expect = 4.5
Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 138 KSKRNNHLPNSQNNEETHSQSNRNSPAKKQKL--IKSKQTLSSNDWDQPNKKSKLQDRDL 195
+SKR P N+ T + + KKQ+L + S Q+ +S+ + + S +++ +
Sbjct: 104 RSKRECFSPY--RNKSTRKREMKQKEGKKQRLDSVSSSQSSASSGFIEDKSLSDVEEDEE 161
Query: 196 CNGPSKLCISMDITIEY 212
+ K ++++ I Y
Sbjct: 162 GDELYKEPLTLEDLISY 178
>gnl|CDD|217970 pfam04220, YihI, Der GTPase activator (YihI). YihI activates the
GTPase activity of Der, a 50S ribosomal subunit
stability factor. The stimulation is specific to Der as
YihI does not stimulate the GTPase activity of Era or
ObgE. The interaction of YihI with Der requires only the
C-terminal 78 amino acids of YihI. A yihI deletion
mutant is viable and shows a shorter lag period, but the
same post-lag growth rate as a wild-type strain. yihI is
expressed during the lag period. Overexpression of yihI
inhibits cell growth and biogenesis of the 50S ribosomal
subunit. YihI is an unusual, highly hydrophilic protein
with an uneven distribution of charged residues,
resulting in an N-terminal region with high pI and a
C-terminal region with low pI.
Length = 169
Score = 27.7 bits (62), Expect = 5.7
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 134 ENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSK 173
E + K KR S++NEE+ SQ + + KK I SK
Sbjct: 28 ERKRKKKRKGLKSGSRHNEESESQKQKGAAQKKDPRIGSK 67
>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
Provisional.
Length = 522
Score = 28.2 bits (63), Expect = 5.7
Identities = 11/43 (25%), Positives = 18/43 (41%)
Query: 126 NRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQK 168
+ N ++N N + NN+ NS N + P K+K
Sbjct: 8 LSVHNNADDNYNNNNNNNNQINSNNPNNNGNNQASKLPRGKKK 50
>gnl|CDD|233741 TIGR02128, G6PI_arch, bifunctional phosphoglucose/phosphomannose
isomerase. This bifunctional isomerase is a member of
the larger PGI superfamily and only distantly related to
other glucose-6-phosphate isomerases. The family is
limited to the archaea.
Length = 308
Score = 27.8 bits (62), Expect = 7.0
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 121 GLDIMNRLRNQFNENQNKSKRNNHLPNSQNNE 152
I R +N+ NEN N LP +NE
Sbjct: 187 TRPIAERWKNEINENAKSPAYYNILPELNHNE 218
>gnl|CDD|113458 pfam04690, YABBY, YABBY protein. YABBY proteins are a group of
plant-specific transcription involved in the
specification of abaxial polarity in lateral organs.
Length = 170
Score = 27.1 bits (60), Expect = 8.8
Identities = 16/84 (19%), Positives = 24/84 (28%), Gaps = 13/84 (15%)
Query: 98 HCFNLSSQESGGAVLIRSLEPVHGLDIMNRL-------RNQFNENQNKSK------RNNH 144
HC NL S + L FN N KS +
Sbjct: 41 HCTNLLSVNLMMRSHLLPALSHLDETGKPELLQNLGVHGQNFNSNMMKSHSASTSVSSYM 100
Query: 145 LPNSQNNEETHSQSNRNSPAKKQK 168
+ ++Q+ E P K+Q+
Sbjct: 101 MSDNQDEEMPRVPPVNRPPEKRQR 124
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
0.316 0.131 0.389
Gapped
Lambda K H
0.267 0.0622 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,276,905
Number of extensions: 1180362
Number of successful extensions: 912
Number of sequences better than 10.0: 1
Number of HSP's gapped: 887
Number of HSP's successfully gapped: 34
Length of query: 281
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 185
Effective length of database: 6,679,618
Effective search space: 1235729330
Effective search space used: 1235729330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.3 bits)