RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4359
(220 letters)
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 71.1 bits (175), Expect = 6e-16
Identities = 35/113 (30%), Positives = 48/113 (42%), Gaps = 15/113 (13%)
Query: 19 IYTDASKNDSSVSAAFWSPD---FSFKVKLNPLLSICNAELMAILYAVYFILANCLSEAR 75
IYTD SK + A F S KL P S+ +AEL+AIL A+ L R
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE---GRR 58
Query: 76 NSSFLLCTDSLSALQSLQDIFS---PNLHTLRQIMSLWHEDWNYLIGNKLRLI 125
+ +DS +AL++L+ S L + I L G K+RL
Sbjct: 59 ARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIREL------ANHGVKVRLH 105
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of
an RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 40.7 bits (96), Expect = 8e-05
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 14/83 (16%)
Query: 14 PQSTKIYTDAS--KNDSSVSAAFWSPDFSFKVKLNPLLSICN--AELMAILYAVYFILAN 69
P++ +YTD S N A + + K + PL N AEL+A++ A
Sbjct: 1 PEAVTVYTDGSCNGNPGPGGAGYVTDGG--KQRSKPLPGTTNQRAELLALIEA------- 51
Query: 70 CLSEARNSSFLLCTDSLSALQSL 92
L + TDS + +
Sbjct: 52 -LEALSGQKVNIYTDSQYVIGGI 73
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 31.9 bits (73), Expect = 0.18
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 7/68 (10%)
Query: 94 DIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGH 153
DIF + + L L+GNK+ L+ ++ KP Q + RL+IG
Sbjct: 42 DIFDFPGSLIPGLAELIGAKPVILVGNKIDLLPKDVKPNRLKQWVKK-------RLKIGG 94
Query: 154 TNLTHVHL 161
+ V L
Sbjct: 95 LKIKDVIL 102
>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
strand of an RNA/DNA hybrid in a sequence non-specific
manner. Ribonuclease H (RNase H) enzymes are divided
into two major families, Type 1 and Type 2, based on
amino acid sequence similarities and biochemical
properties. RNase H is an endonuclease that cleaves the
RNA strand of an RNA/DNA hybrid in a sequence
non-specific manner in the presence of divalent cations.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes. Most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site residues and have the same catalytic
mechanism and functions in cells. RNase H is involved in
DNA replication, repair and transcription. One of the
important functions of RNase H is to remove Okazaki
fragments during DNA replication. RNase H inhibitors
have been explored as an anti-HIV drug target because
RNase H inactivation inhibits reverse transcription.
Length = 123
Score = 29.2 bits (66), Expect = 0.75
Identities = 19/118 (16%), Positives = 35/118 (29%), Gaps = 25/118 (21%)
Query: 20 YTDAS----KNDSSVSAAFWSPD----FSFKVKLNPLLSICNAELMAILYAVYFILANCL 71
TD S + + F+ + P + AEL+A+L A+
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLS-IPAATNNEAELLALLEALE-----LA 54
Query: 72 SEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEEN 129
+ ++ TDS + + W ++ L L L K +
Sbjct: 55 LDLGLKKLIIETDSKYV-----------VDLINSWSKGWKKNNLLLWDILLLLSKFID 101
>gnl|CDD|227073 COG4729, COG4729, Uncharacterized conserved protein [Function
unknown].
Length = 156
Score = 29.0 bits (65), Expect = 1.3
Identities = 24/121 (19%), Positives = 40/121 (33%), Gaps = 32/121 (26%)
Query: 58 AILYAVYFILANCLSEARNSSFLLCTDSLSALQ--------SLQDIFSPNLHTLRQIMSL 109
A AV+ ++A L +L+ +++ +L I H++ + SL
Sbjct: 9 ASGLAVFTLIAGLLP----VMYLVVLGMETSVYCTLPAQEFTLSWI-----HSVEK--SL 57
Query: 110 WHEDWNYLIGNKLRLIK------------EENKPWHPPQTFSRRDQVTLTRLRIGHTNLT 157
W ED+ + G L L + E F R TL LR +
Sbjct: 58 WEEDY-RVSGGGLLLEETRVRSFGAGMPSPEGATLEDGAWFYYRGVRTLQVLRWSRSREA 116
Query: 158 H 158
Sbjct: 117 G 117
>gnl|CDD|225640 COG3098, COG3098, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 109
Score = 27.4 bits (61), Expect = 2.5
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 72 SEARNSSFLLCTDSLSALQSLQDIFSPNLHTL 103
EA S+ D++ + LQ +F P +H L
Sbjct: 31 PEAFLSTEPFFVDTMEPEEWLQWVFIPRMHAL 62
>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor
(ARF-GEF); Provisional.
Length = 1780
Score = 28.6 bits (64), Expect = 3.1
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 10/89 (11%)
Query: 35 WSPDF-SFKVKLNP-----LLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSA 88
W+P +F V L+ + C L +A++ + R++ F+ ++
Sbjct: 880 WAPMLAAFSVPLDQSDDEVVTFQC---LEGFRHAIHVTAVMSMKTHRDA-FVTSLAKFTS 935
Query: 89 LQSLQDIFSPNLHTLRQIMSLWHEDWNYL 117
L S DI N+ ++ I+S+ ED NYL
Sbjct: 936 LHSPADIKQKNIDAIKAIVSIADEDGNYL 964
>gnl|CDD|215868 pfam00343, Phosphorylase, Carbohydrate phosphorylase. The members
of this family catalyze the formation of glucose
1-phosphate from one of the following polyglucoses;
glycogen, starch, glucan or maltodextrin.
Length = 712
Score = 27.7 bits (62), Expect = 6.3
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 92 LQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKP 131
LQ I+ N L+ + W D + L ++ +I E
Sbjct: 283 LQIIYEINERFLKLVWEKWPGDEDKL--RRMSIIDEGAGK 320
>gnl|CDD|213273 cd05905, Dip2, Disco-interacting protein 2 (Dip2). Dip2 proteins
show sequence similarity to other members of the
adenylate forming enzyme family, including insect
luciferase, acetyl CoA ligases and the adenylation
domain of nonribosomal peptide synthetases (NRPS).
However, its function may have diverged from other
members of the superfamily. In mouse embryo, Dip2
homolog A plays an important role in the development of
both vertebrate and invertebrate nervous systems. Dip2A
appears to regulate cell growth and the arrangement of
cells in organs. Biochemically, Dip2A functions as a
receptor of FSTL1, an extracellular glycoprotein, and
may play a role as a cardiovascular protective agent.
Length = 556
Score = 27.5 bits (61), Expect = 6.8
Identities = 12/74 (16%), Positives = 21/74 (28%), Gaps = 3/74 (4%)
Query: 11 SKYPQSTKIYTDASKNDSS---VSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFIL 67
K + + + D++ + V LL+ C A A Y +
Sbjct: 131 KKPIKDWNPHLPPANLDTAYIEYKTSKEGSVMGVTVTHQALLTHCQALKQACQYTEGRTI 190
Query: 68 ANCLSEARNSSFLL 81
N L + F
Sbjct: 191 VNVLDFKKGVGFWH 204
>gnl|CDD|184556 PRK14185, PRK14185, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 293
Score = 26.7 bits (59), Expect = 10.0
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 161 LMKKEQPPECEICSCNLTVKHLLKYCL 187
+M+K P +C + C+ K+L K CL
Sbjct: 177 MMQKAYPGDCTVTVCHSRSKNLKKECL 203
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
0.321 0.134 0.414
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,686,693
Number of extensions: 953307
Number of successful extensions: 719
Number of sequences better than 10.0: 1
Number of HSP's gapped: 716
Number of HSP's successfully gapped: 22
Length of query: 220
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 127
Effective length of database: 6,812,680
Effective search space: 865210360
Effective search space used: 865210360
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: 57 (25.8 bits)