RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12122
(412 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 = 35.3 bits (82), Expect = 0.013
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 53 HVGIAGNEAADREAK 67
H GI GNE ADR AK
Sbjct: 110 HSGIEGNERADRLAK 124
>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 = 29.5 bits (67), Expect = 1.2
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 53 HVGIAGNEAADREAKS 68
H GI GNE AD+ AK
Sbjct: 108 HSGIPGNELADKLAKQ 123
>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 = 1.6
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 25 PKSLWGQKTNLIFFLCPKSPKYGKVSYNHVGIAGNEAADREAK 67
W + L++ + K+ + + HV GNE ADR AK
Sbjct: 78 WSKGWKKNNLLLWDILLLLSKFIDIRFEHVPREGNEVADRLAK 120
>gnl|CDD|221376 pfam12009, Telomerase_RBD, Telomerase ribonucleoprotein complex -
RNA binding domain. Telomeres in most organisms are
comprised of tandem simple sequence repeats. The total
length of telomeric repeat sequence at each chromosome
end is determined in a balance of sequence loss and
sequence addition. One major influence on telomere
length is the enzyme telomerase. It is a reverse
transcriptase that adds these simple sequence repeats
to chromosome ends by copying a template sequence
within the RNA component of the enzyme. The RNA binding
domain of telomerase - TRBD - is made up of twelve
alpha helices and two short beta sheets. How telomerase
and associated regulatory factors physically interact
and function with each other to maintain appropriate
telomere length is poorly understood. It is known
however that TRBD is involved in formation of the
holoenzyme (which performs the telomere extension) in
addition to recognition and binding of RNA.
Length = 136
Score = 28.3 bits (64), Expect = 3.3
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 6 VIFLVRVVLREIKGAPRRPPKSLWGQKTNLIFFLCP-----KSPKYGKVSYNHV 54
V+ +R +LR++ PK LWG K N FL K ++ K+S + +
Sbjct: 3 VVSFLRAILRKLV------PKDLWGSKHNKKVFLKKVSKFLKLRRFEKLSLHEL 50
>gnl|CDD|185519 PTZ00219, PTZ00219, Sec61 alpha subunit; Provisional.
Length = 474
Score = 28.8 bits (65), Expect = 5.3
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 1 MVILLVIFLVRVVLREIKGAPRRPP---KSLWGQKTNLIFFLCPKSPKYGKVS 50
L ++ +L E+ R+ P K LW +F +C + P YG S
Sbjct: 5 TRFLNLLRPAMAILPEVAEPDRKIPFKEKVLWTAIALFVFLVCCQIPLYGIRS 57
>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and
more complex than their prokaryotic counterparts and
unlike prokaryote, RNase H are essential in higher
eukaryote. 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). RNase H is
an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner. 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 is widely present in various organisms,
including bacteria, archaea and eukaryote and 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 (DEDD) residues and have the same catalytic
mechanism and functions in cells. Eukaryotic RNase H is
longer and more complex than in prokaryotes. Almost all
eukaryotic RNase HI have highly conserved regions at the
N-terminal called hybrid binding domain (HBD). It is
speculated that the HBD contributes to binding the
RNA/DNA hybrid. Prokaryotes and some single-cell
eukaryotes do not require RNase H for viability, but
RNase H is essential in higher eukaryotes. RNase H
knockout mice lack mitochondrial DNA replication and die
as embryos.
Length = 150
Score = 27.9 bits (63), Expect = 5.5
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 53 HVGIAGNEAADREAK 67
H GI GNE ADR AK
Sbjct: 132 HSGIYGNEEADRLAK 146
>gnl|CDD|216588 pfam01586, Basic, Myogenic Basic domain. This basic domain is
found in the MyoD family of muscle specific proteins
that control muscle development. The bHLH region of the
MyoD family includes the basic domain and the
Helix-loop-helix (HLH) motif. The bHLH region mediates
specific DNA binding. With 12 residues of the basic
domain involved in DNA binding. The basic domain forms
an extended alpha helix in the structure.
Length = 84
Score = 27.1 bits (60), Expect = 5.5
Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 18/75 (24%)
Query: 218 ELYRRSGLYPGSPGFYRGEDLKRVQSVMYRGYEGVGAPNFRR-------PSHSKEAKTVI 270
EL+ + S FY GE+ S +E + P S E + V
Sbjct: 2 ELFETMPYFFPSDRFYDGEN---FLSSDLEFFEDLE-PREAHEGTLKPEAHGSDEEEHVR 57
Query: 271 L-----CASRSDCLM 280
C + CLM
Sbjct: 58 APSGHHCPGQ--CLM 70
>gnl|CDD|226336 COG3815, COG3815, Predicted membrane protein [Function unknown].
Length = 113
Score = 27.1 bits (60), Expect = 7.3
Identities = 9/30 (30%), Positives = 12/30 (40%)
Query: 135 VCLMRLRIGHTKITHSFLFRREDPPVCDKC 164
+CL + I H SF VC +C
Sbjct: 2 ICLYAVYICHQMPQRSFFIFGHKMAVCARC 31
>gnl|CDD|239650 cd03678, MM_CoA_mutase_1, Coenzyme B12-dependent-methylmalonyl
coenzyme A (CoA) mutase (MCM) family, unknown subfamily
1; composed of uncharacterized bacterial proteins
containing a C-terminal MCM domain. MCM catalyzes the
isomerization of methylmalonyl-CoA to succinyl-CoA. The
reaction proceeds via radical intermediates beginning
with a substrate-induced homolytic cleavage of the Co-C
bond of coenzyme B12 to produce cob(II)alamin and the
deoxyadenosyl radical. MCM plays an important role in
the conversion of propionyl-CoA to succinyl-CoA during
the degradation of propionate for the Krebs cycle. In
some bacteria, MCM is involved in the reverse metabolic
reaction, the rearrangement of succinyl-CoA to
methylmalonyl-CoA. Members of this subfamily also
contain an N-terminal coenzyme B12 binding domain
followed by a domain similar to the E. coli ArgK
membrane ATPase.
Length = 495
Score = 28.6 bits (64), Expect = 7.7
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 10/47 (21%)
Query: 206 LMRFLKRNNFPKELYRRSGLYPGSPGFYR-GEDLKRVQSVMYRGYEG 251
++R+L R N P E +G++P F R GED R M+ G EG
Sbjct: 54 ILRWLLRENVPGEFPFTAGVFP----FKRTGEDPTR----MFAG-EG 91
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 0.137 0.425
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,015,238
Number of extensions: 1981445
Number of successful extensions: 1487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1487
Number of HSP's successfully gapped: 14
Length of query: 412
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 313
Effective length of database: 6,546,556
Effective search space: 2049072028
Effective search space used: 2049072028
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: 60 (26.8 bits)