RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3161
(211 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 = 81.9 bits (203), Expect = 4e-20
Identities = 34/106 (32%), Positives = 50/106 (47%), Gaps = 14/106 (13%)
Query: 29 ICYTDGSKSPDATGCAFSI---GDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSD-- 83
+ YTDGSK TG F+I G + RS L P S+F AEL+AI L+ L
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 84 QFLIVSDSRSAIAALANWNNVPNTN-----KLKSIR-PNIK---HW 120
+ I SDS++A+ AL + + ++ + +K HW
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHW 106
>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 = 44.7 bits (106), Expect = 3e-06
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 31 YTDGSKS--PDATGCAFSI----GDMVRSTSLNPIN-SIFSAELIAIFLCLEAILESPSD 83
TDGS P G + G + + SL+ + AEL+A+ LE L+
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 84 QFLIVSDSRSAIAALANWNNVPNTN 108
+ +I +DS+ + + +W+ N
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKN 85
>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 = 43.4 bits (103), Expect = 8e-06
Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 8/91 (8%)
Query: 26 NHTICYTDGS--KSPDATGCAFSI-GDMVRSTSLNPINSIFSAELIAIFLCLEAILESPS 82
YTDGS +P G + G RS L P + AEL+A+ +EA+
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLAL---IEALEALSG 57
Query: 83 DQFLIVSDSRSAI-AALANWNNVPNTNKLKS 112
+ I +DS+ I W + +K+
Sbjct: 58 QKVNIYTDSQYVIGGITNGWPTKSESKPIKN 88
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term
repeat retroelements. 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 eukaryote. RNase HI has
also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in 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.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 38.4 bits (90), Expect = 5e-04
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 4/73 (5%)
Query: 30 CYTDGSKSPDATGCA-FSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIV 88
+TDGS G A + D++ +L S AELIA+ + A+ + I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58
Query: 89 SDSRSAIAALANW 101
+DS A L
Sbjct: 59 TDSAYAFGILHAL 71
>gnl|CDD|130624 TIGR01561, gde_arch, glycogen debranching enzyme, archaeal type,
putative. The seed for this model is composed of two
uncharacterized archaeal proteins from Methanosarcina
acetivorans and Sulfolobus solfataricus. Trusted cutoff
is set so that essentially only archaeal members hit the
model. The notable exceptions to archaeal membership are
the Gram positive Clostridium perfringens which scores
much better than some other archaea and the
Cyanobacterium Nostoc sp. which scores just above the
trusted cutoff. Noise cutoff is set to exclude the
characterized eukaryotic glycogen debranching enzyme in
S. cerevisiae. These cutoffs leave the prokaryotes
Porphyromonas gingivalis and Deinococcus radiodurans
below trusted but above noise. Multiple alignments
including these last two species exhibit sequence
divergence which may suggest a subtly different function
for these prokaryotic proteins [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 575
Score = 30.0 bits (67), Expect = 0.83
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 98 LANWNNVPNTNKLKSIRPN----IKHWNTSTQDRRIKEVILTRM 137
L + + N K K+IRPN I D I + IL +
Sbjct: 479 LIHQDEAGNQVKDKAIRPNQIFAISLPFPIIDDESIAKAILDLI 522
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 29.2 bits (66), Expect = 0.97
Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 17/94 (18%)
Query: 31 YTDGS----KSPDATGCAFSIGDMVRSTSL-------NPINSIFSAELIAIFLCLEAILE 79
+TDG+ P G GD + S N AEL A+ LEA+ E
Sbjct: 7 FTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNN------RAELRALIEALEALKE 60
Query: 80 SPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSI 113
+ + + +DS+ + + W N K+
Sbjct: 61 LGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTA 94
>gnl|CDD|224704 COG1791, COG1791, Uncharacterized conserved protein, contains
double-stranded beta-helix domain [Function unknown].
Length = 181
Score = 27.4 bits (61), Expect = 3.9
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 106 NTNKLKSIRPNIKHWNTSTQDRRIKEV 132
L S+ P I HW T T+ K V
Sbjct: 123 EKGDLISVPPGIYHWFTLTESPNFKAV 149
>gnl|CDD|233182 TIGR00915, 2A0602, The (Largely Gram-negative Bacterial)
Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. Proteins
scoring above the trusted cutoff (1000) form a tight
clade within the RND (Resistance-Nodulation-Cell
Division) superfamily. Proteins scoring greater than the
noise cutoff (100) appear to form a larger clade,
cleanly separated from more distant homologs that
include cadmium/zinc/cobalt resistance transporters.
This family is one of several subfamilies within the
scope of Pfam model pfam00873 [Cellular processes, Toxin
production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 1044
Score = 28.2 bits (63), Expect = 4.5
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 61 SIFSAELIAIFLCLEAILESPSDQFLIV 88
++++ L+ +FLCL A+ ES S ++
Sbjct: 874 ALYALSLLVVFLCLAALYESWSIPVSVM 901
>gnl|CDD|185081 PRK15127, PRK15127, multidrug efflux system protein AcrB;
Provisional.
Length = 1049
Score = 27.9 bits (62), Expect = 5.0
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 55 SLNPINSIFSAELIAIFLCLEAILESPSDQF 85
S N ++++ LI +FLCL A+ ES S F
Sbjct: 869 SGNQAPALYAISLIVVFLCLAALYESWSIPF 899
>gnl|CDD|181283 PRK08197, PRK08197, threonine synthase; Validated.
Length = 394
Score = 27.7 bits (62), Expect = 5.2
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 157 ICQCGAPLSVRHLLSCPRHGHIRASL--RPP 185
+C+CG PL VR+ L + R +L RP
Sbjct: 25 LCKCGKPLLVRYDLEAVKQAVTREALAGRPA 55
>gnl|CDD|217619 pfam03571, Peptidase_M49, Peptidase family M49.
Length = 550
Score = 27.6 bits (62), Expect = 5.2
Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 13/56 (23%)
Query: 65 AELIAIFLCLEA-ILE-----SPSDQ-----FLIVSDSRSAIAALANWNNVPNTNK 109
AE +A++L +LE + + R+ + AL +N P T K
Sbjct: 360 AEAVALYLSTNKEVLEIFGFTDKEEADDVVYVNWLQMIRAGLLALEFYN--PETKK 413
>gnl|CDD|179352 PRK01911, ppnK, inorganic polyphosphate/ATP-NAD kinase;
Provisional.
Length = 292
Score = 27.2 bits (61), Expect = 7.1
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 8/33 (24%)
Query: 79 ESPSDQFLIVSDSRSAIAALANWNNVPNTNKLK 111
ES SD FL+ DSRS V N +L
Sbjct: 234 ESRSDNFLVSLDSRSET--------VDNGTELT 258
>gnl|CDD|239476 cd03381, PAP2_glucose_6_phosphatase, PAP2_like proteins,
glucose-6-phosphatase subfamily. Glucose-6-phosphatase
converts glucose-6-phosphate into free glucose and is
active in the lumen of the endoplasmic reticulum, where
it is bound to the membrane. The generation of free
glucose is an important control point in metabolism, and
stands at the end of gluconeogenesis and the release of
glucose from glycogen. Deficiency of
glucose-6-phosphatase leads to von Gierke's disease.
Length = 235
Score = 27.0 bits (60), Expect = 8.1
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 44 AFSIGDMVRSTSLNPINSIFSAEL-----IAIFLCLEAI 77
A I + + + + I I+SA L I FL A+
Sbjct: 138 AGVISGIAVAETFSHIRYIYSASLKRYVLITFFLFGFAL 176
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
0.320 0.134 0.405
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,557,991
Number of extensions: 944461
Number of successful extensions: 778
Number of sequences better than 10.0: 1
Number of HSP's gapped: 775
Number of HSP's successfully gapped: 20
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
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 (21.8 bits)
S2: 57 (25.8 bits)