RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16958
(257 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 = 54.6 bits (132), Expect = 1e-09
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 98 TFYCDGSKSPQHCGSAFV--HEGN-TITFKLPNISSSYTAEIIALQKCIQFITQNKK 151
Y DGSK G+ F +G + ++KL S + AE++A+ + +Q + +
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGR 57
>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 = 39.2 bits (92), Expect = 4e-04
Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 13/97 (13%)
Query: 97 ETFYCDGS--KSPQHCGSAFV-HEGNTITFKLPNISSSYTAEIIALQKCIQ-FITQNKKI 152
T Y DGS +P G+ +V G + LP +++ AE++AL + ++ Q I
Sbjct: 4 VTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPG-TTNQRAELLALIEALEALSGQKVNI 62
Query: 153 KPETQY--------WPTSSRQKRIEEVIIARLRIGHT 181
++QY WPT S K I+ I L+ H
Sbjct: 63 YTDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHK 99
>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 = 33.0 bits (76), Expect = 0.058
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 98 TFYCDGSKSPQHCGSAFVHEGNTI-TFKLPNISSSYTAEIIAL 139
T + DGS + G A V + + LP +S+ AE+IAL
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL 43
>gnl|CDD|181842 PRK09422, PRK09422, ethanol-active
dehydrogenase/acetaldehyde-active reductase;
Provisional.
Length = 338
Score = 31.2 bits (71), Expect = 0.57
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 11/32 (34%)
Query: 188 LIDKKPRPI-----------CDTCHTPLSVAH 208
+++K RP+ C CHT L VA+
Sbjct: 15 VVEKTLRPLKHGEALVKMEYCGVCHTDLHVAN 46
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 28.2 bits (64), Expect = 5.6
Identities = 12/40 (30%), Positives = 14/40 (35%), Gaps = 12/40 (30%)
Query: 170 EVIIARLR-----IGHTRVSHSYLIDKKPRPICDTCHTPL 204
+ II L+ HSY P C C TPL
Sbjct: 366 KEIIRDLKERGLLFKAETYEHSY-------PHCWRCDTPL 398
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 28.3 bits (64), Expect = 5.7
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 63 LPETQ--LLLKEKKTNISPNEIKSKFNQLLNKVNRK 96
LP T LLL + ++S N+ L+ VNR
Sbjct: 826 LPPTPVRLLLDKNGNDLSAQVEFESLNRQLSAVNRH 861
>gnl|CDD|217561 pfam03443, Glyco_hydro_61, Glycosyl hydrolase family 61.
Length = 234
Score = 27.6 bits (62), Expect = 6.5
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 100 YCDGSKSPQHCGSAFVHEGNTITFKLP-NISSSY---TAEIIAL 139
DG+K P + N+ + +P +I+ EIIAL
Sbjct: 133 LDDGTKVPTWATDQLIANNNSWSVTIPSSIAPGNYLLRHEIIAL 176
>gnl|CDD|118909 pfam10388, YkuI_C, EAL-domain associated signalling protein domain.
In Bacillus species this highly conserved region of the
YkuI protein lies immediately downstream of the EAL
(diguanylate cyclase/phosphodiesterase domain 2)
pfam00563 domain so that together they form a monomer
which dimerises for its enzymatic action. The region
contains three alpha helices and five beta strands and
is the C-terminal half of the structure.
Length = 166
Score = 27.0 bits (60), Expect = 8.4
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 140 QKCIQFITQNKKIKPETQYWPTSSRQKRIEEVI 172
++ QFIT KK K E QY QKR+ + +
Sbjct: 13 KEFHQFITHEKK-KLEAQYQLAEKLQKRLHQAL 44
>gnl|CDD|220719 pfam10368, YkyA, Putative cell-wall binding lipoprotein. YkyA is a
family of proteins containing a lipoprotein signal and a
hydrolase domain. It is similar to cell wall binding
proteins and might also be recognisable by a host immune
defence system. It is thus likely to belong to pathways
important for pathogenicity.
Length = 205
Score = 26.9 bits (60), Expect = 9.0
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 80 NEIKSKFNQLLNKVNR-KETFY 100
+ K KFN+ K N+ K+ FY
Sbjct: 178 QKAKKKFNEYTKKYNKEKQDFY 199
>gnl|CDD|225644 COG3102, COG3102, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 185
Score = 26.6 bits (59), Expect = 9.8
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 194 RPIC-DTCHTPLSVAHILIECTKFQVERQKLLPH 226
RPIC H PL VAH I+ + + K PH
Sbjct: 75 RPICLIKLHQPLQVAHWQIDIIELPYPKNKRYPH 108
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
0.317 0.132 0.396
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,588,737
Number of extensions: 1127881
Number of successful extensions: 1117
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1115
Number of HSP's successfully gapped: 24
Length of query: 257
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 162
Effective length of database: 6,723,972
Effective search space: 1089283464
Effective search space used: 1089283464
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 (21.7 bits)
S2: 58 (26.2 bits)