RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7385
(208 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 = 43.4 bits (103), Expect = 9e-06
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 18 RSLKSCGKEGTLMWCPSQCGISGNEAVDMAAK 49
R L + G + L W P GI GNE D AK
Sbjct: 93 RELANHGVKVRLHWVPGHSGIEGNERADRLAK 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 = 34.2 bits (79), Expect = 0.012
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 28 TLMWCPSQCGISGNEAVDMAAK 49
+ W P GI GNE D AK
Sbjct: 101 YIQWVPGHSGIPGNELADKLAK 122
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 31.6 bits (72), Expect = 0.29
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 28/86 (32%)
Query: 55 IQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRIKPDKKKKPVVENWASRNRDT 114
I+ LKLC KPI+ + M+ ING+ + +P K+K
Sbjct: 48 IELLKLCKGKGIKPIIG---NEMY------VINGS-IDDPQPKKEK-------------- 83
Query: 115 RYEEVALARMRIGHTRL----THSHL 136
RY V LA+ G+ L T SHL
Sbjct: 84 RYHLVVLAKNATGYKNLVKLTTISHL 109
>gnl|CDD|211667 TIGR01530, nadN, NAD pyrophosphatase/5'-nucleotidase NadN. This
model describes NadN of Haemophilus influenzae and a
small number of close homologs in pathogenic,
Gram-negative bacteria. NadN is a periplasmic enzyme
that cleaves NAD (nicotinamide adenine dinucleotide) to
NMN (nicotinamide mononucleotide) and AMP. The NMN must
be converted by a 5'-nucleotidase to nicotinamide
riboside for import. NadN belongs a large family of
5'-nucleotidases and has NMN 5'-nucleotidase activity
for NMN, AMP, etc [Transport and binding proteins,
Other, Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridine nucleotides].
Length = 545
Score = 30.3 bits (68), Expect = 0.68
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 40 GNEAVDMAAKNPTTPIQPLKL-CSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRIKPDK 98
GN D + ++PLK+ +++ P A I++N W+ ++G K+ I D
Sbjct: 89 GNHEFDAGNEGLLKLLEPLKIPVLSANVIPDKASILYNKWKPYDIFTVDGEKIAIIGLDT 148
Query: 99 KKKPVVENWASRNRDTR-YEEVALAR 123
K V N +S +D + Y+E+A A+
Sbjct: 149 VNKTV--NSSSPGKDVKFYDEIATAQ 172
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide
reductase A/B protein; Provisional.
Length = 521
Score = 27.1 bits (60), Expect = 8.4
Identities = 21/101 (20%), Positives = 31/101 (30%), Gaps = 17/101 (16%)
Query: 85 QINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPA 144
+ LKR + + VVEN +N E H ++P
Sbjct: 302 AVIAAALKREQQKYQLPLVVENEPLKNFYDAEE--------------YHQDYLIKNPNGY 347
Query: 145 CRQDIRRG---PAGKTCCNTSVKAPNRKKEQHCKPHVEKRT 182
C D+R+ GKT K + + KRT
Sbjct: 348 CHIDLRKADEPLPGKTKTAPQGKGFDAATYKKPSDAELKRT 388
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
0.319 0.131 0.410
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,091,846
Number of extensions: 877413
Number of successful extensions: 679
Number of sequences better than 10.0: 1
Number of HSP's gapped: 679
Number of HSP's successfully gapped: 9
Length of query: 208
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 115
Effective length of database: 6,812,680
Effective search space: 783458200
Effective search space used: 783458200
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 (25.9 bits)