RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9306
(98 letters)
>gnl|CDD|181058 PRK07609, PRK07609, CDP-6-deoxy-delta-3,4-glucoseen reductase;
Validated.
Length = 339
Score = 28.7 bits (65), Expect = 0.45
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 32 NFFFIRE-SNCIRESG--GLSGFVHSFVTEVLAILRAH-VTALGGNAMV 76
NF ++ S+ + + G +GFVH V E L H V A G MV
Sbjct: 262 NFRYVPVVSDALDDDAWTGRTGFVHQAVLEDFPDLSGHQVYACGSPVMV 310
>gnl|CDD|235388 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
Length = 344
Score = 27.8 bits (63), Expect = 0.85
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 5/35 (14%)
Query: 36 IRESNCIRESGGLSG---FVHSFVTEVLAILRAHV 67
++ E+GGLSG F S TEV+ L +
Sbjct: 254 LKGLPNADEAGGLSGRPLFERS--TEVIRRLYKEL 286
>gnl|CDD|179651 PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 438
Score = 25.7 bits (57), Expect = 4.0
Identities = 8/26 (30%), Positives = 17/26 (65%)
Query: 24 IERYLGNLNFFFIRESNCIRESGGLS 49
+ER+ G+LN ++ ++ I S G++
Sbjct: 51 VERHTGSLNDEWLLAADLIVASPGIA 76
>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 = 25.3 bits (56), Expect = 4.1
Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 21 GGKIERYLGNLNFFFIRESNCIRESGGLSGFVHSFVTEVLAILRA 65
G K+E G F I I S L + F E+LAIL A
Sbjct: 6 GSKLEGRTGA--GFAIVRKGTISRSYKLGPYCSVFDAELLAILEA 48
>gnl|CDD|220594 pfam10136, SpecificRecomb, Site-specific recombinase. Members of
this family of bacterial proteins are found in various
putative site-specific recombinase transmembrane
proteins.
Length = 647
Score = 26.0 bits (58), Expect = 4.2
Identities = 7/35 (20%), Positives = 16/35 (45%)
Query: 42 IRESGGLSGFVHSFVTEVLAILRAHVTALGGNAMV 76
+ + G + V + ++R+ A+ GN +V
Sbjct: 400 LDDLRGRPEGLEKLVDLIAHLVRSQAAAILGNVLV 434
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 26.0 bits (57), Expect = 4.4
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 10 GVDITPLSYIAGGKIERYLGNLNFFFIRESNCIRESGG----LSGFVHSFVTEVLAILR 64
G+ PL IA KI+R + I + IR +GG LS V +V + + + R
Sbjct: 115 GIVAAPLEGIADVKIKRNEDGSEYLAIYYAGPIRSAGGTAQALSVLVGDYVRKKMGLDR 173
>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
This model represents the large subunit, DP2, of a two
subunit novel Archaeal replicative DNA polymerase first
characterized for Pyrococcus furiosus. Structure of DP2
appears to be organized as a ~950 residue component
separated from a ~300 residue component by a ~150
residue intein. The other subunit, DP1, has sequence
similarity to the eukaryotic DNA polymerase delta small
subunit [DNA metabolism, DNA replication, recombination,
and repair].
Length = 1095
Score = 25.2 bits (55), Expect = 7.2
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 10 GVDITPLSYIAGGKIERYLGNLNFFFIRESNCIRESGG----LSGFVHSFVTEVLAILR 64
GV PL IA +I+R N+ + + IR +GG LS V +V + R
Sbjct: 108 GVVAAPLEGIARVRIKRNFDKSNYLAVYYAGPIRSAGGTAQALSVLVADYVRRAAGLDR 166
>gnl|CDD|237017 PRK11904, PRK11904, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1038
Score = 24.8 bits (55), Expect = 9.1
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 13/38 (34%)
Query: 47 GLSG---------FVHSFVTE-VLAILRAHVTALGGNA 74
GLSG ++ F TE + + + TA GGNA
Sbjct: 1000 GLSGTGPKAGGPHYLLRFATEKTVTV---NTTAAGGNA 1034
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
0.324 0.140 0.419
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,102,223
Number of extensions: 426933
Number of successful extensions: 307
Number of sequences better than 10.0: 1
Number of HSP's gapped: 307
Number of HSP's successfully gapped: 18
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)