RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3694
(61 letters)
>gnl|CDD|220751 pfam10433, MMS1_N, Mono-functional DNA-alkylating methyl
methanesulfonate N-term. MMS1 is a protein that
protects against replication-dependent DNA damage in
Saccharomyces cerevisiae. MMS1 belongs to the DDB1
family of cullin 4 adaptors and the two proteins are
homologous. MMS1 bridges the interaction of MMS22 and
Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein
involved in the regulation of DNA replication subsequent
to DNA damage. The N-terminal region of MMS1 and the
C-terminal of MMS22 are required for the the MMS1-MMS22
interaction. The human HIV-1 virion-associated protein
Vpr assembles with DDB1 through interaction with DCAF1
(chromatin assembly factor) to form an E3 ubiquitin
ligase that targets cellular substrates for
proteasome-mediated degradation and subsequent G2
arrest.
Length = 513
Score = 38.5 bits (90), Expect = 4e-05
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 2 ACGRGPRSTVRVLRHGLEVSEMAVSELP-SNPNAVWTVKRRSDDRVSLF 49
G G R ++R LRHG+E V E +W + S+ L
Sbjct: 339 CSGVGKRGSLRELRHGIEAEIGLVIEEELRGIRGLWLLPSGSNGGYYLL 387
>gnl|CDD|218484 pfam05185, PRMT5, PRMT5 arginine-N-methyltransferase. The human
homologue of yeast Skb1 (Shk1 kinase-binding protein 1)
is PRMT5, an arginine-N-methyltransferase. These
proteins appear to be key mitotic regulators. They play
a role in Jak signalling in higher eukaryotes.
Length = 445
Score = 29.1 bits (66), Expect = 0.079
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 11/55 (20%)
Query: 4 GRGP--RSTVRVLR-HGLEVSEMAVSELPSNPNAVWTVKRRS-----DDRVSLFH 50
GRGP ++ G +V AV + NPNAV T+++R D+V++
Sbjct: 196 GRGPLVDRALKAAEETGRKVKIYAVEK---NPNAVVTLQKRVNFEEWGDKVTIIS 247
>gnl|CDD|227868 COG5581, COG5581, c-di-GMP-binding protein [Signal transduction
mechanisms].
Length = 233
Score = 28.1 bits (63), Expect = 0.19
Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 1/48 (2%)
Query: 10 TVRVLRHGLEVSEMAVSELPSNPNAVWTVKRRSDDRVSLFHQPSISPS 57
T VL E ++ P P + ++RR RVS P
Sbjct: 81 TSEVLEQVKEYLQLPAFSTPP-PETLKRIQRRRYFRVSAPLSPPYYVQ 127
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1172
Score = 25.4 bits (55), Expect = 1.9
Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 18 LEVSEMAVSELPSNPNAVWTVKRRS-DDRVSLFHQPSISPSMI 59
L +E A ++ +V +K S D ++ + P+++
Sbjct: 114 LNKTETAQRKITPRLVSVPKLKFSSPADVPAINDFSNHHPAVV 156
>gnl|CDD|145054 pfam01700, Orbi_VP3, Orbivirus VP3 (T2) protein. The orbivirus VP3
protein is part of the virus core and makes a 'subcore'
shell made up of 120 copies of the 100K protein. VP3
particles can also bind RNA and are fundamental in the
early stages of viral core formation. Also found in the
family is structural core protein VP2 from broadhaven
virus which is similar to VP3 in bluetongue virus.
Orbivirus are part of the larger reoviridae which have a
dsRNA genome of 10-12 linear segments; orbivirus found
in this family include bluetongue virus and epizootic
hemorrhagic disease virus.
Length = 890
Score = 25.5 bits (56), Expect = 2.0
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 27 ELPSNPNAVWTVKRRS 42
+LP NPN +W V R S
Sbjct: 258 QLPVNPNVIWEVPRSS 273
>gnl|CDD|140234 PTZ00207, PTZ00207, hypothetical protein; Provisional.
Length = 591
Score = 24.8 bits (54), Expect = 3.5
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 4 GRGPRSTVRVLRHGLEVSEMAVSELPSNPNAVWTVKRRSDDRV 46
G P + L L AV L + +W+ KRR++DRV
Sbjct: 385 GEAPDDALNTLLTVLNGVGSAVGRLCMSYFEIWSQKRRAEDRV 427
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 24.2 bits (53), Expect = 4.4
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 7 PRSTVRVLRHGLEVSEMAVSELPSNPNAVWTV 38
PR R L L + + LP P +W +
Sbjct: 148 PRRLARALGQLLRSWYIYLFHLPVLPELLWRL 179
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 24.2 bits (53), Expect = 4.9
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 26/76 (34%)
Query: 4 GRGPRSTVRVL----RHGLEVSEMAVSELPSNPNAV--------------WTVKRRS--- 42
GR R+ +R L R E++ +A++EL ++ + W V++
Sbjct: 10 GRIGRNVLRALYESGRRA-EITVVAINEL-ADAEGMAHLLKYDTSHGRFAWDVRQERDQL 67
Query: 43 ---DDRVSLFHQPSIS 55
DD + L H+ I+
Sbjct: 68 FVGDDAIRLLHERDIA 83
>gnl|CDD|219573 pfam07781, Reovirus_Mu2, Reovirus minor core protein Mu-2. This
family represents the Reovirus core protein Mu-2. Mu-2
is a microtubule associated protein and is thought to
play a key role in the formation and structural
organisation of reovirus inclusion bodies.
Length = 735
Score = 23.7 bits (51), Expect = 7.5
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 39 KRRSDDRVSLFHQPSISPS 57
SD R+S + P ISPS
Sbjct: 112 HPPSDFRISDYFSPLISPS 130
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
0.318 0.130 0.386
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,950,312
Number of extensions: 191633
Number of successful extensions: 188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 11
Length of query: 61
Length of database: 10,937,602
Length adjustment: 32
Effective length of query: 29
Effective length of database: 9,518,274
Effective search space: 276029946
Effective search space used: 276029946
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: 53 (24.4 bits)