RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8925
(80 letters)
>gnl|CDD|216628 pfam01652, IF4E, Eukaryotic initiation factor 4E.
Length = 162
Score = 58.0 bits (141), Expect = 2e-12
Identities = 22/40 (55%), Positives = 27/40 (67%), Gaps = 3/40 (7%)
Query: 44 PLHNKWTLWYF---ENDKNKGWEENQREITSFSTVEDFWW 80
PL NKWTLWY DK+K +E+N + I +F TVEDFW
Sbjct: 1 PLQNKWTLWYDRRPPGDKSKDYEDNLKPIGTFDTVEDFWR 40
>gnl|CDD|227386 COG5053, CDC33, Translation initiation factor 4E (eIF-4E)
[Translation, ribosomal structure and biogenesis].
Length = 217
Score = 50.7 bits (121), Expect = 3e-09
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 7 SLYPSSLNKEKEQQPQENTTTTAVTTPEVESELMIKHPLHNKWTLWYFEN--DKNKGWEE 64
+ P T T ++ + M KHPL WTLW+ + D + W +
Sbjct: 4 EEVSKKFEENVSVDPTTKTPRTVLSD---SAHFMNKHPLAFHWTLWFLKPPEDGLESWSD 60
Query: 65 NQREITSFSTVEDFW 79
+ I +F TVE+FW
Sbjct: 61 LLKSIITFETVEEFW 75
>gnl|CDD|240238 PTZ00040, PTZ00040, translation initiation factor E4;
Provisional.
Length = 233
Score = 31.7 bits (72), Expect = 0.022
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 44 PLHNKWTLWYFEND----KNKGWEENQREITSFSTVEDFWW 80
PL KW +W K+ +++ + + SF +V+ FW
Sbjct: 39 PLSYKWVIWEQVVKETIRKSNDYKDYTKPLASFDSVQKFWQ 79
>gnl|CDD|188962 cd09563, SAM_liprin-beta1,2_repeat1, SAM domain of liprin-beta1,2
proteins repeat 1. SAM (sterile alpha motif) domain
repeat 1 of liprin-beta1,2 proteins is a
protein-protein interaction domain. Liprin-beta protein
contain three copies (repeats) of SAM domain. They may
form heterodimers with liprins-alpha through their SAM
domains. It was suggested based on bioinformatic
approaches that the second SAM domain of liprin-beta is
potentially able to form polymers. Liprins were
originally identified as LAR (leukocyte common
antigen-related) transmembrane protein-tyrosine
phosphatase-interacting proteins. They participate in
mammary gland development, in axon guidance, and in the
maintenance of lymphatic vessel integrity.
Length = 64
Score = 26.8 bits (60), Expect = 0.37
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 34 EVESELMIKHPLHNK 48
E+E EL IKHPLH K
Sbjct: 42 ELEKELGIKHPLHRK 56
>gnl|CDD|188893 cd09494, SAM_liprin-kazrin_repeat1, SAM domain of liprin/kazrin
proteins repeat 1. SAM (sterile alpha motif) domain
repeat 1 of liprin/kazrin proteins is a protein-protein
interaction domain. The long form of liprin/kazrin
proteins contains three copies (repeats) of the SAM
domain. Liprin-alpha may form heterodimers with
liprin-beta through their SAM domains. Liprins were
originally identified as LAR (leukocyte common
antigen-related) transmembrane protein-tyrosine
phosphatase-interacting proteins. They participate in
mammary gland development and in axon guidance. In
particular, liprin-alpha is involved in formation of
the presynaptic active zone; liprin-beta is involved in
the maintenance of lymphatic vessel integrity. Kazrins
are involved in interplay between desmosomes and
adherens junctions; additionally they play a role in
regulation of intercellular differentiation, junction
assembly, and cytoskeletal organization.
Length = 58
Score = 26.0 bits (57), Expect = 0.79
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 26 TTTAVTTPEVESELMIKHPLHNK 48
T ++ E+E EL IK+PLH K
Sbjct: 28 TLLTLSDQEMEKELGIKNPLHRK 50
>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
type)/S9(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S9 as well as archaeal
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 162
Score = 25.9 bits (57), Expect = 2.0
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 34 EVESELMIKHPLHNKWTLWYFEN 56
+ E +L+ K+ L NK +W E
Sbjct: 24 DRELKLVGKYGLRNKKEVWKAET 46
>gnl|CDD|187830 cd09699, Csm6_III-A, CRISPR/Cas system-associated protein Csm6.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein of this family often fused to HTH domain;
loosely associated with CRISPR/Cas systems.
Length = 360
Score = 26.0 bits (57), Expect = 2.5
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 23 ENTTTTAVTTPEVESELMIKHP-LHNKWTLWYFENDKNKGWEENQREITSFS 73
NT V+TP S I+ P ++ +W +D G E S +
Sbjct: 70 PNTKAVQVSTPARASNKDIESPNAYDLEEMWDANDDNQPGAPNRCFEANSAA 121
>gnl|CDD|131720 TIGR02672, cas_csm6, CRISPR type III-A/MTUBE-associated protein
Csm6. Members of this family as found in
CRISPR-associated (cas) gene regions in Streptococcus
thermophilus CNRZ1066, Staphylococcus epidermidis RP62A,
and Mycobacterium tuberculosis (strains CDC1551 and
H37Rv), as part of Mtube-type CRISPR/Cas systems. CRISPR
is a widespread form of direct repeat found in archaea
and bacteria, with distinctive subtypes each of which
has a characteristic sporadic distribution [Mobile and
extrachromosomal element functions, Other].
Length = 362
Score = 25.7 bits (56), Expect = 2.5
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 23 ENTTTTAVTTPEVESELMIKHP-LHNKWTLWYFENDKNKGWEENQREITSFS 73
NT V+TP S I+ P ++ +W +D G E S +
Sbjct: 70 PNTKAVQVSTPARASNKDIESPNAYDLEEMWDANDDNQPGAPNRCFEANSAA 121
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 25.4 bits (57), Expect = 3.8
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 67 REITSFSTVEDF 78
REI+S S DF
Sbjct: 347 REISSCSNCTDF 358
>gnl|CDD|217744 pfam03813, Nrap, Nrap protein. Members of this family are
nucleolar RNA-associated proteins (Nrap) which are
highly conserved from yeast (Saccharomyces cerevisiae)
to human. In the mouse, Nrap is ubiquitously expressed
and is specifically localised in the nucleolus. Nrap is
a large nucleolar protein (of more than 1000 amino
acids). Nrap appears to be associated with ribosome
biogenesis by interacting with pre-rRNA primary
transcript.
Length = 929
Score = 24.9 bits (55), Expect = 4.9
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 1 MNETKKSLYPSSLNKEKEQQPQENTTTTAVTTPE 34
+ + S Y S + E P N V TPE
Sbjct: 547 LEASSGSEYKSRVGLENSVPPNLNNAFLDVLTPE 580
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
0.307 0.122 0.381
Gapped
Lambda K H
0.267 0.0565 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,721,040
Number of extensions: 259125
Number of successful extensions: 194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 192
Number of HSP's successfully gapped: 19
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 53 (24.6 bits)