RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10057
(99 letters)
>gnl|CDD|176395 cd01800, SF3a120_C, Ubiquitin-like domain of Mammalian splicing
factor SF3a_120. SF3a120_C Mammalian splicing factor
SF3a consists of three subunits of 60, 66, and 120 kDa
and functions early during pre-mRNA splicing by
converting the U2 snRNP to its active form. The 120kDa
subunit (SF3a120) has a carboxy-terminal ubiquitin-like
domain and two SWAP (suppressor-of-white-apricot)
domains, referred to collectively as the SURP module,
at its amino-terminus.
Length = 76
Score = 55.2 bits (133), Expect = 8e-12
Identities = 25/40 (62%), Positives = 30/40 (75%)
Query: 55 PEWKLNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL 94
PEWKLNGQ L+ +L L V+ LK +IH+ GMPAGKQKL
Sbjct: 1 PEWKLNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKL 40
>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL. UBLs function by
remodeling the surface of their target proteins,
changing their target's half-life, enzymatic activity,
protein-protein interactions, subcellular localization
or other properties. At least 10 different
ubiquitin-like modifications exist in mammals, and
attachment of different ubls to a target leads to
different biological consequences. Ubl-conjugation
cascades are initiated by activating enzymes, which
also coordinate the ubls with their downstream
pathways.
Length = 69
Score = 34.2 bits (79), Expect = 0.001
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 57 WKLNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL 94
L G+T L + +V LK++I G+P +Q+L
Sbjct: 3 KTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRL 40
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A
number of them are thought to carry a distinctive
five-residue motif termed the proteasome-interacting
motif (PIM), which may have a biologically significant
role in protein delivery to proteasomes and recruitment
of proteasomes to transcription sites.
Length = 69
Score = 33.7 bits (78), Expect = 0.002
Identities = 14/36 (38%), Positives = 25/36 (69%)
Query: 59 LNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL 94
L+G+T++L +D +V+ LK +I D G+P +Q+L
Sbjct: 3 LDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRL 38
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 32.2 bits (74), Expect = 0.007
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 59 LNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL 94
L+G+T++L + +V+ LK +I +L G+P +Q+L
Sbjct: 8 LDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRL 43
>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin. Ubiquitin (includes Ubq/RPL40e
and Ubq/RPS27a fusions as well as homopolymeric
multiubiquitin protein chains).
Length = 76
Score = 28.7 bits (64), Expect = 0.19
Identities = 11/36 (30%), Positives = 24/36 (66%)
Query: 59 LNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL 94
L G+T++L ++ ++ +K++I D G+P +Q+L
Sbjct: 8 LTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRL 43
>gnl|CDD|176387 cd01792, ISG15_repeat1, ISG15 ubiquitin-like protein, first
repeat of 2. ISG15 is a ubiquitin-like protein
containing two ubiquitin homology domains that becomes
conjugated to a variety of proteins when cells are
treated with type I interferon or lipopolysaccharide.
Although ISG15 has properties similar to those of other
ubiquitin-like molecules, it is a unique member of the
ubiquitin-like superfamily, whose expression and
conjugation to target proteins are tightly regulated by
specific signaling pathways, indicating it may have
specialized functions in the immune system.
Length = 80
Score = 28.0 bits (62), Expect = 0.36
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 59 LNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL-HLD 97
L G +SL +V+ LK QI IG+PA +Q+L HLD
Sbjct: 10 LGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLD 49
>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein.
Scythe protein (also known as Bat3) is an apoptotic
regulator that is highly conserved in eukaryotes and
contains a ubiquitin-like domain near its N-terminus.
Scythe binds reaper, a potent apoptotic inducer, and
Scythe/Reaper are thought to signal apoptosis, in part
through regulating the folding and activity of
apoptotic signaling molecules.
Length = 72
Score = 26.8 bits (60), Expect = 0.65
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 59 LNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL 94
L+ QT + +++ +V LK +I + +G+P +Q+L
Sbjct: 8 LDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRL 43
>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23. RAD23 belongs
to a family of adaptor molecules having affinity for
both the proteasome and ubiquitinylated proteins and
thought to shuttle these ubiquitinylated proteins to
the proteasome for destruction. RAD23 interacts with
ubiquitin through its C-terminal ubiquitin-associated
domains (UBA) and with the proteasome through its
N-terminal ubiquitin-like domain (UBL).
Length = 77
Score = 26.1 bits (58), Expect = 1.5
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 59 LNGQTLSLSLDLRTSVTALKSQIHDLIG--MPAGKQKL 94
L QT + +D +V LK +I + G P +QKL
Sbjct: 8 LKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKL 45
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell
cycle progression. Other family members are protein
modifiers that perform a wide range of functions.
Ubiquitination usually results in a covalent bond
between the C-terminus of ubiquitin and the
epsilon-amino group of a substrate lysine. The
three-step mechanism requires an activating enzyme (E1)
that forms a thiol ester with the C-terminal carboxy
group, a conjugating enzyme (E2) that transiently
carries the activated ubiquitin molecule as a thiol
ester, and a ligase (E3) that transfers the activated
ubiquitin from the E2 to the substrate lysine residue.
In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 25.9 bits (57), Expect = 1.9
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 57 WKLNGQTLSLSLDLRTSVTALKSQIHDLIGMPAGKQKL 94
+G+T+ L + T+V LK ++ +G+P +Q+L
Sbjct: 3 KLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRL 40
>gnl|CDD|236910 PRK11433, PRK11433, aldehyde oxidoreductase 2Fe-2S subunit;
Provisional.
Length = 217
Score = 26.3 bits (58), Expect = 2.4
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 49 PNMTDKPEWKLNGQTLSLSLDLRTS-VTALKSQIHDLIGMPAG 90
K+NG+T L +D RT+ + AL+ +H L G G
Sbjct: 46 APEISPVTLKVNGKTEQLEVDTRTTLLDALREHLH-LTGTKKG 87
>gnl|CDD|235767 PRK06277, PRK06277, hydrogenase subunit F; Validated.
Length = 478
Score = 26.1 bits (58), Expect = 3.1
Identities = 10/48 (20%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 30 EQVFLSKMATPNVTFNVVVPNMTDKPEWKLNGQTLSLSLDLRTSVTAL 77
+Q+ + ++ + V++ + +K K +G + L L SV+A+
Sbjct: 74 KQIIIFVLSL--IASLVLITGLGEK---KSSGLYVFLMLMGLASVSAI 116
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 26.0 bits (58), Expect = 3.8
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 5/22 (22%)
Query: 38 ATPNVTFNVVVP-----NMTDK 54
A+ N+T N V P +MTDK
Sbjct: 167 ASRNITVNAVAPGFIDTDMTDK 188
>gnl|CDD|236199 PRK08244, PRK08244, hypothetical protein; Provisional.
Length = 493
Score = 25.9 bits (57), Expect = 4.9
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 60 NGQTLSLSLDLRTSVTALKSQIHDLIGMP 88
N + + D AL+S + DL+G P
Sbjct: 336 NTEVQTKLFDFTRPGLALRSMLSDLLGFP 364
>gnl|CDD|233225 TIGR00994, 3a0901s05TIC20, chloroplast protein import component,
Tic20 family. Two families of proteins are involved in
the chloroplast envelope import appartus.They are the
three proteins of the outer membrane (TOC) and four
proteins in the inner membrane (TIC). This family is
specific for the Tic20 protein [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 267
Score = 25.3 bits (55), Expect = 6.1
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 34 LSKMATPNVTFNVVVPNMTDKPEW 57
A + P MT+KP W
Sbjct: 92 EPPRAAKDDFSKFRFPPMTEKPRW 115
>gnl|CDD|218800 pfam05895, DUF859, Siphovirus protein of unknown function (DUF859).
This family consists of several uncharacterized
proteins from the Siphoviruses as well as one bacterial
sequence. Some of the members of this family are
described as putative minor structural proteins.
Length = 534
Score = 25.1 bits (55), Expect = 8.0
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 26 SLIPEQVFLSKMATPNVTFN 45
+++ F+ M+ VTFN
Sbjct: 241 NIVTGNNFVQIMSNIKVTFN 260
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
0.312 0.130 0.371
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,906,020
Number of extensions: 385940
Number of successful extensions: 234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 22
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.3 bits)