RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2142
(168 letters)
>gnl|CDD|218248 pfam04758, Ribosomal_S30, Ribosomal protein S30.
Length = 53
Score = 63.9 bits (156), Expect = 1e-14
Identities = 29/38 (76%), Positives = 33/38 (86%)
Query: 125 TEMVEKQEKKKKKTGRAKRRVQYNRRFVNVVQTFGRRR 162
T VEKQEKKKK TGRAK+R+QYNRRFVNVV FG++R
Sbjct: 16 TPKVEKQEKKKKPTGRAKKRLQYNRRFVNVVPGFGKKR 53
>gnl|CDD|176388 cd01793, Fubi, Fubi ubiquitin-like protein. Fubi is a
ubiquitin-like protein encoded by the fau gene which has
an N-terminal ubiquitin-like domain (also referred to
as FUBI) fused to the ribosomal protein S30. Fubi is
thought to be a tumor suppressor protein and the FUBI
domain may act as a substitute or an inhibitor of
ubiquitin or one of ubiquitin's close relatives UCRP,
FAT10, and Nedd8.
Length = 74
Score = 61.7 bits (150), Expect = 2e-13
Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 54 VRGQSNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSIS---DLESGS 110
VR Q+ + LE ETVS +K VA LE + +ED L+ +G L DD ++ E +
Sbjct: 5 VRAQNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCT 64
Query: 111 IEIFVPLLGG 120
+E+ LLGG
Sbjct: 65 LEVAGRLLGG 74
>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 = 43.0 bits (102), Expect = 2e-06
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 54 VRGQSNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISD--LESGSI 111
LE ++TVS LK K+ E + ++ LI SGK L DD ++S+ ++ GS
Sbjct: 2 TLDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGST 61
>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 = 43.0 bits (102), Expect = 2e-06
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 51 RIIVR--GQSNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISDL 106
+ V+ LE + ++TVS LK K+A L + E LI GK L DD +++D
Sbjct: 2 ELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADY 59
>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 = 41.5 bits (98), Expect = 7e-06
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 55 RGQSNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISD 105
+ LE ++TV+ LK K+A+ E V E LI +GK L DD ++SD
Sbjct: 5 LTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSD 55
>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 = 33.7 bits (77), Expect = 0.007
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 51 RIIVRGQSNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISDLE 107
++ + L TV+ LK K+A + E L+ +GK L D L++ D
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYG 57
>gnl|CDD|185646 PTZ00467, PTZ00467, 40S ribosomal protein S30; Provisional.
Length = 66
Score = 33.2 bits (75), Expect = 0.007
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 124 KTEMVEKQEKKKKKTGRAKRRVQYNRRFV 152
+T V KQEK K+ GRA +R++Y RRF+
Sbjct: 17 QTPKVAKQEKPKQPRGRALKRLKYTRRFL 45
>gnl|CDD|176405 cd01810, ISG15_repeat2, ISG15 ubiquitin-like protein, second repeat
of 2. ISG15 is a ubiquitin-like protein containing two
ubiquitin homology domains and 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 = 74
Score = 33.3 bits (76), Expect = 0.009
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 55 RGQSNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISD 105
+G+S+ + E Q +TV+ LK +V+ E+V + F L G+ + D+ + +
Sbjct: 7 KGRSS-IYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGE 56
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 32.5 bits (74), Expect = 0.019
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 69 TVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISD--LESGS-IEIFVPLLGG 120
TV +K + E + ++ LI SGK ++DDL +SD + GS I + + L GG
Sbjct: 22 TVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRGG 76
>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein. Nedd8 (also known
as Rub1) has a single conserved ubiquitin-like domain
that is part of a protein modification pathway similar
to that of ubiquitin. Nedd8 modifies a family of
molecular scaffold proteins called cullins that are
responsible for assembling the ROC1/Rbx1 RING-based E3
ubiquitin ligases, of which several play a direct role
in tumorigenesis.
Length = 76
Score = 31.7 bits (72), Expect = 0.031
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 62 LECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISD--LESGSI 111
++ + + V +K +V E + + LI SGK + DD + +D LE GS+
Sbjct: 15 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSV 66
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
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 = 378
Score = 33.7 bits (77), Expect = 0.035
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 57 QSNYVLECQQNETVSHLKNKVASL---EKVALEDFSLICSGKTLTDDLSISD 105
Q + ++ + +ETV LK K+ + + + LI SGK L+DD ++ +
Sbjct: 10 QQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKE 61
>gnl|CDD|176393 cd01798, parkin_N, amino-terminal ubiquitin-like of parkin protein.
parkin_N parkin protein is a RING-type E3 ubiquitin
ligase with an amino-terminal ubiquitin-like (Ubl)
domain and an RBR signature consisting of two RING
finger domains separated by an IBR/DRIL domain.
Naturally occurring mutations in parkin are thought to
cause the disease AR_JP (autosomal-recessive juvenile
parkinsonism). Parkin binds the Rpn10 subunit of 26S
proteasomes through its Ubl domain.
Length = 70
Score = 30.5 bits (69), Expect = 0.081
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 52 IIVRGQSNY--VLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSIS--DLE 107
+ VR + + +E + + LK VA + V + +I +GK L + +I DL
Sbjct: 1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLG 60
Query: 108 SGSI 111
SI
Sbjct: 61 QQSI 64
>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 = 30.4 bits (69), Expect = 0.12
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 57 QSNYVLECQQNETVSHLKNKVASLEK---VALEDFSLICSGKTLTDDLSISD 105
Q + +E ++TV+ LK K+ EK E LI SGK L DD ++ +
Sbjct: 10 QQTFPIEVDPDDTVAELKEKIEE-EKGCDYPPEQQKLIYSGKILKDDTTLEE 60
>gnl|CDD|176385 cd01790, Herp_N, Homocysteine-responsive endoplasmic
reticulum-resident ubiquitin-like domain protein. Herp
(Homocysteine-responsive endoplasmic reticulum-resident
ubiquitin-like domain protein) , is an integral membrane
protein that is induced by the endoplasmic reticulum
(ER) stress response pathway and is involved in
improving the balance of folding capacity and protein
loads in the ER. Herp has an N-terminal ubiquitin-like
domain that is involved in Herp degradation, but is not
necessary for its enhancement of amyloid beta-protein
generation.
Length = 79
Score = 29.4 bits (66), Expect = 0.28
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 57 QSNYVLECQQNETVSHLKNKVASL--EKVALEDFSLICSGKTLTDDLSISDL 106
+ + C N TV LK ++ + K +D LI SGK L D L + D+
Sbjct: 13 YEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDV 64
>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin. Ubiquitin (includes Ubq/RPL40e and
Ubq/RPS27a fusions as well as homopolymeric
multiubiquitin protein chains).
Length = 76
Score = 28.3 bits (63), Expect = 0.50
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 62 LECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISD 105
LE + ++T+ ++K K+ E + + LI +GK L D ++SD
Sbjct: 15 LEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD 58
>gnl|CDD|239530 cd03446, MaoC_like, MoaC_like Similar to the MaoC (monoamine
oxidase C) dehydratase regulatory protein but without
the N-terminal PutA domain. This protein family has a
hot-dog fold similar to that of (R)-specific enoyl-CoA
hydratase, the peroxisomal
Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the
fatty acid synthase beta subunit.
Length = 140
Score = 28.0 bits (63), Expect = 1.6
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 123 LKTEMVEKQEKKKKKTGRAKRRVQ-YNRRFVNVVQT 157
+ E+VEK+EK + G RR++ N+R VVQ+
Sbjct: 99 AEAEVVEKEEKDGEDAGVVTRRIEVVNQR-GEVVQS 133
>gnl|CDD|176402 cd01807, GDX_N, ubiquitin-like domain of GDX. GDX contains an
N-terminal ubiquitin-like domain as well as an
uncharacterized c-terminal domain. The function of GDX
is unknown.
Length = 74
Score = 26.4 bits (58), Expect = 2.3
Identities = 18/48 (37%), Positives = 24/48 (50%)
Query: 62 LECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISDLESG 109
L+ + E+VS LK V+ V E L+ GK L DD +SD G
Sbjct: 15 LQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIG 62
>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 = 26.4 bits (59), Expect = 2.6
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 56 GQSNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTDDLSISD 105
+ ++ TV LK K+A + +E LI SG+ L DD ++S+
Sbjct: 9 DSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSE 58
>gnl|CDD|176399 cd01804, midnolin_N, Ubiquitin-like domain of midnolin. midnolin_N
Midnolin (midbrain nucleolar protein) is expressed in
the nucleolus and is thought to regulate genes involved
in neurogenesis. Midnolin contains an amino-terminal
ubiquitin-like domain.
Length = 78
Score = 25.9 bits (57), Expect = 4.7
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 58 SNYVLECQQNETVSHLKNKVASLEKVALEDFSLICSGKTLTD----DLSISDLESGSIEI 113
+ + L +ETV LK +++ KV E +L+ L+ DL + D GS
Sbjct: 12 TRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSGKLQDLGLGD---GSKLT 68
Query: 114 FVP 116
VP
Sbjct: 69 LVP 71
>gnl|CDD|152344 pfam11909, NdhN, NADH-quinone oxidoreductase cyanobacterial subunit
N. The proton-pumping NADH:ubiquinone oxidoreductase
catalyzes the electron transfer from NADH to ubiquinone
linked with proton translocation across the membrane. It
is the largest, most complex and least understood of the
respiratory chain enzymes and is referred to as Complex
I. The subunit composition of the enzyme varies between
groups of organisms. Complex I originating from
mammalian mitochondria contains 45 different proteins,
whereas in bacteria, the corresponding complex NDH-1
consists of 14 different polypeptides. Homologues of
these 14 proteins are found among subunits of the
mitochondrial complex I, and therefore bacterial NDH-1
might be considered a model proton-pumping NADH
dehydrogenase with a minimal set of subunits.
Escherichia coli NDH-1 readily disintegrates into 3
subcomplexes: a water-soluble NADH dehydrogenase
fragment (NuoE, -F, and -G),the connecting fragment
(NuoB, -C, -D, and -I), and the membrane fragment (NuoA,
-H, -J, -K, -L, -M, -N). In cyanobacteria and their
descendants, the chloroplasts of green plants, the
subunit composition of NDH-1 remains obscure. The genes
for eleven subunits NdhA-NdhK, homologous to the
NuoA-NuoD and NuoH-NuoN of the E. coli complex, have
been found in the genome of Synechocystis sp. PCC 6803
which has a family of 6 ndhD genes and a family of 3
ndhF genes. Two reported multisubunit complexes, NDH-1L
and NDH-1M, represent distinct NDH-1 complexes in the
thylakoid membrane of Synechocystis 6803
-cyanobacterium. NDH-1L was shown to be essential for
photoheterotrophic cell growth, whereas expression of
NDH-1M was a prerequisite for CO2 uptake and played an
important role in growth of cells at low CO2. Here we
report the subunit composition of these two complexes.
Fifteen proteins were discovered in NDH-1L including
NdhL, a new component of the membrane fragment, and
Ssl1690 (designated as NdhO), a novel peripheral
subunit. The cyanobacterial NDH-1 complex contains
additional subunits, NdhM and NdhN, compared with the
minimal set of the bacterial enzyme and these seem to be
specific for thylakoid-located NDH-1 of photosynthetic
organisms.
Length = 154
Score = 26.5 bits (59), Expect = 6.2
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 90 LICSGKTLTDDLSISDLESGSIEIFVPLLGG 120
L+ SG+ DL ++G++ ++ PL GG
Sbjct: 3 LLLSGRKFRRDLE----KAGALAVYAPLEGG 29
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 26.8 bits (60), Expect = 6.8
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 121 KLLKTEMVEKQEKKKKKTGRAKRRVQYNRRFVNVVQTFGRRRGPNANS 168
K + + EK+EK+K+K + K+R + + G+RR P+ S
Sbjct: 393 KKVLAKRAEKKEKEKEKP-KVKKRHRDTKN-------IGKRRKPSGTS 432
>gnl|CDD|224644 COG1730, GIM5, Predicted prefoldin, molecular chaperone implicated
in de novo protein folding [Posttranslational
modification, protein turnover, chaperones].
Length = 145
Score = 26.2 bits (58), Expect = 7.8
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 46 IENMKRIIVRGQSNYVLECQQNETVSHLKNKVASLEK 82
+++M ++IV S Y E +E + LK ++ LEK
Sbjct: 72 VKDMDKVIVSIGSGYYAEKSADEAIEFLKKRIEELEK 108
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
0.317 0.131 0.364
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,196,652
Number of extensions: 723916
Number of successful extensions: 795
Number of sequences better than 10.0: 1
Number of HSP's gapped: 790
Number of HSP's successfully gapped: 38
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
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: 55 (25.0 bits)