RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4259
(203 letters)
>gnl|CDD|192241 pfam09280, XPC-binding, XPC-binding domain. Members of this family
adopt a structure consisting of four alpha helices,
arranged in an array. They bind specifically and
directly to the xeroderma pigmentosum group C protein
(XPC) to initiate nucleotide excision repair.
Length = 59
Score = 93.8 bits (234), Expect = 9e-26
Identities = 41/59 (69%), Positives = 48/59 (81%)
Query: 135 LAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAG 193
LAFLR PQFQQ+R +VQQNPELLP +LQQ+GQSNP LL+LI NQE F+R+LNE G
Sbjct: 1 LAFLRNNPQFQQLRQMVQQNPELLPPLLQQLGQSNPQLLQLIQQNQEEFLRLLNEGAEG 59
>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 = 91.6 bits (228), Expect = 1e-24
Identities = 37/61 (60%), Positives = 45/61 (73%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
+D + V +LKEKI+ EKG +Y E QKLIY+GKIL DD L EY IDE F+VVM+SKP
Sbjct: 17 VDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSKP 76
Query: 83 K 83
K
Sbjct: 77 K 77
>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 = 94.2 bits (234), Expect = 5e-23
Identities = 51/111 (45%), Positives = 63/111 (56%), Gaps = 9/111 (8%)
Query: 92 PSDPTQPAGQESEATRPATAT----SDSMLKVFFERVNPYGGESE-----DPLAFLRTQP 142
P DP QP + A A AT + + +E +PL FLR QP
Sbjct: 196 PEDPEQPEPVQQTAASTAAATTETPQHGSVFEQAAQGGTEQPATEAAQGGNPLEFLRNQP 255
Query: 143 QFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPVAG 193
QFQQ+R VVQQNP+LLP +LQQIGQ NP LL+ IS + E F++MLNEPV
Sbjct: 256 QFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQISQHPEQFLQMLNEPVGE 306
Score = 81.5 bits (201), Expect = 2e-18
Identities = 51/114 (44%), Positives = 66/114 (57%), Gaps = 15/114 (13%)
Query: 15 QWQQTVSHLDVQEEVKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
Q Q+ ++ E VK+LKEKI++E+G + Y QKLIY+GKILSDD+ + EY I E
Sbjct: 9 QQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEKD 68
Query: 74 FIVVMLSKPK------------PTPAPYSGPSDPTQPAGQESEATRPATATSDS 115
F+VVM+SKPK PT AP PS P PA S A PA+A +
Sbjct: 69 FVVVMVSKPKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAA--PASAVEEK 120
>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 = 61.1 bits (149), Expect = 6e-13
Identities = 23/68 (33%), Positives = 41/68 (60%), Gaps = 3/68 (4%)
Query: 14 NQWQQTVSH-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
+T++ +D + V +LKEKI+ ++G + Q+LI++GK+L DD LSEY I +
Sbjct: 2 TLDGKTITLEVDPSDTVSELKEKIEDKEGIP--VDQQRLIFSGKVLEDDTTLSEYGIQDG 59
Query: 73 KFIVVMLS 80
+ ++L
Sbjct: 60 STLHLVLR 67
>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 = 61.1 bits (149), Expect = 6e-13
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 14 NQWQQTVSH-LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
+T++ + + V +LKEKI G E Q+LIY GK+L DD+ L++Y I +
Sbjct: 7 TLDGKTITLEVKPSDTVSELKEKIAELTGIP--PEQQRLIYKGKVLEDDRTLADYGIQDG 64
Query: 73 KFIVVMLS 80
I ++L
Sbjct: 65 STIHLVLR 72
>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 = 60.7 bits (148), Expect = 8e-13
Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
+ + V +LK KI +++G E Q+LIYAGKIL DD+ LS+Y I + + ++L
Sbjct: 14 VSPDDTVAELKAKIAAKEG--VPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVLR 69
>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 = 55.7 bits (135), Expect = 6e-11
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFI 75
++ + V LKEKI E G E Q+LIY+G++L DD+ LSEY +++ I
Sbjct: 17 VEEEITVLDLKEKIAEEVGIP--VEQQRLIYSGRVLKDDETLSEYKVEDGHTI 67
>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 = 37.5 bits (87), Expect = 3e-04
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
V LKEK+ + G E Q+L+ GKIL D L +Y + + +V++
Sbjct: 20 VADLKEKLAKKLG--LPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP 68
>gnl|CDD|128966 smart00727, STI1, Heat shock chaperonin-binding motif.
Length = 41
Score = 36.9 bits (86), Expect = 3e-04
Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 5/45 (11%)
Query: 133 DPLAFLRTQ-PQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELI 176
DP LR Q PQ Q + +QQNP++ L Q+ Q NP LL+LI
Sbjct: 1 DPEMALRLQNPQVQSLLQDMQQNPDM----LAQMLQENPQLLQLI 41
>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin. Ubiquitin (includes Ubq/RPL40e
and Ubq/RPS27a fusions as well as homopolymeric
multiubiquitin protein chains).
Length = 76
Score = 37.5 bits (87), Expect = 4e-04
Identities = 19/51 (37%), Positives = 33/51 (64%), Gaps = 2/51 (3%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 23 IENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
>gnl|CDD|220681 pfam10302, DUF2407, DUF2407 ubiquitin-like domain. This is a
family of proteins found in fungi. The function is not
known. This domain is related to the ubiquitin domain.
Length = 90
Score = 36.9 bits (86), Expect = 7e-04
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSE 66
V LK+ I+S E +LIYAG++L+D L+
Sbjct: 26 VAWLKKLIRSRLPQELSNRRLRLIYAGRLLNDSSKLAS 63
>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 = 35.2 bits (81), Expect = 0.003
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 13 QNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSE 66
Q QTVS + V +LK + S+ L + Q+LIY+GK+L D L +
Sbjct: 11 QKYEDQTVS-CFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRD 63
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 33.6 bits (77), Expect = 0.008
Identities = 16/41 (39%), Positives = 28/41 (68%), Gaps = 2/41 (4%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
V+Q+K +Q ++G + + +LIY+GK +SDD LS+Y +
Sbjct: 23 VQQVKMALQEKEGID--VKQIRLIYSGKQMSDDLKLSDYKV 61
>gnl|CDD|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2.
hPLIC-1 and hPLIC-2 (human homologs of the yeast
ubiquitin-like Dsk2 protein) are type2 UBL's
(ubiquitin-like) proteins that are thought to serve as
adaptors that link the ubiquitination machinery to the
proteasome. The hPLIC's have an N-terminal UBL domain
that binds the S5a subunit of the proteasome and a
C-terminal UBA (ubiquitin-associated) domain that binds
a ubiquitylated protein.
Length = 71
Score = 33.2 bits (76), Expect = 0.013
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 28 EVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
VK KE + + + E LI+AGKIL D L+++NI +
Sbjct: 21 SVKDFKEAVSKKFKAN--QEQLVLIFAGKILKDTDTLTQHNIKD 62
>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 = 32.0 bits (73), Expect = 0.032
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 18 QTVSHLDV--QEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
Q L+V QE V +K + +G E Q L+ AG L DD L + ++E
Sbjct: 8 QNTHTLEVTGQETVSDIKAHVAGLEG--IDVEDQVLLLAGVPLEDDATLGQCGVEE 61
>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 = 31.8 bits (72), Expect = 0.044
Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 9/57 (15%)
Query: 26 QEEVKQLKEKIQSEKGSEYL---AEYQKLIYAGKILSDDQALSEYNID-ESKFIVVM 78
+E V LK+ + SE+L E Q+L++ GK L+DD+ LS+Y+I +K +V+
Sbjct: 20 KESVSTLKKLV-----SEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVV 71
>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 = 0.092
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
+D ++KQLKE + +G + ++I+AGK L + + E ++ +
Sbjct: 15 VDPDTDIKQLKEVVAKRQGVP--PDQLRVIFAGKELRNTTTIQECDLGQ 61
>gnl|CDD|206052 pfam13881, Rad60-SLD_2, Ubiquitin-2 like Rad60 SUMO-like.
Length = 111
Score = 31.1 bits (71), Expect = 0.11
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 11/80 (13%)
Query: 29 VKQLKEKIQSEKGSEY-----LAEYQKLIYAGKILSDDQALSEYNIDESKF---IVVM-- 78
V LKEK+ ++ + KLI AGKIL +++ L E + + ++VM
Sbjct: 26 VADLKEKVLAQWPKDKEEGPKSPNDVKLINAGKILENNKTLGECRLPAGETPGGVIVMHV 85
Query: 79 -LSKPKPTPAPYSGPSDPTQ 97
+ P P P + P Q
Sbjct: 86 VVRPPLPEPNSEKKRNKPKQ 105
>gnl|CDD|176389 cd01794, DC_UbP_C, dendritic cell derived ubiquitin-like protein.
DC_UbP (dendritic cell derived ubiquitin-like protein)
is a ubiquitin-like protein from human dendritic cells
that is expressed in the mitochondrion. The
ubiquitin-like domain of this protein is found at the
C-terminus and lacks the canonical gly-gly motif of
ubiquitin required for ubiquitinization. DC_UbP is
expressed in tumor cells but not in normal human adult
tissue suggesting a role for DC_UbP in tumorogenesis.
Length = 70
Score = 30.2 bits (68), Expect = 0.12
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
V QLK+++Q+ +G + Q+ ++GK+L+D L E I + + V+++
Sbjct: 21 VGQLKKQLQAAEGVD--PCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIVN 70
>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 = 30.5 bits (69), Expect = 0.12
Identities = 13/49 (26%), Positives = 35/49 (71%), Gaps = 2/49 (4%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
++ ++V+++KE+++ ++G + Q+LIY+GK ++DD+ ++Y ++
Sbjct: 17 IEPTDKVERIKERVEEKEGIP--PQQQRLIYSGKQMNDDKTAADYKLEG 63
>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 = 30.1 bits (68), Expect = 0.16
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
L + + V LK KI E G A QKL Y G + D +L+ YN+
Sbjct: 14 LQLSDPVSVLKVKIHEETGMP--AGKQKLQYEGIFIKDSNSLAYYNL 58
>gnl|CDD|176392 cd01797, NIRF_N, amino-terminal ubiquitin-like domain of Np95
and NIRF. NIRF_N This CD represents the
amino-terminal ubiquitin-like domain of a family of
nuclear proteins that includes Np95 and NIRF
(Np95/ICBP90-like RING finger) protein. Both Np95 and
NIRF have a domain architecture consisting of a
ubiquitin-like domain, a PHD finger, a YDG/SRA domain,
Rb-binding motifs and a RING finger domain. Both Np95
and NIRF are ubiquitin ligases that ubiquitinate PCNP
(PEST-containing nuclear proteins). While Np95 is
capable of binding histones, NIRF is involved in cell
cycle regulation.
Length = 78
Score = 30.2 bits (68), Expect = 0.18
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 19 TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM 78
TV L +V++L+EKIQ E E Q+L Y GK + D L +YN+ + I+ +
Sbjct: 15 TVDSLSRLTKVEELREKIQELFNVE--PECQRLFYRGKQMEDGHTLFDYNVGLND-IIQL 71
Query: 79 LSKPKP 84
L + P
Sbjct: 72 LVRQDP 77
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 32.3 bits (74), Expect = 0.18
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 12/65 (18%)
Query: 26 QEEVKQLKEKIQ--SEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFI----VVML 79
+E ++ L+E ++ + +G LA A K L + E + ES + +
Sbjct: 492 EEGLRTLEEAVKELASEGLRVLA------VAYKKLDRAEKDDEVDEIESDLVFLGLTGIE 545
Query: 80 SKPKP 84
P+
Sbjct: 546 DPPRE 550
>gnl|CDD|221475 pfam12232, Myf5, Myogenic determination factor 5. This domain
family is found in eukaryotes, and is approximately 70
amino acids in length. The family is found in
association with pfam00010, pfam01586. There is a
conserved CSD sequence motif. Myf5 is responsible for
directing cells to the skeletal myocyte lineage during
development. Myf5 is likely to act in a similar way to
the other MRF4 proteins such as MyoD which perform the
same function. These are histone acetyltransferases and
histone deacetylases which activate and repress genes
involved in the myocyte lineage.
Length = 73
Score = 28.5 bits (64), Expect = 0.52
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 88 PYSGPSDPTQPAGQESEATRPATATSDSM 116
YSG + S+A+ P++ SD M
Sbjct: 3 YYSGDGE--------SDASSPSSNCSDGM 23
>gnl|CDD|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like
domain. DDI1_N DDI1 (DNA damage inducible protein 1)
has an amino-terminal ubiquitin-like domain, an
retroviral protease-like (RVP-like) domain, and a UBA
(ubiquitin-associated) domain. This CD represents the
amino-terminal ubiquitin-like domain of DDI1.
Length = 71
Score = 28.1 bits (63), Expect = 0.78
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
+D E++ K ++E G A Q+LIY G+ L D++ L + +VV+
Sbjct: 15 DVDPDLELENFKALCEAESGIP--ASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLRQ 71
>gnl|CDD|219903 pfam08559, Cut8, Cut8. In Schizosaccharomyces pombe, Cut8 is a
nuclear envelope protein that physically interacts with
and tethers 26S proteasome in the nucleus resulting in
the nuclear accumulation of proteasome. Cut8 is a
proteasome substrate and amino terminal residues 1-72
are polyubiquitinated and function as a degron tag.
Ubiquitination of the amino terminal is essential to the
function of Cut8. Lysine residues in the amino terminal
72 amino acids of Cut8 are required for physical
interaction with proteasome. In fission yeast the
function of Cut8 has been demonstrated to be regulated
by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating
enzymes Ubr1. Cut8 homologs have been identified in
Drosophila melanogaster, Anopheles gambiae and
Dictyostelium discoideum.
Length = 200
Score = 28.8 bits (65), Expect = 1.7
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 102 ESEATRPATATSDSMLKVFFERVN---PYGGESEDPLAFLRTQPQFQQ-MRTVVQQNPEL 157
RP+ +++ +L+ + + PYGG A+LR +P + + +
Sbjct: 57 RKILPRPSISSALEVLRDKKDNLYKSLPYGGSVSSDYAYLRVKPHLMEFLNCLSDFTLHF 116
Query: 158 LPTVLQQIGQS 168
LP Q S
Sbjct: 117 LPPNETQWDAS 127
>gnl|CDD|176397 cd01802, AN1_N, ubiquitin-like domain of AN1. AN1 (also known as
ANUBL1 and RSD-7) is ubiquitin-like protein with a
testis-specific expression in rats that has an
N-terminal ubiquitin-like domain and a C-terminal
zinc-binding domain. Unlike ubiquitin polyproteins and
most ubiquitin fusion proteins, the N-terminal
ubiquitin-like domain of An1 does not undergo
proteolytic processing. The function of AN1 is unknown.
Length = 103
Score = 27.5 bits (61), Expect = 1.8
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 27 EEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES---KFIVVM 78
E V +K KIQ +G Q LI+ L D+ L++YNI E K ++ M
Sbjct: 48 ETVISVKAKIQRLEGIP--VAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAM 100
>gnl|CDD|237612 PRK14108, PRK14108, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 986
Score = 29.2 bits (66), Expect = 1.8
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 17/93 (18%)
Query: 103 SEATRPA-TATSDSMLKVFFERVNPYGGESEDP----LA---FLRTQPQFQQMRTVVQQN 154
S R T + ++LK F E+ L FL+ P Q+ +++Q N
Sbjct: 524 SAEARERLTELTPALLKAF--------AETRRADEALLRFDRFLQGLPAGIQLFSLLQSN 575
Query: 155 PELLPTVLQQIGQSNPALLELISHNQEAFVRML 187
P+LL ++L I + P L ++I+ F +L
Sbjct: 576 PDLL-SLLVLIMGAAPRLADIIARRPHVFDGLL 607
>gnl|CDD|165539 PHA03282, PHA03282, envelope glycoprotein E; Provisional.
Length = 540
Score = 29.1 bits (65), Expect = 1.9
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 75 IVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATAT 112
+V ++ P+P P P G P G E+ A PAT
Sbjct: 155 VVFLVVGPRPVPTPPGGTPPPDDDEGDEAGA--PATPA 190
>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like. The
small ubiquitin-related modifier SUMO-1 is a Ub/Ubl
family member, and although SUMO-1 shares structural
similarity to Ub, SUMO's cellular functions remain
distinct insomuch as SUMO modification alters protein
function through changes in activity, cellular
localisation, or by protecting substrates from
ubiquitination. Rad60 family members contain
functionally enigmatic, integral SUMO-like domains
(SLDs). Despite their divergence from SUMO, each Rad60
SLD interacts with a subset of SUMO pathway enzymes:
SLD2 specifically binds the SUMO E2 conjugating enzyme
(Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also
called Uba2) activating and E3 (Pli1, also called Siz1
and Siz2) specificity enzymes. Structural analysis of
PDB:2uyz reveals a mechanistic basis for the
near-synonymous roles of Rad60 and SUMO in survival of
genotoxic stress and suggest unprecedented
DNA-damage-response functions for SLDs in regulating
SUMOylation. The Rad60 branch of this family is also
known as RENi (Rad60-Esc2-Nip45), and biologically it
should be two distinct families SUMO and RENi
(Rad60-Esc2-Nip45).
Length = 72
Score = 26.3 bits (59), Expect = 3.1
Identities = 11/53 (20%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQK--LIYAGKILSDDQALSEYNIDESKFIVVML 79
+ +L + ++G + Q+ LI+ G+ L + +++Y+I++ I V++
Sbjct: 23 LSKLINAYRKKRG---IPADQQVRLIFDGERLDPNDTVADYDIEDGDTIDVVI 72
>gnl|CDD|183318 PRK11797, PRK11797, D-ribose pyranase; Provisional.
Length = 139
Score = 27.5 bits (62), Expect = 3.2
Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 29/80 (36%)
Query: 135 LAFLRTQPQFQQMRTVV----------------QQNPELLPTVLQQIG-----QSNPALL 173
LA + P F + VV + NPEL +L Q+ Q N +
Sbjct: 42 LALTKGVPSFLDVLDVVLSEMQVEKAILAEEIKEHNPELHEALLTQLEQLEQHQGNTIEI 101
Query: 174 ELISHNQ--------EAFVR 185
E +SH + +A +R
Sbjct: 102 EYVSHEEFKQLTAESKAVIR 121
>gnl|CDD|176409 cd01814, NTGP5, Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4
are plant-specific isoprenylated GTP-binding proteins
with a single fold that resembles ubiquitin. The
function of these proteins is unknown.
Length = 113
Score = 27.1 bits (60), Expect = 3.4
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 29 VKQLKEKIQS------EKGSEYLAEYQKLIYAGKILSDDQALSEY 67
V LKE++ S E G + + E KLI AGKIL + + + E
Sbjct: 28 VDFLKERVVSQWPKDKEVGPKTVNEV-KLISAGKILENSKTVGEC 71
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 28.1 bits (62), Expect = 3.6
Identities = 23/92 (25%), Positives = 34/92 (36%), Gaps = 5/92 (5%)
Query: 81 KPKPTPAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFERVNPYGGESEDPLAFLRT 140
+P Y P P P Q + +P P + + P+A
Sbjct: 770 QPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVA---P 826
Query: 141 QPQFQQMRTVVQQNPE--LLPTVLQQIGQSNP 170
QPQ+QQ + V P+ LL +L + G S P
Sbjct: 827 QPQYQQPQQPVAPQPQDTLLHPLLMRNGDSRP 858
>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1. BAG1_N
N-terminal ubiquitin-like (Ubl) domain of the BAG1
protein. This domain occurs together with the BAG
domain and is closely related to the Ubl domain of a
family of deubiquitinases that includes Rpn11, UBP6
(USP14), USP7 (HAUSP).
Length = 71
Score = 26.1 bits (58), Expect = 3.9
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVV 77
+ Q LK+ + G E QKLI+ GK D + L + D SK +++
Sbjct: 15 SISSQATFGDLKKMLAPVTGVE--PRDQKLIFKGKERDDAETLDMSGVKDGSKVMLL 69
>gnl|CDD|201949 pfam01742, Peptidase_M27, Clostridial neurotoxin zinc protease.
These toxins are zinc proteases that block
neurotransmitter release by proteolytic cleavage of
synaptic proteins such as synaptobrevins, syntaxin and
SNAP-25.
Length = 408
Score = 28.1 bits (63), Expect = 3.9
Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 6 HDISDITQNQWQQTVSH-LDVQEEVKQLKEKIQSE-KGSEYLAEYQKLIYAGKILSDDQA 63
D+ IT + + L+ +++ + K+ S + + KLI+ K D +
Sbjct: 267 QDLKIITTSPYWFIYEKFLNNYKDIAKRLNKVNSAIPSNNAIINSYKLIFKQKYQFDKDS 326
Query: 64 LSEYNIDESKF 74
Y+++ +KF
Sbjct: 327 SGIYSVNLNKF 337
>gnl|CDD|110032 pfam01001, HCV_NS4b, Hepatitis C virus non-structural protein NS4b.
No precise function has been assigned to NS4b. However,
it is known that NS4b interacts with NS4a and NS3 to
form a large replicase complex to direct the viral RNA
replication.
Length = 192
Score = 27.3 bits (61), Expect = 4.0
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 96 TQPAGQESEATRPATATSDSMLKVFFERV 124
PA ++E+ PA A+ D+ + F+ +
Sbjct: 9 LPPAIDKAESITPAVASLDTKFEQFWAKH 37
>gnl|CDD|152424 pfam11989, Dsl1_C, Retrograde transport protein Dsl1 C terminal.
Dsl1 is a peripheral membrane protein required for
transport between the Golgi and the endoplasmic
reticulum. It is localised to the ER membrane, and in
vitro it specifically binds to coatomer, the major
component of the protein coat of COPI vesicles. Binding
sites for coatomer are found on a disorganised region
between the C and N termini of Dsl1. The C terminal
domain is involved in binding to the Sec39 subunit of
the Dsl1p complex. The N terminal complexes with another
subunit of the Dsl1p complex called Tip20 which forms
heterodimers by pairing the N termini of each protein.
Length = 291
Score = 27.8 bits (62), Expect = 4.4
Identities = 14/46 (30%), Positives = 19/46 (41%)
Query: 32 LKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVV 77
L I SEK SE L+E LI G + +Y K ++
Sbjct: 188 LSWDIISEKNSENLSELISLILNGTEIPSLNTYPKYRHLREKLAII 233
>gnl|CDD|151873 pfam11434, CHIPS, Chemotaxis-inhibiting protein CHIPS. The
chemotaxis inhibitory protein, CHIPS, is an excreted
virulence factor which acts by binding to C5a and
formylated peptide receptor (FPR), blocking phagocyte
responses. A fragment of CHIPS, which contains residues
31-121 comprises of an alpha helix packed onto a four
stranded anti-parallel beta-sheet. Most of the conserved
residues of CHIPS are present in the alpha-helix.
Length = 90
Score = 26.2 bits (57), Expect = 5.0
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 13/58 (22%)
Query: 158 LPTVLQQI----------GQSNPALLE---LISHNQEAFVRMLNEPVAGDRRNKNVLG 202
LPT L ++ G N A E +++ N+ + LN P+A DR+N +LG
Sbjct: 4 LPTTLGKLDERLRNYLKKGTKNSAQFEKMVILTENKGYYTVYLNTPLAEDRKNVELLG 61
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 27.6 bits (62), Expect = 5.3
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 24 DVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGK 56
++QE+V KE++ E A ++ I+ GK
Sbjct: 603 EIQEKVVTWKERLDKEVSDTTFATMKENIHEGK 635
>gnl|CDD|146930 pfam04534, Herpes_UL56, Herpesvirus UL56 protein. In herpes
simplex virus type 2, UL56 is thought to be a
tail-anchored type II membrane protein involved in
vesicular trafficking. The C terminal hydrophobic region
is required for association with the cytoplasmic
membrane, and the N terminal proline-rich region is
important for the translocation of UL56 to the Golgi
apparatus and cytoplasmic vesicles.
Length = 198
Score = 27.0 bits (59), Expect = 6.1
Identities = 13/37 (35%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 77 VMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATS 113
V ++ P S P D QP Q S RP T S
Sbjct: 151 VCAARTTEQPMGLSWPFD--QPRSQSSGLWRPPTVNS 185
>gnl|CDD|131213 TIGR02158, PA_CoA_Oxy3, phenylacetate-CoA oxygenase, PaaI subunit.
Phenylacetate-CoA oxygenase is comprised of a five gene
complex responsible for the hydroxylation of
phenylacetate-CoA (PA-CoA) as the second catabolic step
in phenylacetic acid (PA) degradation. Although the
exact function of this enzyme has not been determined,
it has been shown to be required for phenylacetic acid
degradation and has been proposed to function in a
multicomponent oxygenase acting on phenylacetate-CoA
[Energy metabolism, Other].
Length = 237
Score = 27.1 bits (60), Expect = 6.6
Identities = 14/45 (31%), Positives = 21/45 (46%)
Query: 120 FFERVNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQ 164
F GG ED LAF R + +F+ +R N + T+ +Q
Sbjct: 42 FLSLAGQLGGGDEDTLAFFRDEAEFRNLRLTELPNGDFALTIARQ 86
>gnl|CDD|239855 cd04390, RhoGAP_ARHGAP22_24_25, RhoGAP_ARHGAP22_24_25:
GTPase-activator protein (GAP) domain for Rho-like
GTPases found in ARHGAP22, 24 and 25-like proteins;
longer isoforms of these proteins contain an additional
N-terminal pleckstrin homology (PH) domain. ARHGAP25
(KIA0053) has been identified as a GAP for Rac1 and
Cdc42. Short isoforms (without the PH domain) of
ARHGAP24, called RC-GAP72 and p73RhoGAP, and of
ARHGAP22, called p68RacGAP, has been shown to be
involved in angiogenesis and endothelial cell capillary
formation. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 199
Score = 26.6 bits (59), Expect = 7.4
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 124 VNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELL 158
N + EDP + PQ QQ+ TV+ E L
Sbjct: 164 PNILRPKVEDPATIMEGTPQIQQLMTVMISKHEPL 198
>gnl|CDD|235540 PRK05641, PRK05641, putative acetyl-CoA carboxylase biotin carboxyl
carrier protein subunit; Validated.
Length = 153
Score = 26.4 bits (58), Expect = 7.6
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 79 LSKPKPTPAPYSGPSDPTQPAGQESEATRPATA 111
+ + PTPAP P+ P+ P A PA A
Sbjct: 48 VQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAPA 80
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 27.3 bits (60), Expect = 8.5
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 138 LRTQPQFQQMRTVVQQNPEL--LPTVLQQIGQSNPALLELISHNQEAFVRM 186
L T +F V +L + ++ G + LL+ H EA R
Sbjct: 1947 LNTYERFVDTNVAVNPLDQLTRHVLLAKEPGMLSEKLLDRCMH-VEASDRF 1996
>gnl|CDD|233329 TIGR01245, trpD, anthranilate phosphoribosyltransferase. In many
widely different species, including E. coli, Thermotoga
maritima, and Archaeoglobus fulgidus, this enzymatic
domain (anthranilate phosphoribosyltransferase) is found
C-terminal to glutamine amidotransferase; the fusion
protein is designated anthranilate synthase component II
(EC 4.1.3.27) [Amino acid biosynthesis, Aromatic amino
acid family].
Length = 330
Score = 26.8 bits (60), Expect = 9.4
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 24 DVQEEVKQLKEKIQSEKGSEYLAEYQKL 51
D++E V+ E I S +E L E
Sbjct: 303 DLKEGVELALEAIDSGAAAEKLEELVAF 330
>gnl|CDD|235303 PRK04517, PRK04517, hypothetical protein; Provisional.
Length = 216
Score = 26.4 bits (58), Expect = 9.9
Identities = 21/104 (20%), Positives = 42/104 (40%), Gaps = 11/104 (10%)
Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD--QALSEYNIDESKFIVVML 79
++ +K ++ ++ E+G KLI G + D + +EYN V L
Sbjct: 106 ARQAEKAIKTMQWQLVDEQGKAVEVRQDKLIKEGMQIGRDYEREAAEYN---KTGGVAAL 162
Query: 80 SKPKPTPAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFER 123
+ P + + QP Q+ + A T++ ML ++ +
Sbjct: 163 ATP------VTLSAMAVQPVAQQEISNATADNTAEEMLHFWYNK 200
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
0.311 0.128 0.356
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,194,987
Number of extensions: 930835
Number of successful extensions: 1204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1187
Number of HSP's successfully gapped: 85
Length of query: 203
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 111
Effective length of database: 6,857,034
Effective search space: 761130774
Effective search space used: 761130774
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 (21.8 bits)
S2: 57 (25.7 bits)