RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4181
(73 letters)
>gnl|CDD|176386 cd01791, Ubl5, UBL5 ubiquitin-like modifier. UBL5 (also known as
HUB1) is a ubiquitin-like modifier that is both widely
expressed and highly phylogenetically conserved. At
the C-terminal end of the ubiquitin-like fold of UBL5
is a di-tyrosine motif followed by a single variable
residue instead of the characteristic di-glycine found
in all other ubiquitin-like modifiers. ULB5 interacts
with a cyclin-like kinase called CLK4 but not with
other cyclin-like kinase family members.
Length = 73
Score = 146 bits (370), Expect = 3e-48
Identities = 67/73 (91%), Positives = 69/73 (94%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDY 60
MIE+ CNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTR EKIVLKKWYTIFKDHI + DY
Sbjct: 1 MIEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDY 60
Query: 61 EIHDGMNLELYYQ 73
EIHDGMNLELYYQ
Sbjct: 61 EIHDGMNLELYYQ 73
>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 = 64.6 bits (158), Expect = 7e-16
Identities = 25/69 (36%), Positives = 34/69 (49%)
Query: 5 TCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHD 64
T GK ++ +PDDT+ +LK IAA+ G E+ L I KD + DY I D
Sbjct: 1 TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQD 60
Query: 65 GMNLELYYQ 73
G L L +
Sbjct: 61 GSTLHLVLR 69
>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 = 44.8 bits (106), Expect = 3e-08
Identities = 19/63 (30%), Positives = 29/63 (46%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK V + T+ DLK+ +A + G E+ L I D + + DY + DG L L
Sbjct: 7 GKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVL 66
Query: 71 YYQ 73
+
Sbjct: 67 VPR 69
>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 = 32.6 bits (75), Expect = 0.002
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFK-----DHIRIMDYEIHDG 65
GK + ++ +P DT+ +LK+ I + G ++ L IF D + +Y I DG
Sbjct: 5 GKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRL-----IFSGKVLEDDTTLSEYGIQDG 59
Query: 66 MNLELY 71
L L
Sbjct: 60 STLHLV 65
>gnl|CDD|237300 PRK13199, psaB, photosystem I P700 chlorophyll a apoprotein A2;
Provisional.
Length = 742
Score = 30.9 bits (70), Expect = 0.036
Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 47 WYTIFKDHIRIMDYEIHDGMNLELYYQ 73
WY I H D+E HDGM E YQ
Sbjct: 22 WYGIATAH----DFESHDGMTEENLYQ 44
>gnl|CDD|176995 CHL00054, psaB, photosystem I P700 chlorophyll a apoprotein A2.
Length = 734
Score = 29.7 bits (67), Expect = 0.093
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 4/27 (14%)
Query: 47 WYTIFKDHIRIMDYEIHDGMNLELYYQ 73
W+ I H D+E HD + E YQ
Sbjct: 22 WFGIATAH----DFESHDDITEERLYQ 44
>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 = 29.5 bits (66), Expect = 0.11
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGT-RWEKIVLKKWYT--IFKDHIRIMDYEIHDG 65
+K ++ PD+T+ +LK+ I A+ G + K Y+ I D + +Y+I +
Sbjct: 10 QQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEK 67
>gnl|CDD|152797 pfam12362, DUF3646, DNA polymerase III gamma and tau subunits C
terminal. This domain family is found in bacteria, and
is approximately 120 amino acids in length. The family
is found in association with pfam00004. The proteins in
this family are frequently annotated as the gamma and
tau subunits of DNA polymerase III, however there is
little accompanying literature to back this up.
Length = 117
Score = 27.5 bits (62), Expect = 0.34
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 20 PDDTIGDLKKLIAAQTGTRW 39
P D L + + TG RW
Sbjct: 48 PRDLAQRLGRKLQEWTGRRW 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 = 26.8 bits (60), Expect = 0.35
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIR 56
IE+T GK + ++ P DT+ +LK+ IA TG E+ L I+ +D
Sbjct: 1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRL-----IYKGKVLEDDRT 55
Query: 57 IMDYEIHDGMNLELY 71
+ DY I DG + L
Sbjct: 56 LADYGIQDGSTIHLV 70
>gnl|CDD|130403 TIGR01336, psaB, photosystem I core protein PsaB. The core
proteins of photosystem I are PsaA and PsaB, homologous
integral membrane proteins that form a heterodimer. The
heterodimer binds the electron-donating chlorophyll
dimer P700, as well as chlorophyll, phylloquinone, and
4FE-4S electron acceptors. This model describes PsaB
only [Energy metabolism, Photosynthesis].
Length = 734
Score = 27.2 bits (60), Expect = 0.64
Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 47 WYTIFKDHIRIMDYEIHDGMNLELYYQ 73
WY I H D+E HDGM E YQ
Sbjct: 21 WYGIATAH----DFESHDGMTEENLYQ 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 = 0.70
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYT--IFKDHIRIMD 59
++IT + ++ +PDDT+ +LK+ I + G + K Y+ I KD + +
Sbjct: 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEE 60
Query: 60 YEIHDG 65
Y+I +
Sbjct: 61 YKIDEK 66
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 25.9 bits (57), Expect = 0.96
Identities = 15/63 (23%), Positives = 29/63 (46%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GKK PD+T+ +K + + G ++I L D +++ DY++ G + +
Sbjct: 10 GKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHM 69
Query: 71 YYQ 73
Q
Sbjct: 70 VLQ 72
>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 = 25.5 bits (56), Expect = 1.2
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKI 42
G V+ +PD I LK+++A + G +++
Sbjct: 7 TGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQL 39
>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 = 25.3 bits (56), Expect = 1.2
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTG 36
G+ + + T GDLKK++A TG
Sbjct: 9 GESHDLSISSQATFGDLKKMLAPVTG 34
>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 = 25.2 bits (55), Expect = 2.0
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWY---TIFKDHIRIMDYEIHDG 65
GK V++ + DT+G LKK + A G ++W+ + D R+ + +I
Sbjct: 8 GKDVKLSVSSKDTVGQLKKQLQAAEGV---DPCCQRWFFSGKLLTDKTRLQETKIQKD 62
>gnl|CDD|133100 cd06242, M14-like_1_5, Peptidase M14-like domain; uncharacterized
subgroup. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 268
Score = 25.8 bits (57), Expect = 2.1
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 6/36 (16%)
Query: 26 DLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYE 61
D KL QT +K+ ++ F HI I +E
Sbjct: 123 DHTKLARQQT------RDIKEAFSKFNPHIAIDAHE 152
>gnl|CDD|223224 COG0146, HyuB, N-methylhydantoinase B/acetone carboxylase, alpha
subunit [Amino acid transport and metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 563
Score = 25.7 bits (57), Expect = 2.4
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 20 PDDTIGDLKKLIAA 33
PD IGDLK IAA
Sbjct: 176 PDYNIGDLKAQIAA 189
>gnl|CDD|235620 PRK05841, flgE, flagellar hook protein FlgE; Validated.
Length = 603
Score = 25.6 bits (56), Expect = 2.5
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 9/44 (20%)
Query: 2 IEITCNDRLGKK---------VRVKCNPDDTIGDLKKLIAAQTG 36
+ IT GKK N T+GDLKKL+ +TG
Sbjct: 249 LNITIQKEDGKKEDFVFTYGDAEKGENQFKTLGDLKKLLKEKTG 292
>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 = 24.7 bits (54), Expect = 2.7
Identities = 13/50 (26%), Positives = 25/50 (50%)
Query: 21 DDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
D ++ D K+ ++ + E++VL I KD + + I DG+ + L
Sbjct: 19 DASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHL 68
>gnl|CDD|176408 cd01813, UBP_N, UBP ubiquitin processing protease. The UBP
(ubiquitin processing protease) domain (also referred
to as USP which stands for "ubiquitin-specific
protease") is present at in a large family of cysteine
proteases that specifically cleave ubiquitin
conjugates. This family includes Rpn11, UBP6 (USP14),
USP7 (HAUSP). This domain is closely related to the
amino-terminal ubiquitin-like domain of BAG1
(Bcl2-associated anthanogene1) protein and is found
only in eukaryotes.
Length = 74
Score = 24.4 bits (53), Expect = 3.3
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEK 41
G++ V +DT+ DLK+ I TG E+
Sbjct: 9 GQEYSVTTLSEDTVLDLKQFIKTLTGVLPER 39
>gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase. This
subfamily is composed mainly of eukaryotic ornithine
decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes
from prokaryotes represented by Vibrio vulnificus
LysineOrnithine decarboxylase. These are fold type III
PLP-dependent enzymes that differ from most bacterial
ODCs which are fold type I PLP-dependent enzymes. ODC
participates in the formation of putrescine by
catalyzing the decarboxylation of ornithine, the first
step in polyamine biosynthesis. Members of this
subfamily contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain, similar
to bacterial alanine racemases. They exist as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. Homodimer
formation and the presence of the PLP cofactor are
required for catalytic activity. Also members of this
subfamily are proteins with homology to ODC but do not
possess any catalytic activity, the Antizyme inhibitor
(AZI) and ODC-paralogue (ODC-p). AZI binds to the
regulatory protein Antizyme with a higher affinity than
ODC and prevents ODC degradation. ODC-p is a novel
ODC-like protein, present only in mammals, that is
specifically exressed in the brain and testes. ODC-p
may function as a tissue-specific antizyme inhibitory
protein.
Length = 362
Score = 25.1 bits (56), Expect = 3.8
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 16 VKCNPDDTIGDLKKLIAAQTG 36
VKCNPD + L+ L A G
Sbjct: 32 VKCNPDPAV--LRTLAALGAG 50
>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
Length = 981
Score = 24.4 bits (53), Expect = 6.9
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 7 NDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKK 46
N+++G + + D I + K+L +TG WE K
Sbjct: 561 NEKIGGNKLEEMSKSDAIHEFKRLFLEKTGNPWESWEQKT 600
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
0.324 0.141 0.446
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,863,564
Number of extensions: 302205
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 27
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)