RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11489
(433 letters)
>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 = 119 bits (301), Expect = 2e-33
Identities = 45/65 (69%), Positives = 53/65 (81%)
Query: 13 ITIVVKTPKEKQNIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNM 72
I + VKTPK+K+ IEI EDASV DFKEAV+KKF A EQL LIFAGKI+KD + L+ HN+
Sbjct: 1 IKVTVKTPKDKEEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNI 60
Query: 73 KDGLT 77
KDGLT
Sbjct: 61 KDGLT 65
>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 = 63.8 bits (156), Expect = 4e-13
Identities = 26/62 (41%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 17 VKTPKEKQ-NIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMKDG 75
VKT K +E+ D +V + K +A K PEQ LI+AGKI+KD + LS++ ++DG
Sbjct: 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDG 61
Query: 76 LT 77
T
Sbjct: 62 ST 63
>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 = 63.4 bits (155), Expect = 6e-13
Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 13 ITIVVKTPKE-KQNIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHN 71
I I VKT +EE+ +V D KE +A++ EQ LI++G+++KD E LS +
Sbjct: 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYK 60
Query: 72 MKDGLT 77
++DG T
Sbjct: 61 VEDGHT 66
>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 = 58.8 bits (143), Expect = 3e-11
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 18 KTPKEKQN-IEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMKDGL 76
KT K +E++ +V++ KE + K +Q LIF+GK+++D LS + ++DG
Sbjct: 1 KTLDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGS 60
Query: 77 T 77
T
Sbjct: 61 T 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 = 51.1 bits (123), Expect = 1e-08
Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 13 ITIVVKTPKEKQ-NIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHN 71
I + VKT K +E++ +V++ KE +A+ PEQ LI+ GK+++D L+++
Sbjct: 1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYG 60
Query: 72 MKDG 75
++DG
Sbjct: 61 IQDG 64
>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 = 50.6 bits (121), Expect = 2e-08
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 17 VKTPKEKQ-NIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMKDG 75
VK K + + +V D KE +AKK PEQ L+ GKI+ D L ++ ++DG
Sbjct: 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDG 61
Query: 76 LT 77
Sbjct: 62 DE 63
>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 = 46.2 bits (110), Expect = 9e-07
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 13 ITIVVKT-PKEKQNIEIEEDASVTDFKEAVA--KKFNALPEQLCLIFAGKIMKDHENLSN 69
+ I KT ++ IE++ D +V + KE + K + PEQ LI++GKI+KD L
Sbjct: 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEE 60
Query: 70 HNMKDG 75
+ + +
Sbjct: 61 YKIDEK 66
>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 = 45.1 bits (107), Expect = 2e-06
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 26 IEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMKDG 75
+E++ D + KE VAK+ P+QL +IFAGK +++ + ++
Sbjct: 13 VEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQ 62
>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 = 45.0 bits (107), Expect = 2e-06
Identities = 21/63 (33%), Positives = 28/63 (44%)
Query: 13 ITIVVKTPKEKQNIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNM 72
I + VK E ++ I A+ D K+ +A P LIF GK D E L +
Sbjct: 1 IRVRVKHGGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGV 60
Query: 73 KDG 75
KDG
Sbjct: 61 KDG 63
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 39.8 bits (93), Expect = 1e-04
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 15 IVVKT-PKEKQNIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMK 73
I++KT +KQ+ E D +V K A+ +K +Q+ LI++GK M D LS++ +
Sbjct: 3 ILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVV 62
Query: 74 DGLT 77
G T
Sbjct: 63 PGST 66
>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 = 38.2 bits (89), Expect = 5e-04
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 13 ITIVVKTPKEKQ-NIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHN 71
+ I VKT K+ I+IE V KE V +K P+Q LI++GK M D + +++
Sbjct: 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYK 60
Query: 72 MKDG 75
++ G
Sbjct: 61 LEGG 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 = 36.0 bits (83), Expect = 0.003
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 15 IVVKTPKEKQ-NIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMK 73
I VKT K +E+E ++ + K + K P+Q LIFAGK ++D LS++N++
Sbjct: 3 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
>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 = 33.6 bits (77), Expect = 0.020
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 22 EKQNIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMKDGL 76
+K ++ D ++ D K+ +A + PE++ L I KDH +L ++ + DG+
Sbjct: 12 KKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGM 66
>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 = 33.3 bits (77), Expect = 0.028
Identities = 14/65 (21%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 13 ITIVVKTP-KEKQNIEIEEDASVTDFKEAVAKKFN-ALPEQLCLIFAGKIMKDHENLSNH 70
I I +K ++ I+++ +++ A KK +Q+ LIF G+ + ++ ++++
Sbjct: 1 IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKKRGIPADQQVRLIFDGERLDPNDTVADY 60
Query: 71 NMKDG 75
+++DG
Sbjct: 61 DIEDG 65
>gnl|CDD|128966 smart00727, STI1, Heat shock chaperonin-binding motif.
Length = 41
Score = 31.9 bits (73), Expect = 0.034
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 390 LMQNMMQAPYMQSMLQAMSADPSIAQRVIGTNPLLQN 426
M +Q P +QS+LQ M +P + +++ NP L
Sbjct: 3 EMALRLQNPQVQSLLQDMQQNPDMLAQMLQENPQLLQ 39
Score = 27.6 bits (62), Expect = 1.2
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 370 SLFGNAGMQSMMQQMMANPQLMQNMMQA 397
N +QS++Q M NP ++ M+Q
Sbjct: 6 LRLQNPQVQSLLQDMQQNPDMLAQMLQE 33
>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 = 33.0 bits (76), Expect = 0.048
Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 25 NIEIEEDASVTDFKEAVAKKFNALPEQ--LCLIFAGKIMKDHENLSN 69
+I +V K+ + + L LI+AG+++ D L++
Sbjct: 17 DINSPRSTTVAWLKKLIRSRLPQELSNRRLRLIYAGRLLNDSSKLAS 63
>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 = 32.6 bits (74), Expect = 0.056
Identities = 15/48 (31%), Positives = 30/48 (62%)
Query: 25 NIEIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNM 72
++++ E SV+ K+ V++ N EQ L+F GK + D + LS++++
Sbjct: 14 SLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSI 61
>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 = 31.0 bits (70), Expect = 0.18
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 15 IVVKTPKEKQNI-EIEEDASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHNMK 73
I+V+ K + +I E++ +V K+ V+++ +Q L F G+ M+D L + +K
Sbjct: 1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLK 60
Query: 74 DGLTSLKQLPL 84
G T L L
Sbjct: 61 PGCTVFMNLRL 71
>gnl|CDD|188504 TIGR03989, Rxyl_3153, oxidoreductase, Rxyl_3153 family. This model
describes a clade within the family pfam00107 of
zinc-binding dehydrogenases. The family pfam00107
contains class III alcohol dehydrogenases, including
enzymes designated S-(hydroxymethyl)glutathione
dehydrogenase and NAD/mycothiol-dependent formaldehyde
dehydrogenase. Members of the current family occur only
in species that contain the very small protein
mycofactocin (TIGR03969), a possible cofactor precursor,
and radical SAM protein TIGR03962. We name this family
for Rxyl_3153, where the lone member of the family
co-clusters with these markers in Rubrobacter
xylanophilus [Unknown function, Enzymes of unknown
specificity].
Length = 369
Score = 32.3 bits (74), Expect = 0.52
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 105 VLVRWEVSGICHHENLSNHNMKDGLTSLKQLPL 137
VLV+ SG+CH S+ ++ G + + P+
Sbjct: 29 VLVKLVASGLCH----SDEHLVTGDLPMPRYPI 57
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 31.4 bits (72), Expect = 0.98
Identities = 8/35 (22%), Positives = 12/35 (34%), Gaps = 4/35 (11%)
Query: 377 MQSMMQQMMANPQLMQNMMQAPYMQSM----LQAM 407
M+ + +Q NPQ + LQ M
Sbjct: 509 MRQLAEQAQRNPQQGDQPPDQGNSMELTQQDLQRM 543
Score = 31.4 bits (72), Expect = 1.1
Identities = 50/284 (17%), Positives = 77/284 (27%), Gaps = 87/284 (30%)
Query: 165 QMQQMLPQFLQQMQNPEIQGMM---ANPEALSAIQQIQAGIEQLRTAAPGMEWNFRNPEI 221
++ Q LQ+M + I+ +M EA ++Q+Q +E L+ G
Sbjct: 531 NSMELTQQDLQRMMD-RIEELMESGRRAEAQQLLEQLQQMMENLQVTQGGQG-------- 581
Query: 222 NHMLNNPELLRQTMEMARNPSMLQELMRTQDRALSNLESIPGGYSALQRMYRDIQEPMLN 281
EM + L E +R Q LS+ +RD+QE
Sbjct: 582 -----------GQSEMQQAMEGLGETLREQQG-LSD------------ETFRDLQE---- 613
Query: 282 AATQQFSRNPYESNSSGGNPGRVKAPFRRSKRYLGPRQCARPSSSLSTPGLANNQGGNAQ 341
QF+ E G G+ + + +Q G QG A+
Sbjct: 614 ----QFNAQRGEQQGQQGQGGQ-----GQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAE 664
Query: 342 APPEVRYR--SQLDQLTAMGFVNREANLQGSLFGNA------------------------ 375
+R Q L MG EA G A
Sbjct: 665 RQQALRDELGRQRGGLPGMGGEAGEAARDA--LGRAGRAMGGAEEALGQGDLAEAVDRQG 722
Query: 376 --------GMQSMMQQMMANPQLMQNMMQAPYMQSMLQAMSADP 411
G +++ + M Q Q DP
Sbjct: 723 RALEALREGARALGEAMAQQQG--QQQGGQGQQQGRQGGNGRDP 764
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 30.6 bits (70), Expect = 1.5
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 4/24 (16%)
Query: 105 VLVRWEVSGICHHENLSNHNMKDG 128
VLVR +G+CH S+ ++ G
Sbjct: 28 VLVRIAAAGLCH----SDLHVVTG 47
>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 = 28.2 bits (63), Expect = 2.1
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 15 IVVKTPKEKQNIEIEE---DASVTDFKEAVAKKFNALPEQLCLIFAGKIMKDHENLSNHN 71
I V+T K+ ++ V + +E + + FN PE L + GK M+D L ++N
Sbjct: 3 IQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYN 62
Query: 72 MKDGLTSLKQL 82
+ GL + QL
Sbjct: 63 V--GLNDIIQL 71
>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 = 28.2 bits (63), Expect = 2.2
Identities = 15/62 (24%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 13 ITIVVKTPKEK---QNIEIEEDASVTDFKEAVAKKF--NALPEQLCLIFAGKIMKDHENL 67
+T+++K+P +K Q + + +V + K +++ + L + LI++GK++ DH L
Sbjct: 2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKL 61
Query: 68 SN 69
+
Sbjct: 62 RD 63
>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 = 29.9 bits (67), Expect = 3.0
Identities = 20/67 (29%), Positives = 39/67 (58%), Gaps = 4/67 (5%)
Query: 13 ITIVVKT-PKEKQNIEIEEDASVTDFKEAVA--KKFNALP-EQLCLIFAGKIMKDHENLS 68
+T+ KT ++K I++E D +V + KE + + +A P Q LI++GKI+ D + +
Sbjct: 1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVK 60
Query: 69 NHNMKDG 75
+ +K+
Sbjct: 61 EYKIKEK 67
>gnl|CDD|219640 pfam07916, TraG_N, TraG-like protein, N-terminal region. The
bacterial sequences found in this family are similar to
the N-terminal region of the TraG protein. This is a
membrane-spanning protein, with three predicted
transmembrane segments and two periplasmic regions. TraG
protein is known to be essential for DNA transfer in the
process of conjugation, with the N-terminal portion
being required for F pilus assembly. The protein is
thought to interact with the periplasmic domain of TraN
to stabilise mating-cell interactions.
Length = 462
Score = 30.0 bits (68), Expect = 3.1
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 359 GFVNREANLQGSLFGNAGMQSMMQQMMANPQLMQNMMQA-PYMQSMLQAM 407
G A L + A Q++ QQ +A QA P +Q+ L+
Sbjct: 291 GVTRFAAALGDTAAALASTQALAQQSLAWAPAGDAARQALPMVQAFLEMA 340
>gnl|CDD|166612 PLN02971, PLN02971, tryptophan N-hydroxylase.
Length = 543
Score = 29.6 bits (66), Expect = 3.7
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 197 QIQAGIEQLRTAAPGMEWNFRNPEINHMLNNPELLRQTME 236
+I+ I++L AAP N + M+N PE+L + ME
Sbjct: 327 EIKPTIKELVMAAPDNPSNAVEWAMAEMINKPEILHKAME 366
>gnl|CDD|215643 PLN03241, PLN03241, magnesium chelatase subunit H; Provisional.
Length = 1315
Score = 29.5 bits (66), Expect = 4.3
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 238 ARNPSMLQELMRTQDRALSNLESIPGGYSALQRMYRDIQEPMLN-AATQQFSRNPYESNS 296
AR P +LQ+L++T +R + ++S+ G + DIQE N A + + E +
Sbjct: 1110 AR-PEVLQKLLKTTERVVQEIDSVEYGLT-------DIQEYYANTGALKAAAEAAKEIDG 1161
Query: 297 SGGNPGRV 304
G +V
Sbjct: 1162 PTGKKKKV 1169
>gnl|CDD|236646 PRK10064, PRK10064, catecholate siderophore receptor CirA;
Provisional.
Length = 663
Score = 29.5 bits (66), Expect = 4.8
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 251 QDRALSNLESIPGGYSA--LQRMYR-----DIQEPMLNAATQQFSRNPYESNSSG 298
Q RA S PGGY+ ++ ++ +LN + SR+ Y N G
Sbjct: 598 QKRADSATAKTPGGYTIWNTGAAWQVTKDVKLRAGVLNLGDKDLSRDDYSYNEDG 652
>gnl|CDD|226054 COG3523, IcmF, Type VI protein secretion system component VasK
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 1188
Score = 28.9 bits (65), Expect = 6.4
Identities = 21/169 (12%), Positives = 49/169 (28%), Gaps = 17/169 (10%)
Query: 244 LQELMRTQDRALSNL-----ESIPGGYSALQRMYRDIQEPM---LNAATQQFSRNPYESN 295
L + D L++L + AL+++ P+ L P +
Sbjct: 761 LTDYAAQWDAFLNDLRVNPFNDLGQAIDALRQL-ASPDSPLRRLLRTLADNTQLQPSDLL 819
Query: 296 SSGGNPGRVKAPFRRSKRYLGPRQCARPSSSLSTPGLANNQGGNAQAPPE--------VR 347
+ + + + + LG ++ GLA A +
Sbjct: 820 PADELKKALASALDKLAQKLGRLGAPALAALQPQGGLAKRLDSTASLSVSALFEELARLL 879
Query: 348 YRSQLDQLTAMGFVNREANLQGSLFGNAGMQSMMQQMMANPQLMQNMMQ 396
+Q + T + + L+ + +A +QQ+ + +
Sbjct: 880 AANQSNAPTPLDAALKAVQLRFNQLKSADSADALQQLPGGDSRLAVLAA 928
>gnl|CDD|234020 TIGR02801, tolR, TolR protein. The model describes the inner
membrane protein TolR, part of the TolR/TolQ complex
that transduces energy from the proton-motive force,
through TolA, to an outer membrane complex made up of
TolB and Pal (peptidoglycan-associated lipoprotein). The
complex is required to maintain outer membrane
integrity, and defects may cause a defect in the import
of some organic compounds in addition to the resulting
morphologic. While several gene pairs homologous to talR
and tolQ may be found in a single genome, but the scope
of this model is set to favor finding only bone fide
TolR, supported by operon structure as well as by score
[Transport and binding proteins, Other, Cellular
processes, Pathogenesis].
Length = 129
Score = 27.6 bits (62), Expect = 7.8
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 2 AEAQQESEKKLITIVVKTPKE----KQNIEIEEDASVTDFKEAVAKKFNALPEQLCLIFA 57
A+ Q +KK IT+ V + I+ +E + +A A P+ LI A
Sbjct: 41 AKPLQSKDKKPITVSVDADGKIYLNDNKIDKDEQLDADELLAEIAAALAANPDTPVLIRA 100
Query: 58 ------GKIMK 62
G+++K
Sbjct: 101 DKTVPYGEVIK 111
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 28.2 bits (63), Expect = 9.9
Identities = 11/51 (21%), Positives = 26/51 (50%)
Query: 144 PKEEPILMSEQLHLVLVRWEAQMQQMLPQFLQQMQNPEIQGMMANPEALSA 194
P+ + ++ E+L ++ E + + L +M N E+ ++ +PE L +
Sbjct: 502 PQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELLHLLESPELLKS 552
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
0.314 0.128 0.360
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: 21,784,803
Number of extensions: 2082441
Number of successful extensions: 2298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2219
Number of HSP's successfully gapped: 88
Length of query: 433
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 333
Effective length of database: 6,502,202
Effective search space: 2165233266
Effective search space used: 2165233266
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 (21.6 bits)
S2: 60 (26.8 bits)