RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5395
(237 letters)
>gnl|CDD|216301 pfam01105, EMP24_GP25L, emp24/gp25L/p24 family/GOLD. Members of
this family are implicated in bringing cargo forward
from the ER and binding to coat proteins by their
cytoplasmic domains. This domain corresponds closely to
the beta-strand rich GOLD domain described in. The GOLD
domain is always found combined with lipid- or
membrane-association domains.
Length = 178
Score = 146 bits (371), Expect = 2e-44
Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 10/185 (5%)
Query: 48 DYKIHIDPGKEDCFFQYVNPGATFYVNFQVLRGGDGMAGFAVRNPNGQ---IVHPYEWKK 104
+ G+++CF++ V G ++QV+ GG+ F + +P+G I + K
Sbjct: 1 ALTFELPAGEKECFYEEVPKGTLVTGSYQVISGGNLDIDFTITDPDGNGNVIYSKEDRKS 60
Query: 105 NAEYQDTPPHGGYYSVCIDNQFSRNAGKLVNMYLTVVRYDQWDKYHKEIEDLNVSVQNFT 164
++ T G Y C N FS + K V+ + V + ++++ L ++
Sbjct: 61 GGKFSFTATESGEYKFCFSNSFSTFSSKTVSFDIKVGEEAKDIAKKEKLDPLEEELKK-- 118
Query: 165 DSVRTVERNINEILQQQYHARSREARDFNLLEDNNRYVMNWSVIQILVIAATTTVQVYFV 224
+E +N+I ++Q + R REAR E N V+ WS+IQILV+ + +QVY++
Sbjct: 119 -----LEDQLNDIKREQKYLREREARHRETNESTNSRVVWWSIIQILVLIGVSVLQVYYL 173
Query: 225 RQLFN 229
++ F
Sbjct: 174 KRFFE 178
>gnl|CDD|238158 cd00255, nidG2, Nidogen, G2 domain; Nidogen is an important
component of the basement membrane, an extracellular
sheet-like matrix. Nidogen is a multifunctional protein
that interacts with many other basement membrane
proteins, like collagen, perlecan, lamin, and has a
potential role in the assembly and connection of
networks. Nidogen consists of 3 globular domains
(G1-G3), G3 is the lamin-binding domain, while G2 binds
collagen IV and perlecan. Also found in hemicentin, a
protein which functions at various cell-cell and
cell-matrix junctions and might assist in refining broad
regions of cell contact into oriented, line-shaped
junctions. Nidogen G2 consists of an N-terminal EGF-like
domain (excluded from this alignment model) and an
11-stranded beta-barrel with a central helix, a topology
that exhibits high structural similarity to the green
flourescent proteins of Cnidaria.
Length = 224
Score = 30.0 bits (68), Expect = 0.87
Identities = 13/71 (18%), Positives = 24/71 (33%), Gaps = 11/71 (15%)
Query: 42 LPAVAMDYKIHIDPGKEDCFFQYVNPGATFYVNFQVLRGGDGMAGFAVRNPNGQIVHPYE 101
+P V +HI+ E + Y PG + + + V Y+
Sbjct: 126 VPQVPAGATVHIEDYTEL--YHYTGPGVLTSSSTRE---------YTVDEGGESQTLSYQ 174
Query: 102 WKKNAEYQDTP 112
W + Y++ P
Sbjct: 175 WNQTITYEECP 185
>gnl|CDD|219700 pfam08020, DUF1706, Protein of unknown function (DUF1706). This
family contains many hypothetical proteins from bacteria
and yeast.
Length = 166
Score = 29.1 bits (66), Expect = 1.2
Identities = 5/39 (12%), Positives = 17/39 (43%)
Query: 145 QWDKYHKEIEDLNVSVQNFTDSVRTVERNINEILQQQYH 183
++K I+ + +++ + ++N ++L Y
Sbjct: 17 NFEKLIALIDSIPEELKDTPFEEKGRDKNPRDVLAYLYG 55
>gnl|CDD|219083 pfam06548, Kinesin-related, Kinesin-related. This family
represents a region within kinesin-related proteins from
higher plants. Many family members also contain the
pfam00225 domain. Kinesins are ATP-driven microtubule
motor proteins that produce directed force. Some family
members are associated with the phragmoplast, a
structure composed mainly of microtubules that executes
cytokinesis in higher plants.
Length = 488
Score = 29.9 bits (67), Expect = 1.2
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 151 KEIEDLNVSVQNFTDSVRTVERNINEILQQQYHARSREA 189
+EI+DL +Q S ++ R + +L + + R
Sbjct: 229 EEIQDLKSQLQCMLSSSKSTARTRSSLLARSFQLRKSAI 267
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 29.7 bits (67), Expect = 1.5
Identities = 15/76 (19%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 135 NMYLTVVRYDQWDKYHKEIEDLNVSVQNFTDSVRTVERNINEILQQQYHARSREARDFNL 194
V ++ +EI DL ++ +++ ++E+ INE+ +++ E + F
Sbjct: 58 GGKPDVPPSKEFLDLEEEILDLEAEIKEVEENLESLEKEINEL--EEWLNVLDEEKSF-- 113
Query: 195 LEDNNRYVMNWSVIQI 210
L++N + S + I
Sbjct: 114 LDENLEELSELSNLDI 129
>gnl|CDD|219422 pfam07474, G2F, G2F domain. Nidogen, an invariant component of
basement membranes, is a multifunctional protein that
interacts with most other major basement membrane
proteins. The G2 fragment or (G"F domain) contains
binding sites for collagen IV and perlecan. The
structure is composed of an 11-stranded beta-barrel with
a central helix. This domain is structurally related to
that of green fluorescent protein pfam01353. A large
surface patch on the beta-barrel is conserved in all
metazoan nidogens.
Length = 193
Score = 28.6 bits (64), Expect = 2.2
Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 11/71 (15%)
Query: 42 LPAVAMDYKIHIDPGKEDCFFQYVNPGATFYVNFQVLRGGDGMAGFAVRNPNGQIVHPYE 101
+P + ++ I ED + Y PG +L + + VR H Y
Sbjct: 127 VPQIPSGAEVTIKDYTED--YHYTGPG--------ILTSSSTRS-YTVRGGAPSQTHSYT 175
Query: 102 WKKNAEYQDTP 112
W + +++
Sbjct: 176 WDQTITFEECQ 186
>gnl|CDD|216687 pfam01763, Herpes_UL6, Herpesvirus UL6 like. This family consists
of various proteins from the herpesviridae that are
similar to herpes simplex virus type I UL6 virion
protein. UL6 is essential for cleavage and packaging of
the viral genome.
Length = 556
Score = 28.7 bits (65), Expect = 2.8
Identities = 9/45 (20%), Positives = 21/45 (46%)
Query: 151 KEIEDLNVSVQNFTDSVRTVERNINEILQQQYHARSREARDFNLL 195
IEDL ++ +R +E ++ + ++ +R + +LL
Sbjct: 376 DTIEDLKEENEDLLKKLRELESELSRLREEARASRGSASEPADLL 420
>gnl|CDD|100813 PRK01203, PRK01203, prefoldin subunit alpha; Provisional.
Length = 130
Score = 27.6 bits (61), Expect = 2.9
Identities = 10/46 (21%), Positives = 21/46 (45%)
Query: 136 MYLTVVRYDQWDKYHKEIEDLNVSVQNFTDSVRTVERNINEILQQQ 181
+Y+ R ++ + +EDL S+Q D +T+ N + +
Sbjct: 79 VYIAEERERTIERLKENLEDLKDSIQKLNDQRKTLVDQYNTVYITE 124
>gnl|CDD|148050 pfam06212, GRIM-19, GRIM-19 protein. This family consists of
several eukaryotic gene associated with
retinoic-interferon-induced mortality 19 (GRIM-19)
proteins. GRIM-19, was reported to encode a small
protein primarily distributed in the nucleus and was
able to promote cell death induced by IFN-# and RA. A
bovine homologue of GRIM-19 was co-purified with
mitochondrial NADH:ubiquinone oxidoreductase (complex I)
in bovine heart. Therefore, its exact cellular
localisation and function are unclear. It has now been
discovered that GRIM-19 is a specific interacting
protein which negatively regulates Stat3 activity.
Length = 130
Score = 27.3 bits (61), Expect = 3.8
Identities = 28/107 (26%), Positives = 42/107 (39%), Gaps = 16/107 (14%)
Query: 109 QDTPPHGGYYSVCIDNQFSRNAGKLVNMYLTVV--------RYDQWDKYHKEIEDLNVSV 160
QD PP GGY + + M+ T RY +W+K + +E + S
Sbjct: 7 QDMPPPGGYGPIPFKRNLPKTGFSGYAMFATGAGATAFGYYRYYEWNKERRRLEIEDRSA 66
Query: 161 QNFTDSVRTVERNINEILQQQYHARSREARDFNLLEDNNRYVMNWSV 207
+N + ER+ L+Q R EA L++D V W V
Sbjct: 67 RNAILPLLQAERD-RRYLKQLRRNREEEA---ELMKD----VPGWKV 105
>gnl|CDD|241436 cd13282, PH1_PLEKHH1_PLEKHH2, Pleckstrin homology (PH) domain
containing, family H (with MyTH4 domain) members 1 and
2 (PLEKHH1) PH domain, repeat 1. PLEKHH1 and PLEKHH2
(also called PLEKHH1L) are thought to function in
phospholipid binding and signal transduction. There are
3 Human PLEKHH genes: PLEKHH1, PLEKHH2, and PLEKHH3.
There are many isoforms, the longest of which contain a
FERM domain, a MyTH4 domain, two PH domains, a
peroximal domain, a vacuolar domain, and a coiled coil
stretch. The FERM domain has a cloverleaf tripart
structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The
C-lobe/F3 within the FERM domain is part of the PH
domain family. PH domains have diverse functions, but
in general are involved in targeting proteins to the
appropriate cellular location or in the interaction
with a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 96
Score = 26.9 bits (60), Expect = 4.3
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 45 VAMDYKIHIDPGKEDCFFQYVNPGATFYV 73
+A+D I + F+ V T+Y+
Sbjct: 44 IALDGSCEIARAEGAQTFEIVTEKRTYYL 72
>gnl|CDD|218762 pfam05816, TelA, Toxic anion resistance protein (TelA). This
family consists of several prokaryotic TelA like
proteins. TelA and KlA are associated with tellurite
resistance and plasmid fertility inhibition.
Length = 333
Score = 27.5 bits (62), Expect = 6.0
Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 4/67 (5%)
Query: 156 LNVSVQNFTDSVRTVERNINEILQQQYHARSREARDFNLLEDNNRYVMNWSVIQIL--VI 213
S++ + ++V I++IL + + +D +L+ Y N + L I
Sbjct: 82 AKNSIERYFAKYQSVGGQIDKILVELEKGKDELLKDNAMLDQ--LYDKNLEYYEELEKYI 139
Query: 214 AATTTVQ 220
AA
Sbjct: 140 AAGKLKL 146
>gnl|CDD|223287 COG0209, NrdA, Ribonucleotide reductase, alpha subunit [Nucleotide
transport and metabolism].
Length = 651
Score = 27.7 bits (62), Expect = 6.0
Identities = 24/140 (17%), Positives = 45/140 (32%), Gaps = 7/140 (5%)
Query: 69 ATFYVNFQVLRGGDGMAGFAVRNPNGQIVHPYEWKKNAEYQDTPPHGGYYSVCIDNQFSR 128
A +N +R G + +P+ I + K+N + V I + F +
Sbjct: 205 AFDAINQGGVRRGAQAVYLDIWHPD--IEEFLDAKRNNGDEILRAFDISVGVWIPDLFMK 262
Query: 129 NAGKLVNMYLT--VVRYDQWDKYHKEIEDLNVSVQNFTDSVRTVERNINEILQQQYHARS 186
A + + L Y+ D Y E E+ + + + E+ + A
Sbjct: 263 RAKEGEDWTLFSPRDGYEAPDVYGAEFEEYAEYEADPGIRKKRI--KARELFDKLAEAAF 320
Query: 187 REARDFNLLEDN-NRYVMNW 205
+ + D NR N
Sbjct: 321 ETGDPYLIFVDTLNRRNPNA 340
>gnl|CDD|236531 PRK09467, envZ, osmolarity sensor protein; Provisional.
Length = 435
Score = 27.2 bits (61), Expect = 7.9
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 151 KEIEDLNVSVQNFTDSVRTVER------NINEILQQQYHARSREARDFNL 194
K+IE+ N ++ F D +RT + ++N +L + A S R+
Sbjct: 267 KDIEECNAIIEQFIDYLRTGQEMPMEMADLNALLGEVIAAESGYEREIET 316
>gnl|CDD|152844 pfam12410, rpo30_N, Poxvirus DNA dependent RNA polymerase 30kDa
subunit. This family of proteins is found in viruses.
Proteins in this family are typically between 193 and
259 amino acids in length. The family is found in
association with pfam01096. There are two conserved
sequence motifs: GIEYSKD and LRY. This family is N
terminal of the 30 kDa subunit of poxvirus
DNA-d-RNA-pol. It has structural similarity to the
eukaryotic transcriptional elongation factor SII.
Length = 136
Score = 26.6 bits (59), Expect = 8.1
Identities = 9/35 (25%), Positives = 20/35 (57%)
Query: 199 NRYVMNWSVIQILVIAATTTVQVYFVRQLFNSKTN 233
+YV + + + L+ AT +++R + N+K+N
Sbjct: 8 KKYVDDNAEAEELLSWATDKAAKFYLRNIVNTKSN 42
>gnl|CDD|220735 pfam10408, Ufd2P_core, Ubiquitin elongating factor core. This is
the most conserved part of the core region of Ufd2P
ubiquitin elongating factor or E4, running from helix
alpha-11 to alpha-38. It consists of 31 helices of
variable length connected by loops of variable size
forming a compact unit; the helical packing pattern of
the compact unit consists of five structural repeats
that resemble tandem Armadillo (ARM) repeats. This
domain is involved in ubiquitination as it binds Cdc48p
and escorts ubiquitinated proteins from Cdc48p to the
proteasome for degradation. The core is structurally
similar to the nuclear transporter protein
importin-alpha. The core is associated with the U-box at
the C-terminus, pfam04564, which has ligase activity.
Length = 625
Score = 27.2 bits (61), Expect = 8.4
Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 132 KLVNMYLTVVRY--DQWDKYHKEIEDLNVSVQNFTDSVRTVERNINEILQQQYHARSREA 189
+ +N+ L Y D+ Y KEI+ L +Q+ + + E + + R+A
Sbjct: 436 RFINLLLNDATYLLDESLSYLKEIKQLQKELQDRAEWESL-SQEEREERESELRQLERQA 494
Query: 190 RDFNLL 195
+ + L
Sbjct: 495 KSYLQL 500
>gnl|CDD|226371 COG3853, TelA, Uncharacterized protein involved in tellurite
resistance [Inorganic ion transport and metabolism].
Length = 386
Score = 27.0 bits (60), Expect = 8.8
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 4/64 (6%)
Query: 159 SVQNFTDSVRTVERNINEILQQQYHARSREARDFNLLEDNNRYVMNWSVIQIL--VIAAT 216
S+Q +T+ I+ I++ + RD +LE Y N + L IAA
Sbjct: 131 SIQEIFSKYQTIGAQIDRIIESLSKGKDELTRDNKMLEL--LYEKNREYFEHLEKYIAAG 188
Query: 217 TTVQ 220
Sbjct: 189 ELKD 192
>gnl|CDD|200222 TIGR02965, xanthine_xdhB, xanthine dehydrogenase, molybdopterin
binding subunit. Members of the protein family are the
molybdopterin-containing large subunit (or, in,
eukaryotes, the molybdopterin-binding domain) of
xanthine dehydrogenase, and enzyme that reduces the
purine pool by catabolizing xanthine to urate. This
model is based primarily on bacterial sequences; it does
not manage to include all eukaryotic xanthine
dehydrogenases and thereby discriminate them from the
closely related enzyme aldehyde dehydrogenase [Purines,
pyrimidines, nucleosides, and nucleotides, Other].
Length = 758
Score = 27.3 bits (61), Expect = 9.2
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 9/51 (17%)
Query: 152 EIEDLNV---SVQNFTDSVRTVERN-INEILQQ-----QYHARSREARDFN 193
E+ N +N T +TVE N I+EI+++ Y AR R FN
Sbjct: 369 EVRKRNFYGKDERNVTPYHQTVEDNIIHEIIEELEASSDYAARRAAIRAFN 419
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
0.321 0.135 0.419
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,036,826
Number of extensions: 1112307
Number of successful extensions: 1037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1034
Number of HSP's successfully gapped: 25
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.7 bits)