RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10969
(204 letters)
>gnl|CDD|163691 cd08060, MPN_UPF0172, Mov34/MPN/PAD-1 family: UPF0172 family of
unknown function includes neighbor of COX4 (Noc4p).
This family includes Noc4p (neighbor of COX4; neighbor
of Cytochrome c Oxidase 4; nucleolar complex associated
4 homolog) which belongs to the family of unknown
function, UPF0172, with MPN/JAMM-like domains. Proteins
in this family are homologs of the NOC4 gene which is
conserved in eukaryotic members including human, dog,
mouse, rat, chicken, zebrafish, fruit fly, mosquito,
S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa,
A.thaliana, and rice. NOC4 highly expressed in the
pancreas and moderately in liver, heart, lung, kidney,
brain, skeletal muscle, and placenta. This nucleolar
protein forms a complex with Nop14p that mediates
maturation and nuclear export of 40S ribosomal subunits.
This family of eukaryotic MPN-like domains lacks the key
residues that coordinate a metal ion and therefore does
not show catalytic isopeptidase activity.
Length = 182
Score = 235 bits (602), Expect = 9e-80
Identities = 84/188 (44%), Positives = 116/188 (61%), Gaps = 8/188 (4%)
Query: 6 FTDRAYCKMILHAVKYPHCSINGVLLAVTVPTTKESPKKLTYVDAIPLFHLCLQVTPMIE 65
+ AY KM+LHA KYPHC++NG+LL K S + DA+PLFH CL + PM+E
Sbjct: 1 LSTLAYVKMLLHAAKYPHCAVNGLLLG-----KKSSGGSVEITDAVPLFHSCLALAPMLE 55
Query: 66 IALTQISSYAQSNGLVIAGYYLANENIKDVSYDKPYQSRIADKIAEFFPAACLIVLDNRK 125
+AL + +Y +S+GLVI GYY ANE + D S P +IADKIAE F ACL+++DN K
Sbjct: 56 VALALVDAYCKSSGLVIVGYYQANERLDDSSPS-PVAKKIADKIAENFSNACLLMVDNEK 114
Query: 126 LTQTMQESALIVAQNSDGKWKPVSKNSIIVDQT--TLSSVSTLIQRNISRHLVDFDNHLD 183
LT + +AL+V ++ G+WK I + +S L+ R+LVDFD+HLD
Sbjct: 115 LTLDCKGNALVVYKDKGGRWKVKELRGINLLLWESANEILSALLSSKAYRNLVDFDDHLD 174
Query: 184 NLSADWTN 191
++S DW N
Sbjct: 175 DISLDWLN 182
>gnl|CDD|217666 pfam03665, UPF0172, Uncharacterized protein family (UPF0172). In
Chlamydomonas reinhardtii the protein TLA1 (truncated
light-harvesting chlorophyll antenna size) apparently
regulates genes that define the chlorophyll-a antenna
size in the photosynthetic apparatus. This family was
formerly known as UPF0172.
Length = 195
Score = 220 bits (564), Expect = 7e-74
Identities = 88/200 (44%), Positives = 115/200 (57%), Gaps = 11/200 (5%)
Query: 1 MSEISFTDRAYCKMILHAVKYPHCSINGVLLAVTVPTTKESPKKLTYVDAIPLFHLCLQV 60
M+E+ + AY KMILHA KYPHC++NG+LL + DA+PLFH L +
Sbjct: 1 MTEVEISPLAYAKMILHAAKYPHCAVNGLLLG-----KSTKSSSVLITDAVPLFHSTLAL 55
Query: 61 TPMIEIALTQISSYAQSNGLVIAGYYLANENIKDVSYDKPYQSRIADKIAEFFPAACLIV 120
PM+E+AL Q+ SYA+ GLVI GYY ANE D S P +IADKIAE F A L++
Sbjct: 56 APMLEVALAQVESYAKQKGLVIVGYYHANERFDDSSPS-PVAKKIADKIAENFNNAVLLL 114
Query: 121 LDNRKLTQTMQESALIVAQ---NSDGKWKPVSKNSIIVDQT--TLSSVSTLIQRNISRHL 175
+DN KL + AL V + +WK K+ V+ +S L+Q R L
Sbjct: 115 VDNEKLESDPRVPALQVYEKDGKKGWRWKKADKSLEAVEDWEEANEILSALLQSGAYRQL 174
Query: 176 VDFDNHLDNLSADWTNSELN 195
VDFD+HLD++S DW N ELN
Sbjct: 175 VDFDDHLDDISKDWLNQELN 194
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are
found in the N-terminal termini of proteins with a
variety of functions; they are components of the
proteasome regulatory subunits, the signalosome (CSN),
eukaryotic translation initiation factor 3 (eIF3)
complexes, and regulators of transcription factors.
These domains are isopeptidases that release ubiquitin
from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. Catalytically active MPN domains contain a
metalloprotease signature known as the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif. For example, Rpn11 (also
known as POH1 or PSMD14), a subunit of the 19S
proteasome lid is involved in the ATP-dependent
degradation of ubiquitinated proteins, contains the
conserved JAMM motif involved in zinc ion coordination.
Poh1 is a regulator of c-Jun, an important regulator of
cell proliferation, differentiation, survival and death.
JAB1 is a component of the COP9 signalosome (CSN), a
regulatory particle of the ubiquitin (Ub)/26S proteasome
system occurring in all eukaryotic cells; it cleaves the
ubiquitin-like protein NEDD8 from the cullin subunit of
the SCF (Skp1, Cullins, F-box proteins) family of E3
ubiquitin ligases. AMSH (associated molecule with the
SH3 domain of STAM, also known as STAMBP), a member of
JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves
Lys 63-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. Similarly, BRCC36, part
of the nuclear complex that includes BRCA1 protein and
is targeted to DNA damage foci after irradiation,
specifically disassembles K63-linked polyUb. BRCC36 is
aberrantly expressed in sporadic breast tumors,
indicative of a potential role in the pathogenesis of
the disease. Some variants of the JAB1/MPN domains lack
key residues in their JAMM motif and are unable to
coordinate a metal ion. Comparisons of key catalytic and
metal binding residues explain why the MPN-containing
proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the
translation initiation factor 3 subunits f (p47) and h
(p40) do not show catalytic isopeptidase activity. It
has been proposed that the MPN domain in these proteins
has a primarily structural function.
Length = 116
Score = 52.5 bits (126), Expect = 3e-09
Identities = 22/113 (19%), Positives = 37/113 (32%), Gaps = 10/113 (8%)
Query: 12 CKMILHAVKYPH-CSINGVLLAVTVPTTKESPKKLTYVDAIPLFHLCLQVTPMIEIALTQ 70
KM L A K + + G+L KK+ VD + L
Sbjct: 1 LKMFLDAAKSINGKEVIGLLYG-------SKTKKVLDVDEVIAVPFDEGDKDDNVWFLMY 53
Query: 71 ISSYAQSNGLVIAGYYLANENIKDVSYDKPYQSRIADKIAEFFPAACLIVLDN 123
+ + GL I G+Y + + P + +FP +I++D
Sbjct: 54 LDFKKLNAGLRIVGWYHTHPKPS--CFLSPNDLATHELFQRYFPEKVMIIVDV 104
>gnl|CDD|237836 PRK14855, nhaA, pH-dependent sodium/proton antiporter; Provisional.
Length = 423
Score = 28.7 bits (64), Expect = 2.1
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 23 HCSINGVLLAVTVPTTKESP 42
H ++ GVLLA+ VP + P
Sbjct: 228 HPTVAGVLLALAVPIRRRDP 247
>gnl|CDD|223363 COG0286, HsdM, Type I restriction-modification system
methyltransferase subunit [Defense mechanisms].
Length = 489
Score = 28.2 bits (63), Expect = 3.8
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 3 EISFTDRAYCKM--ILHAVKYPHCSINGVLLAVTVPTTKESPKKLTYVDAIPLF 54
EI+ T KM ILH ++ +G L+ K+ K +V A P F
Sbjct: 221 EINDTTYRLAKMNLILHGIEGDANIRHGDTLSNPKHDDKDDKGKFDFVIANPPF 274
>gnl|CDD|218158 pfam04580, Pox_D3, Chordopoxvirinae D3 protein. Chordopoxvirinae
D3 protein conserved region. Region occupies entire
length of D3 protein.
Length = 246
Score = 27.3 bits (61), Expect = 5.4
Identities = 5/48 (10%), Positives = 17/48 (35%)
Query: 3 EISFTDRAYCKMILHAVKYPHCSINGVLLAVTVPTTKESPKKLTYVDA 50
E + K++++ + Y + +L + P ++ +
Sbjct: 95 EKNDRLTDPDKLLIYDICYFENACWKRILFIQCPPLLNPEYEIFLTNP 142
>gnl|CDD|202551 pfam03142, Chitin_synth_2, Chitin synthase. Members of this family
are fungal chitin synthase EC:2.4.1.16 enzymes. They
catalyze chitin synthesis as follows:
UDP-N-acetyl-D-glucosamine +
{(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <=> UDP +
{(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1).
Length = 527
Score = 27.4 bits (61), Expect = 5.9
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 138 AQNSDGKWKPVSKNSIIVDQTTLSSVSTLIQRNI 171
+ DG W P+ + IV++ + + V TL ++N+
Sbjct: 289 PKGGDGYWVPILASPDIVERYSENVVDTLHKKNL 322
>gnl|CDD|182481 PRK10466, hybD, hydrogenase 2 maturation endopeptidase;
Provisional.
Length = 164
Score = 26.6 bits (59), Expect = 7.0
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 22 PH-CSINGVLLAVTVPTTKESPKKLTYVDAIPL-----FHLCLQVTPMIEIALTQISSYA 75
PH + VL A+ T E PKKLT V IP L V MIE AL Q+ +
Sbjct: 92 PHQLGLADVLSALRF--TGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAAL 149
Query: 76 QSNGL 80
+ +G+
Sbjct: 150 RESGV 154
>gnl|CDD|224328 COG1410, MetH, Methionine synthase I, cobalamin-binding domain
[Amino acid transport and metabolism].
Length = 842
Score = 27.3 bits (61), Expect = 7.6
Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 6/59 (10%)
Query: 2 SEISFTDRAYCKMILHAVKYPHCSINGVLLAVTVPTTKESPKKLTYVDAIPLFHLCLQV 60
S +SF R + +L++V G+ +A+ KL D I
Sbjct: 232 SNVSFGLRGAVREVLNSVFLYEAISAGLDMAIVNAG------KLLIYDNITAELREAVE 284
>gnl|CDD|213065 cd11749, GH94N_LBP_like, N-terminal-like domain of Paenibacillus
sp. YM-1 Laminaribiose Phosphorylase and similar
proteins. The glycoside hydrolase family 94
(previously known as glycosyltransferase family 36)
includes bacterial laminaribiose phosphorylase. This
N-terminal domain is involved in oligomerization and
may play a role in catalysis, but it is separate from
the catalytic domain [an (alpha/alpha)(6) barrel].
Bacterial laminaribiose phosphorylase phosphorolyzes
laminaribiose into alpha-glucose 1-phosphate and
glucose, but does not phosphorolyze other glucobioses;
it slightly phosphorolyzed laminaritriose and higher
laminarioligosaccharides. The GH64N domain, as
represented by this model, is also found at the
N-terminus of GH94 members with uncharacterized
specificities.
Length = 229
Score = 26.8 bits (60), Expect = 7.7
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 22 PHCSINGVLLAVTVPTTKESPKKLTYVDAIPLF 54
P N L+ VT+ T + P K T AIPL+
Sbjct: 61 PVDDDNVELMKVTITNTGDEPLKFTPTAAIPLY 93
>gnl|CDD|234035 TIGR02860, spore_IV_B, stage IV sporulation protein B. SpoIVB, the
stage IV sporulation protein B of endospore-forming
bacteria such as Bacillus subtilis, is a serine
proteinase, expressed in the spore (rather than mother
cell) compartment, that participates in a proteolytic
activation cascade for Sigma-K. It appears to be
universal among endospore-forming bacteria and occurs
nowhere else [Cellular processes, Sporulation and
germination].
Length = 402
Score = 26.9 bits (60), Expect = 8.9
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 88 ANENIKDVSYDKPYQSRIADKIAEFFPAACLIVLDNRKLTQTMQESALIVAQNSDGKWKP 147
N+ IK+ Y+KP + D++ E PA L V+D K+ + E +V QNS P
Sbjct: 283 LNQEIKNPLYNKPMPVALRDEVKE-GPAKILTVIDGEKVEKFDIEIVKLVPQNS-----P 336
Query: 148 VSKNSII 154
+K +I
Sbjct: 337 ATKGMVI 343
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
0.318 0.131 0.374
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,919,198
Number of extensions: 880270
Number of successful extensions: 767
Number of sequences better than 10.0: 1
Number of HSP's gapped: 760
Number of HSP's successfully gapped: 19
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.7 bits)