RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14762
(136 letters)
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 71.5 bits (176), Expect = 2e-17
Identities = 28/89 (31%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 45 HFLSSLTAGAIATTMTQPLDVLKTRAMNATPG---QFNSMWALVTYTAKL-GPAGFFKGY 100
L+ AGAIA T+T PLDV+KTR ++ G ++ + K G G +KG
Sbjct: 8 SLLAGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIYKEEGIRGLYKGL 67
Query: 101 FPAFVRLAPQTILTFVFLEQLRLNFGFIK 129
P +R+AP + F E L+
Sbjct: 68 LPNLLRVAPAAAIYFGTYETLKKLLLKKL 96
>gnl|CDD|226317 COG3794, PetE, Plastocyanin [Energy production and conversion].
Length = 128
Score = 28.5 bits (64), Expect = 0.66
Identities = 12/63 (19%), Positives = 17/63 (26%), Gaps = 1/63 (1%)
Query: 56 ATTMTQPLDVLKTRAMNATPGQFNSMWA-LVTYTAKLGPAGFFKGYFPAFVRLAPQTILT 114
A L T A A + G + PA V + P +T
Sbjct: 6 AALRRMFLTGGATLAGVVAGAAGPEAAADEEVASVNKGVDIGAMVFEPAEVTVKPGDTVT 65
Query: 115 FVF 117
+V
Sbjct: 66 WVN 68
>gnl|CDD|205299 pfam13118, DUF3972, Protein of unknown function (DUF3972). This is
a Proteobacterial family of unknown function. Some of
the proteins in this family are annotated as being
kinesin-like proteins.
Length = 126
Score = 28.0 bits (63), Expect = 0.87
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 4 LQGEYDEFKQSVEQLKEQLKQC 25
+Q YDE +++++ L+EQLK
Sbjct: 104 MQELYDEDRKTIDLLREQLKIA 125
>gnl|CDD|181608 PRK09004, PRK09004, FMN-binding protein MioC; Provisional.
Length = 146
Score = 27.5 bits (62), Expect = 1.5
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 7 EYDEFKQSVEQLKEQLKQCKTVKLG 31
EYD F ++++L++ LK ++G
Sbjct: 94 EYDTFCGAIDKLEQLLKAKGAKQIG 118
>gnl|CDD|185494 PTZ00168, PTZ00168, mitochondrial carrier protein; Provisional.
Length = 259
Score = 27.6 bits (61), Expect = 2.2
Identities = 35/115 (30%), Positives = 48/115 (41%), Gaps = 15/115 (13%)
Query: 16 EQLKEQLKQCKTVKLGLLSTPYFEDNATTHFLSSLTAGAIATTMTQPLDVLKTRAMNATP 75
E LKE+ K+ G S Y + T + AG IA +T P+DV+K+R +
Sbjct: 160 ETLKEKAKK----DFGKFSKKY---PSITSAICGGLAGGIAGFLTTPVDVIKSRQIIYG- 211
Query: 76 GQFNSMWALVTYTAKLGPAGFFKGYFPAFVRLAPQTILTFVFLEQLRLNFGFIKE 130
S VT A+ G F+KG R + +F LR F F KE
Sbjct: 212 ---KSYIETVTEIAEEGYLTFYKG---CCFRSSYLFFGGLIFFGSLRF-FSFKKE 259
>gnl|CDD|240579 cd12931, eNOPS_SF, NOPS domain, including C-terminal helical
extension region, in the p54nrb/PSF/PSP1 family. All
members in this family contain a DBHS domain (for
Drosophila behavior, human splicing), which comprises
two conserved RNA recognition motifs (RRM1 and RRM2),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1) domain
with a long helical C-terminal extension. The NOPS
domain specifically binds to RRM2 domain of the partner
DBHS protein via a substantial interaction surface. Its
highly conserved C-terminal residues are critical for
functional DBHS dimerization while the highly conserved
C-terminal helical extension, forming a right-handed
antiparallel heterodimeric coiled-coil, is essential
for localization of these proteins to subnuclear
bodies. PSF has an additional large N-terminal domain
that differentiates it from other family members. The
p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and
DNA-binding protein (p54nrb), polypyrimidine
tract-binding protein (PTB)-associated-splicing factor
(PSF) and paraspeckle protein 1 (PSP1), which are
ubiquitously expressed and are well conserved in
vertebrates. p54nrb, also termed NONO or NMT55, is a
multi-functional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. PSF, also termed POMp100, is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1, also termed PSPC1, is a
novel nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species. For instance, the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore.
Length = 90
Score = 26.4 bits (59), Expect = 2.4
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 1 MKRLQGEYDEFKQSVEQLKEQLKQCK 26
K L Y+ KQ EQL+++LK+ +
Sbjct: 53 WKAL---YELEKQQREQLEKELKEAR 75
>gnl|CDD|129988 TIGR00910, 2A0307_GadC, glutamate:gamma-aminobutyrate antiporter.
Lowered cutoffs from 1000/500 to 800/300, promoted from
subfamily to equivalog, and put into a Genome Property
DHH 9/1/2009 [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 507
Score = 27.2 bits (60), Expect = 3.3
Identities = 20/57 (35%), Positives = 24/57 (42%), Gaps = 13/57 (22%)
Query: 65 VLKTRAMNATP-----GQFNSMWAL-------VTYTAKLGPAGFFKG-YFPAFVRLA 108
+LK A+N P WAL TAK+ AGFF G PAF+ A
Sbjct: 110 ILKFPALNEDPIIKFIAALIIFWALAFSQFGGTKRTAKIAKAGFFAGILIPAFILFA 166
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 26.6 bits (60), Expect = 4.6
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 7 EYDEFKQSVEQLKEQLKQCK 26
E F +SVE +K+ ++ K
Sbjct: 288 EKAAFDKSVEAVKKLIEALK 307
>gnl|CDD|222230 pfam13569, DUF4132, Domain of unknown function (DUF4132). This
domain might be involved in the biosynthesis of the
molybdopterin cofactor in E.coli.
Length = 179
Score = 26.0 bits (58), Expect = 5.6
Identities = 5/21 (23%), Positives = 8/21 (38%)
Query: 7 EYDEFKQSVEQLKEQLKQCKT 27
E K + LK Q + +
Sbjct: 18 AVKELKALKKDLKTQASRQRA 38
>gnl|CDD|237616 PRK14127, PRK14127, cell division protein GpsB; Provisional.
Length = 109
Score = 25.4 bits (56), Expect = 6.2
Identities = 8/35 (22%), Positives = 15/35 (42%)
Query: 2 KRLQGEYDEFKQSVEQLKEQLKQCKTVKLGLLSTP 36
+ LQ E K V++L +Q+ + + P
Sbjct: 47 EELQQENARLKAQVDELTKQVSVGASSSSVATTQP 81
>gnl|CDD|215312 PLN02574, PLN02574, 4-coumarate--CoA ligase-like.
Length = 560
Score = 26.3 bits (58), Expect = 6.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 22 LKQCKTVKLGLLSTPYFEDNATTHFLSSLTAGAIATTM 59
++Q V L L ++ YF FL+ L+ G I TTM
Sbjct: 89 VRQGDVVLLLLPNSVYF----PVIFLAVLSLGGIVTTM 122
>gnl|CDD|213917 TIGR04304, GeoRSP_SPASM, GeoRSP system SPASM domain protein.
Members of this protein family are encoded by one of
two consecutive genes for SPASM domain proteins. The
two are closely homologous in the SPASM domain regions,
and also in a small N-terminal region, but the other
family (TIGR04303) has an intact radical SAM domain
(pfam04055) that this "quasi-rSAM" protein lacks. A
PqqD-family protein, TIGR04302, is always adjacent.
Length = 293
Score = 26.0 bits (57), Expect = 6.9
Identities = 11/52 (21%), Positives = 18/52 (34%)
Query: 20 EQLKQCKTVKLGLLSTPYFEDNATTHFLSSLTAGAIATTMTQPLDVLKTRAM 71
EQ+ + + L + ST L G IA ++T P +
Sbjct: 27 EQIIDLRILSLNVTSTAPTSPGWLLEVLERFRGGPIAVSLTIPPQAHDDAVL 78
>gnl|CDD|218654 pfam05605, Di19, Drought induced 19 protein (Di19). This family
consists of several drought induced 19 (Di19) like
proteins. Di19 has been found to be strongly expressed
in both the roots and leaves of Arabidopsis thaliana
during progressive drought. The precise function of Di19
is unknown.
Length = 209
Score = 25.8 bits (57), Expect = 7.3
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 14 SVEQLKEQLKQCKTVKLGLLST 35
S E+L+E+ K+ + V+ LLST
Sbjct: 187 SKEELEEKAKRSEFVQGLLLST 208
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). 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 = 309
Score = 25.9 bits (57), Expect = 8.7
Identities = 8/40 (20%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 10 EFKQSVEQLKEQLKQCKTVKLGLLST----PYFEDNATTH 45
+ K++ +L+ Q+++ K K ST Y
Sbjct: 200 QHKKNSVKLEMQVEKPKPEKPNTFSTGIKMGYQISLVPVQ 239
>gnl|CDD|193185 pfam12709, Kinetocho_Slk19, Central kinetochore-associated. This
is a family of proteins integrally involved in the
central kinetochore. Slk19 is a yeast member and it may
play an important role in the timing of nuclear
migration. It may also participate, directly or
indirectly, in the maintenance of centromeric tensile
strength during mitotic stagnation, for instance during
activation of checkpoint controls, when cells need to
preserve nuclear integrity until cell cycle progression
can be resumed.
Length = 87
Score = 24.6 bits (54), Expect = 9.3
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 1 MKRLQGEYDEFKQSVEQLKEQLKQCKTVKLGLLST 35
+ L+ E KQ +EQLK+QL + K LL
Sbjct: 51 LDELELENKALKQEIEQLKKQLDTERKEKQELLKL 85
>gnl|CDD|214016 cd12923, iSH2_PI3K_IA_R, Inter-Src homology 2 (iSH2) helical domain
of Class IA Phosphoinositide 3-kinase Regulatory
subunits. PI3Ks catalyze the transfer of the
gamma-phosphoryl group from ATP to the 3-hydroxyl of the
inositol ring of D-myo-phosphatidylinositol (PtdIns) or
its derivatives. They play an important role in a
variety of fundamental cellular processes, including
cell motility, the Ras pathway, vesicle trafficking and
secretion, immune cell activation, and apoptosis. They
are classified according to their substrate specificity,
regulation, and domain structure. Class IA PI3Ks are
heterodimers of a p110 catalytic (C) subunit and a
p85-related regulatory (R) subunit. The R subunit
down-regulates PI3K basal activity, stabilizes the C
subunit, and plays a role in the activation downstream
of tyrosine kinases. All R subunits contain two SH2
domains that flank an intervening helical domain (iSH2),
which binds to the N-terminal adaptor-binding domain
(ABD) of the catalytic subunit. In vertebrates, there
are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode
for different Class IA PI3K R subunits.
Length = 152
Score = 25.3 bits (56), Expect = 9.4
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 2 KRLQGEYDEFKQSVEQLKEQLKQCK 26
+ L+ E ++S EQL+E L++
Sbjct: 82 ELLKSRLKELEESKEQLEEDLRKQV 106
>gnl|CDD|218657 pfam05615, THOC7, Tho complex subunit 7. The Tho complex is
involved in transcription elongation and mRNA export
from the nucleus.
Length = 132
Score = 25.3 bits (56), Expect = 9.4
Identities = 5/26 (19%), Positives = 16/26 (61%)
Query: 1 MKRLQGEYDEFKQSVEQLKEQLKQCK 26
+ + E +E + ++E K+++++ K
Sbjct: 69 RENYEQEKEEIETTIENAKDEIEELK 94
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 26.0 bits (57), Expect = 9.9
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 4 LQGEYDEFKQSVEQLKEQLKQ 24
++G D F + VE L+ LK
Sbjct: 447 IEGVLDVFPEDVEFLRSILKD 467
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 0.134 0.388
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,783,258
Number of extensions: 576810
Number of successful extensions: 899
Number of sequences better than 10.0: 1
Number of HSP's gapped: 898
Number of HSP's successfully gapped: 34
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 54 (24.5 bits)