RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6845
(67 letters)
>gnl|CDD|241300 cd01270, PTB_CAPON-like, Carboxyl-terminal PDZ ligand of neuronal
nitric oxide synthase protein (CAPON)
Phosphotyrosine-binding (PTB) domain. CAPON (also
known as Nitric oxide synthase 1 adaptor protein,
NOS1AP, encodes a cytosolic protein that binds to the
signaling molecule, neuronal NOS (nNOS). It contains a
N-terminal PTB domain that binds to the small monomeric
G protein, Dexras1 and a C-terminal PDZ-binding domain
that mediates interactions with nNOS. Included in this
cd are C. elegan proteins dystrobrevin, DYB-1, which
controls neurotransmitter release and muscle Ca(2+)
transients by localizing BK channels and
DYstrophin-like phenotype and CAPON related,DYC-1,
which is functionally related to dystrophin homolog,
DYS-1. Mutations in the dystrophin gene causes Duchenne
muscular dystrophy. DYS-1 shares sequence similarity,
including key motifs, with their mammalian
counterparts. These CAPON-like proteins all have a
single PTB domain. PTB domains have a common PH-like
fold and are found in various eukaryotic signaling
molecules. This domain was initially shown to binds
peptides with a NPXY motif with differing requirements
for phosphorylation of the tyrosine, although more
recent studies have found that some types of PTB
domains can bind to peptides lack tyrosine residues
altogether. In contrast to SH2 domains, which recognize
phosphotyrosine and adjacent carboxy-terminal residues,
PTB-domain binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 179
Score = 60.4 bits (147), Expect = 3e-13
Identities = 22/34 (64%), Positives = 27/34 (79%)
Query: 4 KKQQYNLVQQDEYDTRIPMHSEEAFQHGITFQAK 37
++ Y + D YDTRIP+H+EEAFQHGITFQAK
Sbjct: 1 SRKTYYNLVDDGYDTRIPLHNEEAFQHGITFQAK 34
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 31.4 bits (72), Expect = 0.018
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 37 KTRQKNKKEEKKKKEEEKKKREK 59
K R+K +K EKK ++EE +K
Sbjct: 413 KLRKKQRKAEKKAEKEEAEKAAA 435
Score = 26.0 bits (58), Expect = 1.5
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 35 QAKTRQKNKKEEKKKKEEEKKKREK 59
Q K +K +KEE +K +KK
Sbjct: 418 QRKAEKKAEKEEAEKAAAKKKAEAA 442
>gnl|CDD|205219 pfam13038, DUF3899, Domain of unknown function (DUF3899).
Putative Tryptophanyl-tRNA synthetase.
Length = 92
Score = 29.2 bits (66), Expect = 0.052
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 10/46 (21%)
Query: 27 AFQHGITFQAKTRQKNKKEEKKKKEE--------EKKKREKMVHVP 64
F +G F+ RQ +K+EK EE KKK+ +
Sbjct: 29 GFSYG--FRRLFRQLVEKKEKDSIEEDEFANDKKVKKKKYSVFTWT 72
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 28.3 bits (63), Expect = 0.22
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 20 IPMHSEEAFQHGITFQAKTRQKNKKEE-----KKKKEEEKKKREKMVHV 63
+P F+ F A ++ ++E+ K+K+EE KR + V
Sbjct: 6 VPEARRYNFKGKGRFSADELRRRREEQQVELRKQKREELLNKRRNLADV 54
>gnl|CDD|152166 pfam11730, DUF3297, Protein of unknown function (DUF3297). This
family is expressed in Proteobacteria and
Actinobacteria. The function is not known.
Length = 71
Score = 26.5 bits (59), Expect = 0.41
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 17 DTRIPMHSEEAFQHGITFQAKTRQKNKKEE 46
+ R P ++ E + G+ + K +++ EE
Sbjct: 7 NPRSPHYNAEVLERGVGIRFKGKERTNVEE 36
>gnl|CDD|237147 PRK12586, PRK12586, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 145
Score = 27.0 bits (60), Expect = 0.45
Identities = 7/55 (12%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 10 LVQQDEYDTRIPMH--SEEAFQHGITFQAKTRQKNKKEEKKKKEEEKKKREKMVH 62
L+ + Y M+ ++ I + ++N E + + +++++ K +
Sbjct: 90 LIARAAYRNGAYMYRKNDAHTHASILLSSN--EQNSTEALQLRAKKREEHRKKWY 142
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 27.2 bits (60), Expect = 0.58
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 33 TFQAKTRQKNKKEEKKKKEEEKKKREKMV 61
T +A R K K +EK ++E K V
Sbjct: 790 TIKAAARAKQKPKEKGPNDKEIKIESPSV 818
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 26.7 bits (60), Expect = 0.71
Identities = 7/25 (28%), Positives = 14/25 (56%)
Query: 39 RQKNKKEEKKKKEEEKKKREKMVHV 63
+ KK+EK++ + K K + + V
Sbjct: 70 HKAQKKKEKQEAKAAKAKSKPRLFV 94
Score = 23.6 bits (52), Expect = 9.2
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 37 KTRQKNKKEEKKKKEEEKKKREK 59
K K + +KKKE+++ K K
Sbjct: 63 KKELKAWHKAQKKKEKQEAKAAK 85
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
This domain is found to the N-terminus of bacterial
signal peptidases of the S49 family (pfam01343).
Length = 154
Score = 26.3 bits (59), Expect = 0.96
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 35 QAKTRQKNKKEEKKKKEEEKKKREK 59
+ K +K +K+ +K K + +KK+ K
Sbjct: 67 ELKAWEKAEKKAEKAKAKAEKKKAK 91
Score = 24.8 bits (55), Expect = 3.5
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 36 AKTRQKNKKEEKKKKEEEKKKR 57
+ K K E+KK K+EE K R
Sbjct: 77 KAEKAKAKAEKKKAKKEEPKPR 98
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 26.1 bits (58), Expect = 1.1
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 35 QAKTRQKNKKEEKKKKEEEKKKREKMVHVPS 65
+ + R + K++++KK++E +K EK P+
Sbjct: 564 KEQKRLRKLKKQEEKKKKELEKLEKAKIPPA 594
Score = 25.0 bits (55), Expect = 3.0
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 35 QAKTRQKNKKEEKKKKEEEKKKREK 59
+ + ++ K+ K KK+EEKKK+E
Sbjct: 559 EKEALKEQKRLRKLKKQEEKKKKEL 583
Score = 23.8 bits (52), Expect = 9.4
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 35 QAKTRQKNKKEEKKKKEEEKKKREK 59
+A QK ++ KK++E++KK+ EK
Sbjct: 561 EALKEQKRLRKLKKQEEKKKKELEK 585
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 25.8 bits (57), Expect = 1.7
Identities = 11/41 (26%), Positives = 21/41 (51%)
Query: 26 EAFQHGITFQAKTRQKNKKEEKKKKEEEKKKREKMVHVPST 66
+A + +K KK+EKKK+EE K++ + + +
Sbjct: 732 DAEFKISDSVEEKTKKKKKKEKKKEEEYKREEKARIEIAEA 772
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 25.3 bits (56), Expect = 2.6
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 39 RQKNKKEEKKKKEEEKKKREK 59
+ K+ EKK+KE+EK K +K
Sbjct: 394 KVLAKRAEKKEKEKEKPKVKK 414
Score = 24.9 bits (55), Expect = 2.9
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 36 AKTRQKNKKEEKKKKEEEKKKREK 59
AK +K +KE++K K +++ + K
Sbjct: 397 AKRAEKKEKEKEKPKVKKRHRDTK 420
Score = 24.9 bits (55), Expect = 3.0
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 36 AKTRQKNKKEEKKKKEEEKKKREK 59
++ KKE++K+K + KK+
Sbjct: 395 VLAKRAEKKEKEKEKPKVKKRHRD 418
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 24.9 bits (55), Expect = 3.1
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 36 AKTRQKNKKEEKKKKEEEKKKREK 59
K R++ KKE+KKK KKK E+
Sbjct: 420 EKKREEEKKEKKKKAFAGKKKEEE 443
Score = 24.9 bits (55), Expect = 3.7
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 34 FQAKTRQKNKKEEKKKKEEEKKKREKMV 61
+ + KK E++KKE++KK
Sbjct: 412 IKKIVEKAEKKREEEKKEKKKKAFAGKK 439
Score = 24.1 bits (53), Expect = 6.8
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 25 EEAFQHGITFQAKTRQKNKKEEKKKKEEEKKKREK 59
E F G K +K ++ +KK+EEEKK+++K
Sbjct: 398 EIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKK 432
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 24.6 bits (54), Expect = 3.6
Identities = 7/23 (30%), Positives = 17/23 (73%)
Query: 36 AKTRQKNKKEEKKKKEEEKKKRE 58
A + ++EE++++EEE+++ E
Sbjct: 71 AAAAAEEEEEEEEEEEEEEEESE 93
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 24.9 bits (54), Expect = 3.7
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 24 SEEAFQHGITFQAKTRQKNKKEEKKKKEEEKKKREK 59
+E + I + + +K KKEEK K++E KK +
Sbjct: 4 TESEAEKKILTEEELERKKKKEEKAKEKELKKLKAA 39
>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization
protein TraG; Provisional.
Length = 942
Score = 24.7 bits (54), Expect = 3.7
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 5 KQQYNLVQQDEYDTRIPMHSEEA-FQHGITFQAKTRQK-----NKKEEKKKKEEEKKKRE 58
+ + N V+ +Y H EA Q+ + K+ Q+ + EE K+ +E + +
Sbjct: 882 RGEENTVKG-QYSELQNHHKTEALSQNNKYNEEKSAQERMPGADSPEELMKRAKEYQDKH 940
Query: 59 K 59
K
Sbjct: 941 K 941
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 24.6 bits (54), Expect = 3.9
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 34 FQAKTRQKNK--KEEKKKKEEEKKKREK 59
F+A+ +K KEEKK + EK+K E+
Sbjct: 94 FKAQKEEKKAMSKEEKKAIKAEKEKLEE 121
>gnl|CDD|115336 pfam06673, L_lactis_ph-MCP, Lactococcus lactis bacteriophage
major capsid protein. This family consists of several
Lactococcus lactis bacteriophage major capsid proteins.
Length = 347
Score = 24.7 bits (53), Expect = 4.0
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 24 SEEAFQHGITFQAKTRQKNKKEEKKKKEEEKKKREKMVHVPS 65
++E + I K R+ K E+ KE E+ K+E+ ++PS
Sbjct: 6 TQEIMKQAIEAGVKVRELEAKVEELNKEREELKKEREANIPS 47
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is
functionally equivalent to L7/L12 in bacteria and the
P1 and P2 proteins in eukaryotes. L12p is homologous to
P1 and P2 but is not homologous to bacterial L7/L12. It
is located in the L12 stalk, with proteins L10, L11,
and 23S rRNA. L12p is the only protein in the ribosome
to occur as multimers, always appearing as sets of
dimers. Recent data indicate that most archaeal species
contain six copies of L12p (three homodimers), while
eukaryotes have four copies (two heterodimers), and
bacteria may have four or six copies (two or three
homodimers), depending on the species. The organization
of proteins within the stalk has been characterized
primarily in bacteria, where L7/L12 forms either two or
three homodimers and each homodimer binds to the
extended C-terminal helix of L10. L7/L12 is attached to
the ribosome through L10 and is the only ribosomal
protein that does not directly interact with rRNA.
Archaeal L12p is believed to function in a similar
fashion. However, hybrid ribosomes containing the large
subunit from E. coli with an archaeal stalk are able to
bind archaeal and eukaryotic elongation factors but not
bacterial elongation factors. In several mesophilic and
thermophilic archaeal species, the binding of 23S rRNA
to protein L11 and to the L10/L12p pentameric complex
was found to be temperature-dependent and cooperative.
Length = 106
Score = 24.4 bits (53), Expect = 4.2
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 35 QAKTRQKNKKEEKKKKEEEKKKRE 58
A + +KEE+KKKEEEK++ E
Sbjct: 72 AAAEEKAEEKEEEKKKEEEKEEEE 95
Score = 23.6 bits (51), Expect = 8.2
Identities = 10/23 (43%), Positives = 19/23 (82%)
Query: 36 AKTRQKNKKEEKKKKEEEKKKRE 58
A+ + + K+EEKKK+EE++++ E
Sbjct: 74 AEEKAEEKEEEKKKEEEKEEEEE 96
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 24.4 bits (53), Expect = 4.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 37 KTRQKNKKEEKKKKEEEKKKR 57
KTR K E K +K+E +KR
Sbjct: 334 KTRTAEKNEAKARKKEIAQKR 354
>gnl|CDD|218437 pfam05107, DUF694, Family of unknown function (DUF694). Family of
hypothetical bacterial proteins.
Length = 278
Score = 24.5 bits (54), Expect = 4.6
Identities = 12/36 (33%), Positives = 23/36 (63%)
Query: 26 EAFQHGITFQAKTRQKNKKEEKKKKEEEKKKREKMV 61
+HG ++ R + +EKKKK+++KKK+E++
Sbjct: 68 LNDEHGELYERADRAEELLKEKKKKKKKKKKKEELR 103
>gnl|CDD|178450 PLN02859, PLN02859, glutamine-tRNA ligase.
Length = 788
Score = 24.3 bits (53), Expect = 4.9
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 37 KTRQKNKKEEKKKKEEEKKKREKMVHV 63
KT N+K KKKKE+ K EK V V
Sbjct: 182 KTAADNEKPVKKKKEKPAKVEEKKVAV 208
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 24.1 bits (53), Expect = 5.2
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 34 FQAKTRQK--NKKEEKKKKEEEKKKREK 59
F+ + +K KEEKK +EEK+K E+
Sbjct: 94 FEEEKEKKKAMSKEEKKAIKEEKEKLEE 121
>gnl|CDD|217286 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
binding fragment. Topoisomerase I promotes the
relaxation of DNA superhelical tension by introducing a
transient single-stranded break in duplex DNA and are
vital for the processes of replication, transcription,
and recombination. This family may be more than one
structural domain.
Length = 215
Score = 24.1 bits (53), Expect = 6.2
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 34 FQAKTRQKN--KKEEKKKKEEEKKKREK 59
F+A+ +K KEEKK +EEK K E+
Sbjct: 95 FEAEKEKKKAMSKEEKKAIKEEKDKLEE 122
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 23.4 bits (51), Expect = 8.4
Identities = 7/16 (43%), Positives = 15/16 (93%)
Query: 43 KKEEKKKKEEEKKKRE 58
+K+E++++EEEK++ E
Sbjct: 79 EKKEEEEEEEEKEESE 94
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 23.7 bits (51), Expect = 8.5
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 36 AKTRQKNKKEEKKKKEEEKK 55
A + + KKEEKK++EEE++
Sbjct: 84 AGAKAEAKKEEKKEEEEEEE 103
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
0.304 0.120 0.319
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,167,948
Number of extensions: 228433
Number of successful extensions: 2223
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1813
Number of HSP's successfully gapped: 403
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 53 (24.0 bits)