RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy280
(156 letters)
>gnl|CDD|217836 pfam04000, Sas10_Utp3, Sas10/Utp3/C1D family. This family
contains Utp3 and LCP5 which are components of the U3
ribonucleoprotein complex. It also includes the human
C1D protein and Saccharomyces cerevisiae YHR081W
(rrp47), an exosome-associated protein required for the
3' processing of stable RNAs, and Sas10 which has been
identified as a regulator of chromatin silencing. This
family also includes the human protein Neuroguidin an
initiation factor 4E (eIF4E) binding protein.
Length = 81
Score = 36.5 bits (85), Expect = 5e-04
Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 5 LIDELLSKFINSQHDLESLVDEISEIIKQVQAVDFTKLPNDKKIEADLLVLYAINSLYFI 64
L++EL + L+ L+ ++ E ++ K + +LL+ Y IN L+++
Sbjct: 1 LLEELSKSLDELEESLKPLLKKVKEKESELPPASL------LKAKNELLLAYLINLLFYL 54
Query: 65 NLRIKHVDSDF--VKVELKRIQETMKK 89
L++ VD V EL R++ ++K
Sbjct: 55 LLKLSGVDIKDHPVMEELVRLRVYLEK 81
>gnl|CDD|233994 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 31.9 bits (73), Expect = 0.12
Identities = 14/76 (18%), Positives = 25/76 (32%)
Query: 1 MTLNLIDELLSKFINSQHDLESLVDEISEIIKQVQAVDFTKLPNDKKIEADLLVLYAINS 60
L+L+ E+L+ +S H D + Q+ D ++ +E D
Sbjct: 158 DLLSLVREMLNPDPDSIHPWPISYDPNQLLRDQIVDPDTDLEVHEGGLEVDHEDNQGEVK 217
Query: 61 LYFINLRIKHVDSDFV 76
IK +F
Sbjct: 218 TRIRVFSIKRFPEEFT 233
>gnl|CDD|226204 COG3679, COG3679, Regulatory protein involved in competence
development and sporulation [Replication, recombination
and repair; Signal transduction mechanisms].
Length = 118
Score = 27.7 bits (62), Expect = 1.6
Identities = 10/25 (40%), Positives = 19/25 (76%)
Query: 7 DELLSKFINSQHDLESLVDEISEII 31
+E +S F+ ++ L SL+DE+++II
Sbjct: 80 NEKVSAFMEAEQALSSLLDELNKII 104
>gnl|CDD|234447 TIGR04046, MSMEG_0569_nitr, flavin-dependent oxidoreductase,
MSMEG_0569 family. Members of this protein family
belong to a conserved seven-gene biosynthetic cluster
found sparsely in Cyanobacteria, Proteobacteria, and
Actinobacteria. Distant homologies to characterized
proteins suggest that members are enzymes dependent on a
flavinoid cofactor.
Length = 400
Score = 26.9 bits (60), Expect = 5.3
Identities = 10/29 (34%), Positives = 10/29 (34%)
Query: 117 WTPPESDTPCDKKTKDIPPVSKKTKFDAD 145
W P E T D I V T F D
Sbjct: 315 WEPEEEPTELDLAAAGITSVIWCTGFRPD 343
>gnl|CDD|213341 cd05392, RasGAP_Neurofibromin_like, Ras-GTPase Activating Domain of
proteins similar to neurofibromin. Neurofibromin-like
proteins include the Saccharomyces cerevisiae RasGAP
proteins Ira1 and Ira2, the closest homolog of
neurofibromin, which is responsible for the human
autosomal dominant disease neurofibromatosis type I
(NF1). The RasGAP Ira1/2 proteins are negative
regulators of the Ras-cAMP signaling pathway and
conserved from yeast to human. In yeast Ras proteins are
activated by GEFs, and inhibited by two GAPs, Ira1 and
Ira2. Ras proteins activate the cAMP/protein kinase A
(PKA) pathway, which controls metabolism, stress
resistance, growth, and meiosis. Recent studies showed
that the kelch proteins Gpb1 and Gpb2 inhibit Ras
activity via association with Ira1 and Ira2. Gpb1/2 bind
to a conserved C-terminal domain of Ira1/2, and loss of
Gpb1/2 results in a destabilization of Ira1 and Ira2,
leading to elevated levels of Ras2-GTP and uninhibited
cAMP-PKA signaling. Since the Gpb1/2 binding domain on
Ira1/2 is conserved in the human neurofibromin protein,
the studies suggest that an analogous signaling
mechanism may contribute to the neoplastic development
of NF1.
Length = 317
Score = 26.5 bits (59), Expect = 5.8
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 11/91 (12%)
Query: 11 SKFINSQHDLESLVDEISEIIKQVQA-------VDFTKLPNDK----KIEADLLVLYAIN 59
F + LESL + + + ++Q + T D+ I ADL L+
Sbjct: 223 VLFSLKEPYLESLNEFLKKNSDRIQQFLSEVSTIPPTDPIFDESDEEPITADLRYLHKFL 282
Query: 60 SLYFINLRIKHVDSDFVKVELKRIQETMKKF 90
L+F+ +R + + + K + ET K
Sbjct: 283 YLHFLEIRKEVLKGSSSQGSDKELVETFKLI 313
>gnl|CDD|165155 PHA02792, PHA02792, ankyrin-like protein; Provisional.
Length = 631
Score = 26.8 bits (59), Expect = 6.3
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 95 DKLTIMPRLDKDASKRFVRNALWT 118
D LT+M +L+K KR+V N ++T
Sbjct: 550 DMLTVMYKLNKPTKKRYVNNPVFT 573
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 26.6 bits (59), Expect = 6.5
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 46 KKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKF 90
K AD+L LY +S + +LR F LK++ E +K
Sbjct: 627 NKYGADILRLYVASSDPWEDLR-------FSDEILKQVVEKYRKI 664
>gnl|CDD|217408 pfam03177, Nucleoporin_C, Non-repetitive/WGA-negative nucleoporin
C-terminal. This is the C-termainl half of a family of
nucleoporin proteins. Nucleoporins are the main
components of the nuclear pore complex in eukaryotic
cells, and mediate bidirectional nucleocytoplasmic
transport, especially of mRNA and proteins. Two
nucleoporin classes are known: one is characterized by
the FG repeat pfam03093; the other is represented by
this family, and lacks any repeats. RNA undergoing
nuclear export first encounters the basket of the
nuclear pore and many nucleoporins are accessible on the
basket side of the pore.
Length = 559
Score = 26.7 bits (59), Expect = 6.8
Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 2/99 (2%)
Query: 3 LNLIDELLSKFINSQHDL-ESLVDEISEIIKQVQAVDFTKLPNDKKIEADLLVLYAINSL 61
L+ I+ELL + Q DL E L++ I + A KL L YA+ +
Sbjct: 422 LSEIEELL-EVAKIQKDLLEQLLEADQRISDEKAAAALAKLDGLILSLTKLFNDYALPAE 480
Query: 62 YFINLRIKHVDSDFVKVELKRIQETMKKFKQTKDKLTIM 100
Y I+L S + L+ + + +DK I
Sbjct: 481 YLIDLLTLMDPSTEFYLALRLLCLLIFALADYRDKDLIR 519
>gnl|CDD|222672 pfam14314, Methyltrans_Mon, Virus-capping methyltransferase. This
is the methyltransferase region of the Mononegavirales
single-stranded RNA viral RNA polymerase enzymes. This
region is involved in the mRNA-capping of the virion
particles.
Length = 674
Score = 26.5 bits (59), Expect = 7.2
Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 8/72 (11%)
Query: 50 ADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQTKDKLTIMPRLDKDASK 109
+ L +A+ S + + + K S K L+++ E + + + K
Sbjct: 174 IEFLGPFAL-SSHLLKILYKPNLSKRDKNRLRKLSELSRNVRSGEG-------WSDLHIK 225
Query: 110 RFVRNALWTPPE 121
R ++ L+ P E
Sbjct: 226 RLTKDILFCPQE 237
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
0.317 0.135 0.372
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,856,012
Number of extensions: 708532
Number of successful extensions: 1125
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1119
Number of HSP's successfully gapped: 59
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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: 55 (25.0 bits)