RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5876
(143 letters)
>gnl|CDD|149648 pfam08662, eIF2A, Eukaryotic translation initiation factor eIF2A.
This is a family of eukaryotic translation initiation
factors.
Length = 194
Score = 79.6 bits (197), Expect = 2e-19
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 1/84 (1%)
Query: 6 RGTHIVLAELRDT-GSLEFVDTGDFSVMNAAEHHQATDVEWDPTGRYVMSGVSLWKTKAD 64
G ++LA + G +EF D + + AE ATD EW P GRY ++ + + + D
Sbjct: 111 FGRLVLLAGFGNLAGQIEFWDVKNKKKIATAEASNATDCEWSPDGRYFLTATTSPRLRVD 170
Query: 65 TGYWQWSFQGKIIKRFNSPTFCQL 88
G+ W + GK++ +++ Q+
Sbjct: 171 NGFKIWHYSGKLVYKYDFDELYQV 194
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 59.9 bits (145), Expect = 2e-11
Identities = 27/96 (28%), Positives = 42/96 (43%)
Query: 35 AEHHQATDVEWDPTGRYVMSGVSLWKTKADTGYWQWSFQGKIIKRFNSPTFCQLRWRPRP 94
A+ + T++ WDP+G+YV + S K K + GY + G + F WRP P
Sbjct: 397 AKVFELTNITWDPSGQYVTTSSSCPKHKVEHGYKIFKIAGALYPEEARGGFKNFAWRPEP 456
Query: 95 ASLLSKEQVDKIKKSLKKYTPAFEAKDRQRMNKASK 130
S L+ E K K + FE + A++
Sbjct: 457 PSKLTIESAKKYVKPSRHRFVPFEKAVIMEADSANR 492
>gnl|CDD|200413 TIGR04162, exo_VPEID, exosortase E/protease, VPEID-CTERM system.
Members of this protein family are fusion proteins of
exosortase (N-terminal) and a CAAX prenyl protease
domain (C-terminal). Members are restricted to the alpha
Proteobacteria. The variant C-terminal protein sequence
VPEID-CTERM occurs only in these species, often
adjacent.
Length = 519
Score = 30.5 bits (69), Expect = 0.29
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 51 YVMSGV---SLWKTKADTGYWQWSFQGKIIKRFNSPTFCQLRWRPRPASLLS 99
+++SGV SLW A + +F + F P L WRP PA LL+
Sbjct: 337 FMLSGVLVQSLWANPAQGYPLRAAFMAAGLWLF-WPALRALDWRPGPADLLT 387
>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 30.4 bits (69), Expect = 0.30
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 3 LRMRGTHIVLAELRDTGSLEFV 24
LRMR I+L ELR + +F+
Sbjct: 215 LRMRPDRIILGELRGDEAFDFI 236
>gnl|CDD|220404 pfam09789, DUF2353, Uncharacterized coiled-coil protein (DUF2353).
Members of this family of uncharacterized proteins have
no known function.
Length = 319
Score = 29.5 bits (66), Expect = 0.49
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 100 KEQVDKIKKSLKKYTPAFEAKDRQRMNKA 128
+E+ + IK +L KY EAK+++ M KA
Sbjct: 209 EEESELIKMTLAKYKQMLEAKNKKTMVKA 237
>gnl|CDD|220059 pfam08890, XkdN, Phage XkdN-like protein. This family of proteins
are functionally uncharacterized. They are found in
prophage sequence in various bacteria.
Length = 136
Score = 27.3 bits (61), Expect = 1.9
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 76 IIKRFNSPTFCQLRWRPRPASLLSKEQVDKIKKSLKKYTPAFEAKDRQRMNK--ASKYAD 133
+KR ++ + + LS+E++D+I+K K Q + + +K+
Sbjct: 20 ALKRLGDKGGNEIPFELKA---LSEEEIDEIRKECTKRVK----VKGQYIKEFDQNKFIA 72
Query: 134 LLVVLSCVY 142
LL+V + VY
Sbjct: 73 LLIVAAVVY 81
>gnl|CDD|215355 PLN02658, PLN02658, homogentisate 1,2-dioxygenase.
Length = 435
Score = 27.7 bits (62), Expect = 2.2
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 5/26 (19%)
Query: 74 GKIIKRFNSPTFC-----QLRWRPRP 94
K++ F+ C QLRWRP P
Sbjct: 74 EKLVGEFDPSNSCETTPTQLRWRPFP 99
>gnl|CDD|226967 COG4608, AppF, ABC-type oligopeptide transport system, ATPase
component [Amino acid transport and metabolism].
Length = 268
Score = 27.6 bits (62), Expect = 2.4
Identities = 11/43 (25%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 71 SFQGKIIKRFNSPTFCQLRWRPRPASLLSK-EQVDKIKKSLKK 112
S G++I PT ++ + + + LSK E+ +++ + L+K
Sbjct: 53 STLGRLILGLEEPTSGEILFEGKDITKLSKEERRERVLELLEK 95
>gnl|CDD|180485 PRK06245, cofG, FO synthase subunit 1; Reviewed.
Length = 336
Score = 27.6 bits (62), Expect = 2.5
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 80 FNSPTFCQLRWRPRPASLLSKEQVDKIKKSLKKY 113
N +C R P SLLS E+V +I +
Sbjct: 23 RNRCGYCTFRRDPGQPSLLSPEEVKEILRRGADA 56
>gnl|CDD|165679 PLN00107, PLN00107, FAD-dependent oxidoreductase; Provisional.
Length = 257
Score = 27.3 bits (60), Expect = 2.6
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 71 SFQGKIIKRFNSPTFCQLRWRPRPASLLSKEQVDKI 106
+F G I K + F +++ R P L S E DKI
Sbjct: 167 AFDGAIAKYKKAGEFLKVKERLDPEGLFSSEWSDKI 202
>gnl|CDD|211421 cd11580, eIF2D_N_like, N-terminal domain of eIF2D, malignant T
cell-amplified sequence 1 and related proteins. This
N-terminal domain of various proteins co-occurs with a
PUA domain. Members of this family are: (1) MCTS-1
(malignant T cell-amplified sequence 1) or MCT-1
(multiple copies T cell malignancies), which may play
roles in the regulation of the cell cycle, (2) the
eukayotic translation initiation factor 2D, and (3) an
uncharacterized archaeal family.
Length = 72
Score = 25.4 bits (56), Expect = 4.5
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 98 LSKEQVDKIKKSLKKYTPAFEAKDRQRMNK 127
LSK+ V K+++ L + P E + K
Sbjct: 9 LSKKDVKKLREQLIEQFPLLEEILDEIFPK 38
>gnl|CDD|215793 pfam00213, OSCP, ATP synthase delta (OSCP) subunit. The ATP D
subunit from E. coli is the same as the OSCP subunit
which is this family. The ATP D subunit from metazoa are
found in family pfam00401.
Length = 171
Score = 26.3 bits (59), Expect = 5.2
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 98 LSKEQVDKIKKSLKKYT 114
LS+EQ+ +K +L+K T
Sbjct: 113 LSEEQLKALKAALEKKT 129
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 26.5 bits (59), Expect = 5.5
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 3 LRMRGTHIVLAELRDTGSLEFV 24
LR R I++ E+RD + + +
Sbjct: 196 LRQRPDRIMVGEIRDGETADIL 217
>gnl|CDD|235593 PRK05758, PRK05758, F0F1 ATP synthase subunit delta; Validated.
Length = 177
Score = 26.3 bits (59), Expect = 5.6
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 98 LSKEQVDKIKKSLKKYT 114
LS+EQ+DK+K +L+K
Sbjct: 117 LSEEQLDKLKAALEKRL 133
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 26.1 bits (58), Expect = 7.7
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 125 MNKASKYADLLVVLS 139
+N+AS+Y D LVVL+
Sbjct: 198 LNQASRYCDHLVVLA 212
>gnl|CDD|226384 COG3866, PelB, Pectate lyase [Carbohydrate transport and
metabolism].
Length = 345
Score = 25.9 bits (57), Expect = 8.0
Identities = 10/60 (16%), Positives = 20/60 (33%), Gaps = 1/60 (1%)
Query: 55 GVSLWKTKADTGYWQWSFQGKII-KRFNSPTFCQLRWRPRPASLLSKEQVDKIKKSLKKY 113
G+ TK +GY + + S + W P + + + +K + Y
Sbjct: 279 GLGFLDTKGTSGYANQDSGSYLNSSKSMSVRAGGVTWNPSSYYSYTVDPPEDVKSFVTNY 338
>gnl|CDD|183911 PRK13239, PRK13239, alkylmercury lyase; Provisional.
Length = 206
Score = 25.7 bits (57), Expect = 8.5
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 39 QATDVEWDPTGRYVMSGVSLWKT 61
D E+D GR + G++L T
Sbjct: 59 AMPDTEYDEDGRIIGYGLTLRPT 81
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and host
eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 25.7 bits (57), Expect = 9.2
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 3 LRMRGTHIVLAELRDTGSLEFV 24
LRMR I++ E+R +L+ +
Sbjct: 97 LRMRPDRIIVGEVRGGEALDLL 118
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM3 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 86
Score = 24.9 bits (55), Expect = 9.7
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 72 FQGKIIKRFNSPTFCQLRW 90
F GK K F S C + +
Sbjct: 63 FNGKKWKNFKSKKVCDITY 81
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
0.320 0.132 0.411
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,170,353
Number of extensions: 607916
Number of successful extensions: 773
Number of sequences better than 10.0: 1
Number of HSP's gapped: 773
Number of HSP's successfully gapped: 29
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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 (24.8 bits)