RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3925
(210 letters)
>gnl|CDD|211398 cd11560, W2_eIF5C_like, C-terminal W2 domain of the eukaryotic
translation initiation factor 5C and similar proteins.
eIF5C appears to be essential for the initiation of
protein translation; its actual function, and
specifically that of the C-terminal W2 domain, are not
well understood. The Drosophila ortholog, kra
(krasavietz) or exba (extra bases), may be involved in
translational inhibition in neural development. The
structure of this C-terminal domain resembles that of a
set of concatenated HEAT repeats.
Length = 194
Score = 201 bits (514), Expect = 4e-66
Identities = 74/119 (62%), Positives = 95/119 (79%), Gaps = 1/119 (0%)
Query: 86 VLINIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCY 145
V+ +W+ +M VEW+KKE+ +AEQAL+HLK++ PL AF T RAELAL+ K+QE+CY
Sbjct: 76 VVGLLWTALMDAVEWSKKEDQIAEQALRHLKKYAPLLAAFC-TTARAELALLNKIQEYCY 134
Query: 146 ENMNLMRVFQKIILLFYKTDVISEEVILKWYKEGHSIKGKIMFLEQMKKFVEWLQSAEE 204
ENM M+VFQKI+ L YK DV+SE+ ILKWYK+GHS KGK +FL+QM+ FVEWLQ AEE
Sbjct: 135 ENMKFMKVFQKIVKLLYKADVLSEDAILKWYKKGHSPKGKQVFLKQMEPFVEWLQEAEE 193
>gnl|CDD|216850 pfam02020, W2, eIF4-gamma/eIF5/eIF2-epsilon. This domain of
unknown function is found at the C-terminus of several
translation initiation factors.
Length = 75
Score = 83.8 bits (208), Expect = 1e-21
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 131 RAELALMLKVQEFCY-ENMNLMRVFQKIILLFYKTDVISEEVILKWYKE--GHSIKGKIM 187
A+ L+ ++ FC EN L+++ KI+ L Y D++ EE ILKWY++ +G
Sbjct: 1 DAQKDLLGALERFCGKENPELIKLLPKILKLLYDLDILEEEAILKWYEKSKKVDGEGSKK 60
Query: 188 FLEQMKKFVEWLQSA 202
+Q K FV WL+ A
Sbjct: 61 VRKQAKPFVTWLEEA 75
>gnl|CDD|214705 smart00515, eIF5C, Domain at the C-termini of GCD6, eIF-2B epsilon,
eIF-4 gamma and eIF-5.
Length = 83
Score = 82.3 bits (204), Expect = 7e-21
Identities = 31/83 (37%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 120 PLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKEG 179
PL F +L L+ ++EFC E L ++ KI+ Y D++ EE ILKWY++
Sbjct: 2 PLL-KFLAKDEEEQLELLYAIEEFCVELEKLGKLLPKILKSLYDADILEEEAILKWYEKA 60
Query: 180 HSIKGKIMFLEQMKKFVEWLQSA 202
S +GK + K FV WLQ A
Sbjct: 61 VSAEGKKKVRKNAKPFVTWLQEA 83
>gnl|CDD|211396 cd11558, W2_eIF2B_epsilon, C-terminal W2 domain of eukaryotic
translation initiation factor 2B epsilon. eIF2B is a
heteropentameric complex which functions as a guanine
nucleotide exchange factor in the recycling of eIF-2
during the initiation of translation in eukaryotes. The
epsilon and gamma subunits are sequence similar and both
are essential in yeast. Epsilon appears to be the
catalytically active subunit, with gamma enhancing its
activity. The C-terminal domain of the eIF2B epsilon
subunit contains bipartite motifs rich in acidic and
aromatic residues, which are responsible for the
interaction with eIF2. The structure of the domain
resembles that of a set of concatenated HEAT repeats.
Length = 169
Score = 71.5 bits (176), Expect = 7e-16
Identities = 32/99 (32%), Positives = 55/99 (55%), Gaps = 3/99 (3%)
Query: 108 AEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVI 167
E K L ++ PL + + ++ L+L ++EFC E+ +F K++ Y D++
Sbjct: 69 LEALKKLLSKWGPLLENYVKSQ-DDQVELLLALEEFCLESEEGGPLFAKLLHALYDLDIL 127
Query: 168 SEEVILKWYKEGHSIKGKIM--FLEQMKKFVEWLQSAEE 204
EE IL+W++E + + M E +KKF+EWL+ AEE
Sbjct: 128 EEEAILEWWEEPDAGADEEMKKVRELVKKFIEWLEEAEE 166
>gnl|CDD|211399 cd11561, W2_eIF5, C-terminal W2 domain of eukaryotic translation
initiation factor 5. eIF5 functions as a GTPase
acceleration protein (GAP), as well as a GDP
dissociation inhibitor (GDI) during translational
initiation in eukaryotes. The structure of this
C-terminal domain resembles that of a set of
concatenated HEAT repeats.
Length = 157
Score = 63.0 bits (154), Expect = 1e-12
Identities = 33/106 (31%), Positives = 54/106 (50%), Gaps = 6/106 (5%)
Query: 104 EELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYE-NMNLMRVFQKIILLFY 162
E L E +K +K+ L T +A+ AL+ ++ FC + + L++ I+ Y
Sbjct: 50 EVLFDENIVKEIKKRKALLLKLV-TDEKAQKALLGGIERFCGKHSPELLKKVPLILKALY 108
Query: 163 KTDVISEEVILKWYKEGH----SIKGKIMFLEQMKKFVEWLQSAEE 204
D++ EEVILKWY++ S + + + FVEWL+ AEE
Sbjct: 109 DNDILEEEVILKWYEKVSKKYVSKEKSKKVRKAAEPFVEWLEEAEE 154
>gnl|CDD|211395 cd11473, W2, C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon.
This domain is found at the C-terminus of several
translation initiation factors, including the epsilon
chain of eIF2b, where it has been found to catalyze the
conversion of eIF2.GDP to its active eIF2.GTP form. The
structure of the domain resembles that of a set of
concatenated HEAT repeats.
Length = 135
Score = 56.7 bits (137), Expect = 1e-10
Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 3/90 (3%)
Query: 90 IWSTVMAQVEWNK-KEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENM 148
+ + V+ VE EQ + LK++ P+ + +L L+LK+++ C +
Sbjct: 46 LLTAVVNAVESADSISLTQKEQLVLVLKKYGPVLRELLKLIKKDQLYLLLKIEKLCLQLK 105
Query: 149 N--LMRVFQKIILLFYKTDVISEEVILKWY 176
L+ + +KI+ L Y DV+SEE IL W+
Sbjct: 106 LSELISLLEKILDLLYDADVLSEEAILSWF 135
>gnl|CDD|211397 cd11559, W2_eIF4G1_like, C-terminal W2 domain of eukaryotic
translation initiation factor 4 gamma 1 and similar
proteins. eIF4G1 is a component of the multi-subunit
eukaryotic translation initiation factor 4F, which
facilitates recruitment of the mRNA to the ribosome, a
rate-limiting step during translation initiation. This
C-terminal domain, whose structure resembles that of a
set of concatenated HEAT repeats, has been associated
with binding to/recruiting the kinase Mnk1, which
phosphorylates eIF4E.
Length = 134
Score = 33.8 bits (78), Expect = 0.021
Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 11/91 (12%)
Query: 91 WSTVMAQV-EWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYE--- 146
+M V ++ +E+ + E+ L+++ PL + D + +L + +Q +
Sbjct: 42 VRALMTAVLKYAIEEKSLPEKEKALLEKYAPLLQKYLDDDEQLQLQALYALQALVHTLEF 101
Query: 147 --NMNLMRVFQKIILLFYKTDVISEEVILKW 175
+ L+R F Y DVI EE LKW
Sbjct: 102 PKGL-LLRFFD----ALYDEDVIEEEAFLKW 127
>gnl|CDD|236409 PRK09201, PRK09201, amidase; Provisional.
Length = 465
Score = 29.9 bits (68), Expect = 1.0
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 107 VAEQALKHLKQFTPLFGAFTD-TAPRA 132
VA+ L + + P AFT TA RA
Sbjct: 26 VAQATLARIARANPQLNAFTAVTAERA 52
>gnl|CDD|182353 PRK10280, PRK10280, dipeptidyl carboxypeptidase II; Provisional.
Length = 681
Score = 29.0 bits (65), Expect = 2.2
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 28 QVFIKLMRRYKYLEKMFD---EEMKKVLVFIKGFNETERIKLARMTALW 73
QVF + R Y+ E M D E+M+ +F KG++ +E + A + W
Sbjct: 513 QVFARYARHYQSGEAMPDELQEKMRNASLFNKGYDMSELLSAALLDMRW 561
>gnl|CDD|213910 TIGR04297, thauma_sortase, thaumarchaeosortase. This member of the
archaeosortase/exosortase family occurs exclusively in
the Thaumarchaeota, where the corresponding proposed
sorting signal is PEFG-CTERM (see model TIGR04296). This
family is unusual in that the suspected active site
residue, Cys in every other defined subfamily of
archaeosortases and exosortases is replaced by Ser.
Length = 307
Score = 27.6 bits (61), Expect = 4.3
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 118 FTPLFGAF--TDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKW 175
F+ + GAF PRA ++ + +NL+R+F L +Y V ++ K
Sbjct: 209 FSLVIGAFLLKMNIPRARKSIYFGIGIAGTIGINLIRIFS---LSWYALKVTTD---PKA 262
Query: 176 YKEGHSIKGKIMFLEQMKKFV 196
++E H I G+IMFL + F+
Sbjct: 263 WEEFHKIAGEIMFLPWLFAFI 283
>gnl|CDD|128350 smart00035, CLa, CLUSTERIN alpha chain.
Length = 216
Score = 27.0 bits (60), Expect = 5.7
Identities = 25/120 (20%), Positives = 49/120 (40%), Gaps = 25/120 (20%)
Query: 21 QSLKNFEQVFIKLMRRYKYLEKMFDEEMKKVLVFIKGFNE--------------TERIKL 66
Q L Q+ + ++Y L + + ++M ++ NE ++ L
Sbjct: 98 QELDESLQLAERFTQQYDQLLQSYQKKMLNTSSLLEQLNEQFGWVSQLANLTQGEDQYYL 157
Query: 67 ARMTALWITNG--SVPPTVLQVLI------NIWSTVMAQVEWN--KKEELVAEQALKHLK 116
++T + SVP +V++ I T+ +V + K E VAE+AL+H +
Sbjct: 158 -QVTTVPSHTSDSSVPSGTTKVVVKLFDSDPITLTIPEEVSADNPKFMETVAEKALQHYR 216
>gnl|CDD|216236 pfam01003, Flavi_capsid, Flavivirus capsid protein C. Flaviviruses
are small enveloped viruses with virions comprised of 3
proteins called C, M and E. Multiple copies of the C
protein form the nucleocapsid, which contains the ssRNA
molecule.
Length = 117
Score = 26.1 bits (58), Expect = 7.6
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 16/56 (28%)
Query: 63 RIKLARMTALWITNGSVPPTVLQVLINIWSTVMAQVEWNKKEELVAEQALKHLKQF 118
R+ LA + T ++ PT L W TV K+ QA+KHL++F
Sbjct: 39 RLVLAFLAFFRFT--AIAPT--PGLKKRWRTV------PKR------QAIKHLRKF 78
>gnl|CDD|185751 cd09238, V_Alix_like_1, Protein-interacting V-domain of an
uncharacterized family of the V_Alix_like superfamily.
This domain family is comprised of uncharacterized plant
proteins. It belongs to the V_Alix_like superfamily
which includes the V-shaped (V) domains of Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, mammalian Alix (apoptosis-linked gene-2
interacting protein X), (His-Domain) type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23), and
related domains. Alix, also known as apoptosis-linked
gene-2 interacting protein 1 (AIP1), participates in
membrane remodeling processes during the budding of
enveloped viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), and the abscission
reactions of mammalian cell division. It also functions
in apoptosis. HD-PTP functions in cell migration and
endosomal trafficking, Bro1 in endosomal trafficking,
and Rim20 in the response to the external pH via the
Rim101 pathway. Alix, HD-PTP, Bro1, and Rim20 all
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. The mammalian Alix
V-domain (belonging to a different family) contains a
binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
The Alix V-domain is also a dimerization domain. In
addition to this V-domain, members of the
V_Alix_Rim20_Bro1_like superfamily also have an
N-terminal Bro1-like domain, which binds components of
the ESCRT-III complex. The Bro1-like domains of Alix and
HD-PTP can also bind to human immunodeficiency virus
type 1 (HIV-1) nucleocapsid. Many members of the
V_Alix_like superfamily also have a proline-rich region
(PRR).
Length = 339
Score = 27.1 bits (60), Expect = 7.9
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 17 QEDMQSLKNFEQVFIKLMRRYKYLEKMFDEEMKK 50
++ M++LK + + K+M + +F EE+KK
Sbjct: 215 EDMMKALKRNDNILAKVMATTGSYDALFKEELKK 248
>gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional.
Length = 1092
Score = 26.9 bits (60), Expect = 8.7
Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 14 FEAQ-EDMQSLKNFEQVFIKLMRR 36
F AQ ED+ LK EQV +LM R
Sbjct: 388 FIAQIEDINELKRTEQVNERLMER 411
>gnl|CDD|222560 pfam14127, DUF4294, Domain of unknown function (DUF4294). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 192 and 226 amino
acids in length.
Length = 157
Score = 26.4 bits (59), Expect = 9.5
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 13 IFEAQEDMQSLKN--FEQVFIKLMRRYKYLEKMFDEEMKK 50
+ E E +++L N + + K + KY+++ F E+KK
Sbjct: 50 LIELYEYLETLPNKKARKKYTKRVE--KYIKEEFTPELKK 87
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 26.5 bits (59), Expect = 9.5
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 17/52 (32%)
Query: 146 ENMNLMRVFQKIILLFYKTDVISEEVILKWYKEGHSIKGKIMFLEQMKKFVE 197
E M L II+L K D++ EE L+ Y EQ+K+FV+
Sbjct: 127 EIMGLK----HIIILQNKIDLVKEEQALENY-------------EQIKEFVK 161
>gnl|CDD|219580 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 26.9 bits (60), Expect = 9.7
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 14/62 (22%)
Query: 62 ERIKLARMTALW-----ITNGSVPPTVLQVLINIWSTVMAQV---------EWNKKEELV 107
R++LAR + S+P V+ +L WS V+ W + L+
Sbjct: 480 ARLELARQQVQQELEQRLAGRSLPEVVVTLLRQAWSDVLVLTYLREGEESPAWQEALALL 539
Query: 108 AE 109
+
Sbjct: 540 DD 541
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
0.322 0.134 0.387
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,766,961
Number of extensions: 1023563
Number of successful extensions: 1113
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1105
Number of HSP's successfully gapped: 35
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
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 (22.0 bits)
S2: 57 (25.7 bits)