RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11013
(176 letters)
>gnl|CDD|216245 pfam01015, Ribosomal_S3Ae, Ribosomal S3Ae family.
Length = 195
Score = 101 bits (253), Expect = 3e-27
Identities = 38/64 (59%), Positives = 45/64 (70%)
Query: 73 THVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVL 132
+ R IRKKM EII E + D KE V KL+P SIAK+IEK + IYPL V IRKVKVL
Sbjct: 132 SQKRAIRKKMTEIITKEASELDFKEFVQKLIPGSIAKDIEKAAKKIYPLRRVEIRKVKVL 191
Query: 133 KKPR 136
K+P+
Sbjct: 192 KRPK 195
>gnl|CDD|224802 COG1890, RPS1A, Ribosomal protein S3AE [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 79.3 bits (196), Expect = 1e-18
Identities = 34/82 (41%), Positives = 47/82 (57%)
Query: 73 THVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVL 132
+ R IRK M EII + + +E V +L+P IA EIE+ + IYPL V IRK KVL
Sbjct: 133 SQKRAIRKIMFEIIEEKASELTFEEFVQELIPGRIAAEIEEAAKKIYPLRKVEIRKSKVL 192
Query: 133 KKPRFELSKLLELHGEGKGGAT 154
K+P+ + LHGE + +
Sbjct: 193 KEPKEAEPEQAVLHGESEEVGS 214
>gnl|CDD|235216 PRK04057, PRK04057, 30S ribosomal protein S3Ae; Validated.
Length = 203
Score = 59.1 bits (144), Expect = 3e-11
Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 73 THVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVL 132
+ IRK M EII + + +E V +++ +A EI K+ + IYPL V IRK KVL
Sbjct: 125 SQKHAIRKIMEEIIEEKASELTFEEFVQEIVFGKLASEIYKEAKKIYPLRRVEIRKSKVL 184
Query: 133 KKP 135
+P
Sbjct: 185 ARP 187
>gnl|CDD|213205 cd03238, ABC_UvrA, ATP-binding cassette domain of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 176
Score = 31.5 bits (72), Expect = 0.14
Identities = 28/120 (23%), Positives = 45/120 (37%), Gaps = 21/120 (17%)
Query: 41 GYLHLSQSLNTFLLGDCGPRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKSDLKEVVN 100
GYL L Q L+T G+ +KL +LF + I++E L +
Sbjct: 77 GYLTLGQKLSTLSGGEL----QRVKLASELFSEPPGTL------FILDEPSTG-LHQQDI 125
Query: 101 KLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVLKKPRFELSKLLEL-HGEGKGGATIDESG 159
L + I I+ I H++ VL + +++ G GK G + SG
Sbjct: 126 NQLLEVIKGLIDLGNTVILIEHNL-----DVLSSADW----IIDFGPGSGKSGGKVVFSG 176
>gnl|CDD|239494 cd03400, Band_7_1, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and are known to interact
with a variety of proteins. Stomatin interacts with and
regulates members of the degenerin/epithelia Na+ channel
family in mechanosensory cells of Caenorhabditis elegans
and vertebrate neurons and participates in trafficking
of Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth during
lambda phage infection. Flotillins have been implicated
in the progression of prion disease, in the pathogenesis
of neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis. Mutations in the podicin gene give rise to
autosomal recessive steroid resistant nephritic
syndrome.
Length = 124
Score = 29.6 bits (67), Expect = 0.39
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 69 QLFKTHVRQIRKKMVEIIINEVVKS--DLKEVV--NKLLPDSIAKEIEKK 114
Q++ T ++I + + +I E V L+EV+ N LPD IA IE K
Sbjct: 74 QIYSTKRKEIESAIKKELIEEFVGDGLILEEVLLRNIKLPDQIADAIEAK 123
>gnl|CDD|129744 TIGR00659, TIGR00659, TIGR00659 family protein. Members of this
small but broadly distibuted (Gram-positive,
Gram-negative, and Archaeal) family appear to have
multiple transmembrane segments. The function is
unknown. A homolog, LrgB of Staphylococcus aureus, in
the same small superfamily but in an outgroup to this
subfamily, is regulated by LytSR and is suggested to act
as a murein hydrolase. Of the three paralogous proteins
in B. subtilis, one is a full length member of this
family, one lacks the C-terminal 60 residues and has an
additional 128 N-terminal residues but branches within
the family in a phylogenetic tree, and one is closely
related to LrgB and part of the outgroup [Hypothetical
proteins, Conserved].
Length = 226
Score = 29.0 bits (65), Expect = 0.99
Identities = 28/104 (26%), Positives = 43/104 (41%), Gaps = 26/104 (25%)
Query: 42 YLHLSQSLNTFLLGDCGPRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKSDLK----- 96
Y+ +N L GP + + L L+K + QI+K EII+N V S +
Sbjct: 54 YMLGGGVINDLL----GP--AVVALAIPLYK-QLPQIKKYWKEIILNVAVGSVIAIISGT 106
Query: 97 ----------EVVNKLLPDS----IAKEIEKKCQGIYPLHDVFI 126
E++ LLP S IA + + GI + VF+
Sbjct: 107 LLALLLGLGPEIIASLLPKSVTTPIAMHVSEMIGGIPAVTAVFV 150
>gnl|CDD|236758 PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA;
Provisional.
Length = 413
Score = 29.3 bits (66), Expect = 1.2
Identities = 17/45 (37%), Positives = 29/45 (64%), Gaps = 7/45 (15%)
Query: 71 FKTHVRQIRKKMVEIIINEVVKSDLKEVVNKLLP---DSIAKEIE 112
+ T+ QIRK+M II+EV ++++ + +LP DS+AK+I
Sbjct: 107 YNTYRNQIRKEM---IISEVRNNEVRRRIT-ILPQEVDSLAKQIG 147
>gnl|CDD|227156 COG4819, EutA, Ethanolamine utilization protein, possible
chaperonin protecting lyase from inhibition [Amino acid
transport and metabolism].
Length = 473
Score = 28.3 bits (63), Expect = 2.5
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 60 RGSSLKLVYQLFKTHVRQIRKKMVEIIINEV---VKSDLKEVV--NKLLPDSIAKEI 111
G ++ +L + Q+ ++M E+++ V S L E + KLLP + EI
Sbjct: 203 CGGAITDGRKLTGAQLVQVTREMAELLVEVVDFGALSPLYEALITTKLLPADVTPEI 259
>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 773
Score = 28.2 bits (63), Expect = 2.8
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 2/72 (2%)
Query: 63 SLKLVYQLFKTHVRQIRKKM-VEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPL 121
L + L K H R++ VEI + K L EV+ +L ++E++ G
Sbjct: 244 LLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQGSGFREA 303
Query: 122 HD-VFIRKVKVL 132
D + K++VL
Sbjct: 304 LDASNLEKLQVL 315
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 27.2 bits (61), Expect = 5.5
Identities = 25/72 (34%), Positives = 31/72 (43%), Gaps = 22/72 (30%)
Query: 83 VEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVLKKPRFE---- 138
+EII +E++ DL E V K L E+ KK RK K KK
Sbjct: 144 LEIISSELILKDL-EFVEKRLD-----ELTKK------------RKKKKKKKEEKVELDV 185
Query: 139 LSKLLELHGEGK 150
L K+LE EGK
Sbjct: 186 LKKVLEWLEEGK 197
>gnl|CDD|143458 cd07140, ALDH_F1L_FTFDH, 10-formyltetrahydrofolate dehydrogenase,
ALDH family 1L. 10-formyltetrahydrofolate dehydrogenase
(FTHFDH, EC=1.5.1.6), also known as aldehyde
dehydrogenase family 1 member L1 (ALDH1L1) in humans, is
a multi-domain homotetramer with an N-terminal formyl
transferase domain and a C-terminal ALDH domain. FTHFDH
catalyzes an NADP+-dependent dehydrogenase reaction
resulting in the conversion of 10-formyltetrahydrofolate
to tetrahydrofolate and CO2. The ALDH domain is also
capable of the oxidation of short chain aldehydes to
their corresponding acids.
Length = 486
Score = 27.1 bits (60), Expect = 6.0
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 19/70 (27%)
Query: 121 LHDVFIRK-VKVLKKPRF-----------------ELSKLLELHGEG-KGGATIDESGET 161
+HD F+R+ V+ +KK + L KL+E G K GAT+ G+
Sbjct: 303 IHDEFVRRVVEEVKKMKIGDPLDRSTDHGPQNHKAHLDKLVEYCERGVKEGATLVYGGKQ 362
Query: 162 VDRPEGYEPP 171
VDRP + P
Sbjct: 363 VDRPGFFFEP 372
>gnl|CDD|222689 pfam14335, DUF4391, Domain of unknown function (DUF4391). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 220 and
257 amino acids in length.
Length = 221
Score = 26.5 bits (59), Expect = 6.6
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 59 PRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKSDLKEVVNKLLP-DSIAKEIEK 113
G +L +Y+ V QI K K DLKE V +L + + KEI K
Sbjct: 141 FSGLNLDALYESI---VNQIIKLNASSNTGVYEKEDLKERVERLEQIEELEKEIAK 193
>gnl|CDD|233220 TIGR00978, asd_EA, aspartate-semialdehyde dehydrogenase
(non-peptidoglycan organisms). Two closely related
families of aspartate-semialdehyde dehydrogenase are
found. They differ by a deep split in phylogenetic and
percent identity trees and in gap patterns. Separate
models are built for the two types in order to exclude
the USG-1 protein, found in several species, which is
specifically related to the Bacillus subtilis type of
aspartate-semialdehyde dehydrogenase. Members of this
type are found primarily in organisms that lack
peptidoglycan [Amino acid biosynthesis, Aspartate
family].
Length = 341
Score = 26.6 bits (59), Expect = 7.6
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 84 EIIINEVVKSDLKEVVNKLLPDSIAKEIEKKC 115
I+ E + D ++V LP +A+E+E K
Sbjct: 62 PIVEPEPIAEDDVDIVFSALPSEVAEEVEPKL 93
>gnl|CDD|241283 cd01252, PH_GRP1-like, General Receptor for
Phosphoinositides-1-like Pleckstrin homology (PH)
domain. GRP1/cytohesin3 and the related proteins ARNO
(ARF nucleotide-binding site opener)/cytohesin-2 and
cytohesin-1 are ARF exchange factors that contain a
pleckstrin homology (PH) domain thought to target these
proteins to cell membranes through binding
polyphosphoinositides. The PH domains of all three
proteins exhibit relatively high affinity for
PtdIns(3,4,5)P3. Within the Grp1 family, diglycine (2G)
and triglycine (3G) splice variants, differing only in
the number of glycine residues in the PH domain,
strongly influence the affinity and specificity for
phosphoinositides. The 2G variants selectively bind
PtdIns(3,4,5)P3 with high affinity,the 3G variants bind
PtdIns(3,4,5)P3 with about 30-fold lower affinity and
require the polybasic region for plasma membrane
targeting. These ARF-GEFs share a common, tripartite
structure consisting of an N-terminal coiled-coil
domain, a central domain with homology to the yeast
protein Sec7, a PH domain, and a C-terminal polybasic
region. The Sec7 domain is autoinhibited by conserved
elements proximal to the PH domain. GRP1 binds to the
DNA binding domain of certain nuclear receptors
(TRalpha, TRbeta, AR, ER, but not RXR), and can repress
thyroid hormone receptor (TR)-mediated transactivation
by decreasing TR-complex formation on thyroid hormone
response elements. ARNO promotes sequential activation
of Arf6, Cdc42 and Rac1 and insulin secretion. Cytohesin
acts as a PI 3-kinase effector mediating biological
responses including cell spreading and adhesion,
chemotaxis, protein trafficking, and cytoskeletal
rearrangements, only some of which appear to depend on
their ability to activate ARFs. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 118
Score = 25.7 bits (57), Expect = 8.0
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 117 GIYPLHDVFIRKVKVLKKPR-FEL 139
GI PL ++ +R+V+ KKP FEL
Sbjct: 44 GIIPLENLSVREVEDSKKPFCFEL 67
>gnl|CDD|147581 pfam05475, Chlam_vir, Chlamydia virulence protein PGP3-D. This
family consists of Chlamydia virulence proteins which
are thought to be required for growth within mammalian
cells.
Length = 264
Score = 26.4 bits (58), Expect = 9.2
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 70 LFKTHVRQIRKKMVEIIINEVVKSDLKEVVNKLLPD 105
+ K + QI ++V+ II + +S ++EV++K+ D
Sbjct: 76 VIKLILTQIEDELVKDIIKNITQSLIQEVIDKIHID 111
>gnl|CDD|223731 COG0658, ComEC, Predicted membrane metal-binding protein [General
function prediction only].
Length = 453
Score = 26.3 bits (58), Expect = 9.3
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 84 EIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVLKKPRFELSKLL 143
+ INE +K +L + E QGI L VF + PRF S++
Sbjct: 138 ALWINETLKLELPQGALN--LGGFDLEAYLGAQGIGALGTVFQAAIISRSLPRFLRSRIR 195
Query: 144 EL 145
L
Sbjct: 196 RL 197
>gnl|CDD|238499 cd01017, AdcA, Metal binding protein AcdA. These proteins have
been shown to function in the ABC uptake of Zn2+ and
Mn2+ and in competence for genetic transformation and
adhesion. The AcdA proteins belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and they bind their ligand in the
cleft between these domains. In addition, many of these
proteins have a low complexity region containing metal
binding histidine-rich motif (repetitive HDH sequence).
Length = 282
Score = 26.1 bits (58), Expect = 9.6
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 80 KKMVEIIINEVVKSDLK-----EVVNKLLPDSIAKEIEKKCQGIYPLH 122
K++ E++ V KSD+K E + + +++AKE K + PL
Sbjct: 207 KQLAELV-EFVKKSDVKYIFFEENASSKIAETLAKETGAKLLVLNPLE 253
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 26.6 bits (58), Expect = 9.8
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 64 LKLVYQLFKTHVRQIR--KKMVEIIINEVVK--SDLKEVVNKLLPDSIAKEIEKKCQGI 118
+K + Q H++ + KK E I+E+ +DL++V +K + + +EIEKK + I
Sbjct: 1120 IKNLDQKIDHHIKALEEIKKKSENYIDEIKAQINDLEDVADKAISNDDPEEIEKKIENI 1178
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
0.318 0.136 0.394
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,747,261
Number of extensions: 795221
Number of successful extensions: 829
Number of sequences better than 10.0: 1
Number of HSP's gapped: 829
Number of HSP's successfully gapped: 40
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
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 (21.7 bits)
S2: 56 (25.4 bits)