RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6417
(194 letters)
>gnl|CDD|202504 pfam02996, Prefoldin, Prefoldin subunit. This family comprises of
several prefoldin subunits. The biogenesis of the
cytoskeletal proteins actin and tubulin involves
interaction of nascent chains of each of the two
proteins with the oligomeric protein prefoldin (PFD) and
their subsequent transfer to the cytosolic chaperonin
CCT (chaperonin containing TCP-1). Electron microscopy
shows that eukaryotic PFD, which has a similar structure
to its archaeal counterpart, interacts with unfolded
actin along the tips of its projecting arms. In its
PFD-bound state, actin seems to acquire a conformation
similar to that adopted when it is bound to CCT.
Length = 120
Score = 75.0 bits (185), Expect = 9e-18
Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 26 IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
+ TDKV + LGA +E +L +A ++K IE +K L +E +L+ L+DQ TT E N+
Sbjct: 55 VIDTDKVLVDLGAGYYVEKSLEEAIEFLKKRIEELEKQLEKLEEELEKLKDQITTLEANL 114
Query: 86 ARVYNW 91
+V
Sbjct: 115 QQVQQK 120
>gnl|CDD|238327 cd00584, Prefoldin_alpha, Prefoldin alpha subunit; Prefoldin is a
hexameric molecular chaperone complex, found in both
eukaryotes and archaea, that binds and stabilizes newly
synthesized polypeptides allowing them to fold
correctly. The complex contains two alpha and four beta
subunits, the two subunits being evolutionarily related.
In archaea, there is usually only one gene for each
subunit while in eukaryotes there two or more paralogous
genes encoding each subunit adding heterogeneity to the
structure of the hexamer. The structure of the complex
consists of a double beta barrel assembly with six
protruding coiled-coils.
Length = 129
Score = 62.2 bits (152), Expect = 8e-13
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 25 SIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVN 84
+ TDKV + LG +E +L +A + K IE K + ++ +L L+DQ T E
Sbjct: 64 KVKDTDKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAE 123
Query: 85 MARVYN 90
+ +
Sbjct: 124 LQELQQ 129
>gnl|CDD|238453 cd00890, Prefoldin, Prefoldin is a hexameric molecular chaperone
complex, found in both eukaryotes and archaea, that
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The complex contains
two alpha and four beta subunits, the two subunits being
evolutionarily related. In archaea, there is usually
only one gene for each subunit while in eukaryotes there
two or more paralogous genes encoding each subunit
adding heterogeneity to the structure of the hexamer.
The structure of the complex consists of a double beta
barrel assembly with six protruding coiled-coils.
Length = 129
Score = 57.0 bits (138), Expect = 6e-11
Identities = 18/66 (27%), Positives = 35/66 (53%)
Query: 25 SIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVN 84
+ DKV + LG V +E +L +A ++K +E +K + +E L+ L+DQ T +
Sbjct: 64 EVKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEE 123
Query: 85 MARVYN 90
+ ++
Sbjct: 124 LQQLQQ 129
>gnl|CDD|178997 PRK00391, rpsR, 30S ribosomal protein S18; Reviewed.
Length = 79
Score = 37.9 bits (89), Expect = 2e-04
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 152 KNPFQKEKVVCILCKMKIK-PDYKNIKLLSQFVS 184
+ F + K VC C KI+ DYK+++LL +F+S
Sbjct: 7 RRRFFRRKKVCRFCAEKIEYIDYKDVELLKKFIS 40
>gnl|CDD|223316 COG0238, RpsR, Ribosomal protein S18 [Translation, ribosomal
structure and biogenesis].
Length = 75
Score = 37.6 bits (88), Expect = 3e-04
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 152 KNPFQKEKVVCILCKMKIKP-DYKNIKLLSQFVS 184
+ PF + + VC I+ DYK+++LL +F+S
Sbjct: 8 RAPFFRRRKVCRFTAEGIEEIDYKDVELLKRFIS 41
>gnl|CDD|201589 pfam01084, Ribosomal_S18, Ribosomal protein S18.
Length = 54
Score = 30.1 bits (69), Expect = 0.10
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 165 CKMKIKPDYKNIKLLSQFVS 184
DYK+++LL +F+S
Sbjct: 1 ADKIEYIDYKDVELLRRFIS 20
>gnl|CDD|216101 pfam00755, Carn_acyltransf, Choline/Carnitine o-acyltransferase.
Length = 590
Score = 31.1 bits (71), Expect = 0.38
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 10/79 (12%)
Query: 8 DATALVQKNIEAAKKNSSIPPTDKVCLWLGANVM-------LEYNLTDATALVQKNIEAA 60
D +V K + I + L +G+ + LE+ +T +Q +IE A
Sbjct: 314 DGIPVVHLCEFVYKVDEQILKSTPEGLPVGSPSVSLPLPEKLEFEITPE---IQSDIEKA 370
Query: 61 KKNLSYIEHDLDFLRDQFT 79
K+ + DLD + QFT
Sbjct: 371 KEKFDKLISDLDLVVLQFT 389
>gnl|CDD|153308 cd07624, BAR_SNX7_30, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 7 and 30. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX7, SNX30, and similar proteins.
The specific functions of SNX7 and SNX30 have not been
elucidated. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 200
Score = 28.9 bits (65), Expect = 1.3
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 34 LWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHD-LDFLRDQFTTTEVNMARVYNWD 92
LW + L L ++ V++ A + LS E L LR+ ++
Sbjct: 60 LWSASETELAPLLEGVSSAVERCTAALEVLLSDHEFVFLPPLREYLLYSDAVKDV----- 114
Query: 93 VKRRNQLKMGLEKS 106
+KRR+Q ++ E S
Sbjct: 115 LKRRDQFQIEYELS 128
>gnl|CDD|177016 CHL00077, rps18, ribosomal protein S18.
Length = 86
Score = 27.6 bits (62), Expect = 1.6
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 172 DYKNIKLLSQFVS 184
DYKN+ LLS+F+S
Sbjct: 29 DYKNMSLLSRFIS 41
>gnl|CDD|184030 PRK13400, PRK13400, 30S ribosomal protein S18; Provisional.
Length = 147
Score = 28.1 bits (62), Expect = 1.8
Identities = 11/44 (25%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 142 EASNKPAEDLKNPFQKEKVVCILCKMKI-KPDYKNIKLLSQFVS 184
+ N+PA + + ++ +C C K+ + DYK+ L++++S
Sbjct: 5 DRPNRPARGGRGRYTPKRKICSFCAEKVSRIDYKDSAKLARYIS 48
>gnl|CDD|216408 pfam01279, Parathyroid, Parathyroid hormone family.
Length = 101
Score = 27.2 bits (60), Expect = 2.3
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 92 DVKRRNQLKMGLEKSNRLRQMTRPVYLSSTRFE--SKSTNNIYEIDFTLGDPEASNKPAE 149
DVKRR L+M LE+ + P + + + +T N+ E F L D E +N P E
Sbjct: 20 DVKRRMWLQMLLEEVHTAEIRGAPATSRDSPHQKPAGNTKNVPER-FGLEDGEGTNLPQE 78
Query: 150 DLKNPFQKE 158
K+ KE
Sbjct: 79 TNKSLTYKE 87
>gnl|CDD|197237 cd09139, PLDc_pPLD_like_1, Catalytic domain, repeat 1, of plant
phospholipase D and similar proteins. Catalytic domain,
repeat 1, of plant phospholipase D (PLD, EC 3.1.4.4) and
similar proteins. Plant PLDs have broad substrate
specificity and can hydrolyze the terminal
phosphodiester bond of several common membrane
phospholipids such as phosphatidylcholine (PC),
phosphatidylethanolamine (PE), phosphatidylglycerol
(PG), and phosphatidylserine (PS), with the formation of
phosphatidic acid and alcohols. Phosphatidic acid is an
essential compound involved in signal transduction. PLDs
also catalyze the transphosphatidylation of
phospholipids to acceptor alcohols, by which various
phospholipids can be synthesized. Most plant PLDs
possess a regulatory calcium-dependent
phospholipid-binding C2 domain in the N-terminus and
require calcium for activity, which is unique to plant
PLDs and is not present in animal or fungal PLDs. Like
other PLD enzymes, the monomer of plant PLDs consists of
two catalytic domains, each of which contains one copy
of the conserved HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue). Two HKD motifs from
two domains form a single active site. Plant PLDs may
utilize a common two-step ping-pong catalytic mechanism
involving an enzyme-substrate intermediate to cleave
phosphodiester bonds. The two histidine residues from
the two HKD motifs play key roles in the catalysis. Upon
substrate binding, a histidine residue from one HKD
motif could function as the nucleophile, attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other histidine
residue from the second HKD motif could serve as a
general acid, stabilizing the leaving group. This
subfamily includes two types of plant PLDs, alpha-type
and beta-type PLDs, which are derived from different
gene products and distinctly regulated. The zeta-type
PLD from Arabidopsis is not included in this subfamily.
Length = 176
Score = 28.1 bits (63), Expect = 2.4
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 149 EDLKNPFQKEKVVCILCKMKIKPDYKNIKLLSQFVS-AFT 187
E+ +N F+ KV C+LC D N + VS AFT
Sbjct: 92 EETRNFFRNTKVNCLLCPR--NGDAGNTYVEQIEVSTAFT 129
>gnl|CDD|236158 PRK08132, PRK08132, FAD-dependent oxidoreductase; Provisional.
Length = 547
Score = 27.9 bits (63), Expect = 3.8
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 130 NIYEIDFTLG---DPEASNKPA 148
N++ IDF LG DPEA KP
Sbjct: 241 NVWRIDFQLGWDADPEAEKKPE 262
>gnl|CDD|223016 PHA03233, PHA03233, DNA packaging protein UL32; Provisional.
Length = 518
Score = 27.8 bits (62), Expect = 3.8
Identities = 11/37 (29%), Positives = 14/37 (37%)
Query: 34 LWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHD 70
+W G NV LTD ++A S IE
Sbjct: 259 MWSGTNVFFNTPLTDLAIKKHHRLKALYSRKSEIEKS 295
>gnl|CDD|183089 PRK11337, PRK11337, DNA-binding transcriptional repressor RpiR;
Provisional.
Length = 292
Score = 27.8 bits (62), Expect = 3.9
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 36 LGANV---MLEYNLTDA--TALVQKNIEAAKKNLSYIEHDLDFLR 75
LG N + + N+ DA ++ Q NIE A+ NL +DF R
Sbjct: 246 LGENAAARIAQLNILDAFFVSVAQLNIEQAEINLQKTGAAVDFFR 290
>gnl|CDD|232851 TIGR00165, S18, ribosomal protein S18. This ribosomal small
subunit protein is found in all eubacteria so far, as
well as in chloroplasts. YER050C from Saccharomyces
cerevisiae and a related protein from Caenorhabditis
elegans appear to be homologous and may represent
mitochondrial forms. The trusted cutoff is set high
enough that these two candidate S18 proteins are not
categorized automatically [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 70
Score = 25.8 bits (57), Expect = 4.8
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 155 FQKEKVVCILCKMKIKP-DYKNIKLLSQFVS 184
+ + K C I+ DYK++ LL +F+S
Sbjct: 1 YFRRKKYCRFTAEGIQFIDYKDLDLLKKFIS 31
>gnl|CDD|217321 pfam03018, Dirigent, Dirigent-like protein. This family contains a
number of proteins which are induced during disease
response in plants. Members of this family are involved
in lignification.
Length = 144
Score = 26.4 bits (59), Expect = 7.0
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 112 MTRPVYLSSTRFESKSTNNIYEIDFTL 138
M R L+ T F S + I E++ +
Sbjct: 116 MARGYALARTYFSLTSGDAIVELNVYV 142
>gnl|CDD|234919 PRK01209, cobD, cobalamin biosynthesis protein; Provisional.
Length = 312
Score = 26.7 bits (60), Expect = 7.5
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 49 ATALVQKNIEAAKKNLSYI 67
A AL ++E A++ +S I
Sbjct: 106 ARALRAGDLEEARRAVSMI 124
>gnl|CDD|217412 pfam03186, CobD_Cbib, CobD/Cbib protein. This family includes CobD
proteins from a number of bacteria, in Salmonella this
protein is called Cbib. Salmonella CobD is a different
protein. This protein is involved in cobalamin
biosynthesis and is probably an enzyme responsible for
the conversion of adenosylcobyric acid to
adenosylcobinamide or adenosylcobinamide phosphate.
Length = 295
Score = 26.7 bits (60), Expect = 9.3
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 49 ATALVQKNIEAAKKNLSYI 67
A AL ++EAA++ LS I
Sbjct: 103 ARALEAGDLEAARRALSMI 121
>gnl|CDD|226566 COG4080, COG4080, SpoU rRNA Methylase family enzyme [General
function prediction only].
Length = 147
Score = 25.8 bits (57), Expect = 10.0
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 1/72 (1%)
Query: 2 LEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAK 61
+ Y A LV + + S IP K+ LG V++ +L DA +++ ++
Sbjct: 22 IAYGF-GAKRLVLTKAKGSAAQSGIPEVLKLAFKLGKPVLVFPDLDDALEVLRPDVTLLV 80
Query: 62 KNLSYIEHDLDF 73
+ S E LD
Sbjct: 81 GSASEGEKKLDP 92
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 0.131 0.377
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,460,922
Number of extensions: 839406
Number of successful extensions: 733
Number of sequences better than 10.0: 1
Number of HSP's gapped: 731
Number of HSP's successfully gapped: 36
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
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 (25.2 bits)