RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4234
(177 letters)
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
Length = 181
Score = 199 bits (509), Expect = 4e-66
Identities = 102/174 (58%), Positives = 114/174 (65%), Gaps = 41/174 (23%)
Query: 4 NRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLT 63
R HSKTY TPRRP+EK RLD ELK+ GEYGL+NKRE+WRV+Y LAKIRKAARELLT
Sbjct: 2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLT 61
Query: 64 LDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRL 123
LDEK+ +RLFEG ALLRR+
Sbjct: 62 LDEKDPKRLFEG-----------------------------------------EALLRRM 80
Query: 124 VRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
R+G+LDE KLDYVLGL +E LERRLQT+VFKLGLAKSIHHARVLIRQRHI
Sbjct: 81 HRLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHI 134
>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional.
Length = 194
Score = 184 bits (470), Expect = 5e-60
Identities = 97/177 (54%), Positives = 113/177 (63%), Gaps = 41/177 (23%)
Query: 1 MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
MV+ + KT+ PRRPYEK RLD ELK++GEYGLRNKRE+WRV+YAL++IR AAR
Sbjct: 1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARM 60
Query: 61 LLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALL 120
LLTLDEK RR+FEG ALL
Sbjct: 61 LLTLDEKNPRRIFEG-----------------------------------------EALL 79
Query: 121 RRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
RR+ R G+LDES+ KLDYVL L +E+FLERRLQT VFK G+AKSIHHARVLIRQRHI
Sbjct: 80 RRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHI 136
>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
type)/S9(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S9 as well as archaeal
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 162
Score = 151 bits (384), Expect = 2e-47
Identities = 84/172 (48%), Positives = 101/172 (58%), Gaps = 43/172 (25%)
Query: 6 VPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLD 65
P K Y TPR P+ K RLD+ELK++G+YGLRNK+EVW+ + L K R+AARELL LD
Sbjct: 3 DPRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD 62
Query: 66 EKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVR 125
++ +RLFEGN LLRRLVR+G+LDE KLD VLGL +EDFLER
Sbjct: 63 DE--QRLFEGNQLLRRLVRLGILDEENAKLDDVLGLTVEDFLER---------------- 104
Query: 126 IGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
RLQTQVFK GLA++IH AR LI HI
Sbjct: 105 -------------------------RLQTQVFKKGLARTIHQARQLIVHGHI 131
>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
Length = 177
Score = 129 bits (326), Expect = 2e-38
Identities = 61/171 (35%), Positives = 83/171 (48%), Gaps = 44/171 (25%)
Query: 7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDE 66
P K Y TP P++K R+ +E +++G+YGLRNKRE+W+ + L K R+ AR LL L
Sbjct: 4 PKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPP 63
Query: 67 KEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRI 126
+E+ + E LL +L R G+L E NA
Sbjct: 64 EERAK--EEEQLLGKLKRYGILKE--------------------------NA-------- 87
Query: 127 GVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LD VL L +ED LERRLQT V++ GLA++ AR I HI
Sbjct: 88 --------TLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHI 130
>gnl|CDD|215762 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal domain.
This family includes small ribosomal subunit S9 from
prokaryotes and S16 from metazoans. This domain is
predicted to bind to ribosomal RNA. This domain is
composed of four helices in the known structure. However
the domain is discontinuous in sequence and the
alignment for this family contains only the first three
helices.
Length = 93
Score = 78.9 bits (195), Expect = 9e-20
Identities = 44/98 (44%), Positives = 53/98 (54%), Gaps = 9/98 (9%)
Query: 11 SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQR 70
T PRR E RL + K+ GEYGLR + WRVK + +R LL LDEK++
Sbjct: 5 GPTLKLPRRLGELPRLTAKTKLAGEYGLRPGQHGWRVKKG-----RLSRYLLRLDEKQKL 59
Query: 71 RLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLE 108
R F G L R+L R GVL KLD LGL + D LE
Sbjct: 60 RFFYG-LLERQLRRYGVLA---KKLDGSLGLNLLDLLE 93
>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 205
Score = 68.5 bits (168), Expect = 9e-15
Identities = 32/162 (19%), Positives = 48/162 (29%), Gaps = 55/162 (33%)
Query: 16 TPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEG 75
P+ K RL +E K+ + G ++ +E W+ + ++L
Sbjct: 15 LGFNPWLKERLCKERKLPYKPG-QHGQERWKKLSDYGLQLREKQKLRAF------YGVLE 67
Query: 76 NALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMK 135
R L G L
Sbjct: 68 KQFRRYLKEAGRLKG--------------------------------------------- 82
Query: 136 LDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
V GL + LERRL V++LG AK+ AR L+ HI
Sbjct: 83 ---VTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHI 121
>gnl|CDD|201819 pfam01479, S4, S4 domain. The S4 domain is a small domain
consisting of 60-65 amino acid residues that was
detected in the bacterial ribosomal protein S4,
eukaryotic ribosomal S9, two families of pseudouridine
synthases, a novel family of predicted RNA methylases, a
yeast protein containing a pseudouridine synthetase and
a deaminase domain, bacterial tyrosyl-tRNA synthetases,
and a number of uncharacterized, small proteins that may
be involved in translation regulation. The S4 domain
probably mediates binding to RNA.
Length = 48
Score = 35.2 bits (82), Expect = 0.001
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177
RL + +LGLA S AR LIR H+
Sbjct: 1 MRLDKVLARLGLASSRSEARQLIRHGHV 28
>gnl|CDD|235411 PRK05327, rpsD, 30S ribosomal protein S4; Validated.
Length = 203
Score = 35.1 bits (82), Expect = 0.009
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 148 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LE RL V++LG A + AR L+ HI
Sbjct: 91 LESRLDNVVYRLGFAPTRRQARQLVSHGHI 120
>gnl|CDD|177038 CHL00113, rps4, ribosomal protein S4; Reviewed.
Length = 201
Score = 34.4 bits (80), Expect = 0.015
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 147 FLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LE RL +F+LG+A +I AR L+ HI
Sbjct: 86 LLEMRLDNILFRLGMAPTIPAARQLVNHGHI 116
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. IleRS has an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids.
Length = 338
Score = 33.4 bits (77), Expect = 0.040
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 11/60 (18%)
Query: 29 ELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVL 88
ELK+ E G+ K+++ K +A+ RE EQ F+ R+GV
Sbjct: 55 ELKVEKELGISGKKDI--EKMGIAEFNAKCREFALRYVDEQEEQFQ---------RLGVW 103
>gnl|CDD|200066 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle
type. This model finds organelle (chloroplast and
mitochondrial) ribosomal protein S4 as well as bacterial
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 200
Score = 32.7 bits (75), Expect = 0.065
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 148 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 177
LE RL V++LG A + AR L+ HI
Sbjct: 88 LESRLDNVVYRLGFAPTRFAARQLVSHGHI 117
>gnl|CDD|227584 COG5259, RSC8, RSC chromatin remodeling complex subunit RSC8
[Chromatin structure and dynamics / Transcription].
Length = 531
Score = 32.9 bits (75), Expect = 0.075
Identities = 26/107 (24%), Positives = 41/107 (38%), Gaps = 21/107 (19%)
Query: 49 YALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRM-KLDYVLGL--KIED 105
YAL ++ A+ T +E++ RL VL ++++ KL LG ++E
Sbjct: 399 YALDSGKEKAKLQATNEERKMERL------------RNVLIQAQLEKLKMKLGHLKELEK 446
Query: 106 FLERRLQTQVSNALLRRL------VRIGVLDESRMKLDYVLGLKIED 146
Q +N LLRRL I + + L K D
Sbjct: 447 STSLERQELDANLLLRRLNAEEKLFAIDEVLSKCLNLISDDQGKNPD 493
>gnl|CDD|226145 COG3618, COG3618, Predicted metal-dependent hydrolase of the
TIM-barrel fold [General function prediction only].
Length = 279
Score = 31.2 bits (71), Expect = 0.24
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 51 LAKIRKAARELLTLDEKEQRRLFEGNALLRRLVR 84
A A REL+ D E+ R+ NA RRL R
Sbjct: 246 FASWVAATRELVPGDAAERARILVDNA--RRLYR 277
>gnl|CDD|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain
surface is populated by conserved, charged residues that
define a likely RNA-binding site; Found in stress
proteins, ribosomal proteins and tRNA synthetases; This
may imply a hitherto unrecognized functional similarity
between these three protein classes.
Length = 70
Score = 29.1 bits (66), Expect = 0.30
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177
RL + +LGLA S AR LI+ H+
Sbjct: 1 MRLDKILARLGLAPSRSEARQLIKHGHV 28
>gnl|CDD|235231 PRK04160, PRK04160, diphthine synthase; Provisional.
Length = 258
Score = 29.8 bits (68), Expect = 0.62
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 54 IRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDF 106
+A LL L+EK + + L + R G D ++ + L DF
Sbjct: 177 ANEALELLLELEEKRGEGVISEDTLAVVVARAGSPDP-VVRAGRLEELADYDF 228
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 27.6 bits (62), Expect = 0.87
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177
RRL + +LGLA S AR LI Q +
Sbjct: 1 RRLDKFLARLGLAPSRSQARRLIEQGRV 28
>gnl|CDD|235458 PRK05427, PRK05427, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 308
Score = 29.0 bits (66), Expect = 1.0
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 16/76 (21%)
Query: 33 IGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDESR 92
I YGL E+ + K ++ K+A EL+ +D KE FE N + V IG ++
Sbjct: 176 IEAYGL----EMLKAKSDVSG--KSAEELIDMDAKE----FEMNG---KKVGIGQVET-- 220
Query: 93 MKLDYVLGLKIEDFLE 108
+ L VL K +
Sbjct: 221 VDLSEVLDRK-AELEA 235
>gnl|CDD|129242 TIGR00136, gidA, glucose-inhibited division protein A. GidA, the
longer of two forms of GidA-related proteins, appears to
be present in all complete eubacterial genomes so far,
as well as Saccharomyces cerevisiae. A subset of these
organisms have a closely related protein. GidA is absent
in the Archaea. It appears to act with MnmE, in an
alpha2/beta2 heterotetramer, in the
5-carboxymethylaminomethyl modification of uridine 34 in
certain tRNAs. The shorter, related protein, previously
called gid or gidA(S), is now called TrmFO (see model
TIGR00137) [Protein synthesis, tRNA and rRNA base
modification].
Length = 617
Score = 28.9 bits (65), Expect = 1.5
Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 9/100 (9%)
Query: 60 ELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVS-NA 118
+L+T KE R+F A R L+R D ++ LGL ++ R L+ + +
Sbjct: 411 DLVTKGTKEPYRMFTSRAEYRLLLREDNADFRLTEIGRELGLIDDERYARFLKKKENIEE 470
Query: 119 LLRRL--VRIGVLDESRMKLDYVLGLKI------EDFLER 150
++RL + E + +L L + ED L R
Sbjct: 471 EIQRLKSTWLTPSKEVKEELKNHLQSPLKREASGEDLLRR 510
>gnl|CDD|218495 pfam05203, Hom_end_hint, Hom_end-associated Hint. Homing
endonucleases are encoded by mobile DNA elements that
are found inserted within host genes in all domains of
life. The crystal structure of the homing nuclease
PI-Sce revealed two domains: an endonucleolytic centre
resembling the C-terminal domain of Drosophila
melanogaster Hedgehog protein, and a a second domain
containing the protein-splicing active site. This Domain
corresponds to the latter protein-splicing domain.
Length = 392
Score = 28.2 bits (63), Expect = 2.8
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 8/56 (14%)
Query: 58 ARELLTLDEKEQR--------RLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIED 105
AR+L L + + L+E L L L L Y+LGL + D
Sbjct: 103 ARDLDKLSPQVRVASKQFRNPVLYENGILSEFLTPQKFLITPAPTLAYLLGLWLGD 158
>gnl|CDD|238599 cd01194, INT_Tn554A_C, Tn544A and related transposases, DNA
breaking-rejoining enzymes, integrase/recombinases,
C-terminal catalytic domain. This CD includes various
bacterial transposases similar to TnpA from transposon
Tn554.
Length = 186
Score = 27.0 bits (60), Expect = 5.0
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 64 LDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDF 106
L E +RL LR +L E+ +++ LGL+IED
Sbjct: 1 LTPSEVQRLINACGNLRDKFLFALLYETGLRIGEALGLRIEDI 43
>gnl|CDD|225819 COG3280, TreY, Maltooligosyl trehalose synthase [Carbohydrate
transport and metabolism].
Length = 889
Score = 27.4 bits (61), Expect = 5.3
Identities = 26/95 (27%), Positives = 38/95 (40%), Gaps = 13/95 (13%)
Query: 18 RRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAAREL----------LTLDEK 67
P A LD+ L + R Y LA R AA E+ L
Sbjct: 216 ATPNIAACLDECLARFNADPEQLDALHERQHYRLASWRVAADEINYRRFFDVNSLAGLRV 275
Query: 68 EQRRLFEG-NALLRRLVRIGVLDESRMKLDYVLGL 101
E +FE + L+ L+R G++D R +D++ GL
Sbjct: 276 EDPAVFEATHRLIFELLREGLIDGLR--IDHIDGL 308
>gnl|CDD|218322 pfam04909, Amidohydro_2, Amidohydrolase. These proteins are
amidohydrolases that are related to pfam01979.
Length = 272
Score = 27.2 bits (60), Expect = 5.6
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 44 VWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRI 85
++ LA + L L E+E+ ++ GNA RL +
Sbjct: 234 HPPLERPLAAL-DLLDLLDALSEEEREKILGGNA--ARLYGL 272
>gnl|CDD|181554 PRK08776, PRK08776, cystathionine gamma-synthase; Provisional.
Length = 405
Score = 26.9 bits (59), Expect = 6.3
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 45 WRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRI 85
WR+ ALAK K L+T D + R L + A +LV I
Sbjct: 113 WRLFNALAK--KGHFALITADLTDPRSLADALAQSPKLVLI 151
>gnl|CDD|217010 pfam02387, IncFII_repA, IncFII RepA protein family. This protein
is plasmid encoded and found to be essential for plasmid
replication.
Length = 279
Score = 26.6 bits (59), Expect = 7.3
Identities = 19/73 (26%), Positives = 28/73 (38%), Gaps = 14/73 (19%)
Query: 21 YEKARLDQELKIIG--EYGLRNKREVWRV-------KYALAKIRKAARELLTLDEKEQRR 71
K + L + E R K + A K R+ AR+L LDEK+ R+
Sbjct: 179 ENKKLKKKGLIPLTLDEARRRAKEFHIERAFSYRTERKAFGKKRRRARKLAKLDEKDIRK 238
Query: 72 LFEGNALLRRLVR 84
+L LV+
Sbjct: 239 K-----ILNALVK 246
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
0.325 0.141 0.390
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,600,694
Number of extensions: 960511
Number of successful extensions: 1410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1392
Number of HSP's successfully gapped: 83
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.2 bits)