RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17938
(307 letters)
>gnl|CDD|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional.
Length = 220
Score = 202 bits (515), Expect = 2e-64
Identities = 84/108 (77%), Positives = 96/108 (88%)
Query: 4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
KFVADGVF AEL+EFL+RELAEDGYSGVE+R TP RTEIII ATRT+ VLGDKGRRIREL
Sbjct: 10 KFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIREL 69
Query: 64 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
TS++QKRF F +G +EL+AE+V RGLCA+AQAESLRYKL+ GL VRR
Sbjct: 70 TSLLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRR 117
>gnl|CDD|239096 cd02413, 40S_S3_KH, K homology RNA-binding (KH) domain of the
eukaryotic 40S small ribosomal subunit protein S3. S3
is part of the head region of the 40S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 81
Score = 158 bits (402), Expect = 2e-49
Identities = 67/81 (82%), Positives = 74/81 (91%)
Query: 9 GVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQ 68
GVF AEL+EFLTRELAEDGYSGVE+R TP RTEIII ATRTQNVLG+KGRRIRELTS+VQ
Sbjct: 1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQ 60
Query: 69 KRFKFADGAIELYAEKVATRG 89
KRF F +G++ELYAEKVA RG
Sbjct: 61 KRFNFPEGSVELYAEKVANRG 81
>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal
type. This model describes ribosomal protein S3 of the
eukaryotic cytosol and of the archaea. TIGRFAMs model
TIGR01009 describes the bacterial/organellar type,
although the organellar types have a different
architecture with long insertions and may score poorly
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 195
Score = 122 bits (309), Expect = 4e-34
Identities = 53/108 (49%), Positives = 66/108 (61%), Gaps = 2/108 (1%)
Query: 4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
KFVA+GV R +DEFL +EL E GYSGV++R TP T++II A R V+G GRRIREL
Sbjct: 4 KFVAEGVKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIREL 63
Query: 64 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
T +QK KF ++ E+V L A QAE + L GL RR
Sbjct: 64 TEKLQK--KFGLENPQIDVEEVENPELNAQVQAERIARSLERGLHFRR 109
>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
structure and biogenesis].
Length = 233
Score = 96.6 bits (241), Expect = 9e-24
Identities = 38/116 (32%), Positives = 56/116 (48%), Gaps = 8/116 (6%)
Query: 2 SAKFVADG------VFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 55
S F V ++ EFL +EL+ G SGVEI TP T + I A R V+G
Sbjct: 9 SRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGK 68
Query: 56 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
KG I +L ++K F + +++ E+V L A AES+ +L ++ RR
Sbjct: 69 KGSNIEKLRKELEKLFGKEN--VQINIEEVKKPELDAQLVAESIAQQLERRVSFRR 122
>gnl|CDD|239094 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of
the archaeal 30S small ribosomal subunit S3 protein. S3
is part of the head region of the 30S ribosomal
subunit and is believed to interact with mRNA as it
threads its way from the latch into the channel. The
KH motif is a beta-alpha-alpha-beta-beta unit that
folds into an alpha-beta structure with a three
stranded beta-sheet interupted by two contiguous
helices. In general, KH binds single-stranded RNA or
DNA. It is found in a wide variety of proteins
including ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 85
Score = 76.5 bits (189), Expect = 7e-18
Identities = 33/76 (43%), Positives = 47/76 (61%)
Query: 4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
KFV +GV R +DE+L +EL GY G+EI TP T+I I A R V+G G+ IREL
Sbjct: 4 KFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIREL 63
Query: 64 TSVVQKRFKFADGAIE 79
T +++ +F + I+
Sbjct: 64 TEILETKFGLENPQID 79
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 76.8 bits (190), Expect = 8e-17
Identities = 40/101 (39%), Positives = 56/101 (55%), Gaps = 12/101 (11%)
Query: 4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
KFV +G+ + +DE+L +EL GY G+EI+ TP T I I A R V+G G+ IREL
Sbjct: 6 KFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIREL 65
Query: 64 TSVVQKRFKFADGAI--------ELYAEKVATRGLCAIAQA 96
T +++K+F + I EL A VA R +A A
Sbjct: 66 TEILEKKFGLENPQIDVKEVENPELNARVVAFR----LANA 102
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 67.9 bits (167), Expect = 8e-15
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 14 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 73
E+ EFL EL + G S +EI TP R ++I ++ V+G G I++L ++K +
Sbjct: 1 EIREFLAVELKKAGISDIEIERTPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIEL 60
Query: 74 ADGAIELYAEKV 85
+ L +V
Sbjct: 61 EGKKVYLNIVEV 72
>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II).
KH binds single-stranded RNA or DNA. It is found in a
wide variety of proteins including ribosomal proteins
(e.g. ribosomal protein S3), transcription factors
(e.g. NusA_K), and post-transcriptional modifiers of
mRNA (e.g. hnRNP K). There are two different KH domains
that belong to different protein folds, but they share
a single KH motif. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In addition to
their KH core domain, KH-II proteins have an N-terminal
alpha helical extension while KH-I proteins have a
C-terminal alpha helical extension.
Length = 68
Score = 55.3 bits (134), Expect = 2e-10
Identities = 29/60 (48%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 16 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQ--NVLGDKGRRIRELTSVVQKRFKF 73
EFL + LA G SGVEI TP R EIII+ R Q V+G KG+ IR L ++QK +
Sbjct: 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRK 60
>gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type. This
model describes the bacterial type of ribosomal protein
S3. Chloroplast and mitochondrial forms have large,
variable inserts between conserved N-terminal and
C-terminal domains. This model recognizes all bacterial
forms and many chloroplast forms above the trusted
cutoff score. TIGRFAMs model TIGR01008 describes S3 of
the eukaryotic cytosol and of the archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 211
Score = 35.0 bits (81), Expect = 0.025
Identities = 17/54 (31%), Positives = 26/54 (48%)
Query: 17 EFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKR 70
++ +EL+ G S VEI + + I R V+G KG I +L +QK
Sbjct: 41 NYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKL 94
>gnl|CDD|239095 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the
prokaryotic 30S small ribosomal subunit protein S3. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 109
Score = 31.7 bits (73), Expect = 0.14
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 17 EFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK 72
+F+ ++L + G S +EI R E+ I R ++G KG I +L +QK
Sbjct: 40 KFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKELQKLLG 95
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 29.6 bits (67), Expect = 0.31
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 36 TPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 73
P E++I A + ++G G I+++ +
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI 38
>gnl|CDD|237397 PRK13488, PRK13488, chemoreceptor glutamine deamidase CheD;
Provisional.
Length = 157
Score = 30.3 bits (69), Expect = 0.80
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 52 VLGDKGRRIRELTSVV---------QKRFKFADGAIELYAEKVATRGLCAIAQAESLRYK 102
+L D+G++I L V+ + K+AD AI L E++ G A+ L K
Sbjct: 32 ILYDRGKKIGGLAHVMLPESSGAGDRNPGKYADTAIPLLIEEMVKLG----ARKSKLEAK 87
Query: 103 LIGGLAV 109
L GG A+
Sbjct: 88 LAGGAAM 94
>gnl|CDD|233314 TIGR01211, ELP3, histone acetyltransferase, ELP3 family. The
Saccharomyces cerevisiae member YPL086C has been
characterized in vitro as an N-terminal
acetyltransferase for all four core histones. It is a
component of the RNA polymerase II holoenzyme,
designated Elp3p for Elongator Protein 3. Members of
this family are found in eukaryotes and archaea. These
proteins are part of the larger set of GNAT
acetyltransferases [Transcription, DNA-dependent RNA
polymerase].
Length = 522
Score = 29.7 bits (67), Expect = 1.9
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 3 AKFVADGVFRAELDEFLTRELAEDGYSGVEIRF 35
A + GV ++ L E + R + E G + IR
Sbjct: 348 APLIVAGVKKSNLRELVYRRMKEHGITCRCIRC 380
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 29.4 bits (67), Expect = 2.0
Identities = 17/56 (30%), Positives = 27/56 (48%)
Query: 17 EFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK 72
+FL ++L + G S +EI R + I R V+G KG I +L ++K
Sbjct: 41 KFLKKKLKKAGVSRIEIERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKELEKLTG 96
>gnl|CDD|214993 smart01047, C1_4, TFIIH C1-like domain. The carboxyl-terminal
region of TFIIH is essential for transcription activity.
This regions binds three zinc atoms through two
independent domain. The first contains a C4 zinc finger
motif, whereas the second is characterised by a
CX(2)CX(2-4)FCADCD motif. The solution structure of the
second C-terminal domain revealed homology with the
regulatory domain of protein kinase C.
Length = 49
Score = 26.6 bits (59), Expect = 2.3
Identities = 7/8 (87%), Positives = 7/8 (87%)
Query: 139 TLHQCPGC 146
TLH CPGC
Sbjct: 41 TLHNCPGC 48
>gnl|CDD|227818 COG5531, COG5531, SWIB-domain-containing proteins implicated in
chromatin remodeling [Chromatin structure and dynamics].
Length = 237
Score = 28.6 bits (64), Expect = 3.4
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 156 LDSIVSLKEVCKPDIIIALWEYFHK 180
L +I+ L+ +P+ + LW+Y K
Sbjct: 131 LAAILGLEPGTRPEAVKKLWKYIKK 155
>gnl|CDD|224164 COG1243, ELP3, Histone acetyltransferase [Transcription / Chromatin
structure and dynamics].
Length = 515
Score = 28.9 bits (65), Expect = 4.3
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 3 AKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEI 42
A+ + DGV ++ L E + + E+G IR +
Sbjct: 340 AELIVDGVKKSNLRELVENRMREEGIKCRCIRCREVGIVV 379
>gnl|CDD|235601 PRK05773, PRK05773, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Validated.
Length = 219
Score = 28.1 bits (63), Expect = 4.7
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 55 DKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYK 102
D+ IREL VV+ + A E + E + G I +R +
Sbjct: 112 DRALTIRELHKVVELAKTNPEEAREEFYENFYSPGHVPILIGRGIRER 159
>gnl|CDD|234062 TIGR02924, ICDH_alpha, isocitrate dehydrogenase. This family of
mainly alphaproteobacterial enzymes is a member of the
isocitrate/isopropylmalate dehydrogenase superfamily
described by pfam00180. Every member of the seed of this
model appears to have a TCA cycle lacking only a
determined isocitrate dehydrogenase. The precise
identity of the cofactor (NADH -- 1.1.1.41 vs. NADPH --
1.1.1.42) is unclear [Energy metabolism, TCA cycle].
Length = 473
Score = 28.2 bits (63), Expect = 5.6
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 15 LDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRT 49
L+ + RE ED Y+G+E R TP E + TR+
Sbjct: 111 LNIVIVRENEEDLYTGIEYRQTPDTYECTKLITRS 145
>gnl|CDD|116585 pfam07975, C1_4, TFIIH C1-like domain. The carboxyl-terminal
region of TFIIH is essential for transcription activity.
This regions binds three zinc atoms through two
independent domain. The first contains a C4 zinc finger
motif, whereas the second is characterized by a
CX(2)CX(2-4)FCADCD motif. The solution structure of the
second C-terminal domain revealed homology with the
regulatory domain of protein kinase C (pfam00130).
Length = 48
Score = 25.8 bits (57), Expect = 5.6
Identities = 6/8 (75%), Positives = 7/8 (87%)
Query: 139 TLHQCPGC 146
+LH CPGC
Sbjct: 40 SLHNCPGC 47
>gnl|CDD|182682 PRK10729, nudF, ADP-ribose pyrophosphatase NudF; Provisional.
Length = 202
Score = 27.8 bits (62), Expect = 6.3
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 10 VFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIM 45
+F E+ + RE+ E G++ V + F P R E++++
Sbjct: 32 LFNGEMSGEVRREIFERGHAAVLLPFDPVRDEVVLI 67
>gnl|CDD|217825 pfam03975, CheD, CheD chemotactic sensory transduction. This
chemotaxis protein stimulates methylation of MCP
proteins. The chemotaxis machinery of Bacillus subtilis
is similar to that of the well characterized system of
Escherichia coli. However, B. subtilis contains several
chemotaxis genes not found in the E. coli genome, such
as CheC and CheD, indicating that the B. subtilis
chemotactic system is more complex. CheD plays an
important role in chemotactic sensory transduction for
many organisms. CheD deamidates other B. subtilis
chemoreceptors including McpB and McpC. Deamidation by
CheD is required for B. subtilis chemoreceptors to
effectively transduce signals to the CheA kinase. The
structure of a complex between the signal-terminating
phosphatase, CheC, and the receptor-modifying deamidase,
CheD, reveals how CheC mimics receptor substrates to
inhibit CheD and how CheD stimulates CheC phosphatase
activity. CheD resembles other cysteine deamidases from
bacterial pathogens that inactivate host Rho-GTPases.
Phospho-CheY, the intracellular signal and CheC target,
stabilises the CheC-CheD complex and reduces
availability of CheD. A model is proposed whereby CheC
acts as a CheY-P-induced regulator of CheD; CheY-P would
cause CheC to sequester CheD from the chemoreceptors,
inducing adaptation of the chemotaxis system.
Length = 111
Score = 26.7 bits (60), Expect = 6.5
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 65 SVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGG 106
++ D A+EL ++ G A+ E L KL GG
Sbjct: 10 DGDSNPGRYGDTAMELLINELLKLG----ARRERLEAKLFGG 47
>gnl|CDD|214348 CHL00048, rps3, ribosomal protein S3.
Length = 214
Score = 27.5 bits (62), Expect = 7.2
Identities = 15/71 (21%), Positives = 30/71 (42%)
Query: 41 EIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLR 100
++II + ++ KGR I EL +QK + + + +V AE +
Sbjct: 69 QVIIYTGFPKLLIERKGRGIEELQINLQKELNSVNRKLNINITEVKKPYGEPNILAEYIA 128
Query: 101 YKLIGGLAVRR 111
+L ++ R+
Sbjct: 129 GQLENRVSFRK 139
>gnl|CDD|238250 cd00443, ADA_AMPD, Adenosine/AMP deaminase. Adenosine deaminases
(ADAs) are present in pro- and eukaryotic organisms and
catalyze the zinc dependent irreversible deamination
of adenosine nucleosides to inosine nucleosides and
ammonia. The eukaryotic AMP deaminase catalyzes a
similar reaction leading to the hydrolytic removal of
an amino group at the 6 position of the adenine
nucleotide ring, a branch point in the adenylate
catabolic pathway.
Length = 305
Score = 27.7 bits (62), Expect = 8.5
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 13 AELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVL 53
A + + E AED +E+R TP E T+ Q L
Sbjct: 45 ARALKEVIEEFAEDNVQYLELRTTPRLLETEKGLTKEQYWL 85
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
0.327 0.140 0.423
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,843,315
Number of extensions: 1536561
Number of successful extensions: 1664
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1660
Number of HSP's successfully gapped: 34
Length of query: 307
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 210
Effective length of database: 6,635,264
Effective search space: 1393405440
Effective search space used: 1393405440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 59 (26.6 bits)