RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026316
(240 letters)
>gnl|CDD|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional.
Length = 220
Score = 388 bits (999), Expect = e-139
Identities = 169/222 (76%), Positives = 193/222 (86%), Gaps = 8/222 (3%)
Query: 3 TQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEK 62
QISKKRKFVADGVF+AELNE L+RELAEDGYSGVEVRVTP+RTEIIIRATRT+ VLG+K
Sbjct: 3 GQISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDK 62
Query: 63 GRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGV 122
GRRIRELTS++QKRF FPE VEL+AE+V NRGLCA+AQAESLRYKLL GL VRRA YGV
Sbjct: 63 GRRIRELTSLLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGV 122
Query: 123 LRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDSAVRH 182
LR +MESGAKGCE VIVSGKLRAQRAKSMKF+DGYMIS+GQP +++DSAVRH
Sbjct: 123 LRHVMESGAKGCE--------VIVSGKLRAQRAKSMKFRDGYMISTGQPKKDFVDSAVRH 174
Query: 183 VLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEE 224
VL+RQGV+G+KVKIML +D GK GP+ PLPD++T+ KEE
Sbjct: 175 VLMRQGVIGVKVKIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216
>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 = 219 bits (561), Expect = 8e-73
Identities = 100/212 (47%), Positives = 126/212 (59%), Gaps = 19/212 (8%)
Query: 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
+RKFVA+GV ++E L +EL E GYSGV+VRVTP+ T++II A R V+G GRRI
Sbjct: 1 IERKFVAEGVKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRI 60
Query: 67 RELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFI 126
RELT +QK+F EN + E+V N L A QAE + L GL RRA Y +R I
Sbjct: 61 RELTEKLQKKFG-LENPQ-IDVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRI 118
Query: 127 MESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDSAVRHVLLR 186
ME+GAKG E V +SGKL +RA++ KF GY+ SG+PV E +D LL+
Sbjct: 119 MEAGAKGVE--------VTISGKLTGERARTEKFAAGYLKHSGEPVEELVDKGFAIALLK 170
Query: 187 QGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTI 218
GVLG+KVKIM P LPD V I
Sbjct: 171 LGVLGVKVKIM---------PPDVKLPDEVEI 193
>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
structure and biogenesis].
Length = 233
Score = 170 bits (433), Expect = 7e-53
Identities = 59/199 (29%), Positives = 92/199 (46%), Gaps = 19/199 (9%)
Query: 7 KKRKFVADGVFF------AELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
K R F + ++ E L +EL+ G SGVE+ TP T + I A R V+G
Sbjct: 8 KSRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIG 67
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120
+KG I +L ++K F V++ E+V L A AES+ +L ++ RRA
Sbjct: 68 KKGSNIEKLRKELEKLFGKEN--VQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMK 125
Query: 121 GVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQR-AKSMKFKDGYMISSGQPVNEYIDSA 179
++ M +GAKG K+ VSG+L A++ K+++G + + ID
Sbjct: 126 RAIQRAMRAGAKGI--------KIQVSGRLGGAEIARTEKYREGRVPLHTLRAD--IDYG 175
Query: 180 VRHVLLRQGVLGIKVKIML 198
GV+G+KV I
Sbjct: 176 TAEAHTTYGVIGVKVWIYK 194
>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 (403), Expect = 2e-50
Identities = 74/81 (91%), Positives = 76/81 (93%)
Query: 15 GVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74
GVF+AELNE LTRELAEDGYSGVEVRVTP RTEIIIRATRTQNVLGEKGRRIRELTS+VQ
Sbjct: 1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQ 60
Query: 75 KRFKFPENSVELYAEKVNNRG 95
KRF FPE SVELYAEKV NRG
Sbjct: 61 KRFNFPEGSVELYAEKVANRG 81
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 151 bits (385), Expect = 5e-46
Identities = 76/218 (34%), Positives = 116/218 (53%), Gaps = 19/218 (8%)
Query: 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
++KFV +G+ ++E L +EL GY G+E++ TP+ T I I A R V+G G+ I
Sbjct: 3 IEKKFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNI 62
Query: 67 RELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFI 126
RELT +++K+F ++ ++V N L A A L L G RRA + +R I
Sbjct: 63 RELTEILEKKFGLENPQID--VKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRI 120
Query: 127 MESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDSAVRHVLLR 186
ME+GA G E +I+SGKL +RA++ KF +GY+ SG+P E +D L+
Sbjct: 121 MEAGALGVE--------IIISGKLTGERARTEKFTEGYIKKSGEPAEELVDRGFAIAKLK 172
Query: 187 QGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEE 224
G++G++V+IM P LPD + I E
Sbjct: 173 LGIIGVEVRIMP---------PDAKLPDEIEIKEPVEV 201
>gnl|CDD|215779 pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C-terminal domain.
This family contains a central domain pfam00013, hence
the amino and carboxyl terminal domains are stored
separately. This is a minimal carboxyl-terminal domain.
Some are much longer.
Length = 85
Score = 89.1 bits (222), Expect = 4e-23
Identities = 29/95 (30%), Positives = 48/95 (50%), Gaps = 12/95 (12%)
Query: 104 SLRYKLLGGLAVRRACYGVLRFI-MESGAKGCEFNFLVSSKVIVSGKLR-AQRAKSMKFK 161
+ +L ++ RRA +R I + GAKG K+ +SG+L A+RA++ K+K
Sbjct: 1 RIAQQLERRISFRRAIKQAIRRIMKKGGAKGI--------KIQISGRLNGAERARTEKYK 52
Query: 162 DGYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKI 196
+G + + ID A + GV+G+KV I
Sbjct: 53 EGRV--PLHTLRADIDYAFAEAKTKYGVIGVKVWI 85
>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 = 66.9 bits (164), Expect = 1e-14
Identities = 30/79 (37%), Positives = 47/79 (59%)
Query: 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
+RKFV +GV ++E L +EL GY G+E+ TP+ T+I I A R V+G G+ I
Sbjct: 1 VERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNI 60
Query: 67 RELTSVVQKRFKFPENSVE 85
RELT +++ +F ++
Sbjct: 61 RELTEILETKFGLENPQID 79
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 64.9 bits (159), Expect = 4e-14
Identities = 23/77 (29%), Positives = 39/77 (50%)
Query: 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79
E+ E L EL + G S +E+ TP R ++IR ++ V+G+ G I++L ++K +
Sbjct: 1 EIREFLAVELKKAGISDIEIERTPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIEL 60
Query: 80 PENSVELYAEKVNNRGL 96
V L +V L
Sbjct: 61 EGKKVYLNIVEVKKPWL 77
>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 = 50.7 bits (122), Expect = 6e-09
Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 22 NEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQ--NVLGEKGRRIRELTSVVQKRFKF 79
E L + LA G SGVE+ TP R EIII R Q V+G+KG+ IR L ++QK +
Sbjct: 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRK 60
Query: 80 PENSVEL 86
+++
Sbjct: 61 KRVKIDV 67
>gnl|CDD|214348 CHL00048, rps3, ribosomal protein S3.
Length = 214
Score = 44.4 bits (106), Expect = 1e-05
Identities = 35/154 (22%), Positives = 62/154 (40%), Gaps = 17/154 (11%)
Query: 47 EIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR 106
++II + ++ KGR I EL +QK + + +V AE +
Sbjct: 69 QVIIYTGFPKLLIERKGRGIEELQINLQKELNSVNRKLNINITEVKKPYGEPNILAEYIA 128
Query: 107 YKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLR-AQRAKSMKFKDGYM 165
+L ++ R+A + ++ KG K+ +SG+L A+ A+ ++G +
Sbjct: 129 GQLENRVSFRKAMKKAIELAEKADIKGI--------KIQISGRLNGAEIARVEWIREGRV 180
Query: 166 ISSGQPVNEY---IDSAVRHVLLRQGVLGIKVKI 196
P+ ID GVLGIK+ I
Sbjct: 181 -----PLQTLRAKIDYCSYPARTIYGVLGIKIWI 209
>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 = 44.2 bits (105), Expect = 2e-05
Identities = 48/173 (27%), Positives = 82/173 (47%), Gaps = 14/173 (8%)
Query: 25 LTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSV 84
+ +EL+ G S VE+ + + I R V+G+KG I +L +QK V
Sbjct: 43 IKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTGKE---V 99
Query: 85 ELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKV 144
++ +V L A A+++ +L ++ RRA ++ M++GAKG KV
Sbjct: 100 QINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGI--------KV 151
Query: 145 IVSGKLR-AQRAKSMKFKDGYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKI 196
VSG+L A+ A++ +K+G + + ID A G++G+KV I
Sbjct: 152 QVSGRLGGAEIARTEWYKEGRV--PLHTLRADIDYATAEAHTTYGIIGVKVWI 202
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 33.4 bits (77), Expect = 0.009
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 42 TPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVE 85
PV E++I A + ++G+ G I+++ + P E
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSE 44
>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 = 32.7 bits (75), Expect = 0.15
Identities = 14/46 (30%), Positives = 19/46 (41%)
Query: 14 DGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVL 59
G A + + E AED +E+R TP E T+ Q L
Sbjct: 40 KGEALARALKEVIEEFAEDNVQYLELRTTPRLLETEKGLTKEQYWL 85
>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 = 30.9 bits (70), Expect = 0.68
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 18 FAELNEVLTRELAEDGYSGVEVRVTP---VRTEIIIRAT 53
LN V+ RE ED Y+G+E R TP T++I R+
Sbjct: 108 SPNLNIVIVRENEEDLYTGIEYRQTPDTYECTKLITRSG 146
>gnl|CDD|220467 pfam09911, DUF2140, Uncharacterized protein conserved in bacteria
(DUF2140). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 187
Score = 29.5 bits (67), Expect = 1.1
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 10/50 (20%)
Query: 183 VLLRQ-----GVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEVYV 227
VLL+ G L + + +L + ++ + LP+ VTI+P K+ +Y+
Sbjct: 111 VLLKAKSLSVGTLSLPISFVLNYIKR-----SYKLPEWVTINPKKKTIYL 155
>gnl|CDD|235682 PRK06041, PRK06041, flagellar assembly protein J; Reviewed.
Length = 553
Score = 28.7 bits (65), Expect = 3.4
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 149 KLRAQRAKSMKFKD-----GYMISSGQPVNEYI 176
+ A+R S F D Y I SG+P+ E++
Sbjct: 132 RFVAKRTPSELFADFLDRLAYSIDSGEPLKEFL 164
>gnl|CDD|221132 pfam11543, UN_NPL4, Nuclear pore localisation protein NPL4. Npl4
is part of the heterodimer UN along with Ufd1 which is
involved in the recruitment of p97, an AAA ATPase, for
tasks involving the ubiquitin pathway. Npl4 has a
ubiquitin-like domain which has within its structure a
beta-grasp fold with a helical insert.
Length = 80
Score = 26.2 bits (58), Expect = 4.4
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 47 EIIIR---ATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90
EIIIR T+ + + L S V + FP N LY E+
Sbjct: 4 EIIIRVQSPDGTKRIEISSTSTLSTLLSKVAEELGFPNNGFSLYLER 50
>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 = 26.7 bits (60), Expect = 5.6
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 25 LTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78
+ ++L + G S +E+ R E+ I R ++G+KG I +L +QK
Sbjct: 42 IKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKELQKLLG 95
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
0.320 0.136 0.380
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,215,213
Number of extensions: 1164059
Number of successful extensions: 879
Number of sequences better than 10.0: 1
Number of HSP's gapped: 859
Number of HSP's successfully gapped: 25
Length of query: 240
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 146
Effective length of database: 6,768,326
Effective search space: 988175596
Effective search space used: 988175596
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 (21.8 bits)
S2: 57 (25.7 bits)