RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046473
(120 letters)
>gnl|CDD|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional.
Length = 220
Score = 179 bits (457), Expect = 9e-59
Identities = 78/109 (71%), Positives = 91/109 (83%)
Query: 1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
S +QKRF FPE VEL+AE+V NRGLCA+AQAESLR + L + + A YGVLR +MESG
Sbjct: 71 SLLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESG 130
Query: 61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
AKGCEVIVSGKLRAQRA SMKF+DGYMIS+G P K+++DSAVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFRDGYMISTGQPKKDFVDSAVRHVLMRQ 179
>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 = 100 bits (250), Expect = 1e-27
Identities = 42/107 (39%), Positives = 59/107 (55%), Gaps = 2/107 (1%)
Query: 3 VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAK 62
+QK+F EN + E+V N L A QAE + + + + A Y +R IME+GAK
Sbjct: 67 LQKKFG-LENPQ-IDVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAK 124
Query: 63 GCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
G EV +SGKL +RA + KF GY+ SG PV+E +D L +
Sbjct: 125 GVEVTISGKLTGERARTEKFAAGYLKHSGEPVEELVDKGFAIALLKL 171
>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
structure and biogenesis].
Length = 233
Score = 78.1 bits (193), Expect = 7e-19
Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 5/109 (4%)
Query: 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGA 61
++K F V++ E+V L A AES+ ++ + + A ++ M +GA
Sbjct: 79 ELEKLFGKEN--VQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGA 136
Query: 62 KGCEVIVSGKLRAQR-ATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
KG ++ VSG+L A + K+++G + ID
Sbjct: 137 KGIKIQVSGRLGGAEIARTEKYREGRVPLHTLRAD--IDYGTAEAHTTY 183
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 75.7 bits (187), Expect = 3e-18
Identities = 25/59 (42%), Positives = 36/59 (61%)
Query: 48 ACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVL 106
A + +R IME+GA G E+I+SGKL +RA + KF +GY+ SG P +E +D
Sbjct: 112 AAHSAIRRIMEAGALGVEIIISGKLTGERARTEKFTEGYIKKSGEPAEELVDRGFAIAK 170
>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 = 57.1 bits (139), Expect = 3e-12
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 48 ACYGVLRFI-MESGAKGCEVIVSGKLR-AQRATSMKFKDGYMISSGYPVKEYIDSAVRHV 105
A +R I + GAKG ++ +SG+L A+RA + K+K+G + + ++ ID A
Sbjct: 15 AIKQAIRRIMKKGGAKGIKIQISGRLNGAERARTEKYKEGRV--PLHTLRADIDYAFAEA 72
Query: 106 LXRQ 109
+
Sbjct: 73 KTKY 76
>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 = 48.4 bits (116), Expect = 9e-09
Identities = 21/25 (84%), Positives = 21/25 (84%)
Query: 1 SAVQKRFKFPENSVELYAEKVNNRG 25
S VQKRF FPE SVELYAEKV NRG
Sbjct: 57 SLVQKRFNFPEGSVELYAEKVANRG 81
>gnl|CDD|185125 PRK15203, PRK15203, 4-hydroxyphenylacetate degradation bifunctional
isomerase/decarboxylase; Provisional.
Length = 429
Score = 26.9 bits (59), Expect = 3.0
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 66 VIVSGKL--RAQRATSMKFKDGYMISSGYPVKEYIDSAVR 103
V+V GK + A +M + GY + + Y +++Y+++ R
Sbjct: 280 VVVIGKQARKVSEADAMDYVAGYTVCNDYAIRDYLENYYR 319
>gnl|CDD|234625 PRK00090, bioD, dithiobiotin synthetase; Reviewed.
Length = 222
Score = 26.7 bits (60), Expect = 3.3
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 27 CAIAQAESLRKEGLAVIVCKMA 48
A+AQA LR+ G +V K
Sbjct: 18 AALAQA--LREAGYSVAGYKPV 37
>gnl|CDD|223940 COG1008, NuoM, NADH:ubiquinone oxidoreductase subunit 4 (chain M)
[Energy production and conversion].
Length = 497
Score = 26.8 bits (60), Expect = 3.4
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 40 LAVIVCKMACYGVLRFIME 58
LA I+ KM YG+LRF +
Sbjct: 246 LAGILLKMGGYGLLRFSLP 264
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 26.2 bits (58), Expect = 4.2
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 58 ESGAKGCEVIVSGKLRAQR 76
ES KG VIV+G+L+ QR
Sbjct: 69 ESLTKGMRVIVTGRLK-QR 86
>gnl|CDD|200147 TIGR01972, NDH_I_M, proton-translocating NADH-quinone
oxidoreductase, chain M. This model describes the 13th
(based on E. coli) structural gene, M, of bacterial NADH
dehydrogenase I, as well as chain 4 of the corresponding
mitochondrial complex I and of the chloroplast NAD(P)H
dehydrogenase complex [Energy metabolism, Electron
transport].
Length = 481
Score = 26.4 bits (59), Expect = 4.5
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 40 LAVIVCKMACYGVLRFIM 57
LA ++ KM YG LRF +
Sbjct: 241 LAGVLLKMGTYGFLRFNL 258
>gnl|CDD|216712 pfam01803, LIM_bind, LIM-domain binding protein. The LIM-domain
binding protein, binds to the LIM domain pfam00412 of
LIM homeodomain proteins which are transcriptional
regulators of development. Nuclear LIM interactor (NLI)
/ LIM domain-binding protein 1 (LDB1) is located in the
nuclei of neuronal cells during development, it is
co-expressed with Isl1 in early motor neuron
differentiation and has a suggested role in the Isl1
dependent development of motor neurons. It is suggested
that these proteins act synergistically to enhance
transcriptional efficiency by acting as co-factors for
LIM homeodomain and Otx class transcription factors both
of which have essential roles in development. The
Drosophila protein Chip is required for segmentation and
activity of a remote wing margin enhancer. Chip is a
ubiquitous chromosomal factor required for normal
expression of diverse genes at many stages of
development. It is suggested that Chip cooperates with
different LIM domain proteins and other factors to
structurally support remote enhancer-promoter
interactions.
Length = 230
Score = 25.7 bits (57), Expect = 5.8
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSI 113
G +V+ G LRA +K + + + +EYI R VL AS +
Sbjct: 106 DDGSQVVTEGTLRAHFDPDLKIEWWDFCTRSH--EEYIP---RSVLEPLASPL 153
>gnl|CDD|143182 cd04981, IgV_H, Immunoglobulin (Ig) heavy chain (H), variable (V)
domain. IgV_H: Immunoglobulin (Ig) heavy chain (H),
variable (V) domain. The basic structure of Ig molecules
is a tetramer of two light chains and two heavy chains
linked by disulfide bonds. In Ig, each chain is composed
of one variable domain (IgV) and one or more constant
domains (IgC); these names reflect the fact that the
variability in sequences is higher in the variable
domain than in the constant domain. There are five types
of heavy chains (alpha, gamma, delta, epsilon, and mu),
which determine the type of immunoglobulin: IgA, IgG,
IgD, IgE, and IgM, respectively. In higher vertebrates,
there are two types of light chain, designated kappa and
lambda, which can associate with any of the heavy
chains. This family includes alpha, gamma, delta,
epsilon, and mu heavy chains.
Length = 117
Score = 24.6 bits (54), Expect = 9.6
Identities = 16/61 (26%), Positives = 19/61 (31%), Gaps = 8/61 (13%)
Query: 17 YAEKVNNRGLC--------AIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIV 68
YA+ V R Q SL E AV C G + +G V V
Sbjct: 57 YADSVKGRFTITRDTSKSTVYLQLNSLTPEDTAVYYCARGLGGYGYGYFDYWGQGTLVTV 116
Query: 69 S 69
S
Sbjct: 117 S 117
>gnl|CDD|235622 PRK05846, PRK05846, NADH:ubiquinone oxidoreductase subunit M;
Reviewed.
Length = 497
Score = 25.2 bits (56), Expect = 9.8
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 40 LAVIVCKMACYGVLRF 55
LA I+ KM YG+LRF
Sbjct: 249 LAGILLKMGAYGLLRF 264
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
0.323 0.135 0.388
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: 5,696,970
Number of extensions: 474210
Number of successful extensions: 400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 395
Number of HSP's successfully gapped: 27
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)