RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3
[Candidatus Liberibacter asiaticus str. psy62]
(227 letters)
>gnl|CDD|30441 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
structure and biogenesis].
Length = 233
Score = 255 bits (653), Expect = 6e-69
Identities = 118/217 (54%), Positives = 154/217 (70%), Gaps = 1/217 (0%)
Query: 12 LGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSA 71
LG+ W SRWFA EY LL EDLKIRE+L+ L AG++ + IERT K R+ +++A
Sbjct: 1 LGITKDWKSRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAA 60
Query: 72 RPGLIIGKKGTDIEKIRKKLSNMTNSE-IHLSVNEVPKPEINATLIAQSIAQQLERRVVF 130
RPGL+IGKKG++IEK+RK+L + E + +++ EV KPE++A L+A+SIAQQLERRV F
Sbjct: 61 RPGLVIGKKGSNIEKLRKELEKLFGKENVQINIEEVKKPELDAQLVAESIAQQLERRVSF 120
Query: 131 RRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAE 190
RRAMKRA+Q AMR GA G+K+ SGRL GAE++RTE Y EGRVPL TLRA IDYGTA A
Sbjct: 121 RRAMKRAIQRAMRAGAKGIKIQVSGRLGGAEIARTEKYREGRVPLHTLRADIDYGTAEAH 180
Query: 191 TAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS 227
T YG G+KV++ + + D AE ++S
Sbjct: 181 TTYGVIGVKVWIYKGEVLPDKVEIKEPAEVEEPAEES 217
>gnl|CDD|176989 CHL00048, rps3, ribosomal protein S3.
Length = 214
Score = 233 bits (597), Expect = 3e-62
Identities = 94/209 (44%), Positives = 135/209 (64%), Gaps = 7/209 (3%)
Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIRE----YLQCHLKQAGVAKIL 56
MGQKINP+ FRLG +S WFA+ Y L ED KIR+ Y+Q ++K G+A+I
Sbjct: 1 MGQKINPLGFRLGTTQKHHSLWFAQPKNYSEGLQEDKKIRDCIKNYVQKNIKYEGIARIE 60
Query: 57 IERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNS---EIHLSVNEVPKPEINA 113
I+R ++I+Y+ P L+I +KG IE+++ L NS ++++++ EV KP
Sbjct: 61 IQRKIDLIQVIIYTGFPKLLIERKGRGIEELQINLQKELNSVNRKLNINITEVKKPYGEP 120
Query: 114 TLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRV 173
++A+ IA QLE RV FR+AMK+A++ A + G+K+ SGRLNGAE++R E EGRV
Sbjct: 121 NILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQISGRLNGAEIARVEWIREGRV 180
Query: 174 PLQTLRAHIDYGTAVAETAYGSCGIKVYV 202
PLQTLRA IDY + A T YG GIK+++
Sbjct: 181 PLQTLRAKIDYCSYPARTIYGVLGIKIWI 209
>gnl|CDD|48410 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 = 145 bits (367), Expect = 1e-35
Identities = 52/109 (47%), Positives = 80/109 (73%), Gaps = 1/109 (0%)
Query: 2 GQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTH 61
GQK+NP+ FRLG+ W+SRW+A +Y LLHEDLKIR++++ LK+AG+++I IER
Sbjct: 1 GQKVNPLGFRLGITKDWDSRWYADKKDYAELLHEDLKIRKFIKKKLKKAGISRIEIERKA 60
Query: 62 KNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNS-EIHLSVNEVPKP 109
+ +++ARPG+IIGKKG IEK+RK+L + + ++ +++ EV KP
Sbjct: 61 DRVEVTIHTARPGIIIGKKGAGIEKLRKELQKLLGNKKVRINIVEVKKP 109
>gnl|CDD|143952 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 = 120 bits (304), Expect = 3e-28
Identities = 52/85 (61%), Positives = 65/85 (76%), Gaps = 1/85 (1%)
Query: 119 SIAQQLERRVVFRRAMKRAVQSAMRF-GADGVKVIASGRLNGAELSRTECYLEGRVPLQT 177
IAQQLERR+ FRRA+K+A++ M+ GA G+K+ SGRLNGAE +RTE Y EGRVPL T
Sbjct: 1 RIAQQLERRISFRRAIKQAIRRIMKKAGAKGIKIQISGRLNGAERARTEKYKEGRVPLHT 60
Query: 178 LRAHIDYGTAVAETAYGSCGIKVYV 202
LRA IDY A A+T YG G+KV++
Sbjct: 61 LRADIDYAFAEAKTKYGVIGVKVWI 85
>gnl|CDD|109474 pfam00417, Ribosomal_S3_N, Ribosomal protein S3, N-terminal
domain. This family contains a central domain
pfam00013, hence the amino and carboxyl-terminal
domains are stored separately.
Length = 62
Score = 86.9 bits (216), Expect = 4e-18
Identities = 34/60 (56%), Positives = 44/60 (73%)
Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
MGQK+NPI FRLG+ W+S+WFA Y LL+EDLKIR Y+ +LK AG+++I IER
Sbjct: 1 MGQKVNPIGFRLGITRNWDSKWFANKKNYAKLLNEDLKIRNYINKNLKPAGISRIEIERK 60
>gnl|CDD|38391 KOG3181, KOG3181, KOG3181, 40S ribosomal protein S3 [Translation,
ribosomal structure and biogenesis].
Length = 244
Score = 52.3 bits (125), Expect = 1e-07
Identities = 42/172 (24%), Positives = 79/172 (45%), Gaps = 6/172 (3%)
Query: 38 KIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIR---KKLSNM 94
++ E+L L + G + + + T II+ + R ++G+KG I ++ +K
Sbjct: 20 ELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKF 79
Query: 95 TNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIAS 154
+ L +V + A A+S+ +L + RRA ++ M GA G +VI S
Sbjct: 80 PEGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVS 139
Query: 155 GRLNGAELSRTECYLEGRV--PLQTLRAHIDYGTAVAETAYGSCGIKVYVSL 204
G+L G +++ +++G + Q ++ +ID G GIKV + L
Sbjct: 140 GKLRGQR-AKSMKFVDGLMIHSGQPVKDYIDTAVRHVLLRQGVLGIKVKIML 190
>gnl|CDD|48409 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 = 49.4 bits (118), Expect = 8e-07
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 37 LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN 96
I EYL+ L++AG + I RT +I +Y+ RPG++IG+ G +I ++ + L
Sbjct: 13 TMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFG 72
Query: 97 SE-IHLSVNEVPK 108
E + V EV
Sbjct: 73 LENPQIDVQEVEN 85
>gnl|CDD|48407 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 = 49.5 bits (118), Expect = 8e-07
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 40 REYLQCHLKQAGVAKILIERTHKNCRIIVYSAR--PGLIIGKKGTDIEKIRKKLSNMTN 96
RE+L+ L AG++ + IERT II+ AR PGL+IGKKG +I ++K L +
Sbjct: 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLR 59
>gnl|CDD|36877 KOG1664, KOG1664, KOG1664, Vacuolar H+-ATPase V1 sector, subunit E
[Energy production and conversion].
Length = 220
Score = 32.9 bits (75), Expect = 0.065
Identities = 28/117 (23%), Positives = 52/117 (44%), Gaps = 20/117 (17%)
Query: 35 EDLKIREYLQCHLKQAGVAKILIERTHKN-CRIIVYSARPGLIIGKKGTDI-EKIRKKLS 92
+ LKI +Y + KQ + K + + N R+ V AR +I DI ++ +K+LS
Sbjct: 47 QRLKIMQYYEKKEKQVELQKKIAKSNLLNQSRLKVLRARDDII-----DDILDEAKKRLS 101
Query: 93 NMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFR------RAMKRAVQSAMR 143
++ + ++ LI Q + Q LE V+ R + ++ A+ A+
Sbjct: 102 KVSK-------DTDRYKKLLKDLIVQGLLQLLEPEVIVRCREKDLKLVEAALPKAIE 151
>gnl|CDD|29006 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like Hen4,
a protein that plays a role in AGAMOUS (AG) pre-mRNA
processing and important step in plant development. 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 = 65
Score = 32.4 bits (74), Expect = 0.12
Identities = 16/45 (35%), Positives = 30/45 (66%), Gaps = 4/45 (8%)
Query: 63 NCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVP 107
R++V S++ G IIGK G+ I++IR++ T ++I +S + +P
Sbjct: 1 TLRLLVPSSQAGSIIGKGGSTIKEIREE----TGAKIRVSKSVLP 41
>gnl|CDD|31968 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 31.4 bits (71), Expect = 0.22
Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 31 ALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKK 90
L + + L+ ++AG+ I + +I+ + +PGL+IGK G+ + +I +
Sbjct: 70 VLKPPEEARKIILEIVPEEAGITDIYFDDD--TGEVIIEAKKPGLVIGKGGSTLREITAE 127
>gnl|CDD|37402 KOG2191, KOG2191, KOG2191, RNA-binding protein NOVA1/PASILLA and
related KH domain proteins [RNA processing and
modification, General function prediction only].
Length = 402
Score = 30.4 bits (68), Expect = 0.43
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 38 KIREYLQCHLKQAGVAKILIERTH---KNCRIIVYSARPGLIIGKKGTDIEKIRKK 90
KIRE Q A IL +T K +I+V ++ G+IIGK G I+ I+++
Sbjct: 108 KIREKPQ---AVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160
>gnl|CDD|37401 KOG2190, KOG2190, KOG2190, PolyC-binding proteins alphaCP-1 and
related KH domain proteins [RNA processing and
modification, General function prediction only].
Length = 485
Score = 30.1 bits (67), Expect = 0.53
Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 4/52 (7%)
Query: 56 LIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVP 107
CR++V S++ G +IGK G+ I++IR++ T ++I +S + +P
Sbjct: 132 DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE----TGAKIRVSSDMLP 179
Score = 29.3 bits (65), Expect = 0.85
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPE 110
R++ + G IIGKKG ++KIRK+ T S+I ++ + PE
Sbjct: 46 RLLCHVKEVGSIIGKKGDIVKKIRKE----TESKIRVNESLPGCPE 87
Score = 28.9 bits (64), Expect = 1.2
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP------EINATLIAQ 118
R++V S G IIGK G I +IR+ T + I + E +I L
Sbjct: 341 RLLVPSDLIGCIIGKGGAKISEIRQ----RTGASISILNKEEVSGVREALVQITGMLRED 396
Query: 119 SIAQQL 124
+AQ L
Sbjct: 397 LLAQYL 402
>gnl|CDD|48411 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 = 30.1 bits (68), Expect = 0.55
Identities = 12/49 (24%), Positives = 25/49 (51%)
Query: 39 IREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKI 87
+ E+L L + G + + + T II+ + R ++G+KG I ++
Sbjct: 7 LNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIREL 55
>gnl|CDD|29002 cd00105, KH-I, K homology RNA-binding domain, type I. 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. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension..
Length = 64
Score = 29.8 bits (67), Expect = 0.62
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPE 110
R++V S+ G IIGK G+ I++IR++ T ++I + + E
Sbjct: 3 RVLVPSSLVGRIIGKGGSTIKEIREE----TGAKIKIPDSGSGSEE 44
>gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 29.8 bits (67), Expect = 0.62
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 16/54 (29%)
Query: 53 AKILIER-THKNCRIIVYSARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101
A I +ER + K G+IIGK G I+KI RK + + +++L
Sbjct: 231 ATIYVERESQK-----------GIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273
>gnl|CDD|30042 cd01299, Met_dep_hydrolase_A, Metallo-dependent hydrolases,
subgroup A is part of the superfamily of
metallo-dependent hydrolases, a large group of proteins
that show conservation in their 3-dimensional fold (TIM
barrel) and in details of their active site. The vast
majority of the members have a conserved metal binding
site, involving four histidines and one aspartic acid
residue. In the common reaction mechanism, the metal ion
(or ions) deprotonate a water molecule for a
nucleophilic attack on the substrate. The function of
this subgroup is unknown..
Length = 342
Score = 29.1 bits (65), Expect = 1.1
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 8/70 (11%)
Query: 134 MKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHID----YGTAVA 189
++ AV+ +R GAD +K++A+G + LS + + + + LRA +D G VA
Sbjct: 122 VRAAVREQLRRGADQIKIMATGGV----LSPGDPPPDTQFSEEELRAIVDEAHKAGLYVA 177
Query: 190 ETAYGSCGIK 199
AYG+ I+
Sbjct: 178 AHAYGAEAIR 187
>gnl|CDD|48406 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA
is an essential multifunctional transcription
elongation factor that is universally conserved among
prokaryotes and archaea. NusA anti-termination function
plays an important role in the expression of ribosomal
rrn operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. 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..
Length = 61
Score = 28.2 bits (63), Expect = 1.8
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 39 IREYLQCHLKQAGVAKILIERTHKNCRIIVYSARP-GLIIGKKGTDIEKIRKKL 91
E+++ L A V + + + +V GL IGK G ++ K L
Sbjct: 1 PAEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLL 54
>gnl|CDD|111443 pfam02543, CmcH_NodU, Carbamoyltransferase. This family consists
of NodU from Rhizobium and CmcH from Nocardia
lactamdurans. NodU a Rhizobium nodulation protein
involved in the synthesis of nodulation factors has
6-O-carbamoyltransferase-like activity. CmcH is involved
in cephamycin (antibiotic) biosynthesis and has
3-hydroxymethylcephem carbamoyltransferase activity,
EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate
+ 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate +
3-carbamoyloxymethylcephem.
Length = 360
Score = 27.7 bits (62), Expect = 2.8
Identities = 8/23 (34%), Positives = 10/23 (43%), Gaps = 2/23 (8%)
Query: 6 NPILFRLGV--NCTWNSRWFARG 26
+ GV N WNS+ RG
Sbjct: 165 RNLCIAGGVALNVKWNSKLRRRG 187
>gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 27.5 bits (61), Expect = 3.0
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 25 RGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDI 84
E AL + +I ++ +L G ++ + + + V +IGK G I
Sbjct: 452 EEEESPALKLAEEEIEREIKRYLP--GDVEVEVVGDGR-AVVKVPEKYIPKVIGKGGKRI 508
Query: 85 EKIRKKLS 92
++I KKL
Sbjct: 509 KEIEKKLG 516
>gnl|CDD|48408 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation
specificity factor (CPSF) contains an N-terminal K
homology RNA-binding domain (KH). The archeal CPSFs are
predicted to be metal-dependent RNases belonging to the
beta-CASP family, a subgroup enzymes within the
metallo-beta-lactamase fold. 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
domains are known to bind single-stranded RNA or DNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA..
Length = 145
Score = 27.5 bits (61), Expect = 3.2
Identities = 12/43 (27%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 48 KQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKK 90
++AG+ I + +I+ + +PGL+IGK G+ + +I ++
Sbjct: 64 EEAGITDIYFDDD--TGEVIIEAEKPGLVIGKGGSTLREITRE 104
>gnl|CDD|36249 KOG1031, KOG1031, KOG1031, Predicted Ca2+-dependent
phospholipid-binding protein [General function
prediction only].
Length = 1169
Score = 27.4 bits (60), Expect = 3.7
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 9 LFRLGVNCTWNSRWFARGSEYGALLHEDLKIR 40
+F +N WNS WF + L E L+IR
Sbjct: 42 VFLKSLNPQWNSDWFKFEVDDADLQDEPLQIR 73
>gnl|CDD|153302 cd07618, BAR_Rich1, The Bin/Amphiphysin/Rvs (BAR) domain of
RhoGAP interacting with CIP4 homologs protein 1. BAR
domains are dimerization, lipid binding and curvature
sensing modules found in many different proteins with
diverse functions. RhoGAP interacting with CIP4
homologs protein 1 (Rich1) is also called
Neuron-associated developmentally-regulated protein
(Nadrin) or Rho GTPase activating protein 17
(ARHGAP17). It is a Cdc42- and Rac-specific GAP that
binds to polarity proteins through the scaffold protein
angiomotin and plays a role in maintaining the
integrity of tight junctions. It may be a component of
a sorting mechanism in the recycling of tight junction
transmembrane proteins. Rich1 contains an N-terminal
BAR domain followed by a Rho GAP domain and a
C-terminal proline-rich domain. It interacts with the
BAR domain proteins endophilin and amphiphysin through
its proline-rich region. The BAR domain of Rich1 forms
oligomers and can bind membranes and induce membrane
tubulation.
Length = 246
Score = 26.9 bits (59), Expect = 5.2
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 55 ILIERTHKNCRIIVYSARPGLII---GKKGTDIEKIRKKL 91
+ IER R + ++ LI G+ GTD EK KKL
Sbjct: 18 LQIERRLDTVRSVSHNVHKRLIACFQGQVGTDAEKRHKKL 57
>gnl|CDD|132736 cd06938, NR_LBD_EcR, The ligand binding domain (LBD) of the
Ecdysone receptor, a member of the nuclear receptors
super family. The ligand binding domain (LBD) of the
ecdysone receptor: The ecdysone receptor (EcR) belongs
to the superfamily of nuclear receptors (NRs) of
ligand-dependent transcription factors. Ecdysone
receptor is present only in invertebrates and regulates
the expression of a large number of genes during
development and reproduction. ECR functions as a
heterodimer by partnering with ultraspiracle protein
(USP), the ortholog of the vertebrate retinoid X
receptor (RXR). The natural ligands of ecdysone receptor
are ecdysteroids#the endogenous steroidal hormones found
in invertebrates. In addition, insecticide
bisacylhydrazine used against pests has shown to act on
EcR. EcR must be dimerised with a USP for high-affinity
ligand binding to occur. The ligand binding triggers a
conformational change in the C-terminal part of the EcR
ligand-binding domain that leads to transcriptional
activation of genes controlled by EcR. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, ec dysone
receptors have a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 231
Score = 26.2 bits (58), Expect = 8.1
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 66 IIVYSARPGLIIGKKGTDIEKI 87
I+++S RPGL+ KK I++I
Sbjct: 148 IVIFSDRPGLLQPKKVEKIQEI 169
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.134 0.387
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,624,125
Number of extensions: 130956
Number of successful extensions: 427
Number of sequences better than 10.0: 1
Number of HSP's gapped: 418
Number of HSP's successfully gapped: 35
Length of query: 227
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 137
Effective length of database: 4,318,927
Effective search space: 591692999
Effective search space used: 591692999
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: 56 (25.4 bits)