RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9398
(154 letters)
>gnl|CDD|178888 PRK00132, rpsI, 30S ribosomal protein S9; Reviewed.
Length = 130
Score = 131 bits (332), Expect = 3e-40
Identities = 46/87 (52%), Positives = 62/87 (71%)
Query: 68 NYKYGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKHTKTFDI 127
YGTGRRK+A+ARV +K GSGK+T+N ++YF R+T MV+ QPL+LT+ FD+
Sbjct: 4 VQYYGTGRRKTAVARVRLKPGSGKITVNGRDLEEYFPRETLRMVVRQPLELTETEGKFDV 63
Query: 128 KINVRGGGESGQYGAVRHGITRAFNQL 154
+ V+GGG SGQ GA+RHGI RA +
Sbjct: 64 YVTVKGGGISGQAGAIRHGIARALLEY 90
>gnl|CDD|223181 COG0103, RpsI, Ribosomal protein S9 [Translation, ribosomal
structure and biogenesis].
Length = 130
Score = 112 bits (283), Expect = 8e-33
Identities = 45/83 (54%), Positives = 56/83 (67%)
Query: 71 YGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKHTKTFDIKIN 130
Y TG+RKSA+ARV + G GK+T+N P + YF R+T M I QPL LT FDI +
Sbjct: 7 YTTGKRKSAVARVRLVPGKGKITVNGRPLELYFPRETLRMKIMQPLLLTGTVGKFDIDVT 66
Query: 131 VRGGGESGQYGAVRHGITRAFNQ 153
V+GGG SGQ GA+RHGI RA +
Sbjct: 67 VKGGGISGQAGAIRHGIARALVE 89
>gnl|CDD|201193 pfam00380, Ribosomal_S9, Ribosomal protein S9/S16. This family
includes small ribosomal subunit S9 from prokaryotes and
S16 from eukaryotes.
Length = 121
Score = 107 bits (270), Expect = 5e-31
Identities = 42/77 (54%), Positives = 55/77 (71%)
Query: 74 GRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKHTKTFDIKINVRG 133
GRRK+A+ARV++K GSGK+TIN P ++YF +T M I +PL+LT FDI + V+G
Sbjct: 1 GRRKTAVARVWLKPGSGKITINGKPLEEYFPNETLRMKILEPLELTGTLGKFDIVVTVKG 60
Query: 134 GGESGQYGAVRHGITRA 150
GG SGQ GA+R I RA
Sbjct: 61 GGISGQAGAIRLAIARA 77
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 100 bits (252), Expect = 5e-28
Identities = 36/92 (39%), Positives = 52/92 (56%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHIDTG----------------------- 38
W++IDA+ K+LGR+AS++A LRGKHK +TPH+DTG
Sbjct: 15 WYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIY 74
Query: 39 -----YPGGIRKINFLKMQEDFPGRVLQKAVK 65
YPGG+++I F ++ P RV++KAVK
Sbjct: 75 YRHSGYPGGLKEITFGELLAKKPERVIEKAVK 106
>gnl|CDD|214357 CHL00079, rps9, ribosomal protein S9.
Length = 130
Score = 86.1 bits (214), Expect = 2e-22
Identities = 36/85 (42%), Positives = 52/85 (61%), Gaps = 1/85 (1%)
Query: 71 YGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRK-TGLMVISQPLKLTKHTKTFDIKI 129
GTGRRK+A+A+V + GSG++ IN PA++Y L I PLKL +DI +
Sbjct: 6 IGTGRRKTAVAQVRLVPGSGEIIINGKPAEEYLQYNPNYLNAIKAPLKLLGLENKYDIIV 65
Query: 130 NVRGGGESGQYGAVRHGITRAFNQL 154
V+GGG +GQ A+R G+ RA ++
Sbjct: 66 KVKGGGLTGQAEAIRLGLARALCKI 90
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 79.9 bits (198), Expect = 4e-20
Identities = 36/92 (39%), Positives = 47/92 (51%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W +IDAK +ILGR+ASK+A LRGKHK YTPH+D
Sbjct: 1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKY 60
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
TGYPGG++ E P R+L++AV+
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVR 92
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type. This
model distinguishes ribosomal protein L13 of bacteria
and organelles from its eukarytotic and archaeal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 140
Score = 77.7 bits (192), Expect = 3e-19
Identities = 35/92 (38%), Positives = 47/92 (51%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W+++DA K LGR+AS++A LRGKHK YTPH+D
Sbjct: 13 WYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVY 72
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
+GYPGG++ F +M P RVL+ AVK
Sbjct: 73 YRHSGYPGGLKSRTFEEMIARKPERVLEHAVK 104
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five
proteins required for an early folding intermediate of
23S rRNA in the assembly of the large subunit. L13 is
situated on the bottom of the large subunit, near the
polypeptide exit site. It interacts with proteins L3
and L6, and forms an extensive network of interactions
with 23S rRNA. L13 has been identified as a homolog of
the human breast basic conserved protein 1 (BBC1), a
protein identified through its increased expression in
breast cancer. L13 expression is also upregulated in a
variety of human gastrointestinal cancers, suggesting
it may play a role in the etiology of a variety of
human malignancies.
Length = 114
Score = 75.2 bits (186), Expect = 2e-18
Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHIDTG----------------------- 38
W +IDAK ++LGR+ASK+A L GKHK YTPH+D G
Sbjct: 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60
Query: 39 -----YPGGIRKINFLKMQEDFPGRVLQKAVK 65
YPGG++ + P R+L++AV+
Sbjct: 61 YRHTGYPGGLKNPTAGPLHPRAPERILKRAVR 92
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 72.7 bits (179), Expect = 4e-17
Identities = 33/93 (35%), Positives = 47/93 (50%), Gaps = 29/93 (31%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHIDTG----------------------- 38
W++IDA+ K+LGR+AS++A LRGKHK YTPH+DTG
Sbjct: 15 WYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKY 74
Query: 39 -----YPGGIRKINFLKMQED-FPGRVLQKAVK 65
YPGG++ P R+L++AV+
Sbjct: 75 YRHSGYPGGLKNPTRGGPLAPRRPERILERAVR 107
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 68.1 bits (167), Expect = 2e-15
Identities = 33/92 (35%), Positives = 48/92 (52%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHIDT------------------------ 37
W++IDAK++ LGR+A+KIA LRGK+K Y P +DT
Sbjct: 16 WYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFY 75
Query: 38 ----GYPGGIRKINFLKMQEDFPGRVLQKAVK 65
G PGG++ F ++Q P R+++KAVK
Sbjct: 76 VRHSGRPGGLKIETFEELQNRLPNRIIEKAVK 107
>gnl|CDD|179041 PRK00474, rps9p, 30S ribosomal protein S9P; Reviewed.
Length = 134
Score = 63.7 bits (156), Expect = 9e-14
Identities = 33/89 (37%), Positives = 46/89 (51%), Gaps = 6/89 (6%)
Query: 64 VKVVNYKYGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKH-- 121
+KVV +G+RK+AIAR I+ G G++ IN +P + + + I +PL L
Sbjct: 2 MKVVI---TSGKRKTAIARATIREGKGRVRINGVPLELI-EPELARLKIMEPLILAGEDL 57
Query: 122 TKTFDIKINVRGGGESGQYGAVRHGITRA 150
DI +NV GGG GQ A R I R
Sbjct: 58 RSKVDIDVNVEGGGIMGQADAARTAIARG 86
>gnl|CDD|132666 TIGR03627, arch_S9P, archaeal ribosomal protein S9P. This model
describes exclusively the archaeal ribosomal protein
S9P. Homologous eukaryotic and bacterial ribosomal
proteins are excluded from this model [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 130
Score = 61.2 bits (149), Expect = 9e-13
Identities = 31/79 (39%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 73 TGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKH-TKTFDIKINV 131
+G+RK+AIAR I+ G G++ IN +P + Y + + I +PL L K DI + V
Sbjct: 5 SGKRKTAIARATIREGKGRVRINGVPVELY-PPELARLKIMEPLILAGDIAKEVDIDVKV 63
Query: 132 RGGGESGQYGAVRHGITRA 150
GGG GQ A R I R
Sbjct: 64 SGGGIMGQADAARTAIARG 82
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 49.5 bits (118), Expect = 5e-08
Identities = 26/91 (28%), Positives = 40/91 (43%), Gaps = 28/91 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W + DAK ++LGR+AS+I+ L+GK K Y P+ D
Sbjct: 17 WRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFY 76
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAV 64
TGY G +++ + P V++KAV
Sbjct: 77 RWHTGYIGHLKERSLKDQMAKDPTEVIRKAV 107
>gnl|CDD|177799 PLN00210, PLN00210, 40S ribosomal protein S16; Provisional.
Length = 141
Score = 44.3 bits (105), Expect = 2e-06
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 74 GRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKHT-KTFDIKINVR 132
GR+K+A+A + K G G + IN P + L L +H D++I V+
Sbjct: 9 GRKKTAVAVTYCKRGRGLIKINGCPIELVQPEILRFKAFEPILLLGRHRFAGVDMRIRVK 68
Query: 133 GGGESGQYGAVRHGITRA 150
GGG + Q A+R I +A
Sbjct: 69 GGGHTSQIYAIRQSIAKA 86
>gnl|CDD|185437 PTZ00086, PTZ00086, 40S ribosomal protein S16; Provisional.
Length = 147
Score = 40.8 bits (96), Expect = 5e-05
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 74 GRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMV-ISQPLKL--TKHTKTFDIKIN 130
G++K+A+A + G G + +N +P D L + +PL L + DI++
Sbjct: 15 GKKKTAVAVALVTKGKGLIRVNGVPLDLI--NPETLRAKVFEPLLLVGKERFSRLDIRVR 72
Query: 131 VRGGGESGQYGAVRHGITR---AFNQ 153
VRGGG+ Q A+R I + A+ Q
Sbjct: 73 VRGGGQVAQAYAIRQAIAKGLVAYYQ 98
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 29.5 bits (67), Expect = 0.39
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 5 IDAKNKILGRVASKIA 20
IDA+ +ILGR+AS +A
Sbjct: 7 IDAEGQILGRLASYVA 22
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 27.8 bits (62), Expect = 2.5
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 43 IRKINFLKMQEDFPGRVLQKAVKVVNYKYGTGRRK 77
I K+ +MQ+ + +LQK + VVN G RK
Sbjct: 401 ILKVGMSQMQKQYYKALLQKDLDVVN---AGGERK 432
>gnl|CDD|227038 COG4694, COG4694, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 758
Score = 27.6 bits (61), Expect = 2.9
Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 3/87 (3%)
Query: 43 IRKINFLKMQEDFPGRVLQKAVKVVNYKYGTGRRKSAIARVFIKIGSGKMTINRIPADKY 102
+ Q G KV + G K +A + GSGK T + +
Sbjct: 5 LNGNKDKGQQNVSSGTSQISFGKVALFYAENGAGKETLANINFIYGSGKTTTSSFLKN-- 62
Query: 103 FSRKTGLMVISQPLKLTKHTKTFDIKI 129
+ G+ ++ + ++ I++
Sbjct: 63 -LAENGIEDKFANSEIAYNNESLKIEV 88
>gnl|CDD|234825 PRK00726, murG, undecaprenyldiphospho-muramoylpentapeptide beta-N-
acetylglucosaminyltransferase; Provisional.
Length = 357
Score = 27.0 bits (61), Expect = 5.0
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 9 NKILGRVASKIAVYLRGKHKTEYTPHID-TGYPGGIRK 45
NK+L R A K+A G + P TG P +R+
Sbjct: 130 NKLLARFAKKVATAFPGAFPEFFKPKAVVTGNP--VRE 165
>gnl|CDD|226274 COG3751, EGL-9, Predicted proline hydroxylase [Posttranslational
modification, protein turnover, chaperones].
Length = 252
Score = 26.6 bits (59), Expect = 5.4
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 3/35 (8%)
Query: 15 VASKIAVYLRGKHKTEYTPHIDTGYPGGIRKINFL 49
V +I VY G H D G IR ++
Sbjct: 136 VEGQITVYNPGCF---LLKHDDNGRDKDIRLATYV 167
>gnl|CDD|222280 pfam13640, 2OG-FeII_Oxy_3, 2OG-Fe(II) oxygenase superfamily.
This family contains members of the 2-oxoglutarate
(2OG) and Fe(II)-dependent oxygenase superfamily.
Length = 93
Score = 25.4 bits (56), Expect = 6.6
Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 5/31 (16%)
Query: 19 IAVYLRGKHKTEYTPHIDTGYPGGIRKINFL 49
++ Y G PH D R++ L
Sbjct: 3 LSRYRPGGF---LGPHTDNSKGE--RRVTLL 28
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components,
and related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 26.6 bits (59), Expect = 7.0
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 12 LGRVASKIAVYLRGKHKTEYTPHIDTGYPGGIRK 45
L +A ++A GK +E P +D P G R
Sbjct: 60 LDSLAIRLA-QRSGKPISEANPILDATLPDGSRI 92
>gnl|CDD|241385 cd13231, PH2_SSRP1-like, Structure Specific Recognition protein 1
(SSRP1) Pleckstrin homology (PH) domain, repeat 2.
SSRP1 is a component of FACT (facilitator of chromatin
transcription), an essential chromatin reorganizing
factor. In yeast FACT (yFACT) is composed of three
proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the
Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in
human and mouse, respectively.The middle domain of the
Pob3 subunit (Pob3-M) has an unusual double pleckstrin
homology (PH) architecture. yFACT interacts in a
physiologically important way with the central
single-strand DNA binding factor RPA to promote a step
in DNA Replication. Coordinated function by yFACT and
RPA is important during nucleosome deposition. These
results support the model that the FACT family has an
essential role in constructing nucleosomes during DNA
replication, and suggest that RPA contributes to this
process. Members of this cd are composed of the second
PH-like repeat. PH domains have diverse functions, but
in general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 100
Score = 25.1 bits (56), Expect = 8.5
Identities = 7/15 (46%), Positives = 13/15 (86%)
Query: 122 TKTFDIKINVRGGGE 136
++TFD++I ++GG E
Sbjct: 58 SRTFDLEIELKGGTE 72
>gnl|CDD|153376 cd07364, PCA_45_Dioxygenase_B, Subunit B of the Class III extradiol
dioxygenase, Protocatechuate 4,5-dioxygenase, which
catalyzes the oxidization and subsequent ring-opening of
protocatechuate. Protocatechuate 4,5-dioxygenase
(LigAB) catalyzes the oxidization and subsequent
ring-opening of protocatechuate (or 3,4-dihydroxybenzoic
acid, PCA), an intermediate in the breakdown of lignin
and other compounds. Protocatechuate 4,5-dioxygenase is
an aromatic ring opening dioxygenase belonging to the
class III extradiol enzyme family, a group of enyzmes
that cleaves aromatic rings between a hydroxylated
carbon and an adjacent non-hydroxylated carbon using a
non-heme Fe(II). LigAB is composed of two subunits,
designated A and B, which form a tetramer composed of
two copies of each subunit. The B subunit (LigB) is the
catalytic subunit of LigAB.
Length = 277
Score = 25.8 bits (57), Expect = 9.2
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 52 QEDFPGRVLQKAVKVVNYKYGTGRR 76
E +P +V+ V VV Y TG+R
Sbjct: 138 PEAWPCKVIPLCVNVVQYPQPTGKR 162
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
0.322 0.140 0.411
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,959,251
Number of extensions: 725327
Number of successful extensions: 500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 493
Number of HSP's successfully gapped: 35
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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 (21.9 bits)
S2: 55 (25.1 bits)