RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025294
(255 letters)
>gnl|CDD|223178 COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 86.1 bits (214), Expect = 2e-21
Identities = 51/120 (42%), Positives = 63/120 (52%), Gaps = 13/120 (10%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI NNT VT+TD GN I ASSG + KG K + YAA+ AE + A+ G+
Sbjct: 21 AHIHASFNNTIVTITDLTGNVIIWASSGGM-GFKGSRKSTPYAAQLAAEDAAKKAKEHGI 79
Query: 198 KSVVVRVKGFTYFKKKRQAIMS--FREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
KSV V+VKG R+A + G I IED T PHNGCR PK+RR+
Sbjct: 80 KSVEVKVKGP---GPGREAAIRALAAAGLK-------ITRIEDVTPIPHNGCRPPKRRRV 129
>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
Length = 128
Score = 84.4 bits (210), Expect = 9e-21
Identities = 47/119 (39%), Positives = 63/119 (52%), Gaps = 11/119 (9%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI NNT VT+TD +GN AS+G L KG K + YAA+ AE + A+ G+
Sbjct: 20 AHIHATFNNTIVTITDRQGNVISWASAGGL-GFKGSRKSTPYAAQVAAEDAAKKAKEHGM 78
Query: 198 KSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
K+V V VKG + AI + + G + I+D T PHNGCR PK+RR+
Sbjct: 79 KTVEVFVKGPG--SGRESAIRALQAAGLE-------VTSIKDVTPIPHNGCRPPKRRRV 128
>gnl|CDD|188357 TIGR03632, bact_S11, 30S ribosomal protein S11. This model
describes the bacterial 30S ribosomal protein S11.
Cutoffs are set such that the model excludes archaeal
and eukaryotic ribosomal proteins, but many chloroplast
and mitochondrial equivalents of S11 are detected
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 108
Score = 80.7 bits (200), Expect = 2e-19
Identities = 44/116 (37%), Positives = 60/116 (51%), Gaps = 11/116 (9%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI NNT VT+TD +GN AS+G + KG K + YAA+ AE + A+ G+
Sbjct: 3 AHIHATFNNTIVTITDPQGNVLSWASAGAV-GFKGSKKSTPYAAQLAAEDAAKKAKEFGM 61
Query: 198 KSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKK 252
K+V V VKG + AI + + G + I+D T PHNGCR PK+
Sbjct: 62 KTVDVYVKGPG--AGRESAIRALQAAGLE-------VTSIKDVTPIPHNGCRPPKR 108
>gnl|CDD|189537 pfam00411, Ribosomal_S11, Ribosomal protein S11.
Length = 109
Score = 80.1 bits (198), Expect = 2e-19
Identities = 42/117 (35%), Positives = 63/117 (53%), Gaps = 11/117 (9%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI+ NNT +T+TD G + +S+G KG K + YAA+ AE+ ++A+ G+
Sbjct: 3 AHIQASFNNTIITITDVIGRVVLWSSAGGC-GFKGSRKSTPYAAQTAAENAAKIAKEQGI 61
Query: 198 KSVVVRVKGFTYFKKKRQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKR 253
K++ V++KG ++ A+ + R G I I D T PHNGCR PKKR
Sbjct: 62 KALEVKIKGPGPGRE--SALRALARSGLR-------ITRIRDVTPIPHNGCRPPKKR 109
>gnl|CDD|176982 CHL00041, rps11, ribosomal protein S11.
Length = 116
Score = 64.5 bits (158), Expect = 2e-13
Identities = 38/112 (33%), Positives = 54/112 (48%), Gaps = 13/112 (11%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSG-CLPELKGGPKMSRYAAEATAEHVGRLARNMG 196
+HI+ NNT VTVTD +G +S+G C KG K + +AA+ AE+ R + G
Sbjct: 16 IHIQASFNNTIVTVTDVRGRVISWSSAGAC--GFKGARKGTPFAAQTAAENAIRTVIDQG 73
Query: 197 LKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGC 247
+K V +KG + A+ + R G + I D T PHNGC
Sbjct: 74 MKRAEVMIKGPGLGRDT--ALRAIRRSGL-------KLSSIRDVTPMPHNGC 116
>gnl|CDD|236588 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
Length = 132
Score = 54.6 bits (132), Expect = 1e-09
Identities = 40/124 (32%), Positives = 54/124 (43%), Gaps = 14/124 (11%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI NNT +T+TD G + I SSG + + S YAA AE A+ G+
Sbjct: 12 AHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGI 71
Query: 198 KSVVVRVKGFTYFKKK------RQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLP 250
V ++V+ +K + AI + R G I IED T PH+G R P
Sbjct: 72 TGVHIKVRAPGGNGQKSPGPGAQAAIRALARAGLR-------IGRIEDVTPIPHDGTRPP 124
Query: 251 KKRR 254
RR
Sbjct: 125 GGRR 128
>gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P. This model
describes exclusively the archaeal ribosomal protein
S11P. It excludes homologous ribosomal proteins S14 from
eukaryotes and S11 from bacteria [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 114
Score = 48.2 bits (115), Expect = 2e-07
Identities = 34/117 (29%), Positives = 49/117 (41%), Gaps = 14/117 (11%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI NNT +T+TD G + I SSG + + S YAA A A+ G+
Sbjct: 5 AHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGI 64
Query: 198 KSVVVRVKGFTYFKKK------RQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGC 247
+ ++V+ +K + AI + R G R IED T PH+G
Sbjct: 65 TGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGR-------IEDVTPIPHDGT 114
>gnl|CDD|238246 cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18 (L5e) is a
ribosomal protein found in the central protuberance (CP)
of the large subunit. L18 binds 5S rRNA and induces a
conformational change that stimulates the binding of L5
to 5S rRNA. Association of 5S rRNA with 23S rRNA depends
on the binding of L18 and L5 to 5S rRNA. L18/L5e is
generally described as L18 in prokaryotes and archaea,
and as L5e (or L5) in eukaryotes. In bacteria, the CP
proteins L5, L18, and L25 are required for the ribosome
to incorporate 5S rRNA into the large subunit, one of
the last steps in ribosome assembly. In archaea, both
L18 and L5 bind 5S rRNA; in eukaryotes, only the L18
homolog (L5e) binds 5S rRNA but a homolog to L5 is also
identified.
Length = 103
Score = 37.5 bits (88), Expect = 8e-04
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 2/81 (2%)
Query: 145 NNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSR--YAAEATAEHVGRLARNMGLKSVVV 202
+ + + D G+K + ++S +KG AA + + A G+K VV
Sbjct: 21 KHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVF 80
Query: 203 RVKGFTYFKKKRQAIMSFREG 223
G+ Y + + REG
Sbjct: 81 DRGGYRYHGRVKALAKGAREG 101
>gnl|CDD|185465 PTZ00129, PTZ00129, 40S ribosomal protein S14; Provisional.
Length = 149
Score = 30.6 bits (69), Expect = 0.36
Identities = 31/122 (25%), Positives = 52/122 (42%), Gaps = 10/122 (8%)
Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
HI N+TF+ VTD G + + +G + + S YAA A+ V + +G+
Sbjct: 31 AHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGI 90
Query: 198 KSVVVRVKGFTYFKKK-----RQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKK 252
++ ++++ + K QA + A +R I IED T P + R
Sbjct: 91 NALHIKLRATGGVRTKTPGPGAQAALR-----ALARAGLKIGRIEDVTPIPTDSTRRKGG 145
Query: 253 RR 254
RR
Sbjct: 146 RR 147
>gnl|CDD|176008 cd04043, C2_Munc13_fungal, C2 domain in Munc13 (mammalian
uncoordinated) proteins; fungal group. C2-like domains
are thought to be involved in phospholipid binding in a
Ca2+ independent manner in both Unc13 and Munc13.
Caenorabditis elegans Unc13 has a central domain with
sequence similarity to PKC, which includes C1 and
C2-related domains. Unc13 binds phorbol esters and DAG
with high affinity in a phospholipid manner. Mutations
in Unc13 results in abnormal neuronal connections and
impairment in cholinergic neurotransmission in the
nematode. Munc13 is the mammalian homolog which are
expressed in the brain. There are 3 isoforms (Munc13-1,
-2, -3) and are thought to play a role in
neurotransmitter release and are hypothesized to be
high-affinity receptors for phorbol esters. Unc13 and
Munc13 contain both C1 and C2 domains. There are two C2
related domains present, one central and one at the
carboxyl end. Munc13-1 contains a third C2-like domain.
Munc13 interacts with syntaxin, synaptobrevin, and
synaptotagmin suggesting a role for these as scaffolding
proteins. C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1. However,
there are a few exceptions to this including RIM
isoforms and some splice variants of piccolo/aczonin and
intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-II topology.
Length = 126
Score = 28.0 bits (63), Expect = 2.5
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 146 NTFVTVTDSKGNKRIG 161
+ +VT+ D+ G +RI
Sbjct: 23 DPYVTLVDTNGKRRIA 38
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 27.9 bits (62), Expect = 5.4
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 12/62 (19%)
Query: 191 LARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLP 250
LA+ +GL V R+ F + N + Y TT P + LP
Sbjct: 205 LAKKLGLNFVRYRLVPFGSHS------------YIEKLMVNSVEYNNSTTNAPGDWLILP 252
Query: 251 KK 252
+
Sbjct: 253 VE 254
>gnl|CDD|213950 TIGR04337, AmmeMemoSam_rS, AmmeMemoRadiSam system radical SAM
enzyme. Members of this protein family are
uncharacterized radical SAM enzymes that occur in a
prokaryotic three-gene system along with homologs of
mammalian proteins Memo (Mediator of ErbB2-driven cell
MOtility) and AMMERCR1 (Alport syndrome, Mental
Retardation, Midface hypoplasia, and Elliptocytosis).
Among radical SAM enzymes that have been experimentally
characterized, the most closely related in sequence
include activases of pyruvate formate-lyase and of
benzylsuccinate synthase.
Length = 349
Score = 27.6 bits (62), Expect = 6.6
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 176 MSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTY 209
M A +A+ E + R A +G +SV FTY
Sbjct: 97 MDTLADQASPEQIARAALRLGCRSV-----AFTY 125
>gnl|CDD|218358 pfam04979, IPP-2, Protein phosphatase inhibitor 2 (IPP-2). Protein
phosphotase inhibitor 2 (IPP-2) is a phosphoprotein
conserved among all eukaryotes, and it appears in both
the nucleus and cytoplasm of tissue culture cells.
Length = 123
Score = 26.6 bits (59), Expect = 7.9
Identities = 22/100 (22%), Positives = 34/100 (34%), Gaps = 20/100 (20%)
Query: 47 RGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTGQGDDETGRS-SRPMDF 105
R + S GN + +++ + A + S + E+ S
Sbjct: 36 RMDDEDSDSESEGNESLTPESLAEKLAAAE-------SSDPSFSIEESESSSSEDEEFS- 87
Query: 106 VRGIVEEDEKRFTGPSQFGQFPRYNVEHSSEFVHIKLMRN 145
EE EKR QF H +EF++IKL R
Sbjct: 88 ----PEEKEKRR-------QFEMKRKLHYNEFLNIKLARQ 116
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 0.135 0.400
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,911,368
Number of extensions: 1189805
Number of successful extensions: 911
Number of sequences better than 10.0: 1
Number of HSP's gapped: 897
Number of HSP's successfully gapped: 19
Length of query: 255
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 160
Effective length of database: 6,723,972
Effective search space: 1075835520
Effective search space used: 1075835520
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: 58 (26.1 bits)