RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15723
(243 letters)
>gnl|CDD|240222 cd05796, Ribosomal_P0_like, Ribosomal protein L10 family, P0-like
protein subfamily; composed of uncharacterized
eukaryotic proteins with similarity to the 60S ribosomal
protein P0, including the Saccharomyces cerevisiae
protein called mRNA turnover protein 4 (MRT4). MRT4 may
be involved in mRNA decay. P0 forms a tight complex with
multiple copies of the small acidic protein L12(e). This
complex forms a stalk structure on the large subunit of
the ribosome. It occupies the L7/L12 stalk of the
ribosome. The stalk is known to contain the binding site
for elongation factors EF-G and EF-Tu; however, there is
disagreement as to whether or not P0 is involved in
forming the binding site. The stalk is believed to be
associated with GTPase activities in protein synthesis.
In a neuroblastoma cell line, P0 has been shown to
interact with the SH3 domain of Src and to activate the
binding of the Nck1 adaptor protein with skeletal
proteins such as the Wiskott-Aldrich Syndrome Protein
(WASP) and the WASP-interacting protein (WIP). Some
eukaryotic P0 sequences have an additional C-terminal
domain homologous with acidic proteins P1 and P2.
Length = 163
Score = 252 bits (646), Expect = 5e-86
Identities = 98/163 (60%), Positives = 126/163 (77%)
Query: 21 ERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWKDSRFFFGKNKVMAYALGKS 80
E KQ L + + +AV+KY I+VFSV NMRN+KLKD+R +WKDSRFFFGKNKVM ALG++
Sbjct: 1 ELKQKLVENIREAVDKYKYIYVFSVDNMRNNKLKDIRQEWKDSRFFFGKNKVMQVALGRT 60
Query: 81 QEDEIEKNIHVVSSALKGQCGLLFTNRSKDDVLMWFDVYEDEDFAKSGFISTEDVELKEG 140
EDE + N+H +S LKGQ GLLFTN ++V+ +FD Y + DFA++G I+TE V L EG
Sbjct: 61 PEDEYKPNLHKLSKYLKGQVGLLFTNEPPEEVIEYFDSYSEPDFARAGSIATETVTLPEG 120
Query: 141 PLPEFPHSIEPQLRQLGLQTNLNKGVVTLFKDHTVCKKGDVLT 183
PL +FPHS+EPQLR+LGL T L KGV+TL D+ VC++G VLT
Sbjct: 121 PLEQFPHSMEPQLRKLGLPTKLKKGVITLEADYVVCEEGKVLT 163
>gnl|CDD|238222 cd00379, Ribosomal_L10_P0, Ribosomal protein L10 family; composed
of the large subunit ribosomal protein called L10 in
bacteria, P0 in eukaryotes, and L10e in archaea, as well
as uncharacterized P0-like eukaryotic proteins. In all
three kingdoms, L10 forms a tight complex with multiple
copies of the small acidic protein L12(e). This complex
forms a stalk structure on the large subunit of the
ribosome. The N-terminal domain (NTD) of L10 interacts
with L11 protein and forms the base of the L7/L12 stalk,
while the extended C-terminal helix binds to two or
three dimers of the NTD of L7/L12 (L7 and L12 are
identical except for an acetylated N-terminus). The
L7/L12 stalk is known to contain the binding site for
elongation factors G and Tu (EF-G and EF-Tu,
respectively); however, there is disagreement as to
whether or not L10 is involved in forming the binding
site. The stalk is believed to be associated with GTPase
activities in protein synthesis. In a neuroblastoma cell
line, L10 has been shown to interact with the SH3 domain
of Src and to activate the binding of the Nck1 adaptor
protein with skeletal proteins such as the
Wiskott-Aldrich Syndrome Protein (WASP) and the
WASP-interacting protein (WIP). Some eukaryotic P0
sequences have an additional C-terminal domain
homologous with acidic proteins P1 and P2.
Length = 155
Score = 99.2 bits (248), Expect = 3e-26
Identities = 38/166 (22%), Positives = 71/166 (42%), Gaps = 18/166 (10%)
Query: 21 ERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWKDS--RFFFGKNKVMAYALG 78
E+K+ L +EL + ++KY ++ V + + ++L ++R + ++S + GKN +M AL
Sbjct: 1 EKKEELVEELKELLKKYKSVVVVDYRGLTVAQLTELRKELRESGAKLKVGKNTLMRRALK 60
Query: 79 KSQEDEIEKNIHVVSSALKGQCGLLFTNRSKDDVLMWFDVYE---DEDFAKSGFISTEDV 135
+ +E++ LKG L FTN +V + + FAK G ++ V
Sbjct: 61 GTGFEELKP-------LLKGPTALAFTNEDPVEVAKVLKDFAKENKKLFAKGGVVA-GKV 112
Query: 136 ELKEGPLPEFPHSIEP-QLRQLGLQTNLNKGVVT-LFKDHTVCKKG 179
G + P + L + L K + L + G
Sbjct: 113 LDPAGV---TALAKLPSREELLAMLIGLLKAPIAKLARLLNALGIG 155
>gnl|CDD|240221 cd05795, Ribosomal_P0_L10e, Ribosomal protein L10 family, P0 and
L10e subfamily; composed of eukaryotic 60S ribosomal
protein P0 and the archaeal P0 homolog, L10e. P0 or L10e
forms a tight complex with multiple copies of the small
acidic protein L12(e). This complex forms a stalk
structure on the large subunit of the ribosome. The
stalk is known to contain the binding site for
elongation factors G and Tu (EF-G and EF-Tu,
respectively); however, there is disagreement as to
whether or not L10 is involved in forming the binding
site. The stalk is believed to be associated with GTPase
activities in protein synthesis. In a neuroblastoma cell
line, L10 has been shown to interact with the SH3 domain
of Src and to activate the binding of the Nck1 adaptor
protein with skeletal proteins such as the
Wiskott-Aldrich Syndrome Protein (WASP) and the
WASP-interacting protein (WIP). These eukaryotic and
archaeal P0 sequences have an additional C-terminal
domain homologous with acidic proteins P1 and P2.
Length = 175
Score = 87.6 bits (218), Expect = 1e-21
Identities = 42/175 (24%), Positives = 78/175 (44%), Gaps = 4/175 (2%)
Query: 21 ERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWKD-SRFFFGKNKVMAYALGK 79
E K+ ++L + ++ Y + + N+ + +L+ +R + + GKN ++ AL
Sbjct: 1 EWKKEYVEKLTELLKSYPKVLIVDADNVGSKQLQKIRRSLRGKAEILMGKNTLIRRALRN 60
Query: 80 SQEDEIEKNIHVVSSALKGQCGLLFTNRSKDDVLMWFDVYEDEDFAKSGFISTEDVELKE 139
++ E + LKG G +FTN ++ + + AK G I+ DV +
Sbjct: 61 LGDENPELEK--LLPYLKGNVGFIFTNGDPFEIRKILEENKVPAPAKPGAIAPCDVVVPA 118
Query: 140 GPLPEFPHSIEPQLRQLGLQTNLNKGVVTLFKDHTVCKKGDVLTPEQARILKLLK 194
GP P + LG+ T + KG + + D V KKG+ + +A +L L
Sbjct: 119 GPTGMPPGPT-SFFQALGIPTKIEKGKIEIISDVVVVKKGEKVGASEATLLNKLN 172
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 88.4 bits (220), Expect = 1e-20
Identities = 47/174 (27%), Positives = 91/174 (52%), Gaps = 5/174 (2%)
Query: 21 ERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRND-WKDSRFFFGKNKVMAYALGK 79
E K+ +EL + ++ Y + + ++ + +L+++R + KN ++ AL +
Sbjct: 6 EWKKEEVEELKELIKSYPVVGIVDLEGIPARQLQEIRRKLRGKAELKVSKNTLIKRALEE 65
Query: 80 SQEDEIEKNIHVVSSALKGQCGLLFTNRSKDDVLMWFDVYEDEDFAKSGFISTEDVELKE 139
+ E+++EK + L+GQ L+FTN + + + + AK G I+ ED+ +
Sbjct: 66 AGEEDLEK----LEDYLEGQVALIFTNMNPFKLYKLLEKSKTPAPAKPGDIAPEDIVVPA 121
Query: 140 GPLPEFPHSIEPQLRQLGLQTNLNKGVVTLFKDHTVCKKGDVLTPEQARILKLL 193
GP P I +L++LG+ + KG + + KD V K G+V++PE A +L+ L
Sbjct: 122 GPTGFPPGPILSELQKLGIPARIQKGKIVIKKDTVVAKAGEVISPELANVLQKL 175
>gnl|CDD|215933 pfam00466, Ribosomal_L10, Ribosomal protein L10.
Length = 100
Score = 70.6 bits (174), Expect = 5e-16
Identities = 28/111 (25%), Positives = 51/111 (45%), Gaps = 13/111 (11%)
Query: 18 KGLERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWK--DSRFFFGKNKVMAY 75
E+K+ + EL + +++Y ++ V + + ++L ++R + + GKN +M
Sbjct: 1 MTREKKEEIVAELKELLKEYKSVVVVDYRGLTVAQLTELRKKLREAGAELKVGKNTLMRR 60
Query: 76 ALGKSQEDEIEKNIHVVSSALKGQCGLLFTNRSKDDVLMWFDVYEDEDFAK 126
AL + E+E +S LKG L+FTN V + FAK
Sbjct: 61 ALEGTGEEE------ALSELLKGPTALIFTNEDPVAVAKVL-----KKFAK 100
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 69.3 bits (170), Expect = 8e-14
Identities = 48/187 (25%), Positives = 91/187 (48%), Gaps = 8/187 (4%)
Query: 12 LSKTVKKGLERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWK-DSRFFFGKN 70
++K KK +K+ ++L + +EKY I + SV N+ + +++D+R + + GKN
Sbjct: 1 MAKPEKK--AKKKAYFEKLYELLEKYKKILIVSVDNVGSKQMQDIRRSLRGKAELLMGKN 58
Query: 71 KVMAYALGKSQEDEIEKNIHVVSSALKGQCGLLFTNRSKDDVLMWFDVYEDEDFAKSGFI 130
++ AL K + +E+ + + + +KG G +FT +V + A++G I
Sbjct: 59 TLIRKAL-KQRLEELPE-LEKLLPHVKGNVGFVFTKDDLFEVKPVILENKVPAPARAGVI 116
Query: 131 STEDVELKEGPLPEFPHSIEPQLRQ-LGLQTNLNKGVVTLFKDHTVCKKGDVLTPEQARI 189
+ DV + GP P Q LG+ T + KG + + + + K+G + QA +
Sbjct: 117 APIDVVIPAGPTGMDPSQT--SFFQALGIATKIVKGQIEITNEVHLIKEGQKVGASQAVL 174
Query: 190 LKLLKKK 196
L+ L K
Sbjct: 175 LQKLNIK 181
>gnl|CDD|223322 COG0244, RplJ, Ribosomal protein L10 [Translation, ribosomal
structure and biogenesis].
Length = 175
Score = 51.5 bits (124), Expect = 4e-08
Identities = 16/89 (17%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 20 LERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWKD--SRFFFGKNKVMAYAL 77
E K+ L EL + +++ ++ + + + ++L ++R ++ ++ KN ++ AL
Sbjct: 5 REWKKELVAELKELIKESPSVVIVDYRGLTVAQLTELRKKLREAGAKLKVVKNTLLRRAL 64
Query: 78 GKSQEDEIEKNIHVVSSALKGQCGLLFTN 106
++ + ++ LKG + F+N
Sbjct: 65 EEAGLEGLDD-------LLKGPTAIAFSN 86
>gnl|CDD|140267 PTZ00240, PTZ00240, 60S ribosomal protein P0; Provisional.
Length = 323
Score = 48.0 bits (114), Expect = 1e-06
Identities = 45/191 (23%), Positives = 80/191 (41%), Gaps = 29/191 (15%)
Query: 21 ERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWK-DSRFFFGKNKVMAYALGK 79
K+ + LV + KY+ + + N+R+ ++ DVR + + F GK + A + K
Sbjct: 6 TAKREYEERLVDCLTKYSCVLFVGMDNVRSQQVHDVRRALRGKAEFVMGKKTLQAKIVEK 65
Query: 80 SQEDE-------------IEKNIHVVSSALKGQCGLLFTNRSKDDVLMWFDVYEDEDFAK 126
+ + EKN+ L G GL+FTN ++ D + + A+
Sbjct: 66 RAQAKKASAEAKLFNDQCEEKNL------LSGNTGLIFTNNEVQEITSVLDSHRVKAPAR 119
Query: 127 SGFISTEDVELKEGPLPEFPHSIEPQ----LRQLGLQTNLNKGVVTLFKDHTVCKKGDVL 182
G I+ DV + G +EP + L + T + KG+V + + V GD +
Sbjct: 120 VGAIAPCDVIVPAGST-----GMEPTQTSFFQALNIATKIAKGMVEIVTEKKVLSVGDKV 174
Query: 183 TPEQARILKLL 193
A +L+ L
Sbjct: 175 DNSTATLLQKL 185
>gnl|CDD|240223 cd05797, Ribosomal_L10, Ribosomal protein L10 family, L10
subfamily; composed of bacterial 50S ribosomal protein
and eukaryotic mitochondrial 39S ribosomal protein, L10.
L10 occupies the L7/L12 stalk of the ribosome. The
N-terminal domain (NTD) of L10 interacts with L11
protein and forms the base of the L7/L12 stalk, while
the extended C-terminal helix binds to two or three
dimers of the NTD of L7/L12 (L7 and L12 are identical
except for an acetylated N-terminus). The L7/L12 stalk
is known to contain the binding site for elongation
factors G and Tu (EF-G and EF-Tu, respectively);
however, there is disagreement as to whether or not L10
is involved in forming the binding site. The stalk is
believed to be associated with GTPase activities in
protein synthesis. In a neuroblastoma cell line, L10 has
been shown to interact with the SH3 domain of Src and to
activate the binding of the Nck1 adaptor protein with
skeletal proteins such as the Wiskott-Aldrich Syndrome
Protein (WASP) and the WASP-interacting protein (WIP).
These bacteria and eukaryotic sequences have no
additional C-terminal domain, present in other
eukaryotic and archaeal orthologs.
Length = 157
Score = 33.2 bits (77), Expect = 0.046
Identities = 17/95 (17%), Positives = 43/95 (45%), Gaps = 12/95 (12%)
Query: 20 LERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWKDS--RFFFGKNKVMAYAL 77
E+K+ + EL + +++ ++ V + + ++L ++R + +++ + KN + AL
Sbjct: 2 REKKEEIVAELKEKLKEAKSVVVADYRGLTVAQLTELRKELREAGVKLKVVKNTLAKRAL 61
Query: 78 GKSQEDEIEKNIHVVSSALKGQCGLLFTNRSKDDV 112
+ + LKG + F S++D
Sbjct: 62 EGT-------GFEDLDDLLKGPTAIAF---SEEDP 86
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 31.6 bits (72), Expect = 0.46
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 185 EQARILKLLKKKMAKFKVLLYLWYNKKEGTFENLLDREKTPMDIYDMEDDENNSNEE 241
+ ++L+LLK + K LL Y+ +NL R YD D ENN +E
Sbjct: 1344 QAVKVLQLLKDDLNKLDELLDACYSLNPAEIQNLKSR-------YDPADKENNLPKE 1393
>gnl|CDD|222691 pfam14337, DUF4393, Domain of unknown function (DUF4393). This
family of proteins is found in bacteria, archaea and
viruses. Proteins in this family are typically between
254 and 285 amino acids in length.
Length = 185
Score = 28.9 bits (65), Expect = 1.9
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 182 LTPEQARILKLLKKKMAKFKVLLYLWYNKKEGTFENLLDREKTPMDIYDMEDDENNSNEE 241
L+P++ARILK L K V + L + G FE +L+ ED +
Sbjct: 66 LSPDEARILKYLYKNNIVPTVDVRLIRPEGGG-FEIILEEL-----SLINEDAGISPERI 119
Query: 242 S 242
S
Sbjct: 120 S 120
>gnl|CDD|237223 PRK12839, PRK12839, hypothetical protein; Provisional.
Length = 572
Score = 28.6 bits (64), Expect = 3.6
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 179 GDVLTPEQ---ARILKLLKKKMAKFKVLLYLWYNKKEGTFENLLDREK 223
GD ++ + AR+ + L A V L + N K GTF +++DR K
Sbjct: 305 GDGISLAESVGARLDRDLASPAAWCPVSLVPYRNGKVGTFPHIMDRGK 352
>gnl|CDD|213284 cd05917, FACL_like_2, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 347
Score = 28.3 bits (64), Expect = 3.7
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 175 VCKKGDVLTPEQARILKLLKKKMAKFKVLLYLWY 208
V K G LT E+ ++ + ++A+FKV Y+ +
Sbjct: 298 VLKPGATLTEEE--LIAFCRGRLARFKVPRYVRF 329
>gnl|CDD|215739 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).
Other tRNA synthetase sub-families are too dissimilar to
be included.
Length = 606
Score = 28.1 bits (63), Expect = 4.6
Identities = 28/134 (20%), Positives = 51/134 (38%), Gaps = 22/134 (16%)
Query: 2 PKSKRDKKVTLSKTVKKGLERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWK 61
P R + + + R +NL + +KAVEK + + L++++ DW
Sbjct: 367 PHCWRSGTPIIYRATPQWFVRMKNLAEAALKAVEKV-QFVPKWGEKRYGNWLENIQ-DWC 424
Query: 62 DSR---------FFFGKN--------KVMAYALGKSQEDEIEKNIHVVSSALKGQCGLLF 104
SR ++ K+ + G+ +E+ IE +H + L G+
Sbjct: 425 ISRQRWWGHPIPAWYSKDTGEVYVRGSLKELVAGREEEEGIEAWLHRDAKDLLGKGAGTL 484
Query: 105 TNRSKDDVL-MWFD 117
+DVL WF
Sbjct: 485 --EQDEDVLDTWFS 496
>gnl|CDD|235730 PRK06187, PRK06187, long-chain-fatty-acid--CoA ligase; Validated.
Length = 521
Score = 27.8 bits (63), Expect = 5.4
Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 175 VCKKGDVLTPEQARILKLLKKKMAKFKV 202
V K G L ++ + L+ ++AKFK+
Sbjct: 465 VLKPGATLDAKE--LRAFLRGRLAKFKL 490
>gnl|CDD|236072 PRK07656, PRK07656, long-chain-fatty-acid--CoA ligase; Validated.
Length = 513
Score = 27.9 bits (63), Expect = 5.6
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 175 VCKKGDVLTPEQARILKLLKKKMAKFKV 202
V K G LT E+ ++ ++ +AK+KV
Sbjct: 462 VLKPGAELTEEE--LIAYCREHLAKYKV 487
>gnl|CDD|191735 pfam07381, DUF1495, Winged helix DNA-binding domain (DUF1495).
This family consists of several hypothetical archaeal
proteins of around 110 residues in length. The structure
of this domain possesses a winged helix DNA-binding
domain suggesting these proteins are bacterial
transcription factors.
Length = 90
Score = 26.1 bits (58), Expect = 6.9
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 189 ILKLLKKKMAKFKVLLYLWYNKKEGTFENLLDRE 222
I + L K + K+L+YL+ E T+ + + R
Sbjct: 1 IYRSLNKSEVRRKILVYLYSIYPEPTYLSEISRR 34
>gnl|CDD|234632 PRK00099, rplJ, 50S ribosomal protein L10; Reviewed.
Length = 172
Score = 26.6 bits (60), Expect = 9.6
Identities = 17/95 (17%), Positives = 41/95 (43%), Gaps = 12/95 (12%)
Query: 20 LERKQNLRDELVKAVEKYNNIFVFSVQNMRNSKLKDVRNDWKDS--RFFFGKNKVMAYAL 77
E K+ + EL + ++K + V + + +++ ++R +++ + KN + AL
Sbjct: 3 REEKKEIVAELAEKLKKAQSAVVADYRGLTVAQMTELRKKLREAGVEYKVVKNTLARRAL 62
Query: 78 GKSQEDEIEKNIHVVSSALKGQCGLLFTNRSKDDV 112
+ + ++ LKG + F S +D
Sbjct: 63 EGTGFEGLD-------DLLKGPTAIAF---SYEDP 87
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
0.315 0.133 0.380
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,194,033
Number of extensions: 1153058
Number of successful extensions: 918
Number of sequences better than 10.0: 1
Number of HSP's gapped: 905
Number of HSP's successfully gapped: 39
Length of query: 243
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 149
Effective length of database: 6,768,326
Effective search space: 1008480574
Effective search space used: 1008480574
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.2 bits)