RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17475
(346 letters)
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 359 bits (924), Expect = e-124
Identities = 149/275 (54%), Positives = 194/275 (70%), Gaps = 2/275 (0%)
Query: 2 LVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERLL 61
L+++Y K +V DNVGS+Q Q+IR+SL G +LMGKNT++RKA++ LE P LE+LL
Sbjct: 20 LLEKYKKILIVSVDNVGSKQMQDIRRSLRGKAELLMGKNTLIRKALKQRLEELPELEKLL 79
Query: 62 PHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSFFQ 121
PH+KGNVGFVFT+ DL EV+ +LENKV APAR G IAP V IPA TG+ P +TSFFQ
Sbjct: 80 PHVKGNVGFVFTKDDLFEVKPVILENKVPAPARAGVIAPIDVVIPAGPTGMDPSQTSFFQ 139
Query: 122 ALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGTIF 179
AL I TKI KG IEI N+VH++KEG + +A LL LNI PFSYGL + +YD+G+I+
Sbjct: 140 ALGIATKIVKGQIEITNEVHLIKEGQKVGASQAVLLQKLNIKPFSYGLEVLSIYDNGSIY 199
Query: 180 APQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAATEVDF 239
++LDI ED+ KF EGV +A++ L+ GYPT AS PHSI+N FKN+ A+ + F
Sbjct: 200 DAKVLDITDEDIVAKFQEGVQNVAAISLAAGYPTEASAPHSILNAFKNLAAIGLESGFTF 259
Query: 240 EQAKTVKEFLKDPSKFLAAAAPAAAAPAASNRSEE 274
A+ +KE L +PS AAAA AAAA AA+ +
Sbjct: 260 PLAEKIKEALANPSAAAAAAAAAAAAAAAAAAAPA 294
Score = 92.0 bits (229), Expect = 3e-21
Identities = 34/62 (54%), Positives = 46/62 (74%)
Query: 285 NDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLRVKF 344
N+VH++KEG KVG S+A LL LNI PFSYGL + +YD+G+I+ ++LDI ED+ KF
Sbjct: 156 NEVHLIKEGQKVGASQAVLLQKLNIKPFSYGLEVLSIYDNGSIYDAKVLDITDEDIVAKF 215
Query: 345 LE 346
E
Sbjct: 216 QE 217
>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 = 254 bits (650), Expect = 6e-85
Identities = 98/164 (59%), Positives = 124/164 (75%), Gaps = 2/164 (1%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
+L+ YPK +V ADNVGS+Q Q IR+SL G +LMGKNT++R+A+R + NP LE+L
Sbjct: 12 ELLKSYPKVLIVDADNVGSKQLQKIRRSLRGKAEILMGKNTLIRRALRNLGDENPELEKL 71
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSFF 120
LP++KGNVGF+FT GD E+R+ L ENKV APA+ GAIAPC V +PA TG+ P TSFF
Sbjct: 72 LPYLKGNVGFIFTNGDPFEIRKILEENKVPAPAKPGAIAPCDVVVPAGPTGMPPGPTSFF 131
Query: 121 QALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISP 162
QAL IPTKI KG IEII+DV ++K+G+ + EATLLN LNI P
Sbjct: 132 QALGIPTKIEKGKIEIISDVVVVKKGEKVGASEATLLNKLNIKP 175
Score = 52.6 bits (127), Expect = 3e-08
Identities = 18/28 (64%), Positives = 24/28 (85%)
Query: 284 LNDVHILKEGDKVGPSEATLLNMLNISP 311
++DV ++K+G+KVG SEATLLN LNI P
Sbjct: 148 ISDVVVVKKGEKVGASEATLLNKLNIKP 175
>gnl|CDD|140267 PTZ00240, PTZ00240, 60S ribosomal protein P0; Provisional.
Length = 323
Score = 206 bits (526), Expect = 2e-64
Identities = 109/293 (37%), Positives = 168/293 (57%), Gaps = 25/293 (8%)
Query: 5 EYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLE-----------H 53
+Y VG DNV S+Q ++R++L G +MGK T+ K + + +
Sbjct: 21 KYSCVLFVGMDNVRSQQVHDVRRALRGKAEFVMGKKTLQAKIVEKRAQAKKASAEAKLFN 80
Query: 54 NPGLERLLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLG 113
+ E+ L + GN G +FT ++ E+ L ++V+APAR GAIAPC V +PA +TG+
Sbjct: 81 DQCEEKNL--LSGNTGLIFTNNEVQEITSVLDSHRVKAPARVGAIAPCDVIVPAGSTGME 138
Query: 114 PEKTSFFQALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKM 171
P +TSFFQAL+I TKI+KG +EI+ + +L GD + ATLL LNISPF Y + +
Sbjct: 139 PTQTSFFQALNIATKIAKGMVEIVTEKKVLSVGDKVDNSTATLLQKLNISPFYYQVEVLS 198
Query: 172 VYDSGTIFAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAV 231
V+D G +F + L + + + +EG++ +A++ L G PT A++ +V+ FKN+LAV
Sbjct: 199 VWDRGVLFTREDLSMTEDVVEKMLMEGLSNVAAMSLGAGIPTAATIGPMLVDAFKNLLAV 258
Query: 232 AAATEVDFEQ--AKTVKEFLKD--------PSKFLAAAAPAAAAPAASNRSEE 274
+ AT +FE+ K ++E + + AAAAPAAA+ AA EE
Sbjct: 259 SVATSYEFEEHNGKELREAALEGLLGGGGSAAAEAAAAAPAAASAAAKEEEEE 311
Score = 46.5 bits (110), Expect = 8e-06
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 284 LNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLRVK 343
+ + +L GDKV S ATLL LNISPF Y + + V+D G +F + L + ED+ K
Sbjct: 162 VTEKKVLSVGDKVDNSTATLLQKLNISPFYYQVEVLSVWDRGVLFTREDLSM-TEDVVEK 220
Query: 344 FL 345
L
Sbjct: 221 ML 222
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 146 bits (371), Expect = 3e-41
Identities = 89/281 (31%), Positives = 137/281 (48%), Gaps = 17/281 (6%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIR--GHLEHNPGLE 58
+L+ YP +V + + +RQ Q IR+ L G + + KNT++++A+ G LE
Sbjct: 17 ELIKSYPVVGIVDLEGIPARQLQEIRRKLRGKAELKVSKNTLIKRALEEAG----EEDLE 72
Query: 59 RLLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGL--GPEK 116
+L +++G V +FT + ++ + L ++K APA+ G IAP + +PA TG GP
Sbjct: 73 KLEDYLEGQVALIFTNMNPFKLYKLLEKSKTPAPAKPGDIAPEDIVVPAGPTGFPPGP-I 131
Query: 117 TSFFQALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYD 174
S Q L IP +I KG I I D + K G+ S A +L L I P GL +K Y+
Sbjct: 132 LSELQKLGIPARIQKGKIVIKKDTVVAKAGEVISPELANVLQKLGIKPIEVGLDLKAAYE 191
Query: 175 SGTIFAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAA 234
G I+ P++L I E R E ++ ++ YPT ++ I F+ A+A
Sbjct: 192 DGVIYTPEVLAIDEEKYRSDIQEAAQNAFNLAVNAAYPTPETLETLIQKAFREAKALAV- 250
Query: 235 TEVDFEQAKTVKEFLKDPSKFLAAA-APAAAAPAASNRSEE 274
E +T + L SK +A A A AAA EE
Sbjct: 251 -EAGIVTPETADDIL---SKAVAQALALAAALADKDALDEE 287
Score = 48.7 bits (117), Expect = 2e-06
Identities = 20/56 (35%), Positives = 29/56 (51%)
Query: 286 DVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLR 341
D + K G+ + P A +L L I P GL +K Y+ G I+ P++L I E R
Sbjct: 154 DTVVAKAGEVISPELANVLQKLGIKPIEVGLDLKAAYEDGVIYTPEVLAIDEEKYR 209
>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 = 101 bits (253), Expect = 6e-26
Identities = 38/149 (25%), Positives = 59/149 (39%), Gaps = 13/149 (8%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVL-MGKNTMMRKAIRGHLEHNPGLER 59
+L+ +Y VV + Q +R+ L G L +GKNT+MR+A++G
Sbjct: 12 ELLKKYKSVVVVDYRGLTVAQLTELRKELRESGAKLKVGKNTLMRRALKGTGFEE----- 66
Query: 60 LLPHIKGNVGFVFTRGDLNEVREKLLENKV---QAPARNGAIAPCPVTIPAQNTGLGPEK 116
L P +KG FT D EV + L + + A+ G +A V PA T L
Sbjct: 67 LKPLLKGPTALAFTNEDPVEVAKVLKDFAKENKKLFAKGGVVA-GKVLDPAGVTALAKLP 125
Query: 117 TSFFQALSIPTKISKGTIEIINDVHILKE 145
+ + + I I +L
Sbjct: 126 S---REELLAMLIGLLKAPIAKLARLLNA 151
>gnl|CDD|223322 COG0244, RplJ, Ribosomal protein L10 [Translation, ribosomal
structure and biogenesis].
Length = 175
Score = 88.1 bits (219), Expect = 6e-21
Identities = 38/180 (21%), Positives = 64/180 (35%), Gaps = 23/180 (12%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVL-MGKNTMMRKAIRGHLEHNPGLER 59
+L+ E P +V + Q +R+ L G L + KNT++R+A+ GLE
Sbjct: 17 ELIKESPSVVIVDYRGLTVAQLTELRKKLREAGAKLKVVKNTLLRRALEE-----AGLEG 71
Query: 60 LLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSF 119
L +KG F+ D + L + G AP +P
Sbjct: 72 LDDLLKGPTAIAFSNEDPVAAAKLLKDFAK----EAGDKAPIKGGVPEGK---------- 117
Query: 120 FQALSIPTKISKGTIEIINDVHILKEGD-SSREATLLNMLNISPFSYGLIIKMVYDSGTI 178
L I+ + ++ ++ G + LL L P GL + Y+ G +
Sbjct: 118 --VLGAAEVIALAKLPSKEELVVMLLGVLQAPATKLLRALKAVPDKVGLKLLAAYEKGVV 175
Score = 34.1 bits (79), Expect = 0.049
Identities = 24/109 (22%), Positives = 37/109 (33%), Gaps = 15/109 (13%)
Query: 225 FKNVLAVAAATEVDFEQAKTVKEFLK---DPSKFLAAAAPAAAAPAASNRSEERFSRNAE 281
K A+A + E AK +K+F K D + AA A
Sbjct: 76 LKGPTAIAFSNEDPVAAAKLLKDFAKEAGDKAPIKGGVPEGKVLGAAE--------VIAL 127
Query: 282 TDL---NDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTI 327
L ++ ++ G P+ LL L P GL + Y+ G +
Sbjct: 128 AKLPSKEELVVMLLGVLQAPA-TKLLRALKAVPDKVGLKLLAAYEKGVV 175
>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 = 85.3 bits (212), Expect = 5e-20
Identities = 49/156 (31%), Positives = 73/156 (46%), Gaps = 20/156 (12%)
Query: 3 VDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHL---EHNPGLER 59
VD+Y +V DN+ + + ++IRQ + GKN +M+ A+ G E+ P L +
Sbjct: 14 VDKYKYIYVFSVDNMRNNKLKDIRQEWKD-SRFFFGKNKVMQVAL-GRTPEDEYKPNLHK 71
Query: 60 LLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGP----- 114
L ++KG VG +FT EV E AR G+IA VT+P GP
Sbjct: 72 LSKYLKGQVGLLFTNEPPEEVIEYFDSYSEPDFARAGSIATETVTLPE-----GPLEQFP 126
Query: 115 ---EKTSFFQALSIPTKISKGTIEIINDVHILKEGD 147
E + L +PTK+ KG I + D + +EG
Sbjct: 127 HSMEPQ--LRKLGLPTKLKKGVITLEADYVVCEEGK 160
>gnl|CDD|215933 pfam00466, Ribosomal_L10, Ribosomal protein L10.
Length = 100
Score = 75.3 bits (186), Expect = 5e-17
Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGV-VLMGKNTMMRKAIRGHLEHNPGLER 59
+L+ EY VV + Q +R+ L G + +GKNT+MR+A+ G E E
Sbjct: 15 ELLKEYKSVVVVDYRGLTVAQLTELRKKLREAGAELKVGKNTLMRRALEGTGEE----EA 70
Query: 60 LLPHIKGNVGFVFTRGDLNEVREKLLEN 87
L +KG +FT D V + L +
Sbjct: 71 LSELLKGPTALIFTNEDPVAVAKVLKKF 98
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 71.1 bits (175), Expect = 1e-15
Identities = 23/58 (39%), Positives = 30/58 (51%)
Query: 211 YPTVASVPHSIVNGFKNVLAVAAATEVDFEQAKTVKEFLKDPSKFLAAAAPAAAAPAA 268
PT A + H + K V A V F + K +KE + + S L+AAA AAAA AA
Sbjct: 1 EPTAADIKHVLKAAGKEVEAERLELLVKFLEGKNIKELIANGSAKLSAAAAAAAAAAA 58
>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 = 36.3 bits (85), Expect = 0.007
Identities = 23/74 (31%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 10 FVVGADNVG--SRQFQNIRQSLEGLGVVLM-GKNTMMRKAIRGHLEHNPGLERLLPHIKG 66
VV AD G Q +R+ L GV L KNT+ ++A+ G G E L +KG
Sbjct: 21 SVVVADYRGLTVAQLTELRKELREAGVKLKVVKNTLAKRALEGT-----GFEDLDDLLKG 75
Query: 67 NVGFVFTRGDLNEV 80
F+ D
Sbjct: 76 PTAIAFSEEDPVAA 89
>gnl|CDD|234632 PRK00099, rplJ, 50S ribosomal protein L10; Reviewed.
Length = 172
Score = 34.7 bits (81), Expect = 0.029
Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 21 QFQNIRQSLEGLGVVLM-GKNTMMRKAIRGHLEHNPGLERLLPHIKGNVGFVFTRGDLNE 79
Q +R+ L GV KNT+ R+A+ G E L +KG F+ D
Sbjct: 35 QMTELRKKLREAGVEYKVVKNTLARRALE-----GTGFEGLDDLLKGPTAIAFSYEDPVA 89
Query: 80 V 80
Sbjct: 90 A 90
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 33.2 bits (76), Expect = 0.042
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 231 VAAATEVDFEQAKTVKEFLKDPSKFLAAAAPAAAAPAASNRSEE 274
VAA EV+ ++A +K + AAAAPAAAA AA+ E
Sbjct: 42 VAALEEVNIDEA------IKKAAVAAAAAAPAAAAAAAAEEKAE 79
>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
This model represents the large subunit, DP2, of a two
subunit novel Archaeal replicative DNA polymerase first
characterized for Pyrococcus furiosus. Structure of DP2
appears to be organized as a ~950 residue component
separated from a ~300 residue component by a ~150
residue intein. The other subunit, DP1, has sequence
similarity to the eukaryotic DNA polymerase delta small
subunit [DNA metabolism, DNA replication, recombination,
and repair].
Length = 1095
Score = 31.4 bits (71), Expect = 0.92
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 125 IPTKISKGTIEIINDVHILKEGDSSREATLLNMLNISPFSYGLII---------KMVYDS 175
IP + KG + N V++ K+G + +AT L + + P G+ + + Y +
Sbjct: 690 IPEPLEKGILRAKNGVYVFKDGTARFDATDLPITHFKPAEIGVSVEKLRELGYERDYYGA 749
Query: 176 GTIFAPQILDIRPEDL 191
QI++++P+D+
Sbjct: 750 ELKDENQIVELKPQDV 765
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 29.2 bits (66), Expect = 0.97
Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 231 VAAATEVDFEQAKTVKEFLKDPSKFLAAAAPAAAAPAASNRSEE 274
VAA +V+ E+A +K+ P AAAA AAAA AA + EE
Sbjct: 42 VAALEDVNIEEA--IKKAAAAPVAAAAAAAAAAAAAAAEEKKEE 83
>gnl|CDD|131354 TIGR02301, TIGR02301, TIGR02301 family protein. Members of this
uncharacterized protein family are found in a number of
alphaProteobacteria, including root nodule bacteria,
Brucella suis, Caulobacter crescentus, and
Rhodopseudomonas palustris. Conserved residues include
two well-separated cysteines, suggesting a disulfide
bond. The function is unknown.
Length = 121
Score = 29.0 bits (65), Expect = 1.7
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 248 FLKDPSKFLAAAAPAAAAPAASNRSEERFSRNAETDLNDVHILK 291
FL P AAP AA A ++R R AE L +H L+
Sbjct: 3 FLAQPCLAALIAAPVPAAERAPAPYDQRLLRLAEI-LGSLHYLR 45
>gnl|CDD|179127 PRK00794, flbT, flagellar biosynthesis repressor FlbT; Reviewed.
Length = 132
Score = 28.7 bits (65), Expect = 2.2
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 131 KGTIEIINDVHILKEGD 147
K ++E++ND L+E D
Sbjct: 26 KVSLELLNDATFLRERD 42
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plant species have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site located in the C-terminal
region of P2. TCS inactivates the ribosome by
depurinating a specific adenine in the sarcin-ricin loop
of 28S rRNA.
Length = 103
Score = 28.1 bits (63), Expect = 2.4
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 243 KTVKEFLKDPSKFLAAAAPAAAAPAASNRSEE 274
K +K+ L + AAPAAAA AA+ + E
Sbjct: 49 KDIKDLLSNVGGGGGGAAPAAAAAAAAAAAAE 80
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 28.1 bits (63), Expect = 2.6
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 231 VAAATEVDFEQAKTVKEFLKDPSKFLAAAAPAAAAPAASNRSEE 274
VAA V+ E+A + AAAA AAAA A EE
Sbjct: 42 VAALEGVNIEEAIKKAAAAPVAA---AAAAAAAAAAAEEEEEEE 82
>gnl|CDD|235558 PRK05683, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 676
Score = 29.7 bits (67), Expect = 3.0
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 242 AKTVKEFLKDPSKFLAAAAPAAAAPAASNRSEERFS 277
A ++ L DP K LA AAP A + N +
Sbjct: 424 ASDIETVLTDPKK-LAFAAPLTAEAGSGNSGTGSIT 458
>gnl|CDD|219391 pfam07378, FlbT, Flagellar protein FlbT. This family consists of
several FlbT proteins. FlbT is a post-transcriptional
regulator of flagellin. FlbT is associated with the 5'
untranslated region (UTR) of fljK (25 kDa flagellin)
mRNA and that this association requires a predicted loop
structure in the transcript. Mutations within this loop
abolish FlbT association and result in increased mRNA
stability. It is therefore thought that FlbT promotes
the degradation of flagellin mRNA by associating with
the 5' UTR.
Length = 126
Score = 27.9 bits (63), Expect = 3.4
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 23/81 (28%)
Query: 131 KGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGTIFAPQ---ILD 185
+ +EI ND IL+E D +AT +P ++ +Y FA Q I
Sbjct: 24 RSRLEIENDAPILREKDILQPEDAT-------TP------VRRLY-----FAVQLMLIGP 65
Query: 186 IRPEDLRVKFLEGVATLASVC 206
+D R FLE + L++
Sbjct: 66 EDRDDARALFLELLEELSAAF 86
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 27.8 bits (62), Expect = 3.5
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 11/59 (18%)
Query: 227 NVLAV--AAATEVDFEQAKT---------VKEFLKDPSKFLAAAAPAAAAPAASNRSEE 274
N+ +V AA EV+ +AK + E +K+ ++ AAAA A AA AA+ +E
Sbjct: 21 NLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEA 79
>gnl|CDD|119426 cd05166, PI3Kc_II, Phosphoinositide 3-kinase (PI3K), class II,
catalytic domain; The PI3K catalytic domain family is
part of a larger superfamily that includes the catalytic
domains of other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
RIO kinases. PI3Ks catalyze the transfer of the
gamma-phosphoryl group from ATP to the 3-hydroxyl of the
inositol ring of D-myo-phosphatidylinositol (PtdIns) or
its derivatives. PI3Ks play an important role in a
variety of fundamental cellular processes, including
cell motility, the Ras pathway, vesicle trafficking and
secretion, immune cell activation and apoptosis. They
can be divided into three main classes (I, II, and III),
defined by their substrate specificity, regulation, and
domain structure. Class II PI3Ks preferentially use
PtdIns as a substrate to produce PtdIns(3)P, but can
also phosphorylate PtdIns(4)P. They function as monomers
and do not associate with any regulatory subunits. Class
II enzymes contain an N-terminal Ras binding domain, a
lipid binding C2 domain, a PI3K homology domain of
unknown function, an ATP-binding cataytic domain, a Phox
homology (PX) domain, and a second C2 domain at the
C-terminus. They are activated by a variety of stimuli
including chemokines, cytokines, lysophosphatidic acid
(LPA), insulin, and tyrosine kinase receptors.
Length = 353
Score = 28.9 bits (65), Expect = 3.8
Identities = 32/119 (26%), Positives = 50/119 (42%), Gaps = 24/119 (20%)
Query: 74 RGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSFFQALSIPTKISKGT 133
R L V LL+NK + P + P G+ + S+F + ++P KIS
Sbjct: 34 RTGLGRVDSFLLQNKCRLP-----LNPALDV-----KGIDVRECSYFNSNALPLKISFVN 83
Query: 134 IEIINDVH--ILKEGDSSREATL-LNMLNISP---FSYGLIIKMV--------YDSGTI 178
+ + + I K GD R+ L L M+NI GL ++M+ YD G +
Sbjct: 84 ADPMGENISVIFKAGDDLRQDMLVLQMINIMDKIWLQEGLDLRMITFRCLSTGYDRGMV 142
>gnl|CDD|225398 COG2842, COG2842, Uncharacterized ATPase, putative transposase
[General function prediction only].
Length = 297
Score = 28.2 bits (63), Expect = 6.1
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 13/89 (14%)
Query: 2 LVDEYPKCFVVGADNVGSRQFQNIR--QSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLER 59
+VDE AD + R + +R G+GVVL+G + + R E + R
Sbjct: 170 IVDE--------ADRLPYRALEELRRIHDKTGIGVVLVGMPRLFKVLRRPEDELSRLYSR 221
Query: 60 LLPHIKGNVGFVFTRGD-LNEVREKLLEN 87
+ + +G F D L E+ +L
Sbjct: 222 V--RVGKLLGEKFPDADELAEIAALVLPT 248
>gnl|CDD|193226 pfam12750, Maff2, Maff2 family. This family of short membrane
proteins are related to the protein Maff2. Maff2 lies
just outside the direct repeats of a tetracycline
resistance transposable element. This protein may
contain transmembrane helices.
Length = 70
Score = 26.3 bits (58), Expect = 6.8
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 13 GADNVGSRQFQNIRQSLEGLGVVLMG 38
G DN G++ Q I+Q + G GVVL+G
Sbjct: 35 GNDNPGAKS-QGIKQLMAGGGVVLIG 59
>gnl|CDD|138873 PRK12320, PRK12320, hypothetical protein; Provisional.
Length = 699
Score = 28.0 bits (62), Expect = 8.2
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 248 FLKDPSKFLAAAAPAAAAPA 267
F DP+ L AA AA PA
Sbjct: 577 FADDPALLLKTAAEIAARPA 596
>gnl|CDD|180865 PRK07178, PRK07178, pyruvate carboxylase subunit A; Validated.
Length = 472
Score = 27.8 bits (62), Expect = 9.1
Identities = 14/23 (60%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 229 LAVAAATEVDFEQAKTVKEFLKD 251
LAV AA V +E A TV EFL D
Sbjct: 257 LAVRAAKAVGYENAGTV-EFLLD 278
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
0.318 0.136 0.385
Gapped
Lambda K H
0.267 0.0648 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,782,661
Number of extensions: 1743077
Number of successful extensions: 2210
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2142
Number of HSP's successfully gapped: 43
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
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: 41 (21.7 bits)
S2: 59 (26.7 bits)