RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy39
(195 letters)
>gnl|CDD|100101 cd00349, Ribosomal_L11, Ribosomal protein L11. Ribosomal protein
L11, together with proteins L10 and L7/L12, and 23S
rRNA, form the L7/L12 stalk on the surface of the large
subunit of the ribosome. The homologous eukaryotic
cytoplasmic protein is also called 60S ribosomal protein
L12, which is distinct from the L12 involved in the
formation of the L7/L12 stalk. The C-terminal domain
(CTD) of L11 is essential for binding 23S rRNA, while
the N-terminal domain (NTD) contains the binding site
for the antibiotics thiostrepton and micrococcin. L11
and 23S rRNA form an essential part of the
GTPase-associated region (GAR). Based on differences in
the relative positions of the L11 NTD and CTD during the
translational cycle, L11 is proposed to play a
significant role in the binding of initiation factors,
elongation factors, and release factors to the ribosome.
Several factors, including the class I release factors
RF1 and RF2, are known to interact directly with L11. In
eukaryotes, L11 has been implicated in regulating the
levels of ubiquinated p53 and MDM2 in the MDM2-p53
feedback loop, which is responsible for apoptosis in
response to DNA damage. In bacteria, the "stringent
response" to harsh conditions allows bacteria to
survive, and ribosomes that lack L11 are deficient in
stringent factor stimulation.
Length = 131
Score = 171 bits (436), Expect = 2e-55
Identities = 70/134 (52%), Positives = 89/134 (66%), Gaps = 3/134 (2%)
Query: 22 IRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRSYK 81
I+ +PAG ASP PPLGP LG+ GVNI FCK+FN +TKD K GLP+P +I V DRS+
Sbjct: 1 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNARTKDYK-GLPVPVKITVYNDRSFT 59
Query: 82 LIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEYIC 141
+ PP S LK+AAG+ KG KP KE G +TL +YEIAKIK D +TL+
Sbjct: 60 FEVKTPPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKLPDL--NAKTLKSAV 117
Query: 142 TSVIGSARSVGIEV 155
++G+ARS+GI V
Sbjct: 118 KEILGTARSMGITV 131
>gnl|CDD|197819 smart00649, RL11, Ribosomal protein L11/L12.
Length = 132
Score = 166 bits (424), Expect = 2e-53
Identities = 69/135 (51%), Positives = 91/135 (67%), Gaps = 3/135 (2%)
Query: 22 IRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRSYK 81
I+ IPAG A+P PPLGP LG+ G+NI FCK+FN +TKD K+GLP+P +I V D+S+
Sbjct: 1 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNARTKD-KKGLPIPVKITVYNDKSFT 59
Query: 82 LIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEYIC 141
I+ PP S LK+AAG+ KG KPGK+ G +TL +YEIAKIK D + LE
Sbjct: 60 FILKTPPASALLKKAAGIEKGSKKPGKKKVGNITLDQVYEIAKIKRPDL--NAKDLEAAV 117
Query: 142 TSVIGSARSVGIEVV 156
++G+ARS+GI V
Sbjct: 118 KEILGTARSMGITVE 132
>gnl|CDD|233500 TIGR01632, L11_bact, 50S ribosomal protein L11. This model
represents bacterial, chloroplast, and most
mitochondrial forms of 50S ribosomal protein L11
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 140
Score = 152 bits (386), Expect = 8e-48
Identities = 65/138 (47%), Positives = 89/138 (64%), Gaps = 2/138 (1%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
+I+ +PAG A+P PP+GP LG+RGVNI FCK FN +T D + GLP+P I V D+S
Sbjct: 5 GIIKLQVPAGQANPAPPVGPALGQRGVNIMEFCKQFNARTADYEPGLPVPVVITVYEDKS 64
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEY 139
+ I+ PP SY LK+AAG+ KG P KE GK+T K + EIA+IK D + +E
Sbjct: 65 FTFIVKTPPVSYLLKKAAGVEKGSKNPKKEKVGKITRKQVREIAEIKMSD--LNTKDIEA 122
Query: 140 ICTSVIGSARSVGIEVVD 157
+ G+A+S+GIE+V
Sbjct: 123 AMKIIAGTAKSMGIEIVG 140
>gnl|CDD|234661 PRK00140, rplK, 50S ribosomal protein L11; Validated.
Length = 141
Score = 145 bits (368), Expect = 6e-45
Identities = 68/145 (46%), Positives = 86/145 (59%), Gaps = 6/145 (4%)
Query: 13 KKAVDNFRMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRI 72
KK V I+ IPAG A+P PP+GP LG+RGVNI FCK FN +T+D K GLP+P I
Sbjct: 3 KKVV---GYIKLQIPAGKANPAPPVGPALGQRGVNIMEFCKAFNARTQDQK-GLPIPVVI 58
Query: 73 KVNPDRSYKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAF 132
V DRS+ I PP S LK+AAG+ KG +P KE GK+T + EIA+ K D
Sbjct: 59 TVYEDRSFTFITKTPPASVLLKKAAGIEKGSGEPNKEKVGKITRAQVREIAETKMPD--L 116
Query: 133 ECETLEYICTSVIGSARSVGIEVVD 157
+E + G+ARS+GI V
Sbjct: 117 NAADIEAAMRMIAGTARSMGIVVEG 141
>gnl|CDD|223158 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
structure and biogenesis].
Length = 141
Score = 145 bits (368), Expect = 6e-45
Identities = 68/139 (48%), Positives = 88/139 (63%), Gaps = 3/139 (2%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
++I+ +PAG A+P PP+GP LG+ GVNI FCK+FN TKD K GLP+P I V DRS
Sbjct: 6 KIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKDEK-GLPVPVVITVYEDRS 64
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEY 139
+ I+ PP S LK+AAG+ KG KP K GKLTL + EIAK K D + LE
Sbjct: 65 FTFIVKTPPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMPDL--NAKDLEA 122
Query: 140 ICTSVIGSARSVGIEVVDK 158
++G+ARS+G+ V K
Sbjct: 123 AVKEILGTARSMGVTVEGK 141
>gnl|CDD|177049 CHL00127, rpl11, ribosomal protein L11; Validated.
Length = 140
Score = 111 bits (279), Expect = 1e-31
Identities = 58/135 (42%), Positives = 84/135 (62%), Gaps = 3/135 (2%)
Query: 22 IRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRSYK 81
I+ +PAG A+P PP+GP LG+ GVNI FCK++N +TKD K GL +P I V D+SY
Sbjct: 9 IKLALPAGKATPAPPVGPALGQHGVNINLFCKEYNARTKD-KIGLIIPVEISVYEDKSYT 67
Query: 82 LIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEYIC 141
I+ PP S L +AAG+ KG +P K+ G +T+K + EIA+IK D +L
Sbjct: 68 FILKTPPASVLLAKAAGIKKGSGEPNKKKVGSITIKQLEEIAQIKLPD--LNTISLSKAI 125
Query: 142 TSVIGSARSVGIEVV 156
+ G+A+++GI +
Sbjct: 126 KIIEGTAKNMGISIK 140
>gnl|CDD|234908 PRK01143, rpl11p, 50S ribosomal protein L11P; Validated.
Length = 163
Score = 95.0 bits (237), Expect = 5e-25
Identities = 51/155 (32%), Positives = 92/155 (59%), Gaps = 5/155 (3%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPD-R 78
+++ + G A+PGPPLGP LG G+N+ ++ NEKTKD K G+ +P ++ V+ D +
Sbjct: 3 KVVEVLVEGGKATPGPPLGPALGPLGLNVKQVVQEINEKTKDFK-GMQVPVKVIVDTDTK 61
Query: 79 SYKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLE 138
+++ + PPT+ +K+ G+ KG +PG E+ G L+ + + +IA +K +D L+
Sbjct: 62 KFEIEVGIPPTTALIKKELGIEKGSGEPGHEVVGNLSFEQVVKIAIMKKDD--LLSYDLK 119
Query: 139 YICTSVIGSARSVGIEVVDKLDAEEYQQFLEERKI 173
V+G+ S+G+ V+ D +E Q+ ++E K
Sbjct: 120 AAVKEVLGTCVSMGV-TVEGKDPKEVQKEVDEGKY 153
>gnl|CDD|189492 pfam00298, Ribosomal_L11, Ribosomal protein L11, RNA binding
domain.
Length = 69
Score = 86.3 bits (215), Expect = 7e-23
Identities = 40/69 (57%), Positives = 47/69 (68%), Gaps = 2/69 (2%)
Query: 87 PPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEYICTSVIG 146
PP SY LK+AAG+ KG KPGKE GK+TLK +YEIAKIK D LE +IG
Sbjct: 3 PPASYLLKKAAGIEKGSGKPGKEKVGKITLKQVYEIAKIKMPDLN--ANDLEAAVKIIIG 60
Query: 147 SARSVGIEV 155
+ARS+GIEV
Sbjct: 61 TARSMGIEV 69
>gnl|CDD|217808 pfam03946, Ribosomal_L11_N, Ribosomal protein L11, N-terminal
domain. The N-terminal domain of Ribosomal protein L11
adopts an alpha/beta fold and is followed by the RNA
binding C-terminal domain.
Length = 59
Score = 85.2 bits (212), Expect = 2e-22
Identities = 35/59 (59%), Positives = 43/59 (72%), Gaps = 1/59 (1%)
Query: 22 IRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRSY 80
I+ +PAG A+P PPLGP LG+ GVNI FCK+FN TKD K GLP+P +I V DRS+
Sbjct: 2 IKLQVPAGKANPAPPLGPALGQLGVNIMEFCKEFNAATKDYK-GLPVPVKITVYNDRSF 59
>gnl|CDD|240358 PTZ00321, PTZ00321, ribosomal protein L11; Provisional.
Length = 342
Score = 74.6 bits (183), Expect = 4e-16
Identities = 61/208 (29%), Positives = 100/208 (48%), Gaps = 26/208 (12%)
Query: 1 MSKAGKVFSKNV---KKAVDNFRMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNE 57
M+KA +F+ K+ + N+R I AG A+ GPP+G + G+ F K FN+
Sbjct: 32 MAKAKDIFAVPEFPGKRVLHNWRFF---IKAGKAATGPPVGQEFSKLGLKAMDFAKSFND 88
Query: 58 KTK-DLKEGLPLPTRIKVNPDRSYKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIG---GK 113
+TK K+ + L RI+V D+SY I PPT++++ +A + P G
Sbjct: 89 RTKPHFKDDVELIVRIQVYFDKSYLFTIEPPPTAWFILRALRKKRRETGPVPLRGHYCAL 148
Query: 114 LTLKHIYEIAKIKSED-SAFECETLEYICTSVIGSARSVGIEVV-------DKLDAEEYQ 165
+TL+ YEIAK+K E +E V+G AR +G+ + + +
Sbjct: 149 MTLEMAYEIAKMKPRSWGRPEYPLIETRVRRVVGQARRMGVCFIGVDTPHSSPVKGMTEK 208
Query: 166 QFLEE----RKIIVAE----QKKELEEA 185
Q+ EE R + + + +++ELEEA
Sbjct: 209 QYAEESERYRAMHMEQYEALRQRELEEA 236
>gnl|CDD|184732 PRK14539, PRK14539, 50S ribosomal protein L11/unknown domain fusion
protein; Provisional.
Length = 196
Score = 69.2 bits (169), Expect = 6e-15
Identities = 52/173 (30%), Positives = 83/173 (47%), Gaps = 15/173 (8%)
Query: 28 AGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRSYKLIIHKP 87
AG A PGP L G+N+ F K FN+ T+D + G P+P +I V D+S+ +
Sbjct: 16 AGQAKPGPSLAGV----GINMPEFTKQFNDATRD-RGGEPVPVQITVYKDKSFDFKLFTA 70
Query: 88 PTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEYICTSVIGS 147
P S+ +KQAA + G I G +TL + EIAK K D + +E ++ G+
Sbjct: 71 PASFKIKQAAKIKSGSANSKTTIVGTITLSQLEEIAKYKLPD--LNTDDVEEAMHTIAGT 128
Query: 148 ARSVGIEV-----VDKLDAEEYQQFLEERKIIVAEQKKELEEAKEAKMLRTSG 195
A+++G+ V V K E A+ K+ ++ EA++ + G
Sbjct: 129 AKNMGVLVEGYDDVVKAKEEAKAAAKAAAL---AKAKEASLKSAEAELKASKG 178
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 36.3 bits (84), Expect = 0.003
Identities = 33/143 (23%), Positives = 66/143 (46%), Gaps = 7/143 (4%)
Query: 37 LGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRSYKLIIHKPPTSYYLKQA 96
L P +G G++ +D ++T +GL + ++ V ++ ++ P + + +A
Sbjct: 28 LAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVSVV--PSAAALVIKA 85
Query: 97 AGMAKGVMKPGKEIG--GKLTLKHIYEIAKIKSEDSAFECETLEYICTSVIGSARSVGIE 154
+ K K I G ++L + EIAKI S + L ++G+ SVG
Sbjct: 86 LKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRPRSM--AKELAGTVKEILGTCVSVGC- 142
Query: 155 VVDKLDAEEYQQFLEERKIIVAE 177
VD D ++ QQ +++ ++ + E
Sbjct: 143 TVDGKDPKDLQQEIDDGEVEIPE 165
>gnl|CDD|199886 cd02856, E_set_GDE_Isoamylase_N, N-terminal Early set domain
associated with the catalytic domain of Glycogen
debranching enzyme and bacterial isoamylase (also
called glycogen 6-glucanohydrolase). E or "early" set
domains are associated with the catalytic domain of the
glycogen debranching enzyme at the N-terminal end.
Glycogen debranching enzymes have both
4-alpha-glucanotransferase and amylo-1,6-glucosidase
activities. As a transferase, it transfers a segment of
the 1,4-alpha-D-glucan to a new 4-position in an
acceptor, which may be glucose or another
1,4-alpha-D-glucan. As a glucosidase, it catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Bacterial isoamylases are
also included in this subfamily. Isoamylase is one of
the starch-debranching enzymes that catalyze the
hydrolysis of alpha-1,6-glucosidic linkages specific in
alpha-glucans such as amylopectin or glycogen.
Isoamylase contains a bound calcium ion, but this is
not in the same position as the conserved calcium ion
that has been reported in other alpha-amylase family
enzymes. The N-terminal domain of glycogen debranching
enzyme may be related to the immunoglobulin and/or
fibronectin type III superfamilies. These domains are
associated with different types of catalytic domains at
either the N-terminal or C-terminal end and may be
involved in homodimeric/tetrameric/dodecameric
interactions. Members of this family include members of
the alpha amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase,
and chitinase, among others.
Length = 130
Score = 30.7 bits (70), Expect = 0.24
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 35 PPLGPTLGERGVNIATFCKD 54
PLG TL + GVN A F
Sbjct: 1 YPLGATLDDGGVNFAVFSPH 20
>gnl|CDD|240269 PTZ00105, PTZ00105, 60S ribosomal protein L12; Provisional.
Length = 140
Score = 30.0 bits (68), Expect = 0.38
Identities = 37/144 (25%), Positives = 60/144 (41%), Gaps = 8/144 (5%)
Query: 37 LGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRSYKLIIHKPPTSYYLKQA 96
L P +G G++ D + TKD K GL + ++ V +R + + P S L +A
Sbjct: 3 LAPKVGPLGLSPKKVGDDIAKATKDWK-GLKVTVKLTVQ-NRQATVEV-VPTASSLLIKA 59
Query: 97 AGMAKGVMKPGKEI--GGKLTLKHIYEIAKIKSEDSAFECETLEYICTSVIGSARSVGIE 154
K K I G LT + +IA+ S +T + V+G+ S+G
Sbjct: 60 LKEPPRDRKKVKNIKHSGNLTFDQVIKIARTMRPKSM--AKTFKGTVKEVLGTCVSIGCT 117
Query: 155 VVDKLDAEEYQQFLEERKIIVAEQ 178
VD + Q+ + +I V E
Sbjct: 118 -VDGESPRDIQEKINNGEIKVPES 140
>gnl|CDD|219379 pfam07336, DUF1470, Protein of unknown function (DUF1470). This
family consists of several hypothetical bacterial
proteins of around 180 residues in length. Members of
this family are found in Streptomyces, Rhizobium,
Ralstonia, Agrobacterium and Bradyrhizobium species. The
function of this family is unknown.
Length = 121
Score = 29.3 bits (66), Expect = 0.67
Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 140 ICTSVIGSARSVGIEVVDKL-DAEEYQQFLEERKIIVAEQKKELEEAKEAKMLR 192
+ ++ + G VD+L D + +L ++ A + A+ LR
Sbjct: 4 LALDLVNTVALRGGRPVDRLADPADLAAWLAAAGLLPAGAADAAADLAAARALR 57
>gnl|CDD|233118 TIGR00761, argB, acetylglutamate kinase. This model describes
N-acetylglutamate kinases (ArgB) of many prokaryotes and
the N-acetylglutamate kinase domains of multifunctional
proteins from yeasts. This enzyme is the second step in
the "acetylated" ornithine biosynthesis pathway. A
related group of enzymes representing the first step of
the pathway contain a homologous domain and are excluded
from this model [Amino acid biosynthesis, Glutamate
family].
Length = 231
Score = 29.2 bits (66), Expect = 1.0
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 130 SAFECETLEYICTSVIGSARSVGIEVVDKLDAEEYQQFLEERKIIVAEQKKELEEAKEA 188
+A E L + T V G G ++ ++ +E +Q L ++ II ++ A EA
Sbjct: 165 AALGAEKL-VLLTDVPGILNGDGQSLISEIPLDEIEQ-LIKQGIIKGGMIPKVNAALEA 221
>gnl|CDD|153174 cd04902, ACT_3PGDH-xct, C-terminal ACT (regulatory) domain of
D-3-phosphoglycerate dehydrogenase (3PGDH). The
C-terminal ACT (regulatory) domain of
D-3-phosphoglycerate dehydrogenase (3PGDH), with an
extended C-terminal (xct) region from bacteria,
archaea, fungi, and plants. 3PGDH is an enzyme that
belongs to the D-isomer specific, 2-hydroxyacid
dehydrogenase family and catalyzes the oxidation of
D-3-phosphoglycerate to 3- phosphohydroxypyruvate,
which is the first step in the biosynthesis of
L-serine, using NAD+ as the oxidizing agent. In
bacteria, 3PGDH is feedback-controlled by the end
product L-serine in an allosteric manner. Some 3PGDH
enzymes have an additional domain formed by an extended
C-terminal region. This additional domain introduces
significant asymmetry to the homotetramer. Adjacent ACT
(regulatory) domains interact, creating two
serine-binding sites, however, this asymmetric
arrangement results in the formation of two different
and distinct domain interfaces between identical
domains in the asymmetric unit. How this asymmetry
influences the mechanism of effector inhibition is
still unknown. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 73
Score = 27.0 bits (61), Expect = 1.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 37 LGPTLGERGVNIATF 51
+G LGE G+NIA
Sbjct: 16 VGTILGEAGINIAGM 30
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 28.4 bits (64), Expect = 2.1
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 154 EVVDKLDAEEYQQFLEERKIIVAEQKKELEEAKEAKM 190
E +K+ ++ EE + E+KKE EAK AK+
Sbjct: 267 EEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKL 303
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc gene
is often associated with scpB (TIGR00281) and scpA genes,
where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 28.5 bits (64), Expect = 2.7
Identities = 15/30 (50%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 159 LDA-EEYQQFLEERKIIVAEQKKELEEAKE 187
L A EEY++ L+ER + QK++L EAKE
Sbjct: 989 LAAIEEYEE-LKERYDFLTAQKEDLTEAKE 1017
>gnl|CDD|147082 pfam04740, LXG, LXG domain of WXG superfamily. This domain is
present is the N-terminal region of a group of
polymorphic toxin proteins in bacteria. It is predicted
to use Type VII secretion pathway to mediate export of
bacterial toxins.
Length = 204
Score = 27.6 bits (62), Expect = 3.1
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 158 KLDAEEYQQFLEERKIIVAEQKKELEEAKEA 188
LD E +++ + E + +LE K+A
Sbjct: 2 VLDVAELISAIDQTISALKELRDQLESLKKA 32
>gnl|CDD|234925 PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated.
Length = 682
Score = 27.4 bits (62), Expect = 5.5
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 149 RSVGIEVVDKLDAEEYQQFLEERKIIV-AEQKKE--LEEAKEA 188
R +G + +A++Y++ L E K+I E++K LE+ +E
Sbjct: 188 RFLGPGPITIANADDYEEKLREAKVIADPEERKAIILEQIEEL 230
>gnl|CDD|216871 pfam02092, tRNA_synt_2f, Glycyl-tRNA synthetase beta subunit.
Length = 549
Score = 27.4 bits (62), Expect = 5.8
Identities = 10/43 (23%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 149 RSVGIEVVDKLDAEEYQQFLEERKIIV-AEQKKE--LEEAKEA 188
R +G + A++Y++ L + +I E++KE E+ +
Sbjct: 185 RFLGPGPITIASADDYEETLRKAGVIADFEERKELIREQIEAL 227
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 27.1 bits (60), Expect = 6.3
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 154 EVVDKLDAEEYQQFLEE---------RKIIVAEQKKELEEAKEAKMLRTSG 195
VVD++ + FLEE K I A K E AK+A+ + SG
Sbjct: 347 NVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAK--EAAKKAREEKKSG 395
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 27.0 bits (61), Expect = 6.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 37 LGPTLGERGVNIATF 51
+G LGE G+NIA
Sbjct: 469 VGTLLGEAGINIAGM 483
>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 1480
Score = 27.2 bits (60), Expect = 8.3
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 160 DAEEYQQFLEERKIIVAEQKKELEEAKE 187
D EE LEE+ +V E + EE +
Sbjct: 356 DLEELTIRLEEQNEVVEEANERQEENEA 383
>gnl|CDD|189013 cd09606, M3B_PepF_1, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 546
Score = 26.7 bits (60), Expect = 8.4
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 111 GGKLTLKHIYEIAKIKSEDSAFECETLEYICTSV 144
GG +Y+ A +K FE TLE I V
Sbjct: 515 GGSKPFPELYKAAGLK---FPFEEGTLEEIVEFV 545
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
0.314 0.133 0.372
Gapped
Lambda K H
0.267 0.0857 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,953,381
Number of extensions: 934417
Number of successful extensions: 1220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1193
Number of HSP's successfully gapped: 67
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.1 bits)