RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8561
(205 letters)
>gnl|CDD|235534 PRK05618, PRK05618, 50S ribosomal protein L25/general stress
protein Ctc; Reviewed.
Length = 197
Score = 210 bits (536), Expect = 2e-69
Identities = 74/185 (40%), Positives = 121/185 (65%), Gaps = 3/185 (1%)
Query: 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
+ + A R++ G +R LR+ GKVP +IYG K+PV IS++ + ALKK F S++L
Sbjct: 4 ITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGAFLSTLL 63
Query: 61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
+LE+ GK + VL+++ Q H K +LH DF RVD +K+ V+VP+HF+ VKL
Sbjct: 64 DLEVGGKKQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLG- 122
Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
+++ V+ +L + CLP+++P+FIE+++ +E+ SIH+SD+KLP GV ++ + D +A
Sbjct: 123 GVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHVSDLKLPEGVKLL--DDPDEVVA 180
Query: 181 TAIIP 185
T + P
Sbjct: 181 TVVAP 185
>gnl|CDD|233106 TIGR00731, ctc_TL5, ribosomal protein L25, Ctc-form. This model
models a family of proteins with full-length homology to
the general stress protein Ctc of Bacillus subtilis, a
mesophile, and ribosomal protein TL5 of Thermus
thermophilus, a thermophile. Ribosomal protein L25 of
Escherichia coli and H. influenzae appear to be
orthologous but consist only of the N-terminal half of
Ctc and TL5. Both short (L25-like) and full-length
(CTC-like) members of this family bind the E-loop of
bacterial 5S rRNA. This protein appears to be restricted
to bacteria and organelles, and consists of at most one
copy per prokaryotic genome.Ctc of Bacillus subtilis has
now been localized to ribosomes and can be viewed as the
long form, or Ctc form, of L25. The C-terminal domain of
sll1824, an apparent L25 of Synechocystis PCC6803,
matches the N-terminal domain of this family. Examples
of L25 and Ctc are not separated by a UPGMA tree built
on the region of shared homology [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 176
Score = 119 bits (301), Expect = 2e-34
Identities = 58/169 (34%), Positives = 95/169 (56%), Gaps = 4/169 (2%)
Query: 7 ERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYG 66
R G S +R +RK G++P ++YG K+ V + + L+K S++L LEI G
Sbjct: 5 SRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRKGA-TSTVLTLEIGG 63
Query: 67 KVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNV 126
K VL++++Q + V+H DF V K+ V+VP+ I + I VK N I++ V
Sbjct: 64 KEFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGTPI--GVK-NGGILTQV 120
Query: 127 ISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEE 175
+ + C PK++P F+E+++ + V S+ LSD++LP GVS I +E
Sbjct: 121 KRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELPAGVSFITDDDE 169
>gnl|CDD|198379 cd00495, Ribosomal_L25_TL5_CTC, Ribosomal L25/TL5/CTC N-terminal
5S rRNA binding domain. L25 is a single-domain
protein, homologous to the N-terminal domain of TL5 and
CTC. CTC is a known stress protein, and proteins of
this family are believed to have two functions, acting
as both ribosomal and stress proteins. In Escherichia
coli, cells deleted for L25 were found to be viable;
however, these cells grew slowly and had impaired
protein synthesis capability. In Bacillus subtilis, CTC
is induced under stress conditions and located in the
ribosome; it has been proposed that CTC may be
necessary for accurate translation under stress
conditions. Ribosomal_L25_TL5_CTC is mostly found in
bacteria, with a few exceptions such as plants or
stramenopiles. Due to its limited taxonomic diversity
and the viability of cells deleted for L25, this
protein is not believed to be necessary for ribosomal
assembly. Eukaryotes contain a protein called L25,
which is not homologous to bacterial L25, but rather to
bacterial L23.
Length = 90
Score = 99.5 bits (249), Expect = 2e-27
Identities = 35/91 (38%), Positives = 57/91 (62%), Gaps = 1/91 (1%)
Query: 2 KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
+ A +R++ G +R LR+ GKVP +IYG ++P+ IS++ + L+KE ++++
Sbjct: 1 TLKAEKREETGKGAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLLRKEGE-NTVIE 59
Query: 62 LEIYGKVELVLLRNFQLHAYKKLVLHADFQR 92
LEI GK E VL+++ Q H K +LH DF R
Sbjct: 60 LEIDGKKENVLIKDVQRHPVKDEILHVDFLR 90
>gnl|CDD|216471 pfam01386, Ribosomal_L25p, Ribosomal L25p family. Ribosomal
protein L25 is an RNA binding protein, that binds 5S
rRNA. This family includes Ctc from B. subtilis, which
is induced by stress.
Length = 87
Score = 94.1 bits (235), Expect = 2e-25
Identities = 35/88 (39%), Positives = 55/88 (62%), Gaps = 1/88 (1%)
Query: 3 IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNL 62
+ A +R++ G SR LR+ GKVP +IYG K+PV IS++ + L +E ++++ L
Sbjct: 1 LKAEKREETGKGASRRLRREGKVPAVIYGKGKEPVSISVDEKELEKLL-REAGENTVIEL 59
Query: 63 EIYGKVELVLLRNFQLHAYKKLVLHADF 90
+I GK E VL+++ Q H K +LH DF
Sbjct: 60 KIDGKKENVLIKDVQRHPVKDKILHVDF 87
>gnl|CDD|224738 COG1825, RplY, Ribosomal protein L25 (general stress protein Ctc)
[Translation, ribosomal structure and biogenesis].
Length = 93
Score = 91.2 bits (227), Expect = 3e-24
Identities = 36/93 (38%), Positives = 57/93 (61%), Gaps = 1/93 (1%)
Query: 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
++ A R +G SR LR+ GK+P ++YGG K+PV I+++H+ AL+K +S+++
Sbjct: 2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGGGKEPVNIALDHHEFAKALRKLG-YSTVI 60
Query: 61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRV 93
LE+ GK VL+++ Q H V H DF RV
Sbjct: 61 TLEVDGKEIKVLVKDVQRHPLTDEVQHIDFLRV 93
>gnl|CDD|180318 PRK05943, PRK05943, 50S ribosomal protein L25; Reviewed.
Length = 94
Score = 90.3 bits (225), Expect = 6e-24
Identities = 35/93 (37%), Positives = 50/93 (53%)
Query: 1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
I A R ++G SR LR+ GK P IIYGGN+ PV I ++H + + K F+ ++
Sbjct: 2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYKEVI 61
Query: 61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRV 93
L I GK V ++ Q H +K + H DF R
Sbjct: 62 TLVIDGKEVKVKVQAVQRHPFKPKLEHIDFVRA 94
>gnl|CDD|241542 cd13391, PH_PRG, PDZ Rho guanine nucleotide exchange factor
Pleckstrin homology (PH) domain. PRG (also called
RhoGEF11) belongs to regulator of G-protein signaling
(RGS) domain-containing RhoGEFs that are RhoA-selective
and directly activated by the Galpha12/13 family of
heterotrimeric G proteins. RhoGEFs activate Rho GTPases
regulating cytoskeletal structure, gene transcription,
and cell migration. PRG contains an N-terminal PDZ
domain, a regulators of G-protein signaling-like (RGSL)
domain, a linker region, and a C-terminal Dbl-homology
(DH) and pleckstrin-homology (PH) domains which bind and
catalyze the exchange of GDP for GTP on RhoA. As is the
case in p115-RhoGEF, it is thought that the PRG
activated by relieving autoinhibition caused by the
linker region. 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 = 142
Score = 28.1 bits (62), Expect = 2.2
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 98 KIHVKVPLHFINSE--ISPAVKLNSCIISNVISD---LYISCLPKNLPKFIE-INLEKME 151
K H K + +S+ SP +KLNS +I +V +D +I C K P+ E + L E
Sbjct: 68 KCHSKTAVGSSDSKQTFSPVLKLNSVLIRSVATDKRAFFIICTSKLGPQIYELVALTSSE 127
Query: 152 VNTSIHL 158
NT + L
Sbjct: 128 KNTWMEL 134
>gnl|CDD|220467 pfam09911, DUF2140, Uncharacterized protein conserved in bacteria
(DUF2140). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 187
Score = 27.5 bits (62), Expect = 3.8
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 138 NLPKFIEINLEKMEVNTSIHLSDIKLPRGVSV 169
LP+++ IN +K + + LS+IKL G+ V
Sbjct: 139 KLPEWVTINPKKKTIY--LRLSEIKLKNGLYV 168
>gnl|CDD|185268 PRK15370, PRK15370, E3 ubiquitin-protein ligase SlrP; Provisional.
Length = 754
Score = 27.7 bits (61), Expect = 4.5
Identities = 26/91 (28%), Positives = 40/91 (43%), Gaps = 7/91 (7%)
Query: 108 INSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEV-NTSIHLSDIKLPRG 166
IN +L S + S + ISCLP+NLP+ L + V + SI LP G
Sbjct: 250 INRITELPERLPSALQSLDLFHNKISCLPENLPE----ELRYLSVYDNSIRTLPAHLPSG 305
Query: 167 VSVIHSTEEDPTIATAIIPVN--TLESDNNS 195
++ ++ T +P TLE+ N+
Sbjct: 306 ITHLNVQSNSLTALPETLPPGLKTLEAGENA 336
>gnl|CDD|225541 COG2994, HlyC, ACP:hemolysin acyltransferase (hemolysin-activating
protein) [Posttranslational modification, protein
turnover, chaperones].
Length = 148
Score = 26.2 bits (58), Expect = 7.9
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 99 IHVKVPLHFINSEISPAVKLNSCII 123
H P+ I+ I PA+KL +
Sbjct: 32 DHRHYPVAEISRNILPALKLGQFAL 56
>gnl|CDD|234910 PRK01158, PRK01158, phosphoglycolate phosphatase; Provisional.
Length = 230
Score = 26.5 bits (59), Expect = 9.6
Identities = 23/86 (26%), Positives = 33/86 (38%), Gaps = 8/86 (9%)
Query: 27 GIIYGGNKDPVKI--SMNHNMI-YHALKK---ETFHSSILNLEIYGKVELVLLRNFQLHA 80
G+I G + Y LKK E S Y K E+ L R +
Sbjct: 69 GVISVGFDGKRIFLGDIEECEKAYSELKKRFPEASTSLTKLDPDYRKTEVALRRTVPVEE 128
Query: 81 YKKLV--LHADFQRVDTEKKIHVKVP 104
++L+ L D + VD+ IH+K P
Sbjct: 129 VRELLEELGLDLEIVDSGFAIHIKSP 154
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
0.317 0.134 0.374
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,175,146
Number of extensions: 939125
Number of successful extensions: 640
Number of sequences better than 10.0: 1
Number of HSP's gapped: 633
Number of HSP's successfully gapped: 26
Length of query: 205
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 113
Effective length of database: 6,857,034
Effective search space: 774844842
Effective search space used: 774844842
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 (21.6 bits)
S2: 57 (25.8 bits)