RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6291
(79 letters)
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 31.7 bits (73), Expect = 0.015
Identities = 8/34 (23%), Positives = 18/34 (52%)
Query: 3 VMKKAVRWELPRSLIKFRLMARLHIFPDQEVPED 36
++++AVR LP++ + + RL ++ P
Sbjct: 86 ILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHA 119
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five proteins
required for an early folding intermediate of 23S rRNA
in the assembly of the large subunit. L13 is situated on
the bottom of the large subunit, near the polypeptide
exit site. It interacts with proteins L3 and L6, and
forms an extensive network of interactions with 23S
rRNA. L13 has been identified as a homolog of the human
breast basic conserved protein 1 (BBC1), a protein
identified through its increased expression in breast
cancer. L13 expression is also upregulated in a variety
of human gastrointestinal cancers, suggesting it may
play a role in the etiology of a variety of human
malignancies.
Length = 114
Score = 29.4 bits (67), Expect = 0.076
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 3 VMKKAVRWELPRSLIKFRLMARLHIFPD 30
++K+AVR LP++ + + RL ++
Sbjct: 86 ILKRAVRGMLPKNKLGRAALKRLKVYEG 113
>gnl|CDD|200455 cd11316, AmyAc_bac2_AmyA, Alpha amylase catalytic domain found in
bacterial Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes Chloroflexi, Dictyoglomi, and Fusobacteria. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 403
Score = 26.8 bits (60), Expect = 1.1
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 19 FRLMARLHIFPDQEVPEDLLKNV 41
FRL A HI+ + E D +N+
Sbjct: 181 FRLDAAKHIYENGEGQADQEENI 203
>gnl|CDD|236683 PRK10410, PRK10410, hypothetical protein; Provisional.
Length = 100
Score = 26.1 bits (58), Expect = 1.3
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 4 MKKAVRWELPRSLIKFRLMARLHIF 28
MK+ +R+ PR L++ ++A H+F
Sbjct: 75 MKQVMRFSGPRMLLRHPILAIRHLF 99
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 26.4 bits (58), Expect = 1.5
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 2 LVMKKAVRWELPRSLIKFRLMARLHIFPDQEVP 34
V++KAV LPR+ ++ +L IF E P
Sbjct: 101 EVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHP 133
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 25.9 bits (57), Expect = 2.0
Identities = 14/47 (29%), Positives = 20/47 (42%)
Query: 29 PDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKD 75
P +EV + L+ I+ L LA + K EFP D+ D
Sbjct: 217 PTEEVVAEGLEAAKPFIKVLCRAQADLAEKAAKPTGEFPLFPDYQDD 263
>gnl|CDD|215083 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 25.3 bits (56), Expect = 3.7
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 16/38 (42%)
Query: 7 AVRWELPRSLIK---------------FRLMARLHIFP 29
A RW L R+LI+ FRL ++P
Sbjct: 542 ATRW-LDRALIRLCSKFGDYRKDDPSSFRLSPNFSLYP 578
>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein. Rotavirus particles
consist of three concentric proteinaceous capsid layers.
The innermost capsid (core) is made of VP2. The genomic
RNA and the two minor proteins VP1 and VP3 are
encapsidated within this layer. The N-terminus of
rotavirus VP2 is necessary for the encapsidation of VP1
and VP3.
Length = 887
Score = 25.3 bits (55), Expect = 3.8
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 20 RLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPR 53
+ RLHIF +VP+D + + ++R L PV R
Sbjct: 651 DFLKRLHIFDVAKVPDDQMYRLRDRLRLL-PVER 683
>gnl|CDD|239008 cd02053, alpha2AP, Alpha2-antiplasmin (alpha2AP) is the primary
inhibitor of plasmin, a proteinase that digests fibrin,
the main component of blood clots. Alpha2-Antiplasmin
forms an inactive 1 : 1 stoichiometric complex with
plasmin. It also rapidly crosslinks to fibrin during
blood clotting by activated coagulation factor XIII, and
as a consequence fibrin becomes more resistant to
fibrinolysis. Therefore alpha2AP is important in
modulating the effectiveness and persistence of fibrin
with respect to its susceptibility to digestion and
removal by plasmin. This subgroup corresponds to clade
F2 of the serpin superfamily.
Length = 351
Score = 25.1 bits (55), Expect = 4.7
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 19 FRLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKD 75
RL R+++ E+ E L+ S ++ +PV L + ++ IN + K+
Sbjct: 79 LRLATRMYLQKGFEIKESFLEE-SEKLYGAKPVS--LTGTKEDDLAN---INKWVKE 129
>gnl|CDD|178322 PLN02720, PLN02720, complex II.
Length = 140
Score = 24.8 bits (54), Expect = 4.8
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 38 LKNVSSQIRQLRPVPRTLASYSDKEVDEF 66
L+N + ++ +P+P +SD +VDEF
Sbjct: 24 LENYARFSKRDKPLP----PWSDSDVDEF 48
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 25.1 bits (54), Expect = 4.8
Identities = 15/29 (51%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 21 LMARLH-IFPDQEVPEDLLKNVSSQIRQL 48
L++ LH I Q VPE L++N S Q+RQL
Sbjct: 285 LLSLLHQIAIIQTVPEALIENDSEQLRQL 313
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 24.8 bits (55), Expect = 5.4
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 33 VPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKIN 70
+ L V +I++L+ + + ++E +IN
Sbjct: 331 PWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEIN 368
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 24.6 bits (54), Expect = 5.9
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 34 PEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKDY 76
++K +IR+++ + DK V+ FP ++D Y
Sbjct: 37 GPKIVKAREFEIRRVKTASNIVRDRLDKIVERFPSLDDLHPFY 79
>gnl|CDD|165890 PLN02247, PLN02247, indole-3-acetic acid-amido synthetase.
Length = 606
Score = 24.9 bits (54), Expect = 6.0
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 18 KFRLMAR----LHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFP 73
+FR + R L I D+ EDLLK V+ L P+ L Y+ + + P
Sbjct: 434 QFRFVQRRNVVLSIDTDKTNEEDLLKAVTQAKLLLEPLGFLLTEYT-----SYADTSSIP 488
Query: 74 KDYIL 78
Y+L
Sbjct: 489 GHYVL 493
>gnl|CDD|218576 pfam05395, DARPP-32, Protein phosphatase inhibitor 1/DARPP-32.
This family consists of several mammalian protein
phosphatase inhibitor 1 (IPP-1) and dopamine- and
cAMP-regulated neuronal phosphoprotein (DARPP-32)
proteins. Protein phosphatase inhibitor-1 is involved
in signal transduction and is an endogenous inhibitor
of protein phosphatase-1. It has been demonstrated that
DARPP-32, if phosphorylated, can inhibit
protein-phosphatase-1. DARPP-32 has a key role in many
neurotransmitter pathways throughout the brain and has
been shown to be involved in controlling receptors, ion
channels and other physiological factors including the
brain's response to drugs of abuse, such as cocaine,
opiates and nicotine. DARPP-32 is reciprocally
regulated by the two neurotransmitters that are most
often implicated in schizophrenia - dopamine and
glutamate. Dopamine activates DARPP-32 through the D1
receptor pathway and disables DARPP-32 through the D2
receptor. Glutamate, acting through the
N-methyl-d-aspartate receptor, renders DARPP-32
inactive. A mutant form of DARPP-32 has been linked
with gastric cancers.
Length = 170
Score = 24.5 bits (53), Expect = 6.3
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 44 QIRQLRPVPRTLASYSDK---EVDE 65
IR+ RP P TL S++ E+DE
Sbjct: 27 MIRRRRPTPATLVLVSEQSSPEIDE 51
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type. This
model distinguishes ribosomal protein L13 of bacteria
and organelles from its eukarytotic and archaeal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 140
Score = 24.2 bits (53), Expect = 6.8
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 3 VMKKAVRWELPRSLIKFRLMARLHIFPDQEVP 34
V++ AV+ LP++ + +L +L ++ E P
Sbjct: 98 VLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHP 129
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 24.6 bits (53), Expect = 6.8
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 48 LRPVPRTLASYSDKEVDEFPKIN 70
LR +P TL S KE DE K+N
Sbjct: 170 LRTLPFTLEDASRKESDEGAKVN 192
>gnl|CDD|218856 pfam06022, Cir_Bir_Yir, Plasmodium variant antigen protein
Cir/Yir/Bir. This family consists of several Cir, Yir
and Bir proteins from the Plasmodium species P.chabaudi,
P.yoelii and P.berghei.
Length = 279
Score = 24.5 bits (54), Expect = 8.0
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 57 SY--SDKEVDEFPKINDFPKDYI 77
SY + K + +NDF YI
Sbjct: 87 SYKLNLKSENGITNLNDFYTKYI 109
>gnl|CDD|225614 COG3072, CyaA, Adenylate cyclase [Nucleotide transport and
metabolism].
Length = 853
Score = 24.4 bits (53), Expect = 8.2
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 24 RLHIFPDQEVPEDLLKNVSSQIRQLRPVP 52
RLHI + V L+ + + +RQ P+
Sbjct: 510 RLHIKSNGNVDLPKLQEMVTDLRQHFPLR 538
>gnl|CDD|172935 PRK14460, PRK14460, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 354
Score = 24.3 bits (53), Expect = 8.5
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 6/27 (22%)
Query: 3 VMKKAVRWELPRSLIKFRLMARLHIFP 29
+M KA RW L L+A L +P
Sbjct: 231 IMPKAARWPLD------DLIAALKSYP 251
>gnl|CDD|214384 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 24.1 bits (53), Expect = 8.7
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 30 DQEVPEDLLKNVSSQIRQL 48
D VP +LLK V S++ QL
Sbjct: 274 DLIVPRNLLKGVLSELFQL 292
>gnl|CDD|221209 pfam11756, YgbA_NO, Nitrous oxide-stimulated promoter. The
function of ygaB is not known but it is a promoter that
is stimulated by the presence of nitrous oxide. It is
regulated by the gene-product of the bacterial nsrR
gene.
Length = 111
Score = 23.8 bits (52), Expect = 8.8
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 4 MKKAVRWELPRSLIKFRLMARLHIFPDQ-EVPEDLLKNVS 42
M+ +RW PR L++ ++A H+ ++ VPE K S
Sbjct: 72 MRTIMRWSGPRMLLRHPILAIRHLLDERRPVPELPPKEAS 111
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 24.1 bits (53), Expect = 9.8
Identities = 9/40 (22%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 11 ELPRSLIKFRLMARLHI-FPDQEVPEDLLKNVSSQIRQLR 49
EL +L++ +I FP++++ E +L+ + ++ +L
Sbjct: 159 ELREALLELLAQVEANIDFPEEDIEELVLEKIREKLEELI 198
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
0.323 0.140 0.408
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,191,535
Number of extensions: 331492
Number of successful extensions: 364
Number of sequences better than 10.0: 1
Number of HSP's gapped: 364
Number of HSP's successfully gapped: 30
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)