RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6264
(120 letters)
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 73.7 bits (182), Expect = 4e-18
Identities = 23/76 (30%), Positives = 39/76 (51%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ I L G + ++ Y+ HTGYPGG+ A E P ++++AVR LP++ +
Sbjct: 44 NAEKIVLTGKKRDQKKYYRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRA 103
Query: 62 LMARLHIFPDQEVPED 77
+ RL ++ P
Sbjct: 104 ALKRLKVYAGSPHPHA 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 = 71.4 bits (176), Expect = 2e-17
Identities = 24/70 (34%), Positives = 41/70 (58%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ I + G +W+++ Y+ HTGYPGG+ A LH P ++K+AVR LP++ +
Sbjct: 44 NAEKIVITGKKWRQKVYYRHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNKLGRA 103
Query: 62 LMARLHIFPD 71
+ RL ++
Sbjct: 104 ALKRLKVYEG 113
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 48.5 bits (117), Expect = 3e-08
Identities = 21/74 (28%), Positives = 39/74 (52%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ + L G + + Y+ H+GYPGG+ +L P V++KAV+ LP++ +
Sbjct: 58 NAEKVKLTGKKLTDKIYYRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRA 117
Query: 62 LMARLHIFPDQEVP 75
+ +L ++ E P
Sbjct: 118 MFKKLKVYAGAEHP 131
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 49.1 bits (117), Expect = 3e-08
Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 6/102 (5%)
Query: 1 MNSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKF 60
+N++ I++ G + + Y HTGY G + DPT V++KAV LPR+ ++
Sbjct: 59 LNAKDISVTGRKLTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRD 118
Query: 61 RLMARLHIFPDQEVPEDLLKNVS-----SQIRQLRP-VPRTL 96
+L IF E P Q+R++RP R +
Sbjct: 119 DRDRKLRIFAGSEHPFGDKPLEPFVMPPRQVREMRPRARRAM 160
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 47.7 bits (114), Expect = 5e-08
Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ I + G + ++ Y H+G PGG+ +L P +++KAV+ LP+ + +
Sbjct: 59 NAEKIKVTGNKTSQKFYVRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRK 118
Query: 62 LMARLHIFPDQEVP 75
L +L ++ + P
Sbjct: 119 LFTKLKVYKGESHP 132
>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 = 47.7 bits (114), Expect = 5e-08
Identities = 20/74 (27%), Positives = 41/74 (55%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ + L G + +++ Y+ H+GYPGG+ ++ P V++ AV+ LP++ + +
Sbjct: 56 NAEKVRLTGKKLEQKVYYRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRK 115
Query: 62 LMARLHIFPDQEVP 75
L +L ++ E P
Sbjct: 116 LFKKLKVYAGSEHP 129
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 38.8 bits (91), Expect = 1e-04
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 2 NSRHIALPGYEWKKRA---YFHHTGYPGGV-SWTLAWQLHEIDPTLVMKKAVRWELPRSL 57
N+ + + G KK Y+ H+GYPGG+ + T L P ++++AVR LP++
Sbjct: 58 NAEKVVITG---KKLTDKKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNP 114
Query: 58 IKFRLMARLHIF 69
+ + RL ++
Sbjct: 115 LGRAALKRLKVY 126
>gnl|CDD|223348 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 29.7 bits (67), Expect = 0.31
Identities = 24/102 (23%), Positives = 35/102 (34%), Gaps = 10/102 (9%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLV---MKKAVRWELPRSLI 58
++ LP W + G L + PT+ ++ + R L
Sbjct: 220 KNKGERLPSLRWGEALTLSRRYKGKGSYIRLHP--DKPAPTVRGGGNERFIHPLEDREL- 276
Query: 59 KFRLMARLHIFPDQEVPEDLLKNVSSQIRQL-RPVPRTLASY 99
R ARL FPD V + + Q RQ+ VP LA
Sbjct: 277 TVREAARLQGFPDDFV---FPGSKTDQYRQIGNSVPPLLAEA 315
>gnl|CDD|182849 PRK10933, PRK10933, trehalose-6-phosphate hydrolase; Provisional.
Length = 551
Score = 28.6 bits (64), Expect = 0.83
Identities = 15/32 (46%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 4 RHIALPGYEWKKRAYFHH--TGYPGGVSWTLA 33
R+ AL G E FHH YP G WTLA
Sbjct: 262 RYAALTGSELSMTFNFHHLKVDYPNGEKWTLA 293
>gnl|CDD|131451 TIGR02398, gluc_glyc_Psyn, glucosylglycerol-phosphate synthase.
Glucosylglycerol-phosphate synthase catalyzes the key
step in the biosynthesis of the osmolyte
glucosylglycerol. It is known in several cyanobacteria
and in Pseudomonas anguilliseptica. The enzyme is
closely related to the alpha,alpha-trehalose-phosphate
synthase, likewise involved in osmolyte biosynthesis, of
E. coli and many other bacteria. A close homolog from
Xanthomonas campestris is excluded from this model and
scores between trusted and noise.
Length = 487
Score = 27.9 bits (62), Expect = 1.5
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 9 PGYEWKKR-----AYFHHTGYPGG-VSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFRL 62
PGY + R A+FHHT +P V L W+ I +L+ + + +PR + F
Sbjct: 147 PGYIRQLRPDLKIAFFHHTPFPSADVFNILPWREQIIG-SLLCCDYIGFHIPRYVENFVD 205
Query: 63 MAR 65
AR
Sbjct: 206 AAR 208
>gnl|CDD|203124 pfam04928, PAP_central, Poly(A) polymerase central domain. The
central domain of Poly(A) polymerase shares structural
similarity with the allosteric activity domain of
ribonucleotide reductase R1, which comprises a
four-helix bundle and a three-stranded mixed beta-
sheet. Even though the two enzymes bind ATP, the
ATP-recognition motifs are different.
Length = 349
Score = 27.2 bits (61), Expect = 2.2
Identities = 9/20 (45%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 13 W-KKRA-YFHHTGYPGGVSW 30
W K+R Y + G+ GGV+W
Sbjct: 214 WAKRRGIYSNVLGFLGGVAW 233
>gnl|CDD|236683 PRK10410, PRK10410, hypothetical protein; Provisional.
Length = 100
Score = 26.4 bits (59), Expect = 2.4
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 45 MKKAVRWELPRSLIKFRLMARLHIF 69
MK+ +R+ PR L++ ++A H+F
Sbjct: 75 MKQVMRFSGPRMLLRHPILAIRHLF 99
>gnl|CDD|119375 cd06413, GH25_muramidase_1, Uncharacterized bacterial muramidase
containing a glycosyl hydrolase family 25 (GH25)
catalytic domain. Endo-N-acetylmuramidases are
lysozymes (also referred to as peptidoglycan hydrolases)
that degrade bacterial cell walls by catalyzing the
hydrolysis of 1,4-beta-linkages between N-acetylmuramic
acid and N-acetyl-D-glucosamine residues.
Length = 191
Score = 26.9 bits (60), Expect = 2.8
Identities = 8/33 (24%), Positives = 9/33 (27%), Gaps = 1/33 (3%)
Query: 7 ALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEI 39
P Y R+ H WT WQ
Sbjct: 143 EFPDYPLWIRSVAGHPRLYEDRPWTF-WQYTNR 174
>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 = 26.8 bits (59), Expect = 3.4
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 61 RLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPR 94
+ RLHIF +VP+D + + ++R L PV R
Sbjct: 651 DFLKRLHIFDVAKVPDDQMYRLRDRLRLL-PVER 683
>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 = 26.7 bits (59), Expect = 3.5
Identities = 14/47 (29%), Positives = 20/47 (42%)
Query: 70 PDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKD 116
P +EV + L+ I+ L LA + K EFP D+ D
Sbjct: 217 PTEEVVAEGLEAAKPFIKVLCRAQADLAEKAAKPTGEFPLFPDYQDD 263
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 26.1 bits (58), Expect = 5.1
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 75 PEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKDY 117
++K +IR+++ + DK V+ FP ++D Y
Sbjct: 37 GPKIVKAREFEIRRVKTASNIVRDRLDKIVERFPSLDDLHPFY 79
>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 = 26.0 bits (58), Expect = 5.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 60 FRLMARLHIFPDQEVPEDLLKNV 82
FRL A HI+ + E D +N+
Sbjct: 181 FRLDAAKHIYENGEGQADQEENI 203
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 25.9 bits (58), Expect = 5.6
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 74 VPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKIN 111
+ L V +I++L+ + + ++E +IN
Sbjct: 331 PWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEIN 368
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 26.2 bits (57), Expect = 5.7
Identities = 15/29 (51%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 62 LMARLH-IFPDQEVPEDLLKNVSSQIRQL 89
L++ LH I Q VPE L++N S Q+RQL
Sbjct: 285 LLSLLHQIAIIQTVPEALIENDSEQLRQL 313
>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 = 25.9 bits (57), Expect = 6.2
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 60 FRLMARLHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFPKD 116
RL R+++ E+ E L+ S ++ +PV L + ++ IN + K+
Sbjct: 79 LRLATRMYLQKGFEIKESFLEE-SEKLYGAKPVS--LTGTKEDDLAN---INKWVKE 129
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 25.8 bits (56), Expect = 7.4
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 27 GVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDLLKNVSSQI 86
G+ L Q H I ++K +++ + +I L+AR FP +E ED ++ + I
Sbjct: 493 GLMRMLTVQPHLITDKGYLEKTIKYAIDCGVIDQWLLARTRGFPPKEDMEDEVEPDPNGI 552
Query: 87 RQLRPVP-RTLASYSDKE 103
R + RTL YS+ E
Sbjct: 553 RSITEKEYRTLEPYSEPE 570
>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 = 25.2 bits (55), Expect = 7.5
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 85 QIRQLRPVPRTLASYSDK---EVDE 106
IR+ RP P TL S++ E+DE
Sbjct: 27 MIRRRRPTPATLVLVSEQSSPEIDE 51
>gnl|CDD|215083 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 25.7 bits (57), Expect = 7.9
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 16/38 (42%)
Query: 48 AVRWELPRSLIK---------------FRLMARLHIFP 70
A RW L R+LI+ FRL ++P
Sbjct: 542 ATRW-LDRALIRLCSKFGDYRKDDPSSFRLSPNFSLYP 578
>gnl|CDD|227513 COG5186, PAP1, Poly(A) polymerase [RNA processing and
modification].
Length = 552
Score = 25.7 bits (56), Expect = 8.0
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 5 HIALPGYE-WKKR--AYFHHTGYPGGVSWTL 32
H AL + W +R Y + G+PGGV+W +
Sbjct: 208 HSALRAIKYWAQRRAVYANPYGFPGGVAWAM 238
>gnl|CDD|165890 PLN02247, PLN02247, indole-3-acetic acid-amido synthetase.
Length = 606
Score = 25.7 bits (56), Expect = 8.6
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 59 KFRLMAR----LHIFPDQEVPEDLLKNVSSQIRQLRPVPRTLASYSDKEVDEFPKINDFP 114
+FR + R L I D+ EDLLK V+ L P+ L Y+ + + P
Sbjct: 434 QFRFVQRRNVVLSIDTDKTNEEDLLKAVTQAKLLLEPLGFLLTEYT-----SYADTSSIP 488
Query: 115 KDYIL 119
Y+L
Sbjct: 489 GHYVL 493
>gnl|CDD|235868 PRK06826, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1151
Score = 25.6 bits (57), Expect = 8.7
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 12/89 (13%)
Query: 39 IDPTLVMKKAVRWELPRSLIKFRLMARLHIFPDQ--EVPEDLLKNVSSQIRQLRPVPRTL 96
+D + + K+AV SLIK L ++ Q V E +L ++S Q ++ +L
Sbjct: 860 VDTSQINKRAVE-----SLIKAGAFDSLGVYRSQLLAVYEKILDSISKQRKKNIEGQISL 914
Query: 97 ---ASYSDKEVDE--FPKINDFPKDYILK 120
++ E +P I +F K +L
Sbjct: 915 FDLIGEEEESSLEIKYPDIKEFDKKELLA 943
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
0.322 0.138 0.443
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: 6,596,817
Number of extensions: 577424
Number of successful extensions: 505
Number of sequences better than 10.0: 1
Number of HSP's gapped: 504
Number of HSP's successfully gapped: 39
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)