RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6080
(240 letters)
>gnl|CDD|238714 cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an
essential protein in the large ribosomal subunit of
bacteria, mitochondria, and chloroplasts. Large subunits
that lack L16 are defective in peptidyl transferase
activity, peptidyl-tRNA hydrolysis activity, association
with the 30S subunit, binding of aminoacyl-tRNA and
interaction with antibiotics. L16 is required for the
function of elongation factor P (EF-P), a protein
involved in peptide bond synthesis through the
stimulation of peptidyl transferase activity by the
ribosome. Mutations in L16 and the adjoining bases of
23S rRNA confer antibiotic resistance in bacteria,
suggesting a role for L16 in the formation of the
antibiotic binding site. The GTPase RbgA (YlqF) is
essential for the assembly of the large subunit, and it
is believed to regulate the incorporation of L16. L10e
is the archaeal and eukaryotic cytosolic homolog of
bacterial L16. L16 and L10e exhibit structural
differences at the N-terminus.
Length = 112
Score = 120 bits (304), Expect = 4e-35
Identities = 46/108 (42%), Positives = 56/108 (51%), Gaps = 1/108 (0%)
Query: 76 NYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDVKKMFAVWRVDPPWLPVTKKGLGSR 135
N L +YGLVAL GR+ E R A+ R L KK +W P PVTKK L +R
Sbjct: 3 NKLFFGEYGLVALEPGRITAEQLEAARIAINRYL-KKKGGKLWIRVFPDHPVTKKPLETR 61
Query: 136 MGGGKGSIDHYVTPVKTGRIIIEVGGKCSYEEVLPYLRSCASKMPFKC 183
MG GKG + +V VK G+I+ EV G E LR A K+P K
Sbjct: 62 MGKGKGKPEGWVARVKPGQILFEVRGVPEEEVAKEALRRAAKKLPIKT 109
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 118 bits (299), Expect = 5e-34
Identities = 49/124 (39%), Positives = 62/124 (50%), Gaps = 3/124 (2%)
Query: 60 RTTKRLDLLRGPEEIHNYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDVKKMFAVWR 119
R ++ L G N L YGL AL GR+ R E R A+ R L K+ +W
Sbjct: 7 RKYQKGRLEYGGAVPGNKLAFGDYGLKALEPGRITARQIEAARIAINRYL--KRGGKLWI 64
Query: 120 VDPPWLPVTKKGLGSRMGGGKGSIDHYVTPVKTGRIIIEVGGKCSYEEVLPYLRSCASKM 179
P PVTKK +RMG GKG + +V VK G+I+ E+GG S E LR ASK+
Sbjct: 65 RVFPDKPVTKKPAETRMGKGKGKPEGWVARVKPGQILFEIGG-VSEEVAKEALRRAASKL 123
Query: 180 PFKC 183
P K
Sbjct: 124 PIKT 127
>gnl|CDD|236411 PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
Length = 138
Score = 86.7 bits (216), Expect = 1e-21
Identities = 45/109 (41%), Positives = 59/109 (54%), Gaps = 5/109 (4%)
Query: 76 NYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDVKKMFAVW-RVDPPWLPVTKKGLGS 134
N + ++GL AL G + R E R AM R +K+ VW R+ P PVTKK
Sbjct: 25 NTVAFGEFGLKALEPGWITARQIEAARIAMTRH--IKRGGKVWIRIFPD-KPVTKKPAEV 81
Query: 135 RMGGGKGSIDHYVTPVKTGRIIIEVGGKCSYEEVLPYLRSCASKMPFKC 183
RMG GKGS +++V VK GRI+ E+ G S E LR A+K+P K
Sbjct: 82 RMGKGKGSPEYWVAVVKPGRILFEIAG-VSEELAREALRLAAAKLPIKT 129
>gnl|CDD|211627 TIGR01164, rplP_bact, ribosomal protein L16, bacterial/organelle.
This model describes bacterial and organellar ribosomal
protein L16. The homologous protein of the eukaryotic
cytosol is designated L10 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 126
Score = 76.6 bits (189), Expect = 6e-18
Identities = 42/113 (37%), Positives = 59/113 (52%), Gaps = 3/113 (2%)
Query: 68 LRGPEEIHNYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDVKKMFAVWRVDPPWLPV 127
++G + N + +YGL AL G + R E R AM R VK+ +W P P
Sbjct: 16 MKGKAKRGNTVAFGEYGLQALEPGWITARQIEAARVAMTRY--VKRGGKLWIRIFPDKPY 73
Query: 128 TKKGLGSRMGGGKGSIDHYVTPVKTGRIIIEVGGKCSYEEVLPYLRSCASKMP 180
TKK L +RMG GKG+ +++V VK G+I+ E+ G E R ASK+P
Sbjct: 74 TKKPLETRMGKGKGNPEYWVAVVKPGKILFEIAG-VPEEVAREAFRLAASKLP 125
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 74.9 bits (185), Expect = 4e-17
Identities = 44/150 (29%), Positives = 64/150 (42%), Gaps = 18/150 (12%)
Query: 34 HIVMPERPRLKFVDKVPTFIYNHKTPRTTKRLDLLRGPEEIHNYLIHKQYGLVALSGGRM 93
H++ P+R + + K G N + +YGLVAL G++
Sbjct: 1 HMLQPKRTKYRKQHKGRG----------PGITIAKGG-----NKVFFGEYGLVALEPGQI 45
Query: 94 NYRHFETIRFAMMRKLDVKKMFAVWRVDPPWLPVTKKGLGSRMGGGKGSIDHYVTPVKTG 153
R E R A R L K+ +W P P+T+K RMG GKG + + VK G
Sbjct: 46 TARQIEAARIAANRYL--KRGGGLWIRVFPDKPLTEKPGEDRMGKGKGKPEGWAARVKPG 103
Query: 154 RIIIEVGGKCSYEEVLPYLRSCASKMPFKC 183
R++ E+ G E LR A+K+P K
Sbjct: 104 RVLFEIAGV-PEELAREALRRAAAKLPVKT 132
>gnl|CDD|176985 CHL00044, rpl16, ribosomal protein L16.
Length = 135
Score = 56.4 bits (137), Expect = 2e-10
Identities = 38/109 (34%), Positives = 55/109 (50%), Gaps = 5/109 (4%)
Query: 76 NYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDVKKMFAVW-RVDPPWLPVTKKGLGS 134
N + +Y L AL + R E R A+ R ++ +W R+ P PVT + +
Sbjct: 25 NRICFGRYALQALEPAWITSRQIEAGRRAITRY--ARRGGKIWIRIFPD-KPVTMRPAET 81
Query: 135 RMGGGKGSIDHYVTPVKTGRIIIEVGGKCSYEEVLPYLRSCASKMPFKC 183
RMG GKGS +++V VK GRI+ E+GG S ++ A KMP K
Sbjct: 82 RMGSGKGSPEYWVAVVKPGRILYEMGG-VSETIARAAIKIAAYKMPIKT 129
>gnl|CDD|167014 PRK00624, PRK00624, glycine cleavage system protein H; Provisional.
Length = 114
Score = 29.8 bits (67), Expect = 0.54
Identities = 20/61 (32%), Positives = 26/61 (42%), Gaps = 9/61 (14%)
Query: 117 VWRVDPPWLPVTKKGLGSRMGGGKGSIDHYVTPVKTGRIIIEVGGKCSYEEVLPYLRSCA 176
VW ++P + + GL S+M G+I H P VG C EVL L S
Sbjct: 9 VW-IEPIHSRIVRLGLTSKMQENLGNILHIDLP--------SVGSFCKEGEVLVILESSK 59
Query: 177 S 177
S
Sbjct: 60 S 60
>gnl|CDD|233860 TIGR02421, QEGLA, conserved hypothetical protein. Members of this
family include a possible metal-binding motif HEXXXH
and, nearby, a perfectly conserved motif QEGLA. All
members belong to the Proteobacteria, including
Agrobacterium tumefaciens and several species of Vibrio
and Pseudomonas, and are found in only one copy per
chromosome (Vibrio vulnificus, with two chromosomes, has
two). The function is unknown.
Length = 366
Score = 29.2 bits (66), Expect = 1.8
Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 5/64 (7%)
Query: 62 TKRLDLLRGPEEIHNYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDVKKMFAVWRVD 121
TK LRG E+ N++ L L G+ F IR + R L V +
Sbjct: 295 TKDALYLRGFVEVLNHIRQGGELLDLLFVGKTALEDFPVIRELVERGLLVPP-----KYL 349
Query: 122 PPWL 125
PP+L
Sbjct: 350 PPFL 353
>gnl|CDD|185176 PRK15273, PRK15273, putative fimbrial outer membrane usher protein
SteB; Provisional.
Length = 881
Score = 29.0 bits (64), Expect = 2.8
Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 15/101 (14%)
Query: 60 RTTKRLDLLRGPEEIHNYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDVKKMFAVWR 119
R+ R+DL + PE+ K + L+ G + YRHF+ + +KM AV+R
Sbjct: 701 RSLARIDLNKLPEKAE---ATKSVVQITLTEGAIGYRHFDVV--------SGEKMMAVFR 749
Query: 120 VD----PPWLPVTKKGLGSRMGGGKGSIDHYVTPVKTGRII 156
+ PP+ K ++G + ++ VK G +
Sbjct: 750 LADGDFPPFGAEVKNERQQQLGLVADDGNAWLAGVKAGETL 790
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 28.8 bits (64), Expect = 3.3
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 66 DLLR--GPEEIHNYLIHKQYGLVALSGGRMNYRHFETIRFAMMRKLDV 111
D+LR G E + +Y+I + + L G R++ +H E I M++K+++
Sbjct: 2640 DILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEI 2687
>gnl|CDD|132121 TIGR03077, not_gcvH, glycine cleavage protein H-like protein,
Chlamydial. The H protein (GcvH) of the glycine
cleavage system shuttles the methylamine group of
glycine from the P protein to the T protein. Most
Chlamydia but lack the P and T proteins, and have a
single homolog of GcvH that appears deeply split from
canonical GcvH in molecular phylogenetic trees. The
protein family modeled here is observed the Chlamydial
GcvH homolog, so far always seen as part of a two-gene
operon, downstream of a member of the uncharacterized
protein family TIGR03076. The function of this protein
is unknown.
Length = 110
Score = 27.2 bits (60), Expect = 3.9
Identities = 22/63 (34%), Positives = 26/63 (41%), Gaps = 9/63 (14%)
Query: 115 FAVWRVDPPWLPVTKKGLGSRMGGGKGSIDHYVTPVKTGRIIIEVGGKCSYEEVLPYLRS 174
+ VW + P V + GL SRM G+I H P VG C EVL L S
Sbjct: 5 YHVW-ILPIHSQVVRLGLTSRMQENLGNILHIDLP--------SVGSSCKEGEVLVILES 55
Query: 175 CAS 177
S
Sbjct: 56 SKS 58
>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain. This region covers
both the Brf homology II and III regions. This region is
involved in binding TATA binding protein.
Length = 95
Score = 26.8 bits (60), Expect = 4.0
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 187 NEDILREMKEKEEREARDNINP 208
N+D L E +EKE ++ D N
Sbjct: 25 NKDYLEEQEEKELKQKADEGNN 46
>gnl|CDD|220721 pfam10373, EST1_DNA_bind, Est1 DNA/RNA binding domain. Est1 is a
protein which recruits or activates telomerase at the
site of polymerisation. This is the DNA/RNA binding
domain of EST1.
Length = 276
Score = 27.7 bits (62), Expect = 5.0
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 171 YLRSCASKMPFKCMPCN-EDILREMKEKEEREARDNINPY 209
YLRS A + PF N E + ++K + +++ +N
Sbjct: 39 YLRSLAVRNPFPTAKNNLELLFEKIKFLADLVSQELLNKG 78
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 28.1 bits (64), Expect = 5.4
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 8/51 (15%)
Query: 66 DLLR--GPEEIHNYL---IHKQYGLVALSGGRMNYRHFETIRFAMMRKLDV 111
D+LR G E + NYL + K Y L G ++N +H E I M+RK+ +
Sbjct: 993 DILRVLGVEAVQNYLVNEVQKVY---RLQGVKINDKHIEVIVRQMLRKVRI 1040
>gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB;
Provisional.
Length = 211
Score = 27.4 bits (61), Expect = 5.8
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 99 ETIRFAMMRKLDVKK 113
ET R MMRKLDV K
Sbjct: 182 ETHRLNMMRKLDVHK 196
>gnl|CDD|219696 pfam08012, DUF1702, Protein of unknown function (DUF1702). This
family of proteins contains many bacterial proteins that
are encoded by the UnbL gene. The function of these
proteins is unknown.
Length = 318
Score = 27.3 bits (61), Expect = 7.0
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 58 TPRTTKRL-DLLRGPEEIHNYLIH 80
R +R+ LL GP H Y+IH
Sbjct: 90 PGRGGRRVAALLAGPGARHVYMIH 113
>gnl|CDD|217421 pfam03200, Glyco_hydro_63, Mannosyl oligosaccharide glucosidase.
This is a family of eukaryotic enzymes belonging to
glycosyl hydrolase family 63. They catalyze the specific
cleavage of the non-reducing terminal glucose residue
from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide
glucosidase EC:3.2.1.106 is the first enzyme in the
N-linked oligosaccharide processing pathway.
Length = 775
Score = 27.3 bits (61), Expect = 8.5
Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 19/73 (26%)
Query: 39 ERPRLKFVDKVPTFIYN-----------HKTPRTTKRLDLLRGPEEIHNYLIHKQYGLVA 87
+ P L+ V Y +P+ K LDL+R PEE+ + YGL +
Sbjct: 617 DEPSLQLV---CHKGYVSLFPFLLKLLPPDSPKLEKLLDLIRDPEELWS-----DYGLRS 668
Query: 88 LSGGRMNYRHFET 100
LS Y T
Sbjct: 669 LSKSSPLYMTRNT 681
>gnl|CDD|220792 pfam10513, EPL1, Enhancer of polycomb-like. This is a family of
EPL1 (Enhancer of polycomb-like) proteins. The EPL1
protein is a member of a histone acetyltransferase
complex which is involved in transcriptional activation
of selected genes.
Length = 145
Score = 26.6 bits (59), Expect = 8.6
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 188 EDILREMKEKEEREARDNINPYTFEYMI 215
E L E+ EK + E ++ FE ++
Sbjct: 112 EAWLEELNEKRKEEGLAPLSEDDFEKLM 139
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 0.141 0.448
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,846,634
Number of extensions: 1236531
Number of successful extensions: 1025
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1015
Number of HSP's successfully gapped: 25
Length of query: 240
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 146
Effective length of database: 6,768,326
Effective search space: 988175596
Effective search space used: 988175596
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 (21.9 bits)
S2: 57 (25.8 bits)