RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043606
(101 letters)
>gnl|CDD|185465 PTZ00129, PTZ00129, 40S ribosomal protein S14; Provisional.
Length = 149
Score = 179 bits (455), Expect = 1e-59
Identities = 87/99 (87%), Positives = 94/99 (94%)
Query: 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP 60
ETL R+TGGMKVKADRDESSPYAAM+AAQDV+ RCKE GI ALHIKLRATGG +TKTPGP
Sbjct: 51 ETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGINALHIKLRATGGVRTKTPGP 110
Query: 61 GAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGR 99
GAQ+ALRALAR+G+KIGRIEDVTPIPTDSTRRKGGRRGR
Sbjct: 111 GAQAALRALARAGLKIGRIEDVTPIPTDSTRRKGGRRGR 149
>gnl|CDD|236588 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
Length = 132
Score = 163 bits (415), Expect = 7e-54
Identities = 69/101 (68%), Positives = 85/101 (84%)
Query: 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP 60
ET+ + +GGM VKADRDESSPYAAM AA+ ++ KE+GIT +HIK+RA GGN K+PGP
Sbjct: 32 ETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQKSPGP 91
Query: 61 GAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGRRL 101
GAQ+A+RALAR+G++IGRIEDVTPIP D TR GGRRGRR+
Sbjct: 92 GAQAAIRALARAGLRIGRIEDVTPIPHDGTRPPGGRRGRRV 132
>gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P. This model
describes exclusively the archaeal ribosomal protein
S11P. It excludes homologous ribosomal proteins S14 from
eukaryotes and S11 from bacteria [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 114
Score = 137 bits (346), Expect = 1e-43
Identities = 64/90 (71%), Positives = 76/90 (84%)
Query: 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP 60
ET+ R +GGM VKADRDESSPYAAM AA +++ KERGIT LHIK+RA GGN K+PGP
Sbjct: 25 ETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKSPGP 84
Query: 61 GAQSALRALARSGMKIGRIEDVTPIPTDST 90
GAQ+A+RALAR+G++IGRIEDVTPIP D T
Sbjct: 85 GAQAAIRALARAGLRIGRIEDVTPIPHDGT 114
>gnl|CDD|223178 COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 106 bits (267), Expect = 2e-31
Identities = 43/98 (43%), Positives = 62/98 (63%), Gaps = 9/98 (9%)
Query: 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP 60
+ +GGM K R +S+PYAA LAA+D +++ KE GI ++ +K++ PGP
Sbjct: 41 VIIWASSGGMGFKGSR-KSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKG--------PGP 91
Query: 61 GAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRG 98
G ++A+RALA +G+KI RIEDVTPIP + R RR
Sbjct: 92 GREAAIRALAAAGLKITRIEDVTPIPHNGCRPPKRRRV 129
>gnl|CDD|189537 pfam00411, Ribosomal_S11, Ribosomal protein S11.
Length = 109
Score = 105 bits (263), Expect = 6e-31
Identities = 44/96 (45%), Positives = 58/96 (60%), Gaps = 9/96 (9%)
Query: 1 ETLERITGGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP 60
L GG K R +S+PYAA AA++ ++ KE+GI AL +K++ PGP
Sbjct: 23 VVLWSSAGGCGFKGSR-KSTPYAAQTAAENAAKIAKEQGIKALEVKIKG--------PGP 73
Query: 61 GAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGR 96
G +SALRALARSG++I RI DVTPIP + R R
Sbjct: 74 GRESALRALARSGLRITRIRDVTPIPHNGCRPPKKR 109
>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
Length = 128
Score = 64.4 bits (158), Expect = 7e-15
Identities = 31/79 (39%), Positives = 49/79 (62%), Gaps = 8/79 (10%)
Query: 19 SSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78
S+PYAA +AA+D +++ KE G+ + + + K PG G +SA+RAL +G+++
Sbjct: 57 STPYAAQVAAEDAAKKAKEHGMKTVEVFV--------KGPGSGRESAIRALQAAGLEVTS 108
Query: 79 IEDVTPIPTDSTRRKGGRR 97
I+DVTPIP + R RR
Sbjct: 109 IKDVTPIPHNGCRPPKRRR 127
>gnl|CDD|188357 TIGR03632, bact_S11, 30S ribosomal protein S11. This model
describes the bacterial 30S ribosomal protein S11.
Cutoffs are set such that the model excludes archaeal
and eukaryotic ribosomal proteins, but many chloroplast
and mitochondrial equivalents of S11 are detected
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 108
Score = 62.2 bits (152), Expect = 3e-14
Identities = 32/84 (38%), Positives = 52/84 (61%), Gaps = 9/84 (10%)
Query: 8 GGMKVKADRDESSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALR 67
G + K + +S+PYAA LAA+D +++ KE G+ + + + K PG G +SA+R
Sbjct: 30 GAVGFKGSK-KSTPYAAQLAAEDAAKKAKEFGMKTVDVYV--------KGPGAGRESAIR 80
Query: 68 ALARSGMKIGRIEDVTPIPTDSTR 91
AL +G+++ I+DVTPIP + R
Sbjct: 81 ALQAAGLEVTSIKDVTPIPHNGCR 104
>gnl|CDD|176982 CHL00041, rps11, ribosomal protein S11.
Length = 116
Score = 53.7 bits (130), Expect = 8e-11
Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 8/68 (11%)
Query: 19 SSPYAAMLAAQDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGR 78
+P+AA AA++ + ++G+ + + K PG G +ALRA+ RSG+K+
Sbjct: 53 GTPFAAQTAAENAIRTVIDQGMKRAEVMI--------KGPGLGRDTALRAIRRSGLKLSS 104
Query: 79 IEDVTPIP 86
I DVTP+P
Sbjct: 105 IRDVTPMP 112
>gnl|CDD|143477 cd07561, Peptidase_S41_CPP_like, C-terminal processing
peptidase-like; serine protease family S41. Bacterial
protease homologs of the S41 family related to
C-terminal processing peptidase (CPP). CPP-1 is
believed to be important for the degradation of
incorrectly synthesized proteins as well as protection
from thermal and osmotic stresses. CPP is synthesized
with an extension on its carboxyl-terminus and
specifically recognizes a C-terminal tripeptide, but
cleaves at variable distance from the C-terminus. The
CPP active site consists of a serine/lysine catalytic
dyad. Conservation of these residues is seen in the
CPP-like proteins of this group. CPP proteins contain a
PDZ domain that promotes protein-protein interactions
and is important for substrate recognition however, most
of CPP-like proteins only have an internal fragment or
lack the PDZ domain.
Length = 256
Score = 26.1 bits (58), Expect = 3.3
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 29 QDVSQRCKERGITALHIKLRATGG 52
K +G+T L + LR GG
Sbjct: 83 NQAFAEFKAQGVTELVLDLRYNGG 106
>gnl|CDD|241312 cd13158, PTB_APPL, Adaptor protein containing PH domain, PTB
domain, and Leucine zipper motif (APPL; also called
DCC-interacting protein (DIP)-13alpha)
Phosphotyrosine-binding (PTB) domain. APPL interacts
with oncoprotein serine/threonine kinase AKT2, tumor
suppressor protein DCC (deleted in colorectal cancer),
Rab5, GIPC (GAIP-interacting protein, C terminus),
human follicle-stimulating hormone receptor (FSHR), and
the adiponectin receptors AdipoR1 and AdipoR2. There
are two isoforms of human APPL: APPL1 and APPL2, which
share about 50% sequence identity. APPL has a BAR and
a PH domain near its N terminus, and the two domains
are thought to function as a unit (BAR-PH domain).
C-terminal to this is a PTB domain. Lipid binding
assays show that the BAR, PH, and PTB domains can bind
phospholipids. PTB domains have a common PH-like fold
and are found in various eukaryotic signaling
molecules. This domain was initially shown to binds
peptides with a NPXY motif with differing requirements
for phosphorylation of the tyrosine, although more
recent studies have found that some types of PTB
domains can bind to peptides lack tyrosine residues
altogether. In contrast to SH2 domains, which recognize
phosphotyrosine and adjacent carboxy-terminal residues,
PTB-domain binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 135
Score = 25.4 bits (56), Expect = 5.1
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 5 RITGGMKVKADRDESSPYAAM---LAA 28
R G M+VK+DR Y AM LAA
Sbjct: 16 RFLGSMEVKSDRTSEVIYEAMRQILAA 42
>gnl|CDD|222572 pfam14155, DUF4307, Domain of unknown function (DUF4307). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 132 and 153 amino
acids in length. There is a single completely conserved
residue C that may be functionally important.
Length = 112
Score = 25.3 bits (56), Expect = 5.2
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 55 TKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRR 92
T+ PG A +RAL G ++GR E + P + T R
Sbjct: 56 TRDPGTPAYCIVRALDEDGAEVGRREVLVPAGGERTVR 93
>gnl|CDD|236770 PRK10826, PRK10826, 2-deoxyglucose-6-phosphatase; Provisional.
Length = 222
Score = 25.3 bits (56), Expect = 5.4
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 29 QDVSQRCKERGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIG 77
Q+V QR R I+ I +T+ PG + AL G+KIG
Sbjct: 73 QEVVQRIIARVIS--LI-------EETRPLLPGVREALALCKAQGLKIG 112
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence
of some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 25.7 bits (57), Expect = 5.4
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 15 DRDESSPYAAML----AAQDVSQRCKERGITALHI 45
D+ ES P A ++++ C RG +HI
Sbjct: 63 DKAESEPELAYAVNALGPGNLAEACAARGAPLIHI 97
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 25.5 bits (57), Expect = 5.8
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 59 GPGAQSALRALARSGMKIGRIED 81
GP A R A+ G K+ IE
Sbjct: 12 GPAGYVAARRAAKLGKKVALIEK 34
>gnl|CDD|232807 TIGR00068, glyox_I, lactoylglutathione lyase. Lactoylglutathione
lyase is also known as aldoketomutase and glyoxalase I.
Glyoxylase I is a homodimer in many species. In some
eukaryotes, including yeasts and plants, the orthologous
protein carries a tandem duplication, is twice as long,
and hits This model twice [Central intermediary
metabolism, Amino sugars, Energy metabolism, Other].
Length = 150
Score = 25.2 bits (55), Expect = 6.2
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 9/35 (25%)
Query: 26 LAAQDVSQRCKERGITALHIKLRATGGNKTKTPGP 60
+ DV + C+ ++RA GGN + PGP
Sbjct: 92 IGVDDVYKACE---------RVRALGGNVVREPGP 117
>gnl|CDD|213935 TIGR04322, rSAM_QueE_Ecoli, putative 7-cyano-7-deazaguanosine
(preQ0) biosynthesis protein QueE. Members of this
radical SAM domain protein family appear to be the E.
coli form of the queuosine biosynthesis protein QueE.
QueE is involved in making preQ0
(7-cyano-7-deazaquanine), a precursor of both the
bacterial/eukaryotic modified tRNA base queuosine and
the archaeal modified base archaeosine. Members occur
in species that lack known forms of QueE but usually
are not found in queuosine biosynthesis operons.
Members of this family tend to form bi-directional best
hit matches to members of known (TIGR03365) and
putative (TIGR03963) QueE families from other lineages.
Length = 215
Score = 25.3 bits (56), Expect = 6.9
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 18 ESSPYAAMLAAQDVSQRCKERGITALHIKLRATGG 52
SP A L+A+++ K++G TA H+ + TGG
Sbjct: 54 ADSPTWANLSAEEILALIKQQGYTAKHVVI--TGG 86
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
0.315 0.131 0.367
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,189,613
Number of extensions: 427550
Number of successful extensions: 434
Number of sequences better than 10.0: 1
Number of HSP's gapped: 427
Number of HSP's successfully gapped: 38
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 42 (22.0 bits)
S2: 53 (24.1 bits)