RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032139
(146 letters)
>gnl|CDD|185489 PTZ00160, PTZ00160, 60S ribosomal protein L27a; Provisional.
Length = 147
Score = 243 bits (623), Expect = 1e-84
Identities = 104/148 (70%), Positives = 122/148 (82%), Gaps = 3/148 (2%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRY 60
M TRFKK RK RGHVS G+GR+GKHRKHPGGRGNAGG HHHRI FDKYHPG+FGKVGMR+
Sbjct: 1 MPTRFKKCRKMRGHVSHGYGRVGKHRKHPGGRGNAGGQHHHRINFDKYHPGYFGKVGMRH 60
Query: 61 FHKLRNKFHCPIVNIDKLWSMVPQDVKAKASK--DNVPMIDVTQFGYFKVLGKGVLPENQ 118
FH +NK++CP +N+DKLWS+VP++ + K +K D P+IDVT+ GYFKVLGKG LP Q
Sbjct: 61 FHLKKNKYYCPTINVDKLWSLVPEETRYKYAKKGDKAPVIDVTKAGYFKVLGKGHLP-KQ 119
Query: 119 PVVVKAKLVSKTAEKKIKEAGGAVVLTA 146
PV+VKA+ SK AEKKIK GGA VLTA
Sbjct: 120 PVIVKARYFSKKAEKKIKAVGGACVLTA 147
>gnl|CDD|216140 pfam00828, Ribosomal_L18e, Ribosomal protein L18e/L15. This family
includes eukaryotic L18 as well as prokaryotic L15.
Length = 122
Score = 98.5 bits (246), Expect = 1e-27
Identities = 49/131 (37%), Positives = 64/131 (48%), Gaps = 14/131 (10%)
Query: 20 GRIGKHRKH--PGGRGNAGGMHHHRILFDKYHPG--FFGKVGMRYFHKLRNKFHCPIVNI 75
G IGK R GGRG AGG HH P GK G R +++ + P VN+
Sbjct: 1 GIIGKTRGRGRKGGRGRAGGQKHH--FEGGQVPLYRRLGKRGFRK--LFKSRKNRPPVNL 56
Query: 76 DKLWSMVPQDVKAKASKDNVPMIDV-TQFGYFKVLGKGVLPENQPVVVKAKLVSKTAEKK 134
KL + +K D ++ V T KVLG G L +P+ VKA SK+A +K
Sbjct: 57 SKLDRKM---LKDGEEVDGETLVVVGTVTDDVKVLGNGEL--TKPLTVKALKFSKSAREK 111
Query: 135 IKEAGGAVVLT 145
I++AGG VVL
Sbjct: 112 IEKAGGEVVLL 122
>gnl|CDD|235799 PRK06419, rpl15p, 50S ribosomal protein L15P; Reviewed.
Length = 148
Score = 90.3 bits (225), Expect = 5e-24
Identities = 53/149 (35%), Positives = 80/149 (53%), Gaps = 8/149 (5%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRK--HPGGRGNAGGMHHHRILFDKYHPGFFGKVGM 58
M + KK+RK RG + G G HR GGRG AG H KY P ++GK G
Sbjct: 1 MIRKKKKSRKLRGSRTHGGGTHKNHRGAGSRGGRGMAGRHKHKWTWVVKYGPDWYGKHGF 60
Query: 59 RYFHKLRNKFHCPIVNIDKLWSMVPQDV-KAKASKDN-VPMIDVTQFGYFKVLGKGVLPE 116
+ KL + +N+ +L + + KA +++ ++D+T+ GY KVLG G +
Sbjct: 61 KRPPKLIKEVS--TINVGELDELADLLKAEGKAEEEDGKIVVDLTELGYDKVLGGGKV-- 116
Query: 117 NQPVVVKAKLVSKTAEKKIKEAGGAVVLT 145
+P+V+KA S+ A +KI+ AGG VVL+
Sbjct: 117 TRPLVIKADAFSEKAIEKIEAAGGEVVLS 145
>gnl|CDD|223278 COG0200, RplO, Ribosomal protein L15 [Translation, ribosomal
structure and biogenesis].
Length = 152
Score = 68.1 bits (167), Expect = 2e-15
Identities = 39/155 (25%), Positives = 57/155 (36%), Gaps = 17/155 (10%)
Query: 4 RFKKNRKKRGHVSAGHGRIGKHR--KHPGGRGNAGG---MHHHRILFDKYHPG-----FF 53
+ + G GGRG+ G H +
Sbjct: 3 LNDLKPARGSKKTRKRVGRGIGSGLGKTGGRGHKGQKARSGHKWVRPGFEGGQMPLYRRL 62
Query: 54 GKVGMRYFHKLRNKFHCPIVNIDKLWSMVP--QDVKAKASKDNVPMIDVTQFGYFKVLGK 111
K G + K +VN+ KL ++P ++V + K + + KVLG
Sbjct: 63 PKRGFT--NSKFKKVEYAVVNLGKLAELLPEGEEVTLASLKAAGVIRKLKDLV--KVLGN 118
Query: 112 GVLPENQPVVVKAKLVSKTAEKKIKEAGGAVVLTA 146
G L + PV VKAK SK+A +KI+ AGG V L
Sbjct: 119 GKLTKAVPVKVKAK-ASKSAIEKIEAAGGKVELIE 152
>gnl|CDD|235196 PRK04005, PRK04005, 50S ribosomal protein L18e; Provisional.
Length = 111
Score = 41.0 bits (97), Expect = 2e-05
Identities = 18/37 (48%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 107 KVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVV 143
KVLG G L + V V A S+TA++KI+EAGG +
Sbjct: 58 KVLGSGKL--DHKVTVAALSFSETAKEKIEEAGGKAL 92
>gnl|CDD|235523 PRK05592, rplO, 50S ribosomal protein L15; Reviewed.
Length = 146
Score = 37.8 bits (89), Expect = 4e-04
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 105 YFKVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVVLT 145
KVLG G L + + VKA SK+A++ I+ AGG V
Sbjct: 108 GVKVLGNGEL--TKKLTVKAHKFSKSAKEAIEAAGGKVEEI 146
>gnl|CDD|224641 COG1727, RPL18A, Ribosomal protein L18E [Translation, ribosomal
structure and biogenesis].
Length = 122
Score = 34.2 bits (79), Expect = 0.006
Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 107 KVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVV 143
KVLG G L ++ V V A SKTA +KI+EAGG +
Sbjct: 69 KVLGDGKL--DKKVTVAALRFSKTAREKIEEAGGECL 103
>gnl|CDD|233260 TIGR01071, rplO_bact, ribosomal protein L15, bacterial/organelle.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 145
Score = 31.1 bits (71), Expect = 0.099
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 104 GYFKVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVV 143
+ KVLG G L +P+ VKA VSK+A+ I+ AGG+V
Sbjct: 108 KFVKVLGNGKL--TKPLTVKAHRVSKSAKAAIEAAGGSVE 145
>gnl|CDD|149086 pfam07820, TraC, TraC-like protein. The members of this family
are sequences that are similar to TraC. The gene
encoding this protein is one of a group of genes found
on plasmid p42a of Rhizobium etli CFN42 that are
thought to be involved in the process of plasmid
self-transmission. Mobilisation of plasmid p42a is of
importance as it is required for transfer of plasmid
p42a, which is also known as plasmid pSym as it carries
most of the genes required for nodulation and nitrogen
fixation by the symbiotic bacterium. The predicted
protein products of p42a are similar to known transfer
proteins of Agrobacterium tumefaciens plasmid pTiC58.
Length = 92
Score = 29.3 bits (66), Expect = 0.29
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHH 40
+ RF+ + K +AG R GG G A G+
Sbjct: 55 IAARFRGGKGK----AAGGAGAASARTAAGGTGAAAGVPG 90
>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal
protein L7/L12 refers to the large ribosomal subunit
proteins L7 and L12, which are identical except that L7
is acetylated at the N terminus. It is a component of
the L7/L12 stalk, which is located at the surface of the
ribosome. The stalk base consists of a portion of the
23S rRNA and ribosomal proteins L11 and L10. An extended
C-terminal helix of L10 provides the binding site for
L7/L12. L7/L12 consists of two domains joined by a
flexible hinge, with the helical N-terminal domain (NTD)
forming pairs of homodimers that bind to the extended
helix of L10. It is the only multimeric ribosomal
component, with either four or six copies per ribosome
that occur as two or three dimers bound to the L10
helix. L7/L12 is the only ribosomal protein that does
not interact directly with rRNA, but instead has
indirect interactions through L10. The globular
C-terminal domains of L7/L12 are highly mobile. They are
exposed to the cytoplasm and contain binding sites for
other molecules. Initiation factors, elongation factors,
and release factors are known to interact with the
L7/L12 stalk during their GTP-dependent cycles. The
binding site for the factors EF-Tu and EF-G comprises
L7/L12, L10, L11, the L11-binding region of 23S rRNA,
and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12
has minimal effect on factor binding and it has been
proposed that L7/L12 induces the catalytically active
conformation of EF-Tu and EF-G, thereby stimulating the
GTPase activity of both factors. In eukaryotes, the
proteins that perform the equivalent function to L7/L12
are called P1 and P2, which do not share sequence
similarity with L7/L12. However, a bacterial L7/L12
homolog is found in some eukaryotes, in mitochondria and
chloroplasts. In archaea, the protein equivalent to
L7/L12 is called aL12 or L12p, but it is closer in
sequence to P1 and P2 than to L7/L12.
Length = 127
Score = 27.5 bits (62), Expect = 1.5
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 5/33 (15%)
Query: 116 ENQPVVVKAKLVSK-TAE---KKIKEAGGAVVL 144
E+ P V+K VSK AE KK++EAG V L
Sbjct: 96 ESAPKVLKEG-VSKEEAEEIKKKLEEAGAKVEL 127
>gnl|CDD|241271 cd01238, PH_Btk, Bruton's tyrosine kinase pleckstrin homology (PH)
domain. Btk is a member of the Tec family of
cytoplasmic protein tyrosine kinases that includes BMX,
IL2-inducible T-cell kinase (Itk) and Tec. Btk plays a
role in the maturation of B cells. Tec proteins general
have an N-terminal PH domain, followed by a Tek homology
(TH) domain, a SH3 domain, a SH2 domain and a kinase
domain. The Btk PH domain binds phosphatidylinositol
3,4,5-trisphosphate and responds to signalling via
phosphatidylinositol 3-kinase. The PH domain is also
involved in membrane anchoring which is confirmed by the
discovery of a mutation of a critical arginine residue
in the BTK PH domain. This results in severe human
immunodeficiency known as X-linked agammaglobulinemia
(XLA) in humans and a related disorder is mice.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 = 140
Score = 26.8 bits (60), Expect = 2.8
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 40 HHRILFDKYHPGFFGK 55
++ L DKYHPGF+
Sbjct: 104 NNSNLSDKYHPGFWTG 119
>gnl|CDD|239241 cd02931, ER_like_FMN, Enoate reductase (ER)-like FMN-binding
domain. Enoate reductase catalyzes the NADH-dependent
reduction of carbon-carbon double bonds of several
molecules, including nonactivated 2-enoates,
alpha,beta-unsaturated aldehydes, cyclic ketones, and
methylketones. ERs are similar to 2,4-dienoyl-CoA
reductase from E. coli and to the old yellow enzyme from
Saccharomyces cerevisiae.
Length = 382
Score = 27.1 bits (60), Expect = 4.2
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 8/101 (7%)
Query: 40 HHRILFDKYHPGFFGKVGMRYFHKLRNKFHCPIVNIDKLWSMVPQDVKAKASKDNVPMID 99
H L D++ F K +Y L N+ I +V +++KA+ +D +
Sbjct: 173 HEGYLLDQFTISLFNKRTDKYGGSLENRLRFAI-------EIV-EEIKARCGEDFPVSLR 224
Query: 100 VTQFGYFKVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGG 140
+ Y K L +G LP + L KI E G
Sbjct: 225 YSVKSYIKDLRQGALPGEEFQEKGRDLEEGLKAAKILEEAG 265
>gnl|CDD|220457 pfam09888, DUF2115, Uncharacterized protein conserved in archaea
(DUF2115). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 162
Score = 26.1 bits (58), Expect = 6.1
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 9/47 (19%)
Query: 46 DKYHPGFFGKVGMRYFHKLRNK--------FHCPIVNIDKLWSMVPQ 84
KY FF + FH+++N ++ M+
Sbjct: 42 KKYIESFFEYIFGT-FHEIKNYRSGSEIEDEEIDEEEFNEFCDMIED 87
>gnl|CDD|201294 pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal
domain.
Length = 68
Score = 24.8 bits (55), Expect = 8.7
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 116 ENQPVVVKAKLVSK-TAE---KKIKEAGGAVVL 144
E P +K VSK AE KK++EAG V L
Sbjct: 36 EGAPKTIKEG-VSKEEAEEIKKKLEEAGAKVEL 67
>gnl|CDD|223484 COG0407, HemE, Uroporphyrinogen-III decarboxylase [Coenzyme
metabolism].
Length = 352
Score = 26.1 bits (58), Expect = 8.9
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 55 KVGMRYFHKLRNKFHCPIVNIDK-LWSMVPQDVKAKASKDNVPMIDVTQFGYFKVLGKGV 113
+V ++ K N+D L P+ +K + + D + GY LG G+
Sbjct: 272 RVDLKEAKKRLGDKVALQGNLDPALLYAPPEAIKEEVKRILEDGGDGS--GYIFNLGHGI 329
Query: 114 LPENQPVVVKA 124
LPE P VKA
Sbjct: 330 LPETPPENVKA 340
>gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional.
Length = 219
Score = 25.8 bits (57), Expect = 9.8
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 37 GMHHHRILFDKY 48
G+HHHR L+D Y
Sbjct: 130 GLHHHRALYDCY 141
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 0.139 0.430
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,604,135
Number of extensions: 685426
Number of successful extensions: 610
Number of sequences better than 10.0: 1
Number of HSP's gapped: 596
Number of HSP's successfully gapped: 26
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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: 54 (24.6 bits)