RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2553
(134 letters)
>gnl|CDD|240297 PTZ00159, PTZ00159, 60S ribosomal protein L32; Provisional.
Length = 133
Score = 190 bits (484), Expect = 9e-64
Identities = 82/133 (61%), Positives = 105/133 (78%)
Query: 2 SIKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGS 61
+KP + KIVKKR K F R QS+R+ ++ SWRKP+GIDNRVRRRFKG LMP IGYGS
Sbjct: 1 MVKPKVKKKIVKKRTKKFTRFQSERFPRVKPSWRKPRGIDNRVRRRFKGTRLMPKIGYGS 60
Query: 62 AKKTRHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRL 121
KKTR++LP+ F K V NVK+LE+L+M NRKY AEI H VS++KR+ IV+RA++L++R+
Sbjct: 61 DKKTRYLLPSGFYKFPVRNVKDLEMLLMHNRKYAAEIAHNVSARKRKAIVERAKELNVRV 120
Query: 122 TNGNARIRTEENE 134
NGNAR+R EE E
Sbjct: 121 LNGNARLRKEEKE 133
>gnl|CDD|238284 cd00513, Ribosomal_L32_L32e, Ribosomal_L32_L32e: L32 is a protein
from the large subunit that contains a surface-exposed
globular domain and a finger-like projection that
extends into the RNA core to stabilize the tertiary
structure. L32 does not appear to play a role in forming
the A (aminacyl), P (peptidyl) or E (exit) sites of the
ribosome, but does interact with 23S rRNA, which has a
"kink-turn" secondary structure motif. L32 is
overexpressed in human prostate cancer and has been
identified as a stably expressed housekeeping gene in
macrophages of human chronic obstructive pulmonary
disease (COPD) patients. In Schizosaccharomyces pombe,
L32 has also been suggested to play a role as a
transcriptional regulator in the nucleus. Found in
archaea and eukaryotes, this protein is known as L32 in
eukaryotes and L32e in archaea.
Length = 107
Score = 170 bits (432), Expect = 4e-56
Identities = 69/107 (64%), Positives = 85/107 (79%)
Query: 17 KVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFLKV 76
K F RHQSDRYK+L SWRKP+GIDN+VRRRFKG+ MP IGYGS KKTR + P+ F KV
Sbjct: 1 KKFKRHQSDRYKRLGDSWRKPRGIDNKVRRRFKGKPAMPKIGYGSPKKTRGLHPSGFKKV 60
Query: 77 VVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTN 123
+VHNVKELEVL M NR Y A I H V ++KR++IV+RA++L I++ N
Sbjct: 61 LVHNVKELEVLDMHNRTYAARIAHTVGARKRKEIVERAKELGIKVLN 107
>gnl|CDD|190064 pfam01655, Ribosomal_L32e, Ribosomal protein L32. This family
includes ribosomal protein L32 from eukaryotes and
archaebacteria.
Length = 110
Score = 165 bits (420), Expect = 2e-54
Identities = 65/110 (59%), Positives = 85/110 (77%)
Query: 15 RRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHFL 74
+ K F RHQSDRYK+L SWRKP+GIDN+VRRRFKG+ MP IGYGS KK R + P+ F
Sbjct: 1 KTKKFKRHQSDRYKRLKPSWRKPRGIDNKVRRRFKGKPPMPKIGYGSPKKVRGLHPSGFK 60
Query: 75 KVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNG 124
+V+VHNVK+LE L+M NR Y A I H V ++KR++IV+RA++L I++ N
Sbjct: 61 EVLVHNVKDLEKLLMDNRTYAARIAHTVGARKRKEIVERAKELGIKVLNP 110
>gnl|CDD|224631 COG1717, RPL32, Ribosomal protein L32E [Translation, ribosomal
structure and biogenesis].
Length = 133
Score = 119 bits (300), Expect = 1e-35
Identities = 52/127 (40%), Positives = 83/127 (65%), Gaps = 3/127 (2%)
Query: 4 KPVYRPKIVKKRRKV-FIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSA 62
K + + + V KR+K F R +SDRYK+L WR+P+GID+++RR+ KG+ M IGY S
Sbjct: 9 KRLLKIRRVLKRKKPEFKRQESDRYKRLGEKWRRPRGIDSKMRRKLKGKPPMVKIGYRSP 68
Query: 63 KKTRHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLT 122
K R + P+ + +V+VHNVK+LE L + + A I V ++KR +I++RA++L I++
Sbjct: 69 KAVRGLHPSGYEEVLVHNVKDLEKLDPETQ--AARIASTVGARKRIEILERARELGIKVL 126
Query: 123 NGNARIR 129
N R+
Sbjct: 127 NPGGRVE 133
>gnl|CDD|236288 PRK08562, rpl32e, 50S ribosomal protein L32e; Validated.
Length = 125
Score = 92.3 bits (230), Expect = 4e-25
Identities = 41/115 (35%), Positives = 70/115 (60%), Gaps = 2/115 (1%)
Query: 10 KIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHML 69
+K+++ F R RYK+L WR+P+G+D+++R + KG+ + +GY S K R +
Sbjct: 11 LKLKRKKPEFKRQDWHRYKRLGDKWRRPRGLDSKMRLKLKGKPAIVEVGYRSPKAVRGLH 70
Query: 70 PNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTNG 124
P+ + +V+VHNVKELE L A I V +KR +I+++A++L I++ N
Sbjct: 71 PSGYEEVLVHNVKELEKL--DPETQAARIASTVGKRKRLEILKKARELGIKVLNP 123
>gnl|CDD|183731 PRK12766, PRK12766, 50S ribosomal protein L32e; Provisional.
Length = 232
Score = 55.6 bits (134), Expect = 2e-10
Identities = 33/118 (27%), Positives = 57/118 (48%), Gaps = 6/118 (5%)
Query: 10 KIVKKRRKV----FIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKT 65
+++ +RR+ F R + K+ SWR+P+G ++ RR KG+ G+ +
Sbjct: 106 RLLTQRRREGKPQFNRQDYHKKKRTPTSWRRPRGGLSKQRRGIKGKGDTVEAGFRTPTAV 165
Query: 66 RHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTN 123
R P+ F +V VHN +LE + I V ++KR I + A++ IR+ N
Sbjct: 166 RGKHPSGFEEVRVHNTDDLE--GVDGDTEAVRIASKVGARKRERIEEVAEEQGIRVLN 221
>gnl|CDD|216683 pfam01758, SBF, Sodium Bile acid symporter family. This family
consists of Na+/bile acid co-transporters. These
transmembrane proteins function in the liver in the
uptake of bile acids from portal blood plasma a process
mediated by the co-transport of Na+. Also in the family
is ARC3 from S. cerevisiae, this is a putative
transmembrane protein involved in resistance to arsenic
compounds.
Length = 188
Score = 29.9 bits (68), Expect = 0.26
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 26 RYKKLHRSWRKPKGIDNRVRRRFKGQYL-MPNIGYGSAKKTRHMLPN 71
RY+ +R+PK + Q++ MP + + A + P
Sbjct: 16 RYEDFKELFRRPKA----LLLGLLLQWVIMPLLMFILAWFLLRLPPE 58
>gnl|CDD|205511 pfam13331, DUF4093, Domain of unknown function (DUF4093). This
domain lies at the C-terminus of primase proteins
carrying the TOPRIM, pfam01751, domain. The exact
function of the domain is not known.
Length = 87
Score = 27.8 bits (63), Expect = 0.65
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 39 GIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNHF 73
G D++ RR G+ L IGYG+AK+ L N F
Sbjct: 44 GADSKERREKLGEIL--GIGYGNAKQLLKRL-NMF 75
>gnl|CDD|146723 pfam04236, Transp_Tc5_C, Tc5 transposase C-terminal domain. This
family corresponds to a C-terminal cysteine rich region
that probably binds to a metal ion and could be DNA
binding (pers. obs. A Bateman)..
Length = 61
Score = 25.8 bits (56), Expect = 3.1
Identities = 3/22 (13%), Positives = 6/22 (27%)
Query: 51 QYLMPNIGYGSAKKTRHMLPNH 72
++ + K R N
Sbjct: 11 KFCFKVSDHCDQKICRDTGCND 32
>gnl|CDD|227380 COG5047, SEC23, Vesicle coat complex COPII, subunit SEC23
[Intracellular trafficking and secretion].
Length = 755
Score = 27.2 bits (60), Expect = 3.3
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 84 LEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQ 115
+EV +N K IGHAVS KK+ + + ++
Sbjct: 401 MEVKTSKNLKIKGLIGHAVSVKKKANNISDSE 432
>gnl|CDD|237846 PRK14876, PRK14876, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 928
Score = 27.1 bits (60), Expect = 3.6
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 3 IKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDN 42
+KP P I K +KV ++ D YK W P+G+ +
Sbjct: 432 LKPSPLPGIPKLCKKVRVKADCDFYKGQMDCWTDPQGVTH 471
>gnl|CDD|185571 PTZ00349, PTZ00349, dehydrodolichyl diphosphate synthetase;
Provisional.
Length = 322
Score = 26.1 bits (57), Expect = 6.5
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 80 NVKELEVLMMQNRKYCAE------IGHAVSSKKRRDIVQRAQQLSIRL 121
N+K + ++M NR++ E IGH + SK I++ +L I++
Sbjct: 19 NIKHISIIMDGNRRFAKEKGLHSAIGHFMGSKALIQIIEICIKLKIKI 66
>gnl|CDD|192929 pfam12062, HSNSD, heparan sulfate-N-deacetylase. This family of
proteins is are heparan sulfate N-deacetylase enzymes.
This protein is found in eukaryotes. This proteinenzyme
is often found associated with pfam00685.
Length = 487
Score = 25.9 bits (57), Expect = 9.4
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 5/34 (14%)
Query: 66 RHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIG 99
HM P+ F HN LE M N+ + E G
Sbjct: 364 SHMQPHLF-----HNFSYLEEQMALNKLFALEHG 392
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 0.136 0.396
Gapped
Lambda K H
0.267 0.0860 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,872,777
Number of extensions: 606626
Number of successful extensions: 545
Number of sequences better than 10.0: 1
Number of HSP's gapped: 541
Number of HSP's successfully gapped: 26
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
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: 54 (24.3 bits)