RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2844
(100 letters)
>gnl|CDD|110307 pfam01294, Ribosomal_L13e, Ribosomal protein L13e.
Length = 179
Score = 83.3 bits (206), Expect = 1e-21
Identities = 46/80 (57%), Positives = 59/80 (73%), Gaps = 1/80 (1%)
Query: 1 MESLQLNIQRLKEYKSKLIVFPRREKKKLRKGEATPEERKVATQLKGPLMPIRQSKPKSK 60
+E LQ N+QRLKEY+SKLI+FPR KK R G+++ EE K ATQLKGP+MPI Q + +
Sbjct: 101 LEGLQANVQRLKEYQSKLILFPRNPKK-PRAGDSSAEEVKSATQLKGPVMPIAQEAKRVE 159
Query: 61 ARIPSEAEKKFSAFQTLRMA 80
AR ++ EK F AF TLR+A
Sbjct: 160 ARKVTKEEKSFKAFATLRLA 179
>gnl|CDD|240377 PTZ00352, PTZ00352, 60S ribosomal protein L13; Provisional.
Length = 212
Score = 64.4 bits (157), Expect = 4e-14
Identities = 39/106 (36%), Positives = 62/106 (58%), Gaps = 10/106 (9%)
Query: 2 ESLQLNIQRLKEYKSKLIVFPRREKKKLRKGEA---------TPEERKVATQLKGPLMPI 52
ESL LN++RLK Y SKL++FPR+ KK +KG A V ++P
Sbjct: 105 ESLNLNVKRLKAYLSKLVLFPRK-GKKPKKGFAGIPADTSKEEVVALPVKQNKNSEVIPF 163
Query: 53 RQSKPKSKARIPSEAEKKFSAFQTLRMARADAKLVGIREKKAREAA 98
+++ + KAR+ ++ E+ F+A++TLR A+ +AK VG +EKK +
Sbjct: 164 QRTPKREKARVITKEERAFNAYRTLRQAKLNAKFVGKKEKKKQAKE 209
>gnl|CDD|173472 PTZ00192, PTZ00192, 60S ribosomal protein L13; Provisional.
Length = 218
Score = 46.8 bits (111), Expect = 1e-07
Identities = 31/97 (31%), Positives = 52/97 (53%), Gaps = 5/97 (5%)
Query: 2 ESLQLNIQRLKEYKSKLIVFPRREKKKLRKGEATPEERKVATQ----LKGPLMPIRQSKP 57
E + +N+QRLK Y SKL++FP KK++KGEA EE K ATQ + +
Sbjct: 112 EGMNVNVQRLKTYMSKLVLFP-MNHKKVQKGEAKEEEVKAATQDRSRFGDAAVGGVVTPS 170
Query: 58 KSKARIPSEAEKKFSAFQTLRMARADAKLVGIREKKA 94
+ R+ S+ E+ + + L+ + + G+R ++A
Sbjct: 171 REAPRVVSKEERSKNVYAFLKKNHSAVRFFGVRSRRA 207
>gnl|CDD|129308 TIGR00204, dxs, 1-deoxy-D-xylulose-5-phosphate synthase. DXP
synthase is a thiamine diphosphate-dependent enzyme
related to transketolase and the pyruvate dehydrogenase
E1-beta subunit. By an acyloin condensation of pyruvate
with glyceraldehyde 3-phosphate, it produces
1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine
diphosphate (TPP), pyridoxal phosphate, and the
isoprenoid building block isopentenyl diphosphate (IPP)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other, Biosynthesis of cofactors, prosthetic
groups, and carriers, Pyridoxine, Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 617
Score = 34.0 bits (78), Expect = 0.007
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 31 KGEATPEERKVATQLKGPLMPIRQSKPKSKARIPSEAEKKFSAFQTLRMARADAKLVGI 89
KG E+ + GP PKSK+ +PS + K + +A+ D K+VGI
Sbjct: 277 KGYKPAEKDPIGWHGVGPFDLSTGCLPKSKSALPSYS--KIFSDTLCELAKKDNKIVGI 333
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional.
Length = 1195
Score = 27.9 bits (62), Expect = 0.78
Identities = 20/66 (30%), Positives = 23/66 (34%), Gaps = 11/66 (16%)
Query: 21 FPRREK-KKLRKGEATPEERKVATQLKGPLMPIRQSKPKSKARIPSEAEKKFSA--FQTL 77
FP K K K EATP KGPL +QS + SA + L
Sbjct: 984 FPSSVKASKPSKFEATPA--------KGPLTSGKQSTLPMATPAQPPVDLNLSAILYTAL 1035
Query: 78 RMARAD 83
R R
Sbjct: 1036 RKLRTA 1041
>gnl|CDD|226196 COG3670, COG3670, Lignostilbene-alpha,beta-dioxygenase and related
enzymes [Secondary metabolites biosynthesis, transport,
and catabolism].
Length = 490
Score = 27.7 bits (62), Expect = 0.98
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 12 KEYKSKLIVFPRREKKKLRKGEATP 36
E ++++V PR ++R EA P
Sbjct: 270 PELPTRILVLPREGDSEIRWFEAEP 294
>gnl|CDD|132563 TIGR03524, GldJ, gliding motility-associated lipoprotein GldJ.
Members of this protein family are exclusive to the
Bacteroidetes phylum (previously
Cytophaga-Flavobacteria-Bacteroides). GldJ is a
lipoprotein linked to a type of rapid surface gliding
motility found in certain Bacteroidetes, such as
Flavobacterium johnsoniae. Knockouts of GldJ abolish the
gliding phenotype. GldJ is homologous to GldK. There is
a GldJ homolog in Cytophaga hutchinsonii and several
other species that has a different, shorter architecture
and is represented by a separate model. Gliding motility
appears closely linked to chitin utilization in the
model species Flavobacterium johnsoniae. Bacteroidetes
with members of this protein family appear to have all
of the genes associated with gliding motility.
Length = 559
Score = 27.6 bits (61), Expect = 1.2
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 19/71 (26%)
Query: 22 PRREKKKLRKGEATPEERKVATQLK-GPLMPIRQSKPKSKARIPSEAEKKFSAFQTLRMA 80
R +KK A PEE+ Q K G + + R+P+EAE +++A
Sbjct: 232 GRTRRKKGEARPAVPEEKDAYQQRKDGIITQ--------RYRLPTEAEWEYAA------- 276
Query: 81 RADAKLVGIRE 91
VG RE
Sbjct: 277 ---KANVGNRE 284
>gnl|CDD|216819 pfam01973, MAF_flag10, Protein of unknown function DUF115. This
family of archaebacterial proteins has no known
function.
Length = 170
Score = 26.8 bits (60), Expect = 1.4
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 3 SLQLNIQRLKEYKSKLIVF 21
SL ++ LK+ + K ++
Sbjct: 35 SLDKHLPLLKKNRDKAVII 53
>gnl|CDD|184749 PRK14566, PRK14566, triosephosphate isomerase; Provisional.
Length = 260
Score = 26.4 bits (58), Expect = 3.0
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 9 QRLKEYKSKLIVFPRREKKKLRKGEATPEERKVATQLKGPLMPIR---QSKPKSKARIPS 65
Q LK+ + ++ E++++ + K A K L PI +S P +AR
Sbjct: 89 QMLKDAGCRYVIIGHSERRRMYGETSNIVAEKFAAAQKHGLTPILCVGESGPAREARRTF 148
Query: 66 E 66
E
Sbjct: 149 E 149
>gnl|CDD|225324 COG2604, COG2604, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 594
Score = 25.8 bits (57), Expect = 4.9
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 3 SLQLNIQRLKEYKSKLIVF 21
SL+ + LK+Y+ K +F
Sbjct: 235 SLEKQLPLLKKYQDKATIF 253
>gnl|CDD|163560 TIGR03848, MSMEG_4193, probable phosphomutase, MSMEG_4193 family.
A three-gene system broadly conserved among the
Actinobacteria includes MSMEG_4193 and homologs, a
subgroup among the larger phosphoglycerate mutase family
protein (pfam00300). Another member of the trio is a
probable kinase, related to phosphatidylinositol
kinases; that context supports the hypothesis that this
protein acts as a phosphomutase.
Length = 204
Score = 25.4 bits (56), Expect = 5.7
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 14/63 (22%)
Query: 39 RKVATQLKGPLMPIRQSKPKSKARIPS-EAEKKFSAFQTLRMARADAKLV-GIREKKARE 96
R++ K PL P+ Q+ P S A P E+ +A+ A+ V +RE AR
Sbjct: 90 RELKELAKEPLWPVVQAHP-SAAVFPGGES-----------LAQVQARAVAAVREHDARL 137
Query: 97 AAG 99
AA
Sbjct: 138 AAE 140
>gnl|CDD|197331 cd09097, Deadenylase_CCR4, C-terminal deadenylase domain of CCR4
and related domains. This subfamily contains the
C-terminal catalytic domain of the deadenylases,
Saccharomyces cerevisiae Ccr4p and two vertebrate
homologs (CCR4a and CCR4b), and related domains. CCR4
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. CCR4 is the major deadenylase subunit of the
CCR4-NOT transcription complex, which contains two
deadenylase subunits and several noncatalytic subunits.
The other deadenylase subunit, Caf1 (called Pop2 in
yeast), is a DEDD-type protein and does not belong in
this superfamily. Saccharomyces cerevisiae CCR4 (or
Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It
is the catalytic subunit of the yeast mRNA deadenylase
(Ccr4p/Pop2p/Not complex). This complex participates in
various ways in mRNA metabolism, including
transcription initiation and elongation, and mRNA
degradation. Ccr4p degrades both poly(A) and
single-stranded DNA. There are two vertebrate homologs
of Ccr4p, CCR4a (also called CCR4-NOT transcription
complex subunit 6 or CNOT6) and CCR4b (also called
CNOT6-like or CNOT6L), which independently associate
with other components to form distinct CCR4-NOT
multisubunit complexes. The nuclease domain of CNOT6
and CNOT6L exhibits Mg2+-dependent deadenylase
activity, with specificity for poly (A) RNA as
substrate. CCR4a is a component of P-bodies and is
necessary for foci formation. CCR4b regulates p27/Kip1
mRNA levels, thereby influencing cell cycle
progression. They both contribute to the prevention of
cell death by regulating insulin-like growth
factor-binding protein 5.
Length = 329
Score = 25.3 bits (56), Expect = 6.6
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 56 KPKSKARIPSEAEKK 70
KPKS+A+ SEAE+K
Sbjct: 74 KPKSRAKTMSEAERK 88
>gnl|CDD|237332 PRK13281, PRK13281, succinylarginine dihydrolase; Provisional.
Length = 442
Score = 25.2 bits (56), Expect = 8.2
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 64 PSEAEKKFSAFQTLRMARADAKLVGIREKKA 94
K++ A QTL + A A+L + +
Sbjct: 202 NRAPPKRYPARQTLEASEAVARLHQLDPDRV 232
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
0.313 0.128 0.333
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,934,776
Number of extensions: 406147
Number of successful extensions: 411
Number of sequences better than 10.0: 1
Number of HSP's gapped: 402
Number of HSP's successfully gapped: 54
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)