RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7251
(151 letters)
>gnl|CDD|153403 cd08034, LARP_1_2, La RNA-binding domain proteins similar to
La-related proteins 1 and 2. This domain is found in
proteins similar to vertebrate La-related proteins 1
and 2 (LARP1, LARP2). A variety of La-related proteins
(LARPs or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 73
Score = 100 bits (250), Expect = 9e-29
Identities = 39/61 (63%), Positives = 50/61 (81%)
Query: 22 EYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLELVD 81
EYYFS DNL +D FLR+KMDPEG+LP+ LIASF RV++LTTD+N +L A++ S +ELVD
Sbjct: 9 EYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELVD 68
Query: 82 N 82
Sbjct: 69 E 69
>gnl|CDD|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein;
unknown function.
Length = 80
Score = 85.7 bits (213), Expect = 5e-23
Identities = 35/64 (54%), Positives = 50/64 (78%), Gaps = 1/64 (1%)
Query: 22 EYYFSADNLVRDIFLRKKMDP-EGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLELV 80
EYYFS +NL RD FLRKKMD +G++P++ IASF RV+SLTTD+N ++ A++ S KLE+
Sbjct: 12 EYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVS 71
Query: 81 DNFK 84
++
Sbjct: 72 EDGL 75
>gnl|CDD|153396 cd07323, LAM, LA motif RNA-binding domain. This domain is found
at the N-terminus of La RNA-binding proteins as well as
in other related proteins. Typically, the domain
co-occurs with an RNA-recognition motif (RRM), and
together these domains function to bind primary
transcripts of RNA polymerase III in the La autoantigen
(Lupus La protein, LARP3, or Sjoegren syndrome type B
antigen, SS-B). A variety of La-related proteins (LARPs
or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 84.1 bits (209), Expect = 2e-22
Identities = 29/61 (47%), Positives = 47/61 (77%)
Query: 22 EYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLELVD 81
EYYFS +NL +D FLR MD +G++P++L+ASF+RV+ LTTD+ +L A++ S +E+ +
Sbjct: 9 EYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSE 68
Query: 82 N 82
+
Sbjct: 69 D 69
>gnl|CDD|153406 cd08037, LARP_1, La RNA-binding domain of La-related protein 1.
This domain is found in vertebrate La-related protein 1
(LARP1). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 73
Score = 83.8 bits (207), Expect = 3e-22
Identities = 38/60 (63%), Positives = 50/60 (83%)
Query: 22 EYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLELVD 81
EYYFS DNL RD FLR+KMD +GFLPVTLIASF RV++LTTDI+ ++ A++ S +E++D
Sbjct: 9 EYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEIID 68
>gnl|CDD|153407 cd08038, LARP_2, La RNA-binding domain of La-related protein 2.
This domain is found in vertebrate La-related protein 2
(LARP2). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 73
Score = 79.6 bits (196), Expect = 1e-20
Identities = 34/60 (56%), Positives = 50/60 (83%)
Query: 22 EYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLELVD 81
EYYFS +NL RD FLR+KMD +GFLP++LIA F RV++LTT+++ +L A++ S ++E+VD
Sbjct: 9 EYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVD 68
>gnl|CDD|203243 pfam05383, La, La domain. This presumed domain is found at the
N-terminus of La RNA-binding proteins as well as other
proteins. The function of this region is uncertain.
Length = 59
Score = 74.5 bits (184), Expect = 8e-19
Identities = 29/54 (53%), Positives = 43/54 (79%), Gaps = 1/54 (1%)
Query: 22 EYYFSADNLVRDIFLRKKMDPE-GFLPVTLIASFSRVRSLTTDINRVLLAIQKS 74
EYYFS +NL RD FLRK+MD + G++P++ IASF R++ LTTD+N ++ A++ S
Sbjct: 6 EYYFSDENLPRDKFLRKQMDKDPGYVPISTIASFKRIKKLTTDVNLIVEALRSS 59
>gnl|CDD|153402 cd08033, LARP_6, La RNA-binding domain of La-related protein 6.
This domain is found in animal and plant proteins
related to the La autoantigen. A variety of La-related
proteins (LARPs or La ribonucleoproteins), with
differing domain architecture, appear to function as
RNA-binding proteins in eukaryotic cellular processes.
Length = 77
Score = 68.5 bits (168), Expect = 3e-16
Identities = 31/67 (46%), Positives = 46/67 (68%), Gaps = 3/67 (4%)
Query: 22 EYYFSADNLVRDIFLRKKM--DPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLEL 79
EYYFS +NL++D FL K + + EG++P+ LIASF +V++LT D V A+++S KL +
Sbjct: 9 EYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVV 68
Query: 80 V-DNFKV 85
D KV
Sbjct: 69 SEDGKKV 75
>gnl|CDD|153400 cd08031, LARP_4_5_like, La RNA-binding domain of proteins similar
to La-related proteins 4 and 5. This domain is found
in proteins similar to La-related proteins 4 and 5
(LARP4, LARP5). A variety of La-related proteins (LARPs
or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 56.7 bits (137), Expect = 1e-11
Identities = 22/58 (37%), Positives = 43/58 (74%)
Query: 22 EYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLEL 79
EYYFS +NL D +L +MD + ++P+ IA+F++++ LTTDI+ ++ A+++S +++
Sbjct: 9 EYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQV 66
>gnl|CDD|153397 cd08028, LARP_3, La RNA-binding domain of La-related protein 3.
This domain is found at the N-terminus of the La
autoantigen and similar proteins, and co-occurs with an
RNA-recognition motif (RRM). Together these domains
function to bind primary transcripts of RNA polymerase
III at their 3' terminus and protect them from
exonucleolytic degradation. Binding is specific for the
3'-terminal UUU-OH motif. The La autoantigen is also
called Lupus La protein, LARP3, or Sjoegren syndrome
type B antigen (SS-B).
Length = 82
Score = 51.5 bits (124), Expect = 1e-09
Identities = 20/55 (36%), Positives = 39/55 (70%), Gaps = 1/55 (1%)
Query: 22 EYYFSADNLVRDIFLRKKM-DPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSD 75
EYYF NL RD FL++++ + +G++P+ ++ F+R++SL++D + A++KS
Sbjct: 13 EYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSK 67
>gnl|CDD|227520 COG5193, LHP1, La protein, small RNA-binding pol III transcript
stabilizing protein and related La-motif-containing
proteins involved in translation [Posttranslational
modification, protein turnover, chaperones /
Translation, ribosomal structure and biogenesis].
Length = 438
Score = 50.8 bits (121), Expect = 3e-08
Identities = 27/77 (35%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 22 EYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDK-LELV 80
EYYFS +NL D FLRKK GF+P++ I F R S D N +L A+++ +
Sbjct: 279 EYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEVVQNKATN 338
Query: 81 DNFKVNQIIVIADTNGK 97
I A N
Sbjct: 339 HLEIALGSIEDAQKNEA 355
Score = 38.1 bits (88), Expect = 9e-04
Identities = 27/131 (20%), Positives = 49/131 (37%), Gaps = 18/131 (13%)
Query: 20 PFEYYFSA-----DNLVRDIFLR----KKMDPEGFLPVTLIASFSRVRSLTTDINRVLLA 70
E+YFS N +D FL+ K + ++P+ IA+F+R+++ + ++ V A
Sbjct: 78 QVEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGA 137
Query: 71 IQKSDKLELV----DNFKVNQII-----VIADTNGKQRSDYLPNNNHLHSNNNKRLTSLR 121
++KS ++ N+ T+ QR Y NN R
Sbjct: 138 LRKSLDARVLEVSSSGSNKNRTEKLISNNNKSTSQMQRDVYQNGFGKEDVNNASRPEQQE 197
Query: 122 SRLTLLSPNGQ 132
P+
Sbjct: 198 DLEIQFPPHYH 208
>gnl|CDD|153399 cd08030, LA_like_plant, La-motif domain of plant proteins similar
to the La autoantigen. This domain is found in plant
proteins related to the La autoantigen. A variety of
La-related proteins (LARPs or La ribonucleoproteins),
with differing domain architecture, appear to function
as RNA-binding proteins in eukaryotic cellular
processes.
Length = 90
Score = 47.8 bits (114), Expect = 3e-08
Identities = 22/41 (53%), Positives = 30/41 (73%), Gaps = 2/41 (4%)
Query: 22 EYYFSADNLVRDIFLRKKM--DPEGFLPVTLIASFSRVRSL 60
E+YFS NL RD FL +++ DP+G + + LI SFSR+RSL
Sbjct: 10 EFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSL 50
>gnl|CDD|153404 cd08035, LARP_4, La RNA-binding domain of La-related protein 4.
This domain is found in vertebrate La-related protein 4
(LARP4), also known as c-MPL binding protein. La-type
domains often co-occur with RNA-recognition motifs
(RRMs). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 44.3 bits (104), Expect = 6e-07
Identities = 18/54 (33%), Positives = 36/54 (66%)
Query: 21 FEYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKS 74
E+ FS +NL +D++L +MD + F+P+ +A+ ++ LTTD++ +L ++ S
Sbjct: 8 LEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSS 61
>gnl|CDD|153398 cd08029, LA_like_fungal, La-motif domain of fungal proteins
similar to the La autoantigen. This domain is found in
fungal proteins related to the La autoantigen. A
variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 76
Score = 43.8 bits (104), Expect = 1e-06
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 22 EYYFSADNLVRDIFLRKKM--DPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLEL 79
E+YFS NL D FL G++P+ IASF R+R + V+ A+++S+ LE+
Sbjct: 9 EFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRF-QPLEAVVEALRESELLEV 67
Query: 80 VDN 82
++
Sbjct: 68 SED 70
>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7.
LARP7 is a component of the 7SK snRNP, a key factor in
the regulation of RNA polymerase II transcription. 7SK
functionality is dependent on the presence of LARP7,
which is thought to stabilize the 7SK RNA by
interacting with its 3' end. The release of 7SK RNA
from P-TEFb/HEXIM/7SK complexes activates the
cyclin-dependent kinase P-TEFb, which in turn
phosphorylates the C-terminal domain of RNA pol II and
mediates a transition into productive transcription
elongation.
Length = 82
Score = 40.3 bits (94), Expect = 3e-05
Identities = 19/60 (31%), Positives = 41/60 (68%), Gaps = 2/60 (3%)
Query: 22 EYYFSADNLVRDIFLRKKMDP--EGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLEL 79
+++F NL +D FLR++++ +G++ ++L+ SF++++ LTTD + A++ S +EL
Sbjct: 14 DFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVEL 73
>gnl|CDD|153405 cd08036, LARP_5, La RNA-binding domain of La-related protein 5.
This domain is found in vertebrate La-related protein 5
(LARP5). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 38.8 bits (90), Expect = 7e-05
Identities = 17/61 (27%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 21 FEYYFSADNLVRDIFLRKKMDPEGFLPVTLIASFSRVRSLTTDINRVLLAIQKSDKLELV 80
E+ S +NL D++L +MD + ++P+ +A+ ++ L+TD++ +++ + +S L V
Sbjct: 8 LEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVD-LIVDVLRSLPLVQV 66
Query: 81 D 81
D
Sbjct: 67 D 67
>gnl|CDD|197821 smart00658, RPOL8c, RNA polymerase subunit 8. subunit of RNA
polymerase I, II and III.
Length = 143
Score = 30.1 bits (68), Expect = 0.22
Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 30 LVRDIFLRKKMDPEG--FLPVTLI--ASFSRVRSLTTDINRVLLAIQKSDKLELV 80
L DIF K +DP+G F V+ I S L DIN + + DK LV
Sbjct: 4 LFEDIFKVKSVDPDGKKFDKVSRIFAESEYLQMELILDINSEIYPLAVGDKFRLV 58
>gnl|CDD|217771 pfam03870, RNA_pol_Rpb8, RNA polymerase Rpb8. Rpb8 is a subunit
common to the three yeast RNA polymerases, pol I, II
and III. Rpb8 interacts with the largest subunit Rpb1,
and with Rpb3 and Rpb11, two smaller subunits.
Length = 137
Score = 30.1 bits (68), Expect = 0.26
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 33 DIFLRKKMDPEG--FLPVTLI--ASFSRVRSLTTDINRVLLAIQKSDKLELV 80
DIF K +DP+G + V+ I S S L DIN L + DK LV
Sbjct: 2 DIFKVKSVDPDGKKYDRVSRIEAESESFKMELILDINSQLYPLAVGDKFRLV 53
>gnl|CDD|133470 cd01415, SAICAR_synt_PurC, bacterial and archaeal
5-aminoimidazole-4-(N-succinylcarboxamide)
ribonucleotide (SAICAR) synthase. A subfamily of SAICAR
synthetases represented by the Thermotoga maritima (Tm)
enzyme and E. coli PurC. SAICAR synthetase catalyzes the
seventh step of the de novo biosynthesis of purine
nucleotides (also reported as eighth step). It converts
5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP,
and L-aspartate into
5-aminoimidazole-4-(N-succinylcarboxamide)
ribonucleotide (SAICAR), ADP, and phosphate.
Length = 230
Score = 27.0 bits (61), Expect = 3.7
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 7/45 (15%)
Query: 55 SRVRSLTTDINRVLLAIQKSDKLELVDNFKV------NQIIVIAD 93
++ L IN VL + LVD FK+ + IV+AD
Sbjct: 144 KEIKELALKINEVLSEFFAEIGIILVD-FKLEFGRDKDGEIVLAD 187
>gnl|CDD|201944 pfam01735, PLA2_B, Lysophospholipase catalytic domain. This family
consists of Lysophospholipase / phospholipase B
EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which
also has a C2 domain pfam00168. Phospholipase B enzymes
catalyze the release of fatty acids from
lysophsopholipids and are capable in vitro of
hydrolysing all phospholipids extractable form yeast
cells. Cytosolic phospholipase A2 associates with
natural membranes in response to physiological increases
in Ca2+ and selectively hydrolyses arachidonyl
phospholipids, the aligned region corresponds the the
carboxy-terminal Ca2+-independent catalytic domain of
the protein as discussed in.
Length = 490
Score = 26.9 bits (60), Expect = 5.0
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 5/81 (6%)
Query: 65 NRVLLAIQKSDKLELVDNFKVNQIIVIADTNGKQRSDYLPNNNHLHSNNNKRLTSLRSRL 124
N+ LL I + L N + + + S Y PN ++ N+ T
Sbjct: 236 NQFLLVINSTSSLPSFLNILIKHFLKDLSEDSDDISQYPPNPFQDANDINQNATQSIVDS 295
Query: 125 TLL-----SPNGQRMMISLLL 140
L +GQ + + LL
Sbjct: 296 DTLFLVDGGEDGQNIPLWPLL 316
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 26.5 bits (59), Expect = 5.6
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 89 IVIADTNGKQRSDYLPNNNHLHSNNNKRLTS--------LRSRLTLLSPNGQRMMISLLL 140
+ +A++ GK+R N S+ +RL L R+ LLS GQR +SLL+
Sbjct: 103 LALAESRGKKRGLSSALNERRRSSFRERLARLGLGLENRLSDRIGLLS-GGQRQALSLLM 161
Query: 141 LALT 144
L
Sbjct: 162 ATLH 165
>gnl|CDD|213370 cd12836, HpCorA-like, Mg2+ transporter Helicobacter pylori
CorA-like subgroup. A bacterial subgroup of the
Escherichia coli CorA-Salmonella typhimurium ZntB_like
(EcCorA_ZntB-like) family of the MIT superfamily of
essential membrane proteins involved in transporting
divalent cations (uptake or efflux) across membranes.
This subgroup includes the Mg2+ transporter Helicobacter
pylori CorAs (which can also transport Co2+, and Ni2+);
CorA plays an important role in the viability of this
pathogen. Structures of the intracellular domain of
Vibrio parahaemolyticus and Salmonella typhimurium ZntB
(members of the EcCorA_ZntB-like family) form
funnel-shaped homopentamers, the tip of the funnel is
formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, such as
occur in some ZntB family proteins, may be associated
with the transport of different divalent cations, such
as zinc and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 288
Score = 26.5 bits (59), Expect = 6.5
Identities = 30/105 (28%), Positives = 47/105 (44%), Gaps = 21/105 (20%)
Query: 21 FEYYFSAD-----NLVRDI-FLRKKMDPEGFLPVTLIASFSRVRSLTT-------DINRV 67
E D N+ ++I LRKK+ + L L+ SR++ L D RV
Sbjct: 111 LEIRIDYDADLLENISKEISKLRKKLFADEDLDEELLEKISRLQELNMTIRENLIDKQRV 170
Query: 68 LLAIQKSDKL--ELVDNFK-----VNQIIVIADTNGKQRSDYLPN 105
L ++ KS+K +L +N + +N +I N +R DYL N
Sbjct: 171 LSSLLKSEKFPEDLKENLRIMIKDINSLIEHTTFNF-ERLDYLQN 214
>gnl|CDD|165185 PHA02843, PHA02843, hypothetical protein; Provisional.
Length = 73
Score = 25.1 bits (54), Expect = 6.6
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 71 IQKSDKLEL-VDNFKVNQIIVIADTNGKQRSDYLPNNNHLHSNNNKRLTSLRSRLTLLS 128
I+ SD + +DNF N+ + TN N NH NNN + S +S ++ S
Sbjct: 12 IKTSDDYDYYLDNFLDNEYFKFSCTNVNNNKLKNKNKNHTRRNNNNTIDSRKSYCSIKS 70
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 0.137 0.384
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,697,360
Number of extensions: 694367
Number of successful extensions: 658
Number of sequences better than 10.0: 1
Number of HSP's gapped: 649
Number of HSP's successfully gapped: 44
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
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 (24.5 bits)