RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1644
(923 letters)
>gnl|CDD|128594 smart00299, CLH, Clathrin heavy chain repeat homology.
Length = 140
Score = 93.1 bits (232), Expect = 3e-22
Identities = 30/112 (26%), Positives = 54/112 (48%), Gaps = 6/112 (5%)
Query: 528 YEGLFYFLGSIVN-YSQDQEVHFKYIQAACKTGQIKEVERICRESNCYNAERVKNFLKEA 586
E L +L S + S++ + K I+ K KE+ER+ +SN Y+ E+V ++A
Sbjct: 23 LEELIPYLESALKLNSENPALQTKLIELYAKYDPQKEIERLDNKSNHYDIEKVGKLCEKA 82
Query: 587 KLTDQLPLIIVCDRFDFVHDLVLYLYR-NNLQKYIEIYVQKGRKHLLEKWLK 637
KL ++ + D +F +V + N +K IE +V++ E W +
Sbjct: 83 KLYEEAVELYKKD-GNFKDAIVTLIEHLGNYEKAIEYFVKQNNP---ELWAE 130
Score = 65.0 bits (159), Expect = 2e-12
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 841 YSEAAKAACKTGQIKEVERICRESNCYNAERVKNFLKEAKLTDQLPLIIV----FVHDLV 896
++ + K KE+ER+ +SN Y+ E+V ++AKL ++ + F +V
Sbjct: 44 QTKLIELYAKYDPQKEIERLDNKSNHYDIEKVGKLCEKAKLYEEAVELYKKDGNFKDAIV 103
Query: 897 LYLYR-NNLQKYIEIYVQK 914
+ N +K IE +V++
Sbjct: 104 TLIEHLGNYEKAIEYFVKQ 122
Score = 32.6 bits (75), Expect = 0.32
Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 4/84 (4%)
Query: 618 KYIEIYVQKGRKHLLEKWLKEEKLECSEELGDLVKQSDPTLALSVYLRANIKQSRFVHDL 677
K IE+Y + + +E+ + E++G L +++ +V L K F +
Sbjct: 46 KLIELYAKYDPQKEIERLDNKSNHYDIEKVGKLCEKAKLY-EEAVEL--YKKDGNFKDAI 102
Query: 678 VLYLYR-NNLQKYIEIYVQKIRIK 700
V + N +K IE +V++ +
Sbjct: 103 VTLIEHLGNYEKAIEYFVKQNNPE 126
Score = 28.4 bits (64), Expect = 9.8
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 7/53 (13%)
Query: 680 YLYRNNLQKYIEIYVQKIRIKIKQSRFVHDLVLYLYR-NNLQKYIEIYVQKVS 731
+ L Y + + + K F +V + N +K IE +V++ +
Sbjct: 78 LCEKAKL------YEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNN 124
>gnl|CDD|206009 pfam13838, Clathrin_H_link, Clathrin-H-link. This short domain is
found on clathrins, and often appears on proteins
directly downstream from the Clathrin-link domain
pfam09268.
Length = 66
Score = 82.2 bits (204), Expect = 2e-19
Identities = 27/40 (67%), Positives = 34/40 (85%)
Query: 405 RVAANAPKGILRTPQTIVKFQQVPTPAGQTSPLLQYFGIL 444
++AAN+P+GILRTP+TI +F+QVP GQ SPLLQYFG L
Sbjct: 27 KIAANSPRGILRTPETINRFKQVPAQPGQPSPLLQYFGAL 66
Score = 50.6 bits (122), Expect = 3e-08
Identities = 16/29 (55%), Positives = 21/29 (72%)
Query: 820 NLAGAEDLFVRKFNLLFTNGQYSEAAKAA 848
L GA+DL++++FN LF G Y EAAK A
Sbjct: 1 GLPGADDLYIQQFNELFNQGNYEEAAKIA 29
>gnl|CDD|216037 pfam00637, Clathrin, Region in Clathrin and VPS. Each region is
about 140 amino acids long. The regions are composed of
multiple alpha helical repeats. They occur in the arm
region of the Clathrin heavy chain.
Length = 143
Score = 80.0 bits (198), Expect = 2e-17
Identities = 20/110 (18%), Positives = 45/110 (40%), Gaps = 5/110 (4%)
Query: 528 YEGLFYFLGSIV--NYSQDQEVHFKYIQAACKTGQIKEVERICRESNCYNAERVKNFLKE 585
E L +L S + N ++ + ++ K +++E +++N Y+ E+V ++
Sbjct: 23 LEELIPYLESALKENSRENPALQTALLELYAKYEDPEKLEEFLKKNNNYDLEKVAKLCEK 82
Query: 586 AKLTDQLPLIIVCDRFDFVHDLV-LYLYRNNLQKYIEIYVQKGRKHLLEK 634
A L ++ ++ + + L + IE V+ L EK
Sbjct: 83 ADLYEEAVILYKK--NGNYKEAISLLKKLKLYKDAIEYAVKSNDPELWEK 130
Score = 56.1 bits (136), Expect = 3e-09
Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 4/75 (5%)
Query: 845 AKAACKTGQIKEVERICRESNCYNAERVKNFLKEAKLTDQLPLIIV---FVHDLV-LYLY 900
+ K +++E +++N Y+ E+V ++A L ++ ++ + + L
Sbjct: 49 LELYAKYEDPEKLEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKNGNYKEAISLLKK 108
Query: 901 RNNLQKYIEIYVQKR 915
+ IE V+
Sbjct: 109 LKLYKDAIEYAVKSN 123
>gnl|CDD|150065 pfam09268, Clathrin-link, Clathrin, heavy-chain linker. Members of
this family adopt a structure consisting of alpha-alpha
superhelix. They are predominantly found in clathrin,
where they act as a heavy-chain linker domain.
Length = 24
Score = 47.5 bits (114), Expect = 2e-07
Identities = 15/24 (62%), Positives = 18/24 (75%)
Query: 795 EDNIIPYINGTLQNPDLALRIAVR 818
E+ IIPYI L NP+LALR+A R
Sbjct: 1 EETIIPYILNQLNNPELALRLASR 24
>gnl|CDD|216475 pfam01394, Clathrin_propel, Clathrin propeller repeat. Clathrin is
the scaffold protein of the basket-like coat that
surrounds coated vesicles. The soluble assembly unit, a
triskelion, contains three heavy chains and three light
chains in an extended three-legged structure. Each leg
contains one heavy and one light chain. The N-terminus
of the heavy chain is known as the globular domain, and
is composed of seven repeats which form a beta
propeller.
Length = 37
Score = 35.2 bits (82), Expect = 0.004
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 760 NRISSDTIFVTAPHEATGGIIGVN--RKGQVLSVSVD 794
I +D F TA E+ GII +N KG V V V+
Sbjct: 1 GAIFADIDFPTATMESWKGIIAINLTTKGSVQIVDVE 37
Score = 34.8 bits (81), Expect = 0.007
Identities = 8/37 (21%), Positives = 12/37 (32%)
Query: 2 AASFASFKSEGNPEPSTLFCFAVRTPAGGKLHIIEVG 38
A FA S A+ G + I++V
Sbjct: 1 GAIFADIDFPTATMESWKGIIAINLTTKGSVQIVDVE 37
Score = 33.7 bits (78), Expect = 0.015
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 60 AANDFPVAMQVSAKYDVVYLITKFGYIHVYDIE 92
A DFP A S K + +T G + + D+E
Sbjct: 5 ADIDFPTATMESWKGIIAINLTTKGSVQIVDVE 37
Score = 31.7 bits (73), Expect = 0.078
Identities = 9/40 (22%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 353 LNGCQIINYRTDPKQTWLLLIGISAVSNRVVGAMQLYSVE 392
I++ T ++W +I A++ G++Q+ VE
Sbjct: 1 GAIFADIDFPTATMESWKGII---AINLTTKGSVQIVDVE 37
Score = 30.6 bits (70), Expect = 0.20
Identities = 8/37 (21%), Positives = 13/37 (35%), Gaps = 5/37 (13%)
Query: 307 HPMTDDVVFW-----KWISPNTLALVTETSVYHWSME 338
+ D+ F W + L T+ SV +E
Sbjct: 1 GAIFADIDFPTATMESWKGIIAINLTTKGSVQIVDVE 37
Score = 29.4 bits (67), Expect = 0.56
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 126 GINVGSVSFNTLTMESDKFICVREKIAESAQVVIIDMN 163
G + F T TMES K I + V I+D+
Sbjct: 1 GAIFADIDFPTATMESWKGIIAI-NLTTKGSVQIVDVE 37
Score = 29.4 bits (67), Expect = 0.56
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 214 GINVGSVSFNTLTMESDKFICVREKIAESAQVVIIDMN 251
G + F T TMES K I + V I+D+
Sbjct: 1 GAIFADIDFPTATMESWKGIIAI-NLTTKGSVQIVDVE 37
Score = 27.1 bits (61), Expect = 3.7
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 8/45 (17%)
Query: 255 NPIRRPISADSAIMNPASKVIALKGKAGNDNNPNAPKTLQIFNIE 299
I I +A M +IA+ ++QI ++E
Sbjct: 1 GAIFADIDFPTATMESWKGIIAINLTTKG--------SVQIVDVE 37
Score = 26.0 bits (58), Expect = 9.1
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 100 NRISSDTIFVTAPHEATGGIIGLTNVGINVGSV 132
I +D F TA E+ GII + GSV
Sbjct: 1 GAIFADIDFPTATMESWKGIIAI--NLTTKGSV 31
>gnl|CDD|218483 pfam05183, RdRP, RNA dependent RNA polymerase. This family of
proteins are eukaryotic RNA dependent RNA polymerases.
These proteins are involved in post transcriptional gene
silencing where they are thought to amplify dsRNA
templates.
Length = 508
Score = 34.8 bits (80), Expect = 0.24
Identities = 33/144 (22%), Positives = 56/144 (38%), Gaps = 30/144 (20%)
Query: 631 LLEKWLKEEK------LECSEELGDLVKQSDPTLALSVYLRANIKQSRFVHDLVLYLYRN 684
LL + LKE + + L ++D TL L R + F+ L+ L ++
Sbjct: 248 LLREALKELAEALTDWDQALDLLRKQADENDFTLTL----RFMPSEDPFLRKLLRALVKH 303
Query: 685 NLQKYIEIYVQKIRIKIKQSRF---VHDLVLYLYRNNLQKYIEIYVQKVS----AKYDVV 737
L+K E K+RI + +S V D L K E++VQ +Y+ +
Sbjct: 304 TLKKLKE----KLRIPVPKSAALFGVVDETGVL------KEGEVFVQVSDGNDGGQYEYL 353
Query: 738 ---YLITKFGYIHVYDIETATCIY 758
L+ + +H DI +
Sbjct: 354 EGDVLVARNPCLHPGDIRVVRAVD 377
>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family. This
large family includes diverse proteins involved in large
complexes. The alignment contains one highly conserved
negatively charged residue and one highly conserved
positively charged residue that are probably important
for the function of these proteins. The family includes
the yeast nuclear export factor Sac3, and mammalian
GANP/MCM3-associated proteins, which facilitate the
nuclear localisation of MCM3, a protein that associates
with chromatin in the G1 phase of the cell-cycle. The
26S protease (or 26S proteasome) is responsible for
degrading ubiquitin conjugates. It consists of 19S
regulatory complexes associated with the ends of 20S
proteasomes. The 19S regulatory complex is composed of
about 20 different polypeptides and confers
ATP-dependence and substrate specificity to the 26S
enzyme. The conserved region occurs at the C-terminal of
the Nin1-like regulatory subunit. This family includes
several eukaryotic translation initiation factor 3
subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation
factor 3 (eIF3) is a multisubunit complex that is
required for binding of mRNA to 40 S ribosomal subunits,
stabilisation of ternary complex binding to 40 S
subunits, and dissociation of 40 and 60 S subunits.
Length = 155
Score = 31.5 bits (72), Expect = 0.93
Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 653 QSDPTLALSVYLRANIKQSRFVHDLVLYLYRNNLQKYI-EIYVQKIRIKI 701
++DP + ++ L + + + L L + E ++ +IR +
Sbjct: 85 RNDPYIQFALELEQALMEGNYHRFFRLLKKAPYLYACLLERFLDRIRKEA 134
>gnl|CDD|181567 PRK08861, PRK08861, cystathionine gamma-synthase; Provisional.
Length = 388
Score = 31.4 bits (71), Expect = 2.0
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 108 FVTAPHEATGGIIGLTNVGINVGSVSFNTLTMESDKFICVREKIAESAQVVIIDMNDPTN 167
+ APH+ GG L N N G F ++ + +A+ ++++++ P+N
Sbjct: 94 LIVAPHDCYGGTYRLFNTRANKG--DFKVQFVDQSDAAALDAALAKKPKLILLET--PSN 149
Query: 168 PIRRPISADSAIMNPASKVIAL 189
P+ R + + + A V AL
Sbjct: 150 PLVRVVDI-AELCQKAKAVGAL 170
>gnl|CDD|223023 PHA03249, PHA03249, DNA packaging tegument protein UL25;
Provisional.
Length = 653
Score = 31.5 bits (71), Expect = 2.3
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 18/77 (23%)
Query: 679 LYLYRNNLQKYIEIYVQKIRI----KIKQSRFVHDLVLYL--------YRNN---LQKYI 723
LYLYR NLQK + +++ K+ + ++DL + + L+ YI
Sbjct: 379 LYLYRQNLQKLNNGHRGVLKLLSSEKLNEEHTLNDLAFLVGVELMLVHFERTIRVLRCYI 438
Query: 724 EIYVQKVSAKYDVVYLI 740
+ +Q +S +++Y+I
Sbjct: 439 QHQLQNLS---ELIYII 452
>gnl|CDD|219553 pfam07751, Abi_2, Abi-like protein. This family, found in various
bacterial species, contains sequences that are similar
to the Abi group of proteins, which are involved in
bacteriophage resistance mediated by abortive infection
in Lactococcus species. The proteins are thought to have
helix-turn-helix motifs, found in many DNA-binding
proteins, allowing them to perform their function.
Length = 190
Score = 30.0 bits (68), Expect = 3.6
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 561 IKEVERICRESNCYNAERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLY-LYRNNLQKY 619
I+++ +I + S + +K++ K P ++ + F LY +N ++K
Sbjct: 95 IQKLSKIIKRSKDKLEDFIKHYRKNYDTELLFPFWVLVELLTFGTLSKLYRNLKNEVKKK 154
Query: 620 IEIYVQKGRKHLLEKWLK 637
I + LE WLK
Sbjct: 155 IAKRFGPLNRKELESWLK 172
>gnl|CDD|177665 PLN00028, PLN00028, nitrate transmembrane transporter; Provisional.
Length = 476
Score = 30.7 bits (70), Expect = 3.9
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 108 FVTAPHEATGGIIGLTNVGINVGSVSFNTLTMESDKF 144
FV+ + G I GLT G NVG+V L +
Sbjct: 375 FVSRR--SLGVISGLTGAGGNVGAVLTQLLFFTGSSY 409
>gnl|CDD|238772 cd01514, Elongation_Factor_C, Elongation factor G C-terminus. This
domain includes the carboxyl terminal regions of
elongation factors (EFs) bacterial EF-G, eukaryotic and
archeal EF-2 and eukaryotic mitochondrial mtEFG1s and
mtEFG2s. This group also includes proteins similar to
the ribosomal protection proteins Tet(M) and Tet(O),
BipA, LepA and, spliceosomal proteins: human 116kD U5
small nuclear ribonucleoprotein (snRNP) protein (U5-116
kD) and yeast counterpart Snu114p. This domain adopts a
ferredoxin-like fold consisting of an alpha-beta
sandwich with anti-parallel beta-sheets, resembling the
topology of domain III found in the elongation factors
EF-G and eukaryotic EF-2, with which it forms the
C-terminal block. The two domains however are not
superimposable and domain III lacks some of the
characteristics of this domain. EF-2/EF-G in complex
with GTP, promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site, the uncharged tRNA
from the P site to the E-site and, the mRNA is shifted
one codon relative to the ribosome. Tet(M) and Tet(O)
mediate Tc resistance. Typical Tcs bind to the ribosome
and inhibit the elongation phase of protein synthesis,
by inhibiting the occupation of site A by
aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release
of tetracycline (Tc) from the ribosome in a
GTP-dependent manner. BipA is a highly conserved
protein with global regulatory properties in Escherichia
coli. Yeast Snu114p is essential for cell viability and
for splicing in vivo. Experiments suggest that GTP
binding and probably GTP hydrolysis is important for the
function of the U5-116 kD/Snu114p. The function of LepA
proteins is unknown.
Length = 79
Score = 28.2 bits (64), Expect = 4.0
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 769 VTAPHEATGGIIGV--NRKGQVLSVSVDEDN 797
+T P E G +IG R+G++L +
Sbjct: 8 ITVPEEYLGAVIGDLSKRRGEILGMEPRGTG 38
>gnl|CDD|191210 pfam05153, DUF706, Family of unknown function (DUF706). Family of
uncharacterized eukaryotic function. Some members have a
described putative function, but a common theme is not
evident.
Length = 255
Score = 30.0 bits (68), Expect = 5.6
Identities = 27/104 (25%), Positives = 36/104 (34%), Gaps = 26/104 (25%)
Query: 606 DLVLYLYRNNLQKYIEIYVQKGRKHLLEKWLKEEK-----LECSEELGDLVKQSDPTLAL 660
D V YR K +V+K R +LK + E E L LV +SDP L
Sbjct: 8 DRVREFYREQHTKQTVDFVKKARAE----FLKFTRAKMTIWEALELLNTLVDESDPDTDL 63
Query: 661 S--VYL-------RANIKQSR------FVHDL--VLYLYRNNLQ 687
+L R + +HDL VL + Q
Sbjct: 64 PQIQHLLQTAEAIRRDHPDPDWMHLTGLIHDLGKVLAFFGGEPQ 107
>gnl|CDD|223534 COG0458, CarB, Carbamoylphosphate synthase large subunit (split
gene in MJ) [Amino acid transport and metabolism /
Nucleotide transport and metabolism].
Length = 400
Score = 29.6 bits (67), Expect = 7.9
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 22 FAVRTPAGGKLHIIEVGTPPAGNTPLAKKA 51
FAV P GG+L++IE+ + ++ LA KA
Sbjct: 272 FAVD-PGGGELYVIEINPRVSRSSALASKA 300
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 28.9 bits (65), Expect = 9.1
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 13/54 (24%)
Query: 576 AERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYIEIYVQKGRK 629
A ++ L+ A+ + +P+I+V ++ D L + E+ VQ+GR
Sbjct: 91 ASELRIQLRRARQAEDIPIILVGNKSD-------------LVRSREVSVQEGRA 131
>gnl|CDD|237037 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
Length = 368
Score = 29.4 bits (67), Expect = 9.5
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 12/58 (20%)
Query: 528 YEGLFYFLGSIVNYSQDQEVHFKYIQAACKTGQIKEVERICRESNCYNAERVKNFLKE 585
YE L Y L D+E+ K I C++G E +C E AE++ FLKE
Sbjct: 301 YELLLYHL-----EEDDKEL--KEIYEECRSG-----ELLCGECKKEAAEKIAEFLKE 346
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 29.5 bits (67), Expect = 9.5
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 767 IFVTAPHEATGGIIGV--NRKGQVLSVSVDEDN 797
+ +T P E G +IG +R+GQ+L +
Sbjct: 606 VEITTPEEYMGDVIGDLNSRRGQILGMEQRPGG 638
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
0.320 0.136 0.398
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 47,186,206
Number of extensions: 4740803
Number of successful extensions: 3996
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3990
Number of HSP's successfully gapped: 47
Length of query: 923
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 817
Effective length of database: 6,236,078
Effective search space: 5094875726
Effective search space used: 5094875726
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 (21.8 bits)
S2: 64 (28.4 bits)