RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5448
(322 letters)
>gnl|CDD|238166 cd00266, MADS_SRF_like, SRF-like/Type I subfamily of MADS (MCM1,
Agamous, Deficiens, and SRF (serum response factor) box
family of eukaryotic transcriptional regulators. Binds
DNA and exists as hetero- and homo-dimers. Differs from
the MEF-like/Type II subgroup mainly in position of the
alpha 2 helix responsible for the dimerization
interface. Important in homeotic regulation in plants
and in immediate-early development in animals. Also
found in fungi.
Length = 83
Score = 105 bits (265), Expect = 7e-29
Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 1/83 (1%)
Query: 137 GRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFATRK 196
GR KIK++ I+NK +R TFSKR+ G+ KKA ELSTL G +V ++V S +G +Y F
Sbjct: 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSS 60
Query: 197 -LQPMITSEAGKALIQTCLNSPD 218
++ +I+ + ++ + D
Sbjct: 61 EVEGVISRFEVLSALERKKKAVD 83
>gnl|CDD|197721 smart00432, MADS, MADS domain.
Length = 59
Score = 97.6 bits (244), Expect = 6e-26
Identities = 30/59 (50%), Positives = 41/59 (69%)
Query: 137 GRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFATR 195
GR KI+++ I+NK R TFSKR+ G+ KKA+ELS L +V L+V S TG +Y FA+
Sbjct: 1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP 59
>gnl|CDD|238067 cd00120, MADS, MADS: MCM1, Agamous, Deficiens, and SRF (serum
response factor) box family of eukaryotic transcriptonal
regulators. Binds DNA and exists as hetero and
homo-dimers. Composed of 2 main subgroups:
SRF-like/Type I and MEF2-like (myocyte enhancer factor
2)/ Type II. These subgroups differ mainly in position
of the alpha 2 helix responsible for the dimerization
interface; Important in homeotic regulation in plants
and in immediate-early development in animals. Also
found in fungi.
Length = 59
Score = 94.1 bits (235), Expect = 1e-24
Identities = 27/58 (46%), Positives = 39/58 (67%)
Query: 137 GRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFAT 194
GR KI+++ I+NK R TFSKR+ G+ KKA ELS L +V ++V S +G +Y F +
Sbjct: 1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWS 58
>gnl|CDD|109379 pfam00319, SRF-TF, SRF-type transcription factor (DNA-binding and
dimerisation domain).
Length = 51
Score = 81.3 bits (201), Expect = 6e-20
Identities = 23/51 (45%), Positives = 35/51 (68%)
Query: 144 EYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFAT 194
+ I+NK R TFSKR+ GI KKA+ELS L +V +++ S TG +Y +++
Sbjct: 1 KRIENKSNRQVTFSKRRNGIFKKAHELSVLCDAEVAVIIFSSTGKLYEYSS 51
>gnl|CDD|238165 cd00265, MADS_MEF2_like, MEF2 (myocyte enhancer factor 2)-like/Type
II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF
(serum response factor) box family of eukaryotic
transcriptional regulators. Binds DNA and exists as
hetero and homo-dimers. Differs from SRF-like/Type I
subgroup mainly in position of the alpha helix
responsible for the dimerization interface. Important in
homeotic regulation in plants and in immediate-early
development in animals. Also found in fungi.
Length = 77
Score = 77.2 bits (191), Expect = 4e-18
Identities = 27/65 (41%), Positives = 45/65 (69%)
Query: 137 GRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFATRK 196
GR KI+++ I+N R TFSKR+ G++KKA+ELS L +V L++ S +G +Y F++
Sbjct: 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPS 60
Query: 197 LQPMI 201
++ +I
Sbjct: 61 MEKII 65
>gnl|CDD|227400 COG5068, ARG80, Regulator of arginine metabolism and related MADS
box-containing transcription factors [Transcription].
Length = 412
Score = 78.5 bits (193), Expect = 3e-16
Identities = 60/187 (32%), Positives = 78/187 (41%), Gaps = 20/187 (10%)
Query: 135 TKGRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFAT 194
+ KI + YI NK +R TFSKRK GI KKA+ELS LTGT+V+LLV SE G V+TF T
Sbjct: 80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTT 139
Query: 195 RKLQPMITSEAGKALIQT-CLNSPDPCPSGAGDQRMSATGFEETELSYNIGDDEQKVRQL 253
KL+ ++ S GK+LIQ+ C N+P S S + D+
Sbjct: 140 PKLESVVKSLEGKSLIQSPCSNAPS---------DSSEEPSSSASFSVDPNDNNPMGSFQ 190
Query: 254 VYGGSPHLPSQPQSHPHQNYHPAGSPHQHH---LYQS-------SPIIPCSSPGPMIGSY 303
G Q+ Q Y S H + +IP
Sbjct: 191 HNGSPQTNFIPLQNPQTQQYQQHSSRKDHPTVPHSNTNNGRPPAKFMIPELHSSHSTLDL 250
Query: 304 PSPIPHS 310
PS
Sbjct: 251 PSDFISD 257
>gnl|CDD|226193 COG3667, PcoB, Uncharacterized protein involved in copper
resistance [Inorganic ion transport and metabolism].
Length = 321
Score = 33.3 bits (76), Expect = 0.14
Identities = 18/66 (27%), Positives = 22/66 (33%), Gaps = 14/66 (21%)
Query: 257 GSPHLPSQ-PQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAYPHM 315
PH P PH P H H PGP + + + H A PHM
Sbjct: 30 AQPHAHEHAPMDAPHPA-MPGMDHHAHS----------KMPGPEMAA--PQMDHGAMPHM 76
Query: 316 SHSHPQ 321
H+ P
Sbjct: 77 DHAPPP 82
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 33.1 bits (75), Expect = 0.19
Identities = 19/66 (28%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 256 GGSPHLPSQPQSHPHQNYHPAGSPHQHHLYQSSPII--PCSSPGPMIGSYPSPIPHSAYP 313
SP P+ HP ++H G P H L Q + P S+P G S +P P
Sbjct: 251 QQSPQPPAPSSRHPQSSHHGPGPPMPHALQQGPVFLQHPSSNPPQPFGLAQSQVPPLPLP 310
Query: 314 HMSHSH 319
+ H
Sbjct: 311 SQAQPH 316
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 32.3 bits (74), Expect = 0.26
Identities = 23/95 (24%), Positives = 31/95 (32%), Gaps = 8/95 (8%)
Query: 230 SATGFEETELSYNIGDDEQKVRQLVYGGSPHLPSQPQSHPHQNYH---PAGSPHQHHLYQ 286
S G + S + D G P PS P+ + PA S Q
Sbjct: 171 SFPGEDADPASASPSDPPS-----SSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPP 225
Query: 287 SSPIIPCSSPGPMIGSYPSPIPHSAYPHMSHSHPQ 321
SP P + P + P P P P +S + P
Sbjct: 226 PSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPT 260
>gnl|CDD|218581 pfam05416, Peptidase_C37, Southampton virus-type processing
peptidase. Corresponds to Merops family C37.
Norwalk-like viruses (NLVs), including the Southampton
virus, cause acute non-bacterial gastroenteritis in
humans. The NLV genome encodes three open reading frames
(ORFs). ORF1 encodes a polyprotein, which is processed
by the viral protease into six proteins.
Length = 535
Score = 32.5 bits (74), Expect = 0.28
Identities = 25/93 (26%), Positives = 35/93 (37%), Gaps = 22/93 (23%)
Query: 83 VQRGLKRTSDMCYEHDGRSS-----MTNLTGDCGSDIVDEGYSPSTQKGSP-PSNGKKTK 136
V R +KR M E R C S+ DEG+ Q +P GK K
Sbjct: 183 VNRAVKR---MFAEVWSRPPFGHDXEVTYYDGCESEEDDEGWYIEPQDATPEGKKGKNKK 239
Query: 137 GRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYE 169
GR K ++ FS+R G+ + Y+
Sbjct: 240 GRGK-----------KHNAFSRR--GLSDEEYD 259
>gnl|CDD|218163 pfam04592, SelP_N, Selenoprotein P, N terminal region. SelP is the
only known eukaryotic selenoprotein that contains
multiple selenocysteine (Sec) residues, and accounts for
more than 50% of the selenium content of rat and human
plasma. It is thought to be glycosylated. SelP may have
antioxidant properties. It can attach to epithelial
cells, and may protect vascular endothelial cells
against peroxynitrite toxicity. The high selenium
content of SelP suggests that it may be involved in
selenium intercellular transport or storage. The
promoter structure of bovine SelP suggest that it may be
involved in countering heavy metal intoxication, and may
also have a developmental function. The N-terminal
region of SelP can exist independently of the C terminal
region. Zebrafish selenoprotein Pb lacks the C terminal
Sec-rich region, and a protein encoded by the rat SelP
gene and lacking this region has also been reported.
N-terminal region contains a conserved SecxxCys motif,
which is similar to the CysxxCys found in thioredoxins.
It is speculated that the N terminal region may adopt a
thioredoxin fold and catalyze redox reactions. The
N-terminal region also contains a His-rich region, which
is thought to mediate heparin binding. Binding to
heparan proteoglycans could account for the membrane
binding properties of SelP. The function of the
bacterial members of this family is uncharcterised.
Length = 238
Score = 31.8 bits (72), Expect = 0.35
Identities = 12/61 (19%), Positives = 15/61 (24%)
Query: 259 PHLPSQPQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAYPHMSHS 318
P Q HPH + H H HH +S P H
Sbjct: 176 PVEAEPRQDHPHHHSHHEHQGHAHHHPHGHHHPGSNSHSESQQPDPDKPTEPPSGLHHHH 235
Query: 319 H 319
+
Sbjct: 236 N 236
>gnl|CDD|238917 cd01942, ribokinase_group_A, Ribokinase-like subgroup A. Found in
bacteria and archaea, this subgroup is part of the
ribokinase/pfkB superfamily. Its oligomerization state
is unknown at this time.
Length = 279
Score = 30.0 bits (68), Expect = 1.7
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 5 PTESCVVQCVLEIKVMDTPTGGGRDSRFSMGYNMSILNNET 45
E V V +KV+DT TG G D+ F G+ +L
Sbjct: 220 DGEEVEVPAVPAVKVVDT-TGAG-DA-FRAGFLYGLLRGYD 257
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 29.4 bits (66), Expect = 2.0
Identities = 10/56 (17%), Positives = 11/56 (19%), Gaps = 6/56 (10%)
Query: 265 PQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAYPHMSHSHP 320
P G +Q Y P PG Y P P
Sbjct: 127 LPQPPSTAPSYPGPQYQG--YHPMP----PQPGMPAPPYSLQYPPPGLLQPQGPPP 176
>gnl|CDD|221404 pfam12067, Sox_C_TAD, Sox C-terminal transactivation domain. This
domain is found at the C-terminus of the Sox family of
transcription factors. It is found associated with
pfam00505. It binds to the Armadillo repeats (pfam00514)
in Catenin beta-1 (CTNNB1), which is involved in
transcriptional regulation. It functions as a
transactivating domain (TAD).
Length = 197
Score = 28.5 bits (64), Expect = 3.9
Identities = 13/69 (18%), Positives = 22/69 (31%), Gaps = 7/69 (10%)
Query: 256 GGSPHLPSQPQSHPHQNYHPAGSPHQHHLYQSSPIIP-CSSPGPMIGSYPSPIPHSAY-- 312
+ PQ P + G P +Y +P C+ P+ SP P S +
Sbjct: 71 RQMAVTENIPQGSPAPSIM--GCPTPPQMYYGQMYVPECAKHHPVQLGQLSPPPESQHLD 128
Query: 313 --PHMSHSH 319
+ +
Sbjct: 129 TLDQLQQAE 137
>gnl|CDD|227478 COG5149, TOA1, Transcription initiation factor IIA, large chain
[Transcription].
Length = 293
Score = 28.5 bits (63), Expect = 4.6
Identities = 14/75 (18%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 41 LNNETSPEIYSSSVHSRASTSITSGLSRTLINNNNNNNCSSNVQRGLKRTSDMCYEHDGR 100
+ T+P + +S + ++++T+ S S + N +NN +T+D +D
Sbjct: 72 SLDVTAPAVANSPILNQSATN-ISFDSSAIPNVQSNNTAPFPSYSSTNQTADSPIINDHS 130
Query: 101 SSMTNLTGDCGSDIV 115
++ + GD ++++
Sbjct: 131 TANLKIYGDIIAEVI 145
>gnl|CDD|218146 pfam04554, Extensin_2, Extensin-like region.
Length = 57
Score = 25.9 bits (57), Expect = 5.9
Identities = 16/56 (28%), Positives = 19/56 (33%)
Query: 254 VYGGSPHLPSQPQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPH 309
Y P Q P Y P + +Y+S P SP P Y SP P
Sbjct: 2 HYKSPPPPVKQYSPPPPYYYKSPPPPVKSPVYKSPPPPVYKSPPPPKYVYKSPPPP 57
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins is
found in bacteria. Proteins in this family are typically
between 115 and 181 amino acids in length. There are two
completely conserved residues (F and G) that may be
functionally important.
Length = 110
Score = 27.0 bits (60), Expect = 6.1
Identities = 12/58 (20%), Positives = 13/58 (22%), Gaps = 8/58 (13%)
Query: 264 QPQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAYPHMSHSHPQ 321
P Y P Q YQ P + P P H PQ
Sbjct: 1 NPYQQNTNQYPP--QNQQQQPYQQQP------YHQQMPPPPYSPPQQQQGHFMPPQPQ 50
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 28.2 bits (63), Expect = 6.5
Identities = 12/88 (13%), Positives = 19/88 (21%), Gaps = 4/88 (4%)
Query: 239 LSYNIGDDEQKVRQLVYGGSPHLPSQPQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGP 298
L + + Q P QP + P + P +P P
Sbjct: 180 LPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQ 239
Query: 299 M----IGSYPSPIPHSAYPHMSHSHPQR 322
+P P Q+
Sbjct: 240 PPPLQQPQFPGLSQQMPPPPPQPPQQQQ 267
Score = 27.8 bits (62), Expect = 9.0
Identities = 12/69 (17%), Positives = 17/69 (24%), Gaps = 4/69 (5%)
Query: 257 GSPHLPSQPQSHPHQNYHPA----GSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAY 312
P P Q Q P P +PH + +P ++ P
Sbjct: 258 PPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRG 317
Query: 313 PHMSHSHPQ 321
P Q
Sbjct: 318 PQFREQLVQ 326
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 28.2 bits (63), Expect = 6.5
Identities = 17/70 (24%), Positives = 21/70 (30%), Gaps = 8/70 (11%)
Query: 256 GGSPHLPSQPQSHPHQNYHPAGSPHQHHLYQSSP--------IIPCSSPGPMIGSYPSPI 307
P QP PAG QH+ SP +P GP I + P +
Sbjct: 60 AQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGPAGPTIQTEPGQL 119
Query: 308 PHSAYPHMSH 317
P M
Sbjct: 120 YPVQVPVMVT 129
>gnl|CDD|219750 pfam08217, DUF1712, Fungal domain of unknown function (DUF1712).
The function of this family of proteins is unknown.
Length = 466
Score = 28.1 bits (63), Expect = 6.7
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 101 SSMTNLTGDCGSDIVDEGYSPSTQKGSPPSNGKKTKGRVKIKMEYIDNKL 150
S + + TG S + Y+PS + S S +K ++ K ++ + L
Sbjct: 225 SEVGSWTGIRNSPSLFMNYTPSGRVRSGSSENGDSKAKLDGKDGFLISPL 274
>gnl|CDD|215935 pfam00471, Ribosomal_L33, Ribosomal protein L33.
Length = 48
Score = 25.2 bits (56), Expect = 7.6
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 138 RVKIKMEYIDNKLRRYTTF-SKRKT 161
RVKI +E + R YTT +KR T
Sbjct: 1 RVKITLECTECGGRNYTTTKNKRNT 25
>gnl|CDD|217298 pfam02948, Amelogenin, Amelogenin. Amelogenins play a role in
biomineralisation. They seem to regulate the formation
of crystallites during the secretory stage of tooth
enamel development. thought to play a major role in the
structural organisation and mineralisation of developing
enamel. They are found in the extracellular matrix.
Mutations in X-chromosomal amelogenin can cause
Amelogenesis imperfecta.
Length = 174
Score = 27.2 bits (60), Expect = 9.3
Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 6/67 (8%)
Query: 259 PHLPSQPQSHPHQ--NYHPAGSPHQHHLYQS--SPIIPCSSPGPMIGSYPSPIPHSAYPH 314
P +P PQ P Q + HP +PH L P++P PM+ PH P
Sbjct: 49 PIIPLSPQ-MPQQQQSAHPKLTPHHQLLILPPQQPMMPVPGHHPMV-PMTGQQPHLQPPA 106
Query: 315 MSHSHPQ 321
P
Sbjct: 107 QHPLQPT 113
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
0.312 0.128 0.378
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,566,939
Number of extensions: 1399176
Number of successful extensions: 944
Number of sequences better than 10.0: 1
Number of HSP's gapped: 911
Number of HSP's successfully gapped: 63
Length of query: 322
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 225
Effective length of database: 6,635,264
Effective search space: 1492934400
Effective search space used: 1492934400
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 (21.8 bits)
S2: 59 (26.7 bits)