RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6461
(703 letters)
>gnl|CDD|218774 pfam05843, Suf, Suppressor of forked protein (Suf). This family
consists of several eukaryotic suppressor of forked
(Suf) like proteins. The Drosophila melanogaster
Suppressor of forked [Su(f)] protein shares homology
with the yeast RNA14 protein and the 77-kDa subunit of
human cleavage stimulation factor, which are proteins
involved in mRNA 3' end formation. This suggests a role
for Su(f) in mRNA 3' end formation in Drosophila. The
su(f) gene produces three transcripts; two of them are
polyadenylated at the end of the transcription unit, and
one is a truncated transcript, polyadenylated in intron
4. It is thought that su(f) plays a role in the
regulation of poly(A) site utilisation and an important
role of the GU-rich sequence for this regulation to
occur.
Length = 271
Score = 37.3 bits (87), Expect = 0.021
Identities = 15/32 (46%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
Query: 158 PETAVRVFRRYLKLFPEDAE---DYIEYLSSI 186
P+TA ++F LKLF ED E Y++YL S+
Sbjct: 52 PKTAFKIFELGLKLFGEDGEFVLKYLDYLISL 83
>gnl|CDD|214642 smart00386, HAT, HAT (Half-A-TPR) repeats. Present in several
RNA-binding proteins. Structurally and sequentially
thought to be similar to TPRs.
Length = 33
Score = 31.4 bits (72), Expect = 0.078
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 533 ERARDLFEQCLEACPPRYAKTLYLLYAKLEEE 564
ERAR ++E+ LE P + L+L YA+ EE
Sbjct: 4 ERARKIYERALEKFP--KSVELWLKYAEFEER 33
Score = 28.7 bits (65), Expect = 0.74
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 52 IYERSLKELPGSYKLWYNYLKLRRK 76
IYER+L++ P S +LW Y + +
Sbjct: 9 IYERALEKFPKSVELWLKYAEFEER 33
Score = 28.7 bits (65), Expect = 0.82
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 266 GLFERARDIYEEAIQTVTTVRDFTQVFDAYAQFEE 300
G ERAR IYE A+ +++ YA+FEE
Sbjct: 1 GDIERARKIYERAL---EKFPKSVELWLKYAEFEE 32
Score = 27.1 bits (61), Expect = 2.6
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 93 NTFERSLVFMHKMPRIWLDYGRFLM 117
+ER+L K +WL Y F
Sbjct: 8 KIYERALEKFPKSVELWLKYAEFEE 32
>gnl|CDD|219834 pfam08424, NRDE-2, NRDE-2, necessary for RNA interference. This is
a family of eukaryotic proteins. Eukaryotic cells
express a wide variety of endogenous small regulatory
RNAs that regulate heterochromatin formation,
developmental timing, defence against parasitic nucleic
acids, and genome rearrangement. Many small regulatory
RNAs are thought to function in nuclei, and in plants
and fungi small interfering (si)RNAs associate with
nascent transcripts and direct chromatin and/or DNA
modifications. This family protein, NRDE-2, is required
for small interfering (si)RNA-mediated silencing in
nuclei. NRDE-2 associates with the Argonaute protein
NRDE-3 within nuclei and is recruited by NRDE-3/siRNA
complexes to nascent transcripts that have been targeted
by RNA interference, RNAi, the process whereby
double-stranded RNA (dsRNA) directs the
sequence-specific degradation of mRNA.
Length = 324
Score = 35.0 bits (81), Expect = 0.11
Identities = 26/90 (28%), Positives = 37/90 (41%), Gaps = 8/90 (8%)
Query: 20 YEEEILRNPFSVKHWLRYIE--HKKNAPKAIINTIYERSLKELPGSYKLWYNYLKLRRKQ 77
E+ + NP S + L +E K ++ E+ LKE PGS KLW YL R+
Sbjct: 56 LEKALKHNPDSERLLLGLLEEGEKVWDTDELLKRW-EKVLKENPGSPKLWRKYLDFRQGD 114
Query: 78 VKGKVITDPSYEDVNNTFERSLVFMHKMPR 107
SY V T+E+ L +
Sbjct: 115 FSTF-----SYSKVRKTYEKCLRALKAALN 139
Score = 35.0 bits (81), Expect = 0.12
Identities = 27/145 (18%), Positives = 52/145 (35%), Gaps = 31/145 (21%)
Query: 11 TTENEEDLPYEEEILRNPFSVKHWLRYIEH------------KKNAPKAIIN---TIYER 55
N E ++ NP + W+ I K K + +I E+
Sbjct: 2 LKRNAE---LNRKVRENPEDIDAWIELIRFQEELLRLSRRRSTKAERKQLAEKKLSILEK 58
Query: 56 SLKELPGSYKLWYNYLKLRRKQVKGKVITDPSYEDVNNTFERSLVFMHK-MPRIWLDYGR 114
+LK P S +L L+ K + +++ +E ++ + P++W Y
Sbjct: 59 ALKHNPDSERLLLGLLEEGEK-------VWDT-DELLKRWE-KVLKENPGSPKLWRKYLD 109
Query: 115 FLMDQ---HKITQTRHVFDRALRAL 136
F ++ R +++ LRAL
Sbjct: 110 FRQGDFSTFSYSKVRKTYEKCLRAL 134
>gnl|CDD|221958 pfam13176, TPR_7, Tetratricopeptide repeat.
Length = 36
Score = 28.7 bits (65), Expect = 0.81
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 254 LWNSLADYYIRSGLFERARDIYEEAIQTVTTVRD 287
++L Y + G +E+A +YE A+ D
Sbjct: 1 ALSNLGRLYRKLGDYEKAISLYERALALAKDPED 34
>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif). This
model describes a domain called the PPR motif, or
pentatricopeptide repeat. Its consensus sequence is 35
positions long and typically is found in four or more
tandem copies. This family is strongly represented in
plant proteins, particularly those sorted to
chloroplasts or mitochondria. The pfam model pfam01535,
domain of unknown function DUF17, consists of 6 copies
of this repeat. This family has a similar consensus to
the TPR domain (tetratricopeptide), pfam pfam00515, a
33-residue repeat. It is predicted to form a pair of
antiparallel helices similar to that of TPR.
Length = 35
Score = 28.6 bits (65), Expect = 0.94
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 253 HLWNSLADYYIRSGLFERARDIYEE 277
+N+L D ++G E A ++++E
Sbjct: 1 VTYNTLIDGLCKAGRVEEALELFKE 25
>gnl|CDD|239458 cd03342, TCP1_zeta, TCP-1 (CTT or eukaryotic type II) chaperonin
family, zeta subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 484
Score = 32.2 bits (74), Expect = 0.99
Identities = 26/95 (27%), Positives = 44/95 (46%), Gaps = 17/95 (17%)
Query: 1 PESTGFTGI--YTTENEEDLPYEEEILRNPFSV--------KHWLRYIEHK-KNAPKAII 49
PE G+ G+ T EE + E + +NP S H + I+ ++ +A+
Sbjct: 299 PECLGYAGLVYERTLGEEKYTFIEGV-KNPKSCTILIKGPNDHTITQIKDAIRDGLRAVK 357
Query: 50 NTIYERSLKELPGSYKLW---YNYLKLRRKQVKGK 81
N I ++ + +PG+ Y +LK +K VKGK
Sbjct: 358 NAIEDKCV--VPGAGAFEVALYAHLKEFKKSVKGK 390
>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family. This repeat has no known
function. It is about 35 amino acids long and is found
in up to 18 copies in some proteins. The family appears
to be greatly expanded in plants and fungi. The repeat
has been called PPR.
Length = 50
Score = 28.5 bits (65), Expect = 1.1
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 255 WNSLADYYIRSGLFERARDIYEE 277
+N+L D Y + G E A ++ E
Sbjct: 6 YNTLIDGYCKKGKVEEALKLFNE 28
>gnl|CDD|153104 cd01045, Ferritin_like_AB, Uncharacterized family of ferritin-like
proteins found in archaea and bacteria. Ferritin-like
domain found in archaea and bacteria (Ferritin_like_AB).
This uncharacterized domain is a member of a broad
superfamily of ferritin-like diiron-carboxylate proteins
whose function is unknown. This family includes unknown
or hypothetical proteins which were sequenced from
mostly anaerobic or microaerophilic metal-metabolizing
and/or nitrogen-fixing microbes. The family includes
sequences from ferric-, sulfate-, and arsenic-reducing
bacteria, Geobacter, Magnetospirillum, Desulfovibrio,
and Desulfitobacterium. Also included are several
nitrogen-fixing endosymbiotic bacteria, Rhizobium,
Mesorhizobium, and Bradyrhizobium; also phototrophic
purple nonsulfur bacteria, Rhodobacter and
Rhodopseudomonas, as well as, obligate thermophiles,
Thermotoga, Thermoanaerobacter, and Pyrococcus. The
conserved residues of a diiron center are present in
this uncharacterized domain.
Length = 139
Score = 30.4 bits (69), Expect = 1.4
Identities = 24/120 (20%), Positives = 41/120 (34%), Gaps = 20/120 (16%)
Query: 533 ERARDLFEQCLEACPPRYAKTLYLLYAKLEEEHGLARHAMAVYERATGAVLP-------- 584
E A + + + E K L+ A+ E+EH A +YE+ G LP
Sbjct: 11 EEAAEFYLELAEKAKDPELKKLFEELAEEEKEH--AERLEELYEKLFGEELPELEPEDYK 68
Query: 585 -----EEMFEMFNIYIKKAAEIYGIP-----KTRQIYERAIESLPEEPTRQMCLKFAEME 634
E F+ + E + + YE E + +++ + AE E
Sbjct: 69 EEVEEEPEFKKALESLMDPLEALRLAIEIEKDAIEFYEELAEKAEDPEVKKLFEELAEEE 128
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 32.0 bits (73), Expect = 1.4
Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 5/111 (4%)
Query: 89 EDVNNTFERSLVFMHKMPRIWLDYGRFLMDQHKITQTRHVFDRALRALPITQHHRVWPLY 148
E ++E++L + L + + +++ + R + D L A P + L
Sbjct: 142 ELAQKSYEQALAIDPRSLYAKLGLAQLALAENRFDEARALIDEVLTADP--GNVDALLLK 199
Query: 149 LSFVKSHAVPETAVRVFRRYLKLFPEDAEDYI-EYLSSIE--RLDEAAVKL 196
+ S E A+ +R+ + L P + + IE +EA
Sbjct: 200 GDLLLSLGNIELALAAYRKAIALRPNNIAVLLALATILIEAGEFEEAEKHA 250
>gnl|CDD|144943 pfam01535, PPR, PPR repeat. This repeat has no known function. It
is about 35 amino acids long and found in up to 18
copies in some proteins. This family appears to be
greatly expanded in plants. This repeat occurs in
PET309, which may be involved in RNA stabilisation. This
domain occurs in crp1 that is involved in RNA
processing. This repeat is associated with a predicted
plant protein that has a domain organisation similar to
the human BRCA1 protein. The repeat has been called PPR.
Length = 31
Score = 27.4 bits (62), Expect = 1.9
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 255 WNSLADYYIRSGLFERARDIYEE 277
+NSL Y ++G E A ++++E
Sbjct: 3 YNSLISGYCKAGKLEEALELFKE 25
>gnl|CDD|191825 pfam07719, TPR_2, Tetratricopeptide repeat. This Pfam entry
includes outlying Tetratricopeptide-like repeats (TPR)
that are not matched by pfam00515.
Length = 34
Score = 27.1 bits (61), Expect = 2.4
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 254 LWNSLADYYIRSGLFERARDIYEEAIQ 280
+L Y + G +E A + YE+A++
Sbjct: 3 ALYNLGLAYYKLGDYEEALEAYEKALE 29
>gnl|CDD|224377 COG1460, COG1460, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 114
Score = 29.2 bits (66), Expect = 2.6
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 161 AVRVFRRYLKLFPEDAEDYIEYLSSIERLDE-AAVKLAYI 199
A+ ++ KL PE A + +E L SI ++ E AVK+A I
Sbjct: 38 ALEYAEKFAKLDPEKARELVEELLSIVKMSEKIAVKIADI 77
>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain. This family
matches additional variants of the PPR repeat that were
not captured by the model for pfam01535. The exact
function is not known.
Length = 34
Score = 27.1 bits (61), Expect = 2.9
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 253 HLWNSLADYYIRSGLFERARDIYEE 277
+N+L ++G + A + EE
Sbjct: 2 ETYNALLLALAKAGDPDLALAVLEE 26
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 30.7 bits (70), Expect = 3.0
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 346 LLRQNPHNVLEWHKRVRLFDGKPLDIIRTYT--EAVKTVDPKLA---VGKLHTLWIEFGK 400
L+ ++ ++L+ H+ R GK L + T+ EA+ +D A +GKL + G
Sbjct: 44 LINRSVIDILKAHRFARRIVGKELSVRETFPILEALSKLDLGPARVDIGKLAVKYKAEGD 103
Query: 401 FYEVNDQLEDA 411
+V + +
Sbjct: 104 GSDVEAFVAEE 114
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 28.0 bits (63), Expect = 3.2
Identities = 6/27 (22%), Positives = 15/27 (55%)
Query: 254 LWNSLADYYIRSGLFERARDIYEEAIQ 280
+L + + G ++ A + YE+A++
Sbjct: 5 ALKNLGNALFKLGDYDEAIEAYEKALE 31
>gnl|CDD|227518 COG5191, COG5191, Uncharacterized conserved protein, contains HAT
(Half-A-TPR) repeat [General function prediction only].
Length = 435
Score = 30.7 bits (69), Expect = 3.2
Identities = 18/97 (18%), Positives = 32/97 (32%), Gaps = 8/97 (8%)
Query: 20 YEEEILRNPFSVKHWLRYIEH-KKNAPKAIINTIYERSLKELPGSYKLWYNYLKLRRKQV 78
+ K W +Y + K + I+ L + P + LW
Sbjct: 96 LYRSTNKFFNDPKIWSQYAAYVIKKKMYGEMKNIFAECLTKHPLNVDLWIYCCAF----- 150
Query: 79 KGKVITDPSYEDVNNTFERSLVFMHKMPRIWLDYGRF 115
++ + E F + L + PRIW++Y R
Sbjct: 151 --ELFEIANIESSRAMFLKGLRMNSRSPRIWIEYFRM 185
>gnl|CDD|222122 pfam13429, TPR_15, Tetratricopeptide repeat.
Length = 279
Score = 30.0 bits (68), Expect = 4.1
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 418 ATLVPYTKVEDLATVWCEWAELELRAGQEEAALRLMARA 456
A+L P E A AE + GQ +AALR RA
Sbjct: 133 ASLTPEEAAEQSAGFLSARAEYYRQTGQPDAALRDYRRA 171
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 27.7 bits (62), Expect = 4.2
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 250 QLGHLWNSLADYYIRSGLFERARDIYEEAIQ 280
L N+LA R G ++ A ++ E+A++
Sbjct: 3 DLAAALNNLALVLRRLGDYDEALELLEKALE 33
>gnl|CDD|205362 pfam13181, TPR_8, Tetratricopeptide repeat.
Length = 34
Score = 26.7 bits (60), Expect = 4.2
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 253 HLWNSLADYYIRSGLFERARDIYEEAIQ 280
+ L Y++ G +E A++ YE+A++
Sbjct: 2 RAYYLLGQIYLQLGDYEEAKEYYEKALE 29
>gnl|CDD|215274 PLN02496, PLN02496, probable phosphopantothenoylcysteine
decarboxylase.
Length = 209
Score = 29.6 bits (66), Expect = 4.9
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 403 EVNDQLEDARLIFDKATLVPYTKVEDLATVWCEWAELELRAGQEEAALRLMARATATPAR 462
EVN R++ + V K +L + EWA E+RA +A+L + RA + P
Sbjct: 12 EVNTAPRKPRILLAASGSVAAIKFGNLCHCFSEWA--EVRAVVTKASLHFIDRA-SLPKD 68
Query: 463 PVAYHDEAE 471
Y DE E
Sbjct: 69 VTLYTDEDE 77
>gnl|CDD|227438 COG5107, RNA14, Pre-mRNA 3'-end processing (cleavage and
polyadenylation) factor [RNA processing and
modification].
Length = 660
Score = 30.0 bits (67), Expect = 5.5
Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 5/89 (5%)
Query: 50 NTIYERSLKELP-GSYKLWYNYLKLRRKQVKGKVITDPSYEDVNNTFERSLVFMHKMPRI 108
N I R+ + S W N++K + K+ P + ++ + L + + +
Sbjct: 246 NPINLRTANKAARTSDSNWLNWIKWEMEN-GLKLGGRPHEQRIHYIHNQILDYFYYAEEV 304
Query: 109 WLDYGRFLMDQHKITQTRHVFDRALRALP 137
W DY +L+ I+ + R +
Sbjct: 305 WFDYSEYLIG---ISDKQKALKTVERGIE 330
>gnl|CDD|133003 cd02509, GDP-M1P_Guanylyltransferase, GDP-M1P_Guanylyltransferase
catalyzes the formation of GDP-Mannose.
GDP-mannose-1-phosphate guanylyltransferase, also called
GDP-mannose pyrophosphorylase (GDP-MP), catalyzes the
formation of GDP-Mannose from mannose-1-phosphate and
GTP. Mannose is a key monosaccharide for glycosylation
of proteins and lipids. GDP-Mannose is the activated
donor for mannosylation of various biomolecules. This
enzyme is known to be bifunctional, as both
mannose-6-phosphate isomerase and mannose-1-phosphate
guanylyltransferase. This CD covers the N-terminal
GDP-mannose-1-phosphate guanylyltransferase domain,
whereas the isomerase function is located at the
C-terminal half. GDP-MP is a member of the
nucleotidyltransferase family of enzymes.
Length = 274
Score = 29.5 bits (67), Expect = 5.8
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 245 RRYTDQLGHLWNS-----LADYYIRSGLFER-ARDIY---EEAIQTVTTVRDFTQVFDAY 295
+ Y + +LWNS A ++ ++ A DIY E+A+ T + +A+
Sbjct: 180 KEYLESGNYLWNSGIFLFRAKTFLE--ELKKHAPDIYEALEKALAAAGTDDFLRLLEEAF 237
Query: 296 AQFEELS 302
A+ +S
Sbjct: 238 AKIPSIS 244
>gnl|CDD|173172 PRK14709, PRK14709, hypothetical protein; Provisional.
Length = 469
Score = 29.7 bits (67), Expect = 6.0
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 10/78 (12%)
Query: 407 QLEDARLIFDKATLVPYTKVEDLATVWCEWAELEL-RAGQEEAALRLMARATATPARPVA 465
Q + R I D V + ++DL WCE+A E AG + M + R
Sbjct: 391 QWLEERCIVDPGNPVCWDVLQDLYASWCEFARAEGEPAGTAKEFGERMEKLGFKKDR--- 447
Query: 466 YHDEAETVQARVYKSIKL 483
+ R ++ I+L
Sbjct: 448 ------KNRGRGFRGIQL 459
>gnl|CDD|218005 pfam04285, DUF444, Protein of unknown function (DUF444). Bacterial
protein of unknown function. One family member is
predicted to contain a von Willebrand factor (vWF) type
A domain (Smart:VWA).
Length = 421
Score = 29.7 bits (67), Expect = 6.0
Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 7/74 (9%)
Query: 311 AENDTPSEEDDIELELRLARLEDLMERRLLLLNSVLLRQNPHNVLEWHKRVRLFDGKPL- 369
A D E DD E E+ + DL+ L L N L ++ + E+ +
Sbjct: 104 AAGDGEGE-DDFEFEVSREEVLDLLFEDLELPN--LKKKEADQIDEFKTERAGIQKSGVP 160
Query: 370 ---DIIRTYTEAVK 380
+ +RT A+K
Sbjct: 161 ANINKVRTLRSAIK 174
>gnl|CDD|233575 TIGR01783, TonB-siderophor, TonB-dependent siderophore receptor.
This subfamily model encompasses a wide variety of
TonB-dependent outer membrane siderophore receptors. It
has no overlap with TonB receptors known to transport
other substances, but is likely incomplete due to lack
of characterizations. It is likely that genuine
siderophore receptors will be identified which score
below the noise cutoff to this model at which point the
model should be updated [Transport and binding proteins,
Cations and iron carrying compounds, Transport and
binding proteins, Porins].
Length = 651
Score = 29.7 bits (67), Expect = 6.4
Identities = 12/32 (37%), Positives = 12/32 (37%)
Query: 474 QARVYKSIKLWSLYADLEESFGTFKAYEKGIA 505
YK WSLYA ESF KG
Sbjct: 412 LGVAYKPTDDWSLYASYAESFKPGGYAPKGAG 443
>gnl|CDD|153339 cd07655, F-BAR_PACSIN, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Protein
kinase C and Casein kinase Substrate in Neurons (PACSIN)
proteins, also called Synaptic dynamin-associated
proteins (Syndapins), act as regulators of cytoskeletal
and membrane dynamics. They bind both dynamin and
Wiskott-Aldrich syndrome protein (WASP), and may provide
direct links between the actin cytoskeletal machinery
through WASP and dynamin-dependent endocytosis.
Vetebrates harbor three isoforms with distinct
expression patterns and specific functions. PACSINs
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 258
Score = 29.2 bits (66), Expect = 6.4
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 269 ERARDIYEEAIQTVTT-----VRDFTQVFDAYAQFEE 300
+ +D YE+A++ + + D QVFD +FEE
Sbjct: 185 SKTKDKYEKALEDLNKYNPRYMEDMEQVFDKCQEFEE 221
>gnl|CDD|216902 pfam02146, SIR2, Sir2 family. This region is characteristic of
Silent information regulator 2 (Sir2) proteins, or
sirtuins. These are protein deacetylases that depend on
nicotine adenine dinucleotide (NAD). They are found in
many subcellular locations, including the nucleus,
cytoplasm and mitochondria. Eukaryotic forms play in
important role in the regulation of transcriptional
repression. Moreover, they are involved in microtubule
organisation and DNA damage repair processes.
Length = 177
Score = 28.7 bits (65), Expect = 7.2
Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 1/66 (1%)
Query: 5 GFTGIYTTENEEDLPYEEEILRNPFSVKHWLRYIEHKKNAPKAIINTIYERSLKELPGSY 64
G+Y +E+L E NP+ V I + A N + + EL
Sbjct: 15 SDDGLYAKLAKEELASPEAFFSNPYLVWDPFYNIARELLPGPAQPNPAH-YFIAELEDKG 73
Query: 65 KLWYNY 70
KL
Sbjct: 74 KLLRLI 79
>gnl|CDD|106077 PRK13040, PRK13040, superantigen-like protein; Reviewed.
Length = 231
Score = 28.9 bits (64), Expect = 7.2
Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 15/104 (14%)
Query: 231 IRSLNVDAIIRGGLRRYTDQLGHLWNSLADYYIRSGLFERARDIYEEAIQTVTTVRDFTQ 290
I N+D + R + TD+ ++W DY++ GL + + Y +
Sbjct: 52 IELKNLDGLYRQKV---TDKGVYVWKDRKDYFV--GLLGKDIEKYPQ---------GEHD 97
Query: 291 VFDAYAQFEELSLNKRMEEIAE-NDTPSEEDDIELELRLARLED 333
DA+ EE ++N R I + T S+E E+++++ R D
Sbjct: 98 KQDAFLVIEEETVNGRQYSIGGLSKTNSKEFSKEVDVKVTRKID 141
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 29.4 bits (66), Expect = 8.3
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 421 VPYTKVEDLATVWCEWAELELRAGQEEAALRLMARATATPARPVAYHD 468
VP + E + VW E + + + G +AA+ L+ A AR + +D
Sbjct: 133 VPKSSPEITSEVWSELVDFQ-KNGDWDAAVELVVNAGDPKARSLPRND 179
>gnl|CDD|222121 pfam13428, TPR_14, Tetratricopeptide repeat.
Length = 44
Score = 26.0 bits (57), Expect = 8.7
Identities = 5/27 (18%), Positives = 10/27 (37%)
Query: 254 LWNSLADYYIRSGLFERARDIYEEAIQ 280
+LA + G + A + A+
Sbjct: 3 ALLALARALLALGDLDEALALLRRALA 29
>gnl|CDD|237234 PRK12854, PRK12854, glucose-6-phosphate 1-dehydrogenase;
Provisional.
Length = 484
Score = 29.2 bits (66), Expect = 8.9
Identities = 21/88 (23%), Positives = 32/88 (36%), Gaps = 14/88 (15%)
Query: 545 ACPPRYAKTLYLLYAKLEEEHGLARHAMAVYERATGAVLPEEMFEMFNIYIKKAAEIYGI 604
A PP + E GLA + V E+ G L E N A ++ +
Sbjct: 125 AVPPSAFLD----VTRALGEAGLAEGSRVVMEKPFGTDL--ASAEALN------AAVHEV 172
Query: 605 PKTRQIYERAIESLPEEPTRQ-MCLKFA 631
QI+ R L +E + + +FA
Sbjct: 173 FDESQIF-RIDHFLGKEAAQNILAFRFA 199
>gnl|CDD|227633 COG5323, COG5323, Uncharacterized conserved protein [Function
unknown].
Length = 410
Score = 29.1 bits (65), Expect = 9.4
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 15/49 (30%)
Query: 519 YLTKFLSRYGGTKLER---------------ARDLFEQCLEACPPRYAK 552
+L SRYGGT+L R R+ E+C EA P +
Sbjct: 202 FLRTLASRYGGTRLGRQELDGELVEEDGALWRREDLERCREARPAPLDR 250
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 28.9 bits (66), Expect = 9.5
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 309 EIAENDTPSEEDDIELELRL 328
IAEN P EE ++ LEL+L
Sbjct: 138 RIAENGEPGEERELRLELKL 157
>gnl|CDD|233721 TIGR02092, glgD, glucose-1-phosphate adenylyltransferase, GlgD
subunit. This family is GlgD, an apparent regulatory
protein that appears in an alpha2/beta2 heterotetramer
with GlgC (glucose-1-phosphate adenylyltransferase,
TIGR02091) in a subset of bacteria that use GlgC for
glycogen biosynthesis [Energy metabolism, Biosynthesis
and degradation of polysaccharides].
Length = 369
Score = 28.9 bits (65), Expect = 9.5
Identities = 24/106 (22%), Positives = 47/106 (44%), Gaps = 13/106 (12%)
Query: 242 GGLRRYTDQLGHLWNSLADYYIRSGL-------FERARDIYEEAIQTVTTVRDFTQVFDA 294
GG R ++ L L S ++Y + + +EE + +T V + +V A
Sbjct: 97 GGKRYFSQNLEFLKRSTSEYTVVLNSHMVCNIDLKAVLKYHEETGKDITVV--YKKVKPA 154
Query: 295 YAQFEELSLNK----RMEEIAENDTPSEEDDIELELRLARLEDLME 336
A + L +++ I +N P EE++I L++ + + L+E
Sbjct: 155 DASEYDTILRFDESGKVKSIGQNLNPEEEENISLDIYIVSTDLLIE 200
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
0.321 0.136 0.411
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 37,774,874
Number of extensions: 3870117
Number of successful extensions: 4262
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4247
Number of HSP's successfully gapped: 74
Length of query: 703
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 599
Effective length of database: 6,324,786
Effective search space: 3788546814
Effective search space used: 3788546814
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: 63 (28.1 bits)