RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5660
(337 letters)
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 56.9 bits (138), Expect = 7e-11
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 39 ELATTYKDEGNFNFKCNKYRNAIINYTEGLKIKCADNDVNAQLYNNRAASNFFL-KNYRS 97
+ A K+ GN FK Y AI Y + L++ + NA+ Y N A + L K+Y
Sbjct: 1 DNAEALKNLGNALFKLGDYDEAIEAYEKALEL----DPDNAEAYYNLALAYLKLGKDYEE 56
Query: 98 CLTDCQIALKLKP 110
L D + AL+L P
Sbjct: 57 ALEDLEKALELDP 69
Score = 46.2 bits (110), Expect = 5e-07
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 78 NAQLYNNRAASNFFLKNYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHL-KKFEDCTHLC 136
NA+ N + F L +Y + + AL+L PD + A L K +E+
Sbjct: 2 NAEALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALEDL 61
Query: 137 DELLKENP 144
++ L+ +P
Sbjct: 62 EKALELDP 69
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 53.9 bits (130), Expect = 2e-09
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 4/102 (3%)
Query: 44 YKDEGNFNFKCNKYRNAIINYTEGLKIKCADNDVNAQLYNNRAASNFFLKNYRSCLTDCQ 103
+ GN +K Y A+ Y + L++ + NA Y N AA+ + L Y L D +
Sbjct: 3 LLNLGNLYYKLGDYDEALEYYEKALEL----DPDNADAYYNLAAAYYKLGKYEEALEDYE 58
Query: 104 IALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENPT 145
AL+L PD K + L K+E+ ++ L+ +P
Sbjct: 59 KALELDPDNAKAYYNLGLAYYKLGKYEEALEAYEKALELDPN 100
Score = 40.4 bits (95), Expect = 1e-04
Identities = 15/71 (21%), Positives = 29/71 (40%)
Query: 80 QLYNNRAASNFFLKNYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDEL 139
+ N + L +Y L + AL+L PD A + L K+E+ ++
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKA 60
Query: 140 LKENPTDSTVI 150
L+ +P ++
Sbjct: 61 LELDPDNAKAY 71
>gnl|CDD|233223 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 615
Score = 48.8 bits (116), Expect = 2e-06
Identities = 50/184 (27%), Positives = 75/184 (40%), Gaps = 41/184 (22%)
Query: 34 ENTPEELATTYKDEGNFNFKCNKYRNAIINYTEGLKIKCADNDVNAQLYNNRAASNFFLK 93
E ++ A K++GN ++ + AI Y++ I+C + V Y+NRAA + L
Sbjct: 120 EEERKKYAAKLKEKGNKAYRNKDFNKAIKLYSKA--IECKPDPV---YYSNRAACHNALG 174
Query: 94 NYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTDSTVIDLR 153
++ + D AL+L PDY K R A L K+ D ++DL
Sbjct: 175 DWEKVVEDTTAALELDPDYSKALNRRANAYDGLGKYAD----------------ALLDLT 218
Query: 154 TSCINKHKEILRNERKQAQQVKKEEKEKERVLQIIRERKIKLATSGKGDLKSFSDLEPNF 213
SCI RNE + AQ V ER+L+ E K K + N
Sbjct: 219 ASCIIDG---FRNE-QSAQAV-------ERLLKKFAESKAK---------EILETKPENL 258
Query: 214 PEIT 217
P +T
Sbjct: 259 PSVT 262
Score = 33.0 bits (75), Expect = 0.25
Identities = 22/124 (17%), Positives = 40/124 (32%), Gaps = 11/124 (8%)
Query: 55 NKYRNAIINYTEGLKIKCADNDVNAQLYNNRAASNFFLKNYRSCLTDCQIALKLKPD--Y 112
N E N + +Y +RA +F + D Q ++ L PD +
Sbjct: 375 NLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIF 434
Query: 113 PKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTDSTVIDLRTSCINKHKEILRNERKQAQ 172
++L Q + K P V N + E+L ++ K +
Sbjct: 435 SHIQLGVTQ--YKEGSIASSMATFRRCKKNFPEAPDV-------YNYYGELLLDQNKFDE 485
Query: 173 QVKK 176
++K
Sbjct: 486 AIEK 489
>gnl|CDD|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only].
Length = 291
Score = 37.9 bits (86), Expect = 0.005
Identities = 27/166 (16%), Positives = 58/166 (34%), Gaps = 4/166 (2%)
Query: 33 LENTPEELATTYKDEGNFNFKCNKYRNAIINYTEGLKIKCADNDVNAQLYNNRAASNFFL 92
L P+ ++ Y A+ Y + L++ N+ A+ A L
Sbjct: 122 LALDPDPDLAEALLALGALYELGDYEEALELYEKALELDPELNE-LAEALLALGALLEAL 180
Query: 93 KNYRSCLTDCQIALKLKPD-YPKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTDSTVID 151
Y L + ALKL PD + L L K+E+ ++ L+ +P ++ +
Sbjct: 181 GRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALY 240
Query: 152 LRTSCINKHKEI--LRNERKQAQQVKKEEKEKERVLQIIRERKIKL 195
+ + ++A ++ + L ++ ++L
Sbjct: 241 NLALLLLELGRYEEALEALEKALELDPDLYNLGLALLLLLAEALEL 286
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 32.8 bits (76), Expect = 0.011
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 79 AQLYNNRAASNFFLKNYRSCLTDCQIALKLKPDY 112
A+ N + L Y L + AL+L P+
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEKALELNPNN 34
>gnl|CDD|197478 smart00028, TPR, Tetratricopeptide repeats. Repeats present in 4
or more copies in proteins. Contain a minimum of 34
amino acids each and self-associate via a "knobs and
holes" mechanism.
Length = 34
Score = 32.4 bits (75), Expect = 0.016
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 79 AQLYNNRAASNFFLKNYRSCLTDCQIALKLKPDY 112
A+ N + L +Y L + AL+L P+
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 31.9 bits (73), Expect = 0.049
Identities = 11/58 (18%), Positives = 18/58 (31%)
Query: 90 FFLKNYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTDS 147
+Y L + AL P + L + L + + L L +P D
Sbjct: 8 LRAGDYDEALAALEAALARYPLAAEALLLLGEALLRQGRLAEAAALLRAALAADPDDP 65
>gnl|CDD|173112 PRK14649, PRK14649, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 295
Score = 33.3 bits (76), Expect = 0.14
Identities = 25/128 (19%), Positives = 46/128 (35%), Gaps = 35/128 (27%)
Query: 224 DDNDRLVWPVLFLYPEYRITDFVQEFHEDVTFDSMLEEMFSESPGWDEDRKYV-PGRLSI 282
+ ++ + W V DF + S+L+++ ++ W V R +
Sbjct: 146 NGSECVEWSV---------HDFAYGYRT-----SVLKQLRADGITWRP--PLVLAARFRL 189
Query: 283 YYQDP-----------NGKPQRVPTTSTLGEVLTNP------KYVIQAGTPGFSILVAD- 324
+ DP + Q+ P S+ G V NP + + AG G I A+
Sbjct: 190 HRDDPTALAARMEAIAAERKQKTPAGSSCGSVFKNPPGDSAGRLIEAAGLKGTRIGDAEI 249
Query: 325 SKEEAQFI 332
+ A +I
Sbjct: 250 ATRHANYI 257
>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 = 32.4 bits (74), Expect = 0.42
Identities = 25/107 (23%), Positives = 44/107 (41%), Gaps = 11/107 (10%)
Query: 40 LATTYKDEGNFNFKCNKYRNAIINYTEGLKIKCADNDVNAQLYNNRAASNFFLKNYRSCL 99
L G+ N A+ ++ + L + +A A + +KNY +
Sbjct: 607 LGRAQLAAGDLN-------KAVSSFKKLLAL----QPDSALALLLLADAYAVMKNYAKAI 655
Query: 100 TDCQIALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTD 146
T + AL+LKPD + ++ AQ L K+ E + L K++P
Sbjct: 656 TSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKA 702
Score = 32.0 bits (73), Expect = 0.48
Identities = 16/54 (29%), Positives = 21/54 (38%)
Query: 93 KNYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTD 146
KNY Q ALK P+Y L A + L E +++LK P
Sbjct: 275 KNYEDARETLQDALKSAPEYLPALLLAGASEYQLGNLEQAYQYLNQILKYAPNS 328
Score = 30.8 bits (70), Expect = 1.0
Identities = 27/119 (22%), Positives = 44/119 (36%), Gaps = 11/119 (9%)
Query: 26 QQLKYDPLENTPEELATTYKDEGNFNFKCNKYRNAIINYTEGLKIKCADNDVNAQLYNNR 85
L Y + P LA Y +G F +++ G + D++ A+L R
Sbjct: 83 LSLGYPKNQVLPL-LARAYLLQGKFQ--------QVLDELPGKTLL--DDEGAAELLALR 131
Query: 86 AASNFFLKNYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENP 144
+ L + AL + P KL AQ +F++ L DE+L +P
Sbjct: 132 GLAYLGLGQLELAQKSYEQALAIDPRSLYAKLGLAQLALAENRFDEARALIDEVLTADP 190
Score = 28.5 bits (64), Expect = 7.2
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 105 ALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENP 144
A+ L+P+ V L A L +FE+ D LLK+ P
Sbjct: 219 AIALRPNNIAVLLALATILIEAGEFEEAEKHADALLKKAP 258
>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
Length = 897
Score = 32.1 bits (73), Expect = 0.48
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 27/116 (23%)
Query: 202 DLKSFSDLEPNFPEITLRPVHTDDNDRLVWPVLFLYPEYRITDFVQEFHE-DVTFDSMLE 260
+L D E + E + H DD+ + P I D Q + +V D +
Sbjct: 253 ELGDIPDAETRYKE--WKKEHKDDDPSNL-------PPLDIIDTGQPYDIFNVVTDPVWR 303
Query: 261 EMFSES----PGWDEDRK--------YVPG-----RLSIYYQDPNGKPQRVPTTST 299
E F E P W+E RK Y+P + +Y+ P+G +RVP +T
Sbjct: 304 EKFLEKKPPLPYWEETRKGRKAWLKKYIPAIPHGSKYRVYFNTPDGPLERVPAWAT 359
>gnl|CDD|215568 PLN03088, PLN03088, SGT1, suppressor of G2 allele of SKP1;
Provisional.
Length = 356
Score = 31.3 bits (71), Expect = 0.66
Identities = 23/90 (25%), Positives = 33/90 (36%), Gaps = 20/90 (22%)
Query: 78 NAQLYNNRAASNFFLKNYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHLK---------- 127
NA+LY +RA +N L N+ + D A++L P K LR L+
Sbjct: 35 NAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQTAKAALE 94
Query: 128 ----------KFEDCTHLCDELLKENPTDS 147
+F CDE + E D
Sbjct: 95 KGASLAPGDSRFTKLIKECDEKIAEEEKDL 124
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 28.9 bits (65), Expect = 0.79
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 79 AQLYNNRAASNFFLKNYRSCLTDCQIALKLKPDYPKVKLRAAQCLFHL 126
A NN A L +Y L + AL+L + + A+ L +L
Sbjct: 5 AAALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNL 52
>gnl|CDD|227122 COG4783, COG4783, Putative Zn-dependent protease, contains TPR
repeats [General function prediction only].
Length = 484
Score = 31.2 bits (71), Expect = 0.80
Identities = 15/48 (31%), Positives = 23/48 (47%)
Query: 105 ALKLKPDYPKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTDSTVIDL 152
AL L P+ P ++L AQ L K ++ + + L +P D DL
Sbjct: 366 ALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDPEDPNGWDL 413
>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 = 27.5 bits (62), Expect = 0.89
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 79 AQLYNNRAASNFFLKNYRSCLTDCQIALKLKPDY 112
A+ N + + L +Y L + AL+L P+
Sbjct: 1 AEALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
Score = 26.7 bits (60), Expect = 1.7
Identities = 4/34 (11%), Positives = 13/34 (38%)
Query: 113 PKVKLRAAQCLFHLKKFEDCTHLCDELLKENPTD 146
+ + L +E+ ++ L+ +P +
Sbjct: 1 AEALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
>gnl|CDD|204914 pfam12422, Condensin2nSMC, Condensin II non structural maintenance
of chromosomes subunit. This domain family is found in
eukaryotes, and is approximately 150 amino acids in
length. This family is part of a non-SMC subunit of
condensin II which is involved in maintenance of the
structural integrity of chromosomes. Condensin II is
made up of SMC (structural maintenance of chromosomes)
and non-SMC subunits. The non-SMC subunits bind to the
catalytic ends of the SMC subunit dimer. The condensin
holocomplex is able to introduce superhelical tension
into DNA in an ATP hydrolysis- dependent manner,
resulting in the formation of positive supercoils in the
presence of topoisomerase I and of positive knots in the
presence of topoisomerase II.
Length = 152
Score = 29.9 bits (68), Expect = 0.94
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 146 DSTVIDLRTSCINKHKEILRNERKQAQQVKKEEKEKERVLQIIRERKIKLATS 198
+ + L S + + EIL K A KEE E E ++Q + E I T
Sbjct: 39 KNQLPKLSKSVLEAYGEILFRAWKNASGALKEEIE-EVIIQDLMEGAIHAETP 90
>gnl|CDD|99978 cd03806, GT1_ALG11_like, This family is most closely related to the
GT1 family of glycosyltransferases. ALG11 in yeast is
involved in adding the final 1,2-linked Man to the
Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of
the ER. The deletion analysis of ALG11 was shown to
block the early steps of core biosynthesis that takes
place on the cytoplasmic face of the ER and lead to a
defect in the assembly of lipid-linked oligosaccharides.
Length = 419
Score = 31.0 bits (71), Expect = 1.00
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 13/81 (16%)
Query: 203 LKSFSDLEPNFPEITLRPVH--------TDDNDRLVWPVLFLYPEYRITDFVQEFHEDVT 254
L++F+ L PE + +D+++ V + L E + D V EF +
Sbjct: 256 LRAFAKLLKRLPEEIKEKIKLVLIGSCRNEDDEKRVEDLKLLAKELGLEDKV-EFVVNAP 314
Query: 255 FDSMLEEMFSESPG----WDE 271
F+ +LEE+ + S G W+E
Sbjct: 315 FEELLEELSTASIGLHTMWNE 335
>gnl|CDD|227586 COG5261, IQG1, Protein involved in regulation of cellular
morphogenesis/cytokinesis [Cell division and chromosome
partitioning / Signal transduction mechanisms].
Length = 1054
Score = 31.0 bits (70), Expect = 1.0
Identities = 26/124 (20%), Positives = 49/124 (39%), Gaps = 17/124 (13%)
Query: 157 INKHKEILRNERKQAQQVKKEEKEKERVLQIIRERK-------IKLATS---GKGDLKSF 206
+ + L N R Q Q K + K R + ++R++ K + +G L +
Sbjct: 913 LQIYGSYLNNARSQLQPKKSKLKGFSRGVGVVRDKPKSISSGTFKYSAQQLYKRGVLVNI 972
Query: 207 SDLEPNFPEITLRPVHTDDNDRLVWPVLFLYPEYRITDFVQEFHEDVTFDSMLEEMFSES 266
+ EPN I +D D V + P + ++ F FD +L+ ++++
Sbjct: 973 TIPEPNVSNIYFT-FSSDSTDNFV--IEVYQPGHSVSLPEVSFC----FDDLLKRQYNKN 1025
Query: 267 PGWD 270
P D
Sbjct: 1026 PVVD 1029
>gnl|CDD|221837 pfam12895, Apc3, Anaphase-promoting complex, cyclosome, subunit 3.
Apc3, otherwise known as Cdc27, is one of the subunits
of the anaphase-promoting complex or cyclosome. The
anaphase-promoting complex is a multiprotein subunit E3
ubiquitin ligase complex that controls segregation of
chromosomes and exit from mitosis in eukaryotes. The
protein members of this family contain TPR repeats just
as those of Apc7 do, and it appears that these TPR units
bind the C-termini of the APC co-activators CDH1 and
CDC20.
Length = 80
Score = 28.4 bits (64), Expect = 1.5
Identities = 19/82 (23%), Positives = 29/82 (35%), Gaps = 11/82 (13%)
Query: 53 KCNKYRNAIINYTEGLKIKCADNDVN--AQLYNNRAASNFFLKNYRSCLTDCQIALKLKP 110
Y NAI + L + ++ D AQ Y Y+ + LKL
Sbjct: 1 DQGNYENAIFLAEKLLALTPSNEDAYLLAQCYFL-------QGQYKRAYELLR-KLKLDN 52
Query: 111 DYPKVKLRAAQCLFHLKKFEDC 132
+ AQCL L K+++
Sbjct: 53 -SSGCRYLLAQCLLKLGKYDEA 73
>gnl|CDD|135428 PRK05529, PRK05529, cell division protein FtsQ; Provisional.
Length = 255
Score = 29.9 bits (67), Expect = 1.8
Identities = 20/70 (28%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 165 RNERKQAQQVKKEEKEKERVLQI---IRERKIKL--ATSGKGDLKSFSDLEPNFPEITLR 219
+ + +KE K+ ERV + IR R I L A L F L P + LR
Sbjct: 5 DEAYQNLRYARKERKDYERVRRFTTRIRRRFILLACAVGAVLTLLLFVMLSAYSPLLALR 64
Query: 220 PVHTDDNDRL 229
+ N R+
Sbjct: 65 SIEVAGNMRV 74
>gnl|CDD|220549 pfam10069, DICT, Sensory domain found in DIguanylate Cyclases &
Two-component systems. DICT is a sensory domain found
associated with GGDEF, EAL, HD-GYP STAS, and two
component systems. It assumes an alpha+beta fold with a
4-stranded beta-sheet and might have a role in light
response.
Length = 125
Score = 28.4 bits (64), Expect = 2.5
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 207 SDLEPNFPEITLRPVHTDDNDRLV--WPVLFLYPEY 240
D + P +H + +D L W ++ L P+Y
Sbjct: 81 PDTDFPPPSPNDETIHLEPSDPLRREWFLVVLGPDY 116
>gnl|CDD|219155 pfam06741, LsmAD, LsmAD domain. This domain is found associated
with Lsm domain.
Length = 72
Score = 27.3 bits (61), Expect = 2.6
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 151 DLRTSCINKHKEILRNERKQAQQVKKE-EKEKERVLQIIRERKIKLATSGKGDLKSFSD 208
+L T+ ++K I + +A+++ +E E + I ER + SG + +S
Sbjct: 10 ELYTTRLDKSNPIYKEREARAERIAREIEGSATGNIHIAEERGDLVDDSGVDEEDKYSG 68
>gnl|CDD|235895 PRK06945, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 651
Score = 29.2 bits (66), Expect = 4.0
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 277 PGRLSIYYQDPNGKPQRVPTTSTLGEVL 304
P RL++ P G Q +P +S G L
Sbjct: 252 PSRLTVAGYKPPGTTQELPDSSLTGGTL 279
>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 = 29.3 bits (65), Expect = 4.1
Identities = 11/34 (32%), Positives = 23/34 (67%)
Query: 159 KHKEILRNERKQAQQVKKEEKEKERVLQIIRERK 192
K +E + +++A+Q +EE+E+E+ + RER+
Sbjct: 580 KREEAVEKAKREAEQKAREEREREKEKEKERERE 613
>gnl|CDD|182142 PRK09915, PRK09915, putative outer membrane efflux protein MdtP;
Provisional.
Length = 488
Score = 28.3 bits (63), Expect = 5.8
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 62 INYTEGLKIKCADND-VNAQLYNNRAASNFFLKNY 95
N+ GLK+ D +NA L RAASN ++ Y
Sbjct: 353 FNFIPGLKLPLFDGGRLNANLEGTRAASNMMIERY 387
>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011).
This is a family of fungal proteins whose function is
unknown.
Length = 130
Score = 27.2 bits (61), Expect = 6.1
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 159 KHKEILRNERKQAQQVKKEEKEKERVLQIIRERKIK 194
K + I R++ KE EKE+ + RE+K K
Sbjct: 90 KKRRIALRLRRER---TKERAEKEKRTRKNREKKFK 122
>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus. This
family represents the C-terminus (approximately 500
residues) of the eukaryotic coatomer alpha subunit.
Coatomer (COPI) is a large cytosolic protein complex
which forms a coat around vesicles budding from the
Golgi apparatus. Such coatomer-coated vesicles have been
proposed to play a role in many distinct steps of
intracellular transport. Note that many family members
also contain the pfam04053 domain.
Length = 421
Score = 28.3 bits (63), Expect = 6.8
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 107 KLKPDYPKVKLRAAQCLFH-LKKFEDCTHLCDELLKENPTDS 147
KL+P + + LR+A LF LK F+ LL+ P
Sbjct: 292 KLQPVHMILTLRSALNLFFKLKNFKTAASFARRLLELAPKPE 333
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 28.0 bits (63), Expect = 7.5
Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 164 LRNERKQAQQVKKEEKEKERVLQIIRERKIKLATSGKGDLKSFSDLEPN 212
LR ++++A++ ++E+ ++ + E K A G+ K D +P
Sbjct: 414 LRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKV-DPDPL 461
>gnl|CDD|143386 cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X
DNA Polymerases. X family polymerases fill in short
gaps during DNA repair. They are relatively inaccurate
enzymes and play roles in base excision repair, in
non-homologous end joining (NHEJ) which acts mainly to
repair damage due to ionizing radiation, and in V(D)J
recombination. This family includes eukaryotic Pol
beta, Pol lambda, Pol mu, and terminal
deoxyribonucleotidyl transferase (TdT). Pol beta and
Pol lambda are primarily DNA template-dependent
polymerases. TdT is a DNA template-independent
polymerase. Pol mu has both template dependent and
template independent activities. This subgroup belongs
to the Pol beta-like NT superfamily. In the majority of
enzymes in this superfamily, two carboxylates, Dx[D/E],
together with a third more distal carboxylate,
coordinate two divalent metal cations involved in a
two-metal ion mechanism of nucleotide addition. These
three carboxylate residues are fairly well conserved in
this family.
Length = 307
Score = 27.5 bits (62), Expect = 9.1
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 38 EELATTYKDEGNFNFKCNKYRNAI 61
EELA + G F+ YR A
Sbjct: 8 EELADLLELLGGNPFRVRAYRKAA 31
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
0.317 0.136 0.403
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: 17,367,488
Number of extensions: 1690380
Number of successful extensions: 2358
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2324
Number of HSP's successfully gapped: 88
Length of query: 337
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 240
Effective length of database: 6,635,264
Effective search space: 1592463360
Effective search space used: 1592463360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.6 bits)