RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12000
(507 letters)
>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 = 38.4 bits (90), Expect = 5e-04
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 11 WLGYCHFHLGQYKQALGIYETLRHLPNPPEDTEFNIASCYFYLGMYLQANQILEKV 66
L C+F GQYK+A + L+ + + +A C LG Y +A +LEK
Sbjct: 27 LLAQCYFLQGQYKRAYELLRKLKLDNSS--GCRYLLAQCLLKLGKYDEAIAVLEKA 80
>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 = 33.1 bits (76), Expect = 0.070
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 12 LGYCHFHLGQYKQALGIYETLRHLPNPPEDTEFNIASCYFYLGMYLQANQILEKV 66
L ++ LG+Y++AL YE L +N+ Y+ LG Y +A + EK
Sbjct: 40 LAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKLGKYEEALEAYEKA 94
Score = 31.6 bits (72), Expect = 0.24
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 12 LGYCHFHLGQYKQALGIYE-TLRHLPNPPEDTEFNIASCYFYLGMYLQANQILEKV 66
LG ++ LG Y +AL YE L P+ D +N+A+ Y+ LG Y +A + EK
Sbjct: 6 LGNLYYKLGDYDEALEYYEKALELDPDNA-DAYYNLAAAYYKLGKYEEALEDYEKA 60
Score = 30.4 bits (69), Expect = 0.58
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 101 EEQLCLASIHFLRCHYQEAIDIYKRIL-LDHKDLLALNVYGAMCYYKLDYYDVSQEQVAM 159
E L L ++++ Y EA++ Y++ L LD + A A YYKL Y+ + E
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNL-AAAYYKLGKYEEALEDYEK 59
Query: 160 YLAQKPTSRIALNLKACNTYKL 181
L P + A YKL
Sbjct: 60 ALELDPDNAKAYYNLGLAYYKL 81
Score = 30.4 bits (69), Expect = 0.58
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 394 EEQLCLASIHFLRCHYQEAIDIYKRIL-LDHKDLLALNVYGAMCYYKLDYYDVSQEQVAM 452
E L L ++++ Y EA++ Y++ L LD + A A YYKL Y+ + E
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNL-AAAYYKLGKYEEALEDYEK 59
Query: 453 YLAQKPTSRIALNLKACNTYKL 474
L P + A YKL
Sbjct: 60 ALELDPDNAKAYYNLGLAYYKL 81
>gnl|CDD|224581 COG1667, COG1667, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 254
Score = 34.1 bits (78), Expect = 0.13
Identities = 24/143 (16%), Positives = 48/143 (33%), Gaps = 27/143 (18%)
Query: 133 LLALNVYGAMCYYKLDYYDVSQEQVAMYLAQKPTSRIALNLKACNTYKLFTSRAAENQL- 191
L ++ +D Y++ ++ L LN C T EN++
Sbjct: 80 LKVIDHDSFAV---VDVYELDEDLFEKILE--------LNKDECVLSVPITEEEVENEME 128
Query: 192 -------------KPILVSILPPLIDVIPESRLNLVIYHLKQEEHQEAFDLIKNLEPSVP 238
I V + + ++ E+ + Y ++ E +L+K L P
Sbjct: 129 ELKSSEREELLEKYGIRVPEIEEIERILDEAVGS--DYFSEEIEEPSREELLKKLGIKEP 186
Query: 239 QEYILKAVVQVTIGQDTGSREMV 261
E ++ +++V G D E
Sbjct: 187 DENWVETILKVFRGVDEELEEEK 209
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 30.7 bits (70), Expect = 0.22
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 12 LGYCHFHLGQYKQALGIYET-LRHLPNPPEDTEFNIASCYFYLG-MYLQANQILEKV 66
LG F LG Y +A+ YE L P+ E +N+A Y LG Y +A + LEK
Sbjct: 9 LGNALFKLGDYDEAIEAYEKALELDPDNAE-AYYNLALAYLKLGKDYEEALEDLEKA 64
>gnl|CDD|218234 pfam04733, Coatomer_E, Coatomer epsilon subunit. This family
represents the epsilon subunit of the coatomer complex,
which is involved in the regulation of intracellular
protein trafficking between the endoplasmic reticulum
and the Golgi complex.
Length = 288
Score = 32.8 bits (75), Expect = 0.36
Identities = 30/149 (20%), Positives = 61/149 (40%), Gaps = 12/149 (8%)
Query: 17 FHLGQYKQALGIYETLRHLPNPPEDTEFNIASCYFYLGMYLQ-ANQILE-KVPPSRAKTR 74
F+LG Y++A+ + + + + Y LG Y ++I E P +A
Sbjct: 10 FYLGNYQKAINESDVTSLSEEALVERDVYMYRSYLALGSYQIVISEIKESAATPLQAVRL 69
Query: 75 LSFHLSHKLGDEKSLMEYHQKLEDSLEE-----QLCLASIHFLRCHYQEAIDIYKRILLD 129
L+ +L+ E L + + DS +L A I + +A+ + +
Sbjct: 70 LAEYLNSPSRKESILASLKEWVADSHIGSNSTLRLLAAIIFIHEGDFDDALKHLHK--GE 127
Query: 130 HKDLLALNVYGAMCYYKLDYYDVSQEQVA 158
+ + +ALNV K+ D++++Q+
Sbjct: 128 NLEAMALNVQ---ILLKMHRIDLAEQQLK 153
>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 = 33.1 bits (76), Expect = 0.39
Identities = 36/191 (18%), Positives = 62/191 (32%), Gaps = 30/191 (15%)
Query: 8 TDAWL--GYCHFHLGQYKQALGIY-ETLRHLPNPPEDTEFNIASCYFYLGMYLQANQILE 64
DA L G LG + AL Y + + PN +A+ G + +A + +
Sbjct: 193 VDALLLKGDLLLSLGNIELALAAYRKAIALRPNNIAV-LLALATILIEAGEFEEAEKHAD 251
Query: 65 KVPPSRAKTRLSFHLSHKLGDEKSLMEYHQKLEDSLEEQLCLASIHFLRCHYQEAIDIYK 124
+ K L Y + A + F + +Y++A + +
Sbjct: 252 AL---LKKAP-----------NSPLAHYLK------------ALVDFQKKNYEDARETLQ 285
Query: 125 RILLDHKDLLALNVYGAMCYYKLDYYDVSQEQVAMYLAQKPTSRIALNLKACNTYKLFTS 184
L + L + Y+L + + + + L P S A L A +L
Sbjct: 286 DALKSAPEYLPALLLAGASEYQLGNLEQAYQYLNQILKYAPNSHQARRLLASIQLRLGRV 345
Query: 185 RAAENQLKPIL 195
A L P L
Sbjct: 346 DEAIATLSPAL 356
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 29.6 bits (67), Expect = 0.79
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 7/62 (11%)
Query: 12 LGYCHFHLGQYKQALGIYETLRHL-----PNPPE--DTEFNIASCYFYLGMYLQANQILE 64
L LG Y +AL + E L + PE N+A Y LG Y +A + LE
Sbjct: 11 LALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEALEYLE 70
Query: 65 KV 66
K
Sbjct: 71 KA 72
Score = 28.5 bits (64), Expect = 1.6
Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 19/84 (22%)
Query: 44 FNIASCYFYLGMYLQANQILEKVPPSRAKTRLSFHLSHKLGDEKSLMEYHQKLEDSLEEQ 103
N+A LG Y +A ++LEK L + L E H + +L
Sbjct: 9 NNLALVLRRLGDYDEALELLEKA----------------LELARELGEDHPETARAL--- 49
Query: 104 LCLASIHFLRCHYQEAIDIYKRIL 127
LA ++ Y EA++ ++ L
Sbjct: 50 NNLARLYLALGDYDEALEYLEKAL 73
>gnl|CDD|205550 pfam13371, TPR_9, Tetratricopeptide repeat.
Length = 73
Score = 28.7 bits (65), Expect = 1.4
Identities = 12/70 (17%), Positives = 29/70 (41%)
Query: 106 LASIHFLRCHYQEAIDIYKRILLDHKDLLALNVYGAMCYYKLDYYDVSQEQVAMYLAQKP 165
L +I+ ++ A+ + +R+LL D + Y +L + + + +L P
Sbjct: 1 LKAIYLREEDFERALAVVERLLLLAPDDPYERRDRGLLYAQLGCFQAALADLEYFLELCP 60
Query: 166 TSRIALNLKA 175
+ A ++
Sbjct: 61 DAPDAERIRE 70
Score = 28.7 bits (65), Expect = 1.4
Identities = 12/70 (17%), Positives = 29/70 (41%)
Query: 399 LASIHFLRCHYQEAIDIYKRILLDHKDLLALNVYGAMCYYKLDYYDVSQEQVAMYLAQKP 458
L +I+ ++ A+ + +R+LL D + Y +L + + + +L P
Sbjct: 1 LKAIYLREEDFERALAVVERLLLLAPDDPYERRDRGLLYAQLGCFQAALADLEYFLELCP 60
Query: 459 TSRIALNLKA 468
+ A ++
Sbjct: 61 DAPDAERIRE 70
>gnl|CDD|148811 pfam07417, Crl, Transcriptional regulator Crl. This family
contains the bacterial transcriptional regulator Crl
(approximately 130 residues long). This is a
transcriptional regulator of the csgA curlin subunit
gene for curli fibres that are found on the surface of
certain bacteria.
Length = 127
Score = 29.6 bits (67), Expect = 1.8
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 13/68 (19%)
Query: 40 EDTEFNIASCYFYLGMY-LQANQILEKVPPSRAKTRLSFHLSHKLGDEKSLMEYHQKLED 98
E TE Y + G+Y + N + EK+P + + EK+L ++H+KL
Sbjct: 60 EATEDGFEYEYQF-GLYNKEGNWVAEKIPKK-VQEEV----------EKTLEDFHEKLVK 107
Query: 99 SLEEQLCL 106
LEE+ L
Sbjct: 108 LLEEEFEL 115
>gnl|CDD|218166 pfam04598, Gasdermin, Gasdermin family. The precise function of
this protein is unknown. A deletion/insertion mutation
is associated with an autosomal dominant non-syndromic
hearing impairment form. In addition, this protein has
also been found to contribute to acquired etoposide
resistance in melanoma cells. This family also includes
the gasdermin protein.
Length = 451
Score = 30.0 bits (68), Expect = 3.3
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 61 QILEKVPPSRAKTRLSFHLSHKLGDEKSLMEYHQKLEDSLEEQLC 105
Q L ++P L L L D+++L + LED LE+ L
Sbjct: 291 QPLAELPRELRAALLG-SLLALLRDQEALQD----LEDMLEDLLD 330
>gnl|CDD|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only].
Length = 291
Score = 29.8 bits (65), Expect = 3.6
Identities = 42/186 (22%), Positives = 70/186 (37%), Gaps = 25/186 (13%)
Query: 12 LGYCHFHLGQYKQALGIYE-TLRHLPNPPEDTEFNIASCYFYLGMYLQANQILEKVPPSR 70
LG LG+Y++AL + E L P+P + LG Y +A ++ EK
Sbjct: 101 LGLLLEALGKYEEALELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEK----- 155
Query: 71 AKTRLSFHLSHKLGDEKSLMEYHQKLEDSLEEQLCLASIHFLRCHYQEAIDIYKRIL-LD 129
+E +L + E L L ++ Y+EA+++ ++ L L+
Sbjct: 156 ------------------ALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLN 197
Query: 130 HKDLLALNVYGAMCYYKLDYYDVSQEQVAMYLAQKPTSRIALNLKACNTYKLFTSRAAEN 189
D + + Y KL Y+ + E L P + AL A +L A
Sbjct: 198 PDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALE 257
Query: 190 QLKPIL 195
L+ L
Sbjct: 258 ALEKAL 263
Score = 28.3 bits (61), Expect = 9.0
Identities = 36/171 (21%), Positives = 59/171 (34%), Gaps = 7/171 (4%)
Query: 319 FNFAQAKCALGQYKEAEEMFLLVQNEGLKNDYVYISHLTKCSPSRAKTRLSFHLSHKLGD 378
N ALG+Y+EA E+ D + L K
Sbjct: 99 LNLGLLLEALGKYEEALELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEKA-- 156
Query: 379 EKSLMEYHQKLEDSLEEQLCLASIHFLRCHYQEAIDIYKRIL-LDHKDLLALNVYGAMCY 437
+E +L + E L L ++ Y+EA+++ ++ L L+ D + + Y
Sbjct: 157 ----LELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLY 212
Query: 438 YKLDYYDVSQEQVAMYLAQKPTSRIALNLKACNTYKLFTSRAAENQLKPIL 488
KL Y+ + E L P + AL A +L A L+ L
Sbjct: 213 LKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKAL 263
>gnl|CDD|235120 PRK03363, fixB, putative electron transfer flavoprotein FixB;
Provisional.
Length = 313
Score = 29.2 bits (65), Expect = 5.4
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 244 KAVVQVTIGQDTGSREMVKAAQALFQLVGS 273
KA + V++G+ GS+E + A+ L + +G+
Sbjct: 194 KARLVVSVGRGIGSKENIALAEQLCKAIGA 223
>gnl|CDD|204301 pfam09735, Nckap1, Membrane-associated apoptosis protein.
Expression of this protein was found to be markedly
reduced in patients with Alzheimer's disease. It is
involved in the regulation of actin polymerisation in
the brain as part of a WAVE2 signalling complex.
Length = 1118
Score = 29.3 bits (66), Expect = 5.5
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 74 RLSFHLSH--KLGDEKSLMEYHQKLEDSLEEQL 104
+ S +L KL E + + +H K+ DSLEE L
Sbjct: 497 KSSLNLRDNPKLASEMNTIVFHSKMVDSLEEML 529
Score = 29.3 bits (66), Expect = 5.5
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 367 RLSFHLSH--KLGDEKSLMEYHQKLEDSLEEQL 397
+ S +L KL E + + +H K+ DSLEE L
Sbjct: 497 KSSLNLRDNPKLASEMNTIVFHSKMVDSLEEML 529
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 0.136 0.400
Gapped
Lambda K H
0.267 0.0867 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,485,074
Number of extensions: 2473142
Number of successful extensions: 2153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2128
Number of HSP's successfully gapped: 47
Length of query: 507
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 406
Effective length of database: 6,457,848
Effective search space: 2621886288
Effective search space used: 2621886288
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: 61 (27.0 bits)