RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12599
(269 letters)
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 76.9 bits (189), Expect = 7e-16
Identities = 44/105 (41%), Positives = 58/105 (55%), Gaps = 2/105 (1%)
Query: 167 EMRRRRNEVTVELRKNKREETLQKRRNVPLADSTDEDDIEKMAQVNLDML--VVEAARKD 224
E+RRRR E VELRK KREE L KRRN+ E M Q L + + D
Sbjct: 24 ELRRRREEQQVELRKQKREELLNKRRNLADVSEEAESSFIPMEQQFYSELPQLTQQLFSD 83
Query: 225 NPELQLLAVQSARKLLSSDKNPPIEALIHSGILPVLVECLERSDR 269
+ E QL AV RKLLS + +PPI+ +I +G++P VE ++ R
Sbjct: 84 DIEQQLQAVYKFRKLLSKETSPPIQPVIDAGVVPRFVEFMDEIQR 128
>gnl|CDD|201951 pfam01749, IBB, Importin beta binding domain. This family consists
of the importin alpha (karyopherin alpha), importin beta
(karyopherin beta) binding domain. The domain mediates
formation of the importin alpha beta complex; required
for classical NLS import of proteins into the nucleus,
through the nuclear pore complex and across the nuclear
envelope. Also in the alignment is the NLS of importin
alpha which overlaps with the IBB domain.
Length = 97
Score = 59.3 bits (144), Expect = 1e-11
Identities = 34/76 (44%), Positives = 45/76 (59%), Gaps = 7/76 (9%)
Query: 167 EMRRRRNEVTVELRKNKREETLQKRRNVPLAD---STDEDDIEKMAQVNL----DMLVVE 219
EMRRRR EV VELRKNKREE L KRRNV L + E +++ + + ++V+
Sbjct: 22 EMRRRREEVGVELRKNKREEQLLKRRNVGLPPEDGAEPESELDGSSDADQLSLELPVMVQ 81
Query: 220 AARKDNPELQLLAVQS 235
D+PE QL A Q+
Sbjct: 82 GVNSDDPENQLSATQA 97
>gnl|CDD|221732 pfam12719, Cnd3, Nuclear condensing complex subunits, C-term
domain. The Cnd1-3 proteins are the three non-SMC
(structural maintenance of chromosomes) proteins that go
to make up the mitotic condensation complex along with
the two SMC protein families, XCAP-C and XCAP-E, (or in
the case of fission yeast, Cut3 and Cut14). The
five-member complex seems to be conserved from yeasts to
vertebrates. This domain is the C-terminal,
cysteine-rich domain of Cnd3. The complex shuttles
between the nucleus, during mitosis, and the cytoplasm
during the rest of the cycle. Thus this family is made
up of the C-termini of XCAP-Gs, Ycg1 and Ycs5 members.
Length = 302
Score = 33.0 bits (76), Expect = 0.14
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 196 LADSTDEDDIEKMAQVNLDMLVVEAARKDNPELQLLAVQSARKLLSSDKNPPIEALI 252
DED E + V+L ++ + ++PE+Q +A + KLL + + L+
Sbjct: 101 FDSEGDEDSTEDVDSVSLLKILYKFLDSEDPEVQAIAAEGLCKLLLAGRLTDEPDLL 157
>gnl|CDD|201276 pfam00514, Arm, Armadillo/beta-catenin-like repeat. Approx. 40
amino acid repeat. Tandem repeats form super-helix of
helices that is proposed to mediate interaction of
beta-catenin with its ligands. CAUTION: This family does
not contain all known armadillo repeats.
Length = 41
Score = 29.3 bits (67), Expect = 0.19
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 245 NPPIEALIHSGILPVLVECLERSD 268
+A+I +G +P LV+ L D
Sbjct: 2 PENKQAVIEAGAVPPLVQLLSSPD 25
>gnl|CDD|237987 cd00020, ARM, Armadillo/beta-catenin-like repeats. An approximately
40 amino acid long tandemly repeated sequence motif
first identified in the Drosophila segment polarity gene
armadillo; these repeats were also found in the
mammalian armadillo homolog beta-catenin, the junctional
plaque protein plakoglobin, the adenomatous polyposis
coli (APC) tumor suppressor protein, and a number of
other proteins. ARM has been implicated in mediating
protein-protein interactions, but no common features
among the target proteins recognized by the ARM repeats
have been identified; related to the HEAT domain; three
consecutive copies of the repeat are represented by this
alignment model.
Length = 120
Score = 31.1 bits (71), Expect = 0.24
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 217 VVEAARKDNPELQLLAVQSARKLLSSDKNPPIEALIHSGILPVLVECLERSD 268
+V + +Q A + L S+ N I+A++ +G LP LV+ L+ D
Sbjct: 12 LVSLLSSSDENVQREAAWALSNL-SAGNNDNIQAVVEAGGLPALVQLLKSED 62
Score = 27.3 bits (61), Expect = 5.0
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 249 EALIHSGILPVLVECLERSD 268
EA+I +G LP LV L SD
Sbjct: 1 EAVIQAGGLPALVSLLSSSD 20
>gnl|CDD|214547 smart00185, ARM, Armadillo/beta-catenin-like repeats. Approx. 40
amino acid repeat. Tandem repeats form superhelix of
helices that is proposed to mediate interaction of
beta-catenin with its ligands. Involved in transducing
the Wingless/Wnt signal. In plakoglobin arm repeats bind
alpha-catenin and N-cadherin.
Length = 41
Score = 28.9 bits (66), Expect = 0.30
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 244 KNPPIEALIHSGILPVLVECLERSD 268
+ +A++ +G LP LVE L+ D
Sbjct: 1 DDENKQAVVDAGGLPALVELLKSED 25
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.7 bits (68), Expect = 1.9
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 143 KEKTKDIIAIELGKVKHRLIEVDKEMRRRRNEVT-VELRKNKREETLQKR 191
+ K+ + ++ E +KE+R RRNE+ +E R ++EE L ++
Sbjct: 52 EAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRK 101
>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. There are no obvious
homologs to these genes in any other organism.
Length = 255
Score = 28.7 bits (64), Expect = 2.6
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 4/82 (4%)
Query: 165 DKEMRRRRNEVTVELRKNKREETLQKRRNVPLADSTDEDDIEKMAQVNLDMLVVEAARKD 224
DKE+ RN + ++K+K TL NV D + I K+ Q L+ L E +
Sbjct: 78 DKEIAHLRNIIDSHIKKHKERNTLPDLNNV---DKKTKKLINKL-QKELEELKKELDNEM 133
Query: 225 NPELQLLAVQSARKLLSSDKNP 246
N EL + + + + N
Sbjct: 134 NDELTIQPIHDKIIIKKDENNS 155
>gnl|CDD|239652 cd03680, MM_CoA_mutase_ICM_like, Coenzyme
B12-dependent-methylmalonyl coenzyme A (CoA) mutase
(MCM) family, isobutyryl-CoA mutase (ICM)-like
subfamily; contains archaeal and bacterial proteins
similar to the large subunit of Streptomyces
cinnamonensis coenzyme B12-dependent ICM. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA, intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis.
Length = 538
Score = 29.2 bits (66), Expect = 2.8
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 134 GMNRMTGREKEKTKDIIAIELGKVKHRLIEVDKEMRRRRNEVTVE-----LRKNKREET 187
G+N+ +E+ I+ +V+ R IE KE+R R+ V+ LRK +E
Sbjct: 454 GVNKFV--VEEEPPIILLKVDDEVEERQIERLKEVRAERDNAKVQEALDALRKAAEDEE 510
>gnl|CDD|178337 PLN02736, PLN02736, long-chain acyl-CoA synthetase.
Length = 651
Score = 28.9 bits (65), Expect = 3.6
Identities = 30/96 (31%), Positives = 43/96 (44%), Gaps = 19/96 (19%)
Query: 16 LDDL----------VPTLSSRI----RNQSKSSTLPVVEVVEFKAYKRKSKALEDD---- 57
+DDL VP L +RI N K S + E + AY K +ALE+
Sbjct: 301 MDDLAALRPTIFCSVPRLYNRIYDGITNAVKESG-GLKERLFNAAYNAKKQALENGKNPS 359
Query: 58 PADDQLTANDLVPTLSSRIRNQSKSSTPPVVEVVEF 93
P D+L N + L R+R S ++P +V+EF
Sbjct: 360 PMWDRLVFNKIKAKLGGRVRFMSSGASPLSPDVMEF 395
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 27.6 bits (62), Expect = 5.7
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 174 EVTVELRKNKREETLQKRRNVPLADSTDEDDIEK-MAQVNLDMLVVEAARKDNPE 227
EV V R+ + E R D TD D +E+ +A+V D ++ AA+
Sbjct: 24 EVIVLGRRRRSESLNTGRIRFHEGDLTDPDALERLLAEVQPDAVIHLAAQSGVGA 78
>gnl|CDD|239500 cd03406, Band_7_3, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and are known to interact
with a variety of proteins. Stomatin interacts with and
regulates members of the degenerin/epithelia Na+ channel
family in mechanosensory cells of Caenorhabditis elegans
and vertebrate neurons and participates in trafficking
of Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth during
lambda phage infection. Flotillins have been implicated
in the progression of prion disease, in the pathogenesis
of neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis. Mutations in the podicin gene give rise to
autosomal recessive steroid resistant nephritic
syndrome.
Length = 280
Score = 27.8 bits (62), Expect = 5.9
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 12/100 (12%)
Query: 142 EKEKTKDIIAIELGKVKHRLIEVDKEMRRRRNEVTVELRKNKREETLQKRRNVPLADSTD 201
E EKTK +IAI+ KV V+KE R + +E K + + + V +
Sbjct: 169 EAEKTKLLIAIQKQKV------VEKEAETERKKAVIEAEKVAQVAKILFGQKV-----ME 217
Query: 202 EDDIEKMAQVNLDM-LVVEAARKDNPELQLLAVQSARKLL 240
++ ++++++ + L E A+ D A KL
Sbjct: 218 KETEKRISEIEDEAFLAREKAKADAEYYTAQKEAEANKLK 257
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.0 bits (63), Expect = 6.6
Identities = 13/30 (43%), Positives = 23/30 (76%), Gaps = 1/30 (3%)
Query: 163 EVDKEMRRRRNEVT-VELRKNKREETLQKR 191
E+++E++ RRNE+ +E R +REETL ++
Sbjct: 66 ELERELKERRNELQRLERRLLQREETLDRK 95
>gnl|CDD|221313 pfam11917, DUF3435, Protein of unknown function (DUF3435). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 435 to 791 amino acids in
length. This family is related to pfam00589 suggesting
it may be an integrase enzyme.
Length = 418
Score = 27.7 bits (62), Expect = 7.7
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 141 REKEKTKDIIAIELGKV-KHRLIEVDKEMRRRRNEVTVELRKNKREETLQKR----RNVP 195
R+++ K I G+V K + + + + +RR EV E ++ +RE + R P
Sbjct: 295 RKRDHLKKEIIALYGQVAKAKGTPLYERLEKRRREVRNERQRLRRELKKKIREEFDEEQP 354
Query: 196 LADS 199
+ D
Sbjct: 355 VIDI 358
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 27.3 bits (61), Expect = 8.4
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 196 LADSTDEDDIEKMAQVNLDMLVVEAARKDNPELQLLAVQSARKLLSSDKN---PPIEALI 252
+A + +E+ A ++ D+L+VE K+ P ++L V RK+L + + AL+
Sbjct: 76 IAGGPPDPLLERGAFLDCDLLLVEGL-KELPLPKILLVDRERKILDLLEQGSVTNVVALV 134
Query: 253 HSG 255
Sbjct: 135 VPD 137
>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is about 200 amino acids in length. This
domain is found associated with pfam00013, pfam01966.
This domain has a single completely conserved residue A
that may be functionally important.
Length = 201
Score = 27.1 bits (61), Expect = 8.6
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 141 REKEKTKDIIAIELGKVKHRL-IEVDKEMRRRRNEVT-VELRKNKREETLQKR 191
+E E K +E + H+L E ++E++ RRNE+ E R ++EETL ++
Sbjct: 45 KEAEALKKEALLEAKEEIHKLRAEAERELKERRNELQRQEKRLLQKEETLDRK 97
>gnl|CDD|217247 pfam02836, Glyco_hydro_2_C, Glycosyl hydrolases family 2, TIM
barrel domain. This family contains beta-galactosidase,
beta-mannosidase and beta-glucuronidase activities.
Length = 297
Score = 27.4 bits (61), Expect = 9.4
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 201 DEDDIEKMAQVNLDMLVVEAARKDNPELQLLAVQSARKLLSSDKNPP 247
DE ++E DNPE +Q AR+++ DKN P
Sbjct: 77 DETNLETHGLWQ--KFGEINVLADNPEWLKAHLQRAREMVQRDKNHP 121
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 27.2 bits (61), Expect = 9.8
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 19/73 (26%)
Query: 141 REKEKTKDIIAIELGKVKHRLIEVDKEMRRRRNEVTVELRKNKREETLQKRRN-----VP 195
REK K + A+++ K L+E+D+E R+ E+ E LQ RN +
Sbjct: 15 REKLKKRGGDALDVDK----LLELDEERRKLLREL----------EELQAERNELSKEIG 60
Query: 196 LADSTDEDDIEKM 208
A EDD E++
Sbjct: 61 RALKRGEDDAEEL 73
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 0.129 0.337
Gapped
Lambda K H
0.267 0.0877 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,651,073
Number of extensions: 1330654
Number of successful extensions: 1156
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1147
Number of HSP's successfully gapped: 61
Length of query: 269
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 174
Effective length of database: 6,723,972
Effective search space: 1169971128
Effective search space used: 1169971128
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 (21.9 bits)
S2: 58 (25.9 bits)