RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9795
(337 letters)
>gnl|CDD|219873 pfam08506, Cse1, Cse1. This domain is present in Cse1 nuclear
export receptor proteins. Cse1 mediates the nuclear
export of importin alpha. This domain contains HEAT
repeats.
Length = 370
Score = 158 bits (403), Expect = 1e-45
Identities = 51/102 (50%), Positives = 70/102 (68%)
Query: 183 LFKRYRHEFKSQKLWTEIKFVLDNFAKPFTELFKATINLVGEHKDNPTALKVIYNSLVVS 242
+FKR+R F+S +L+ EIK VLD FA+PF +L +AT L+ +K+N ALK+++ L++
Sbjct: 1 IFKRWRPLFRSDELFLEIKLVLDKFAEPFLDLLQATDELIEANKNNKAALKILFEVLLLL 60
Query: 243 CKIFYSLNFQDLPEYFEDNMVVWMPALHNLLVTDVPCLRTDS 284
CK+FY LN QD+PE+FEDNM WM H L D P L TD
Sbjct: 61 CKLFYDLNCQDIPEFFEDNMSEWMGIFHKYLTYDNPLLETDD 102
Score = 40.4 bits (95), Expect = 8e-04
Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 30/98 (30%)
Query: 224 EHKDNPTALKVIYNSLVVSCKIFYSLNFQDLPEYFEDNMVVWMPALHNLLVTDVPCLRTD 283
E +N + LK I +V+ +L D E FED+ + ++
Sbjct: 177 ELFNNESVLKQICEKVVLPN---VTLRESDE-ELFEDDPIEYI----------------- 215
Query: 284 SIFVNSFRRFI--SDVETRRRAACDFVKILCKYMEDKM 319
RR + SD +TRRRAA D ++ L + E +
Sbjct: 216 -------RRDLEGSDSDTRRRAATDLLRGLKEKFEALV 246
>gnl|CDD|227944 COG5657, CSE1, CAS/CSE protein involved in chromosome segregation
[Cell division and chromosome partitioning].
Length = 947
Score = 144 bits (365), Expect = 3e-38
Identities = 66/238 (27%), Positives = 113/238 (47%), Gaps = 5/238 (2%)
Query: 46 NIQLESRSPTENFLESVETNQNYPLLILTLVERADVDMTIRIAGAVAFKNYVKRNWPLVE 105
+ S E L E + L +L++ A M++R A + FKNY+ ++W E
Sbjct: 15 SPDPPSVKCAEERLRQWEKQHGFALKLLSINLSAFNSMSLRWAALIQFKNYIDKHW--RE 72
Query: 106 DEPDKIHASDREAIKGLILHLMLTSPEAIQKQLSDATAIIGKSDFPDKWPSLITDMVAKF 165
+ + I + I+ + L+++S +Q Q + A + I + DFPD+WP+L+ D+++
Sbjct: 73 ENGNSILPDENVLIRDELFSLIISSSNQLQIQNALAVSRIARLDFPDEWPTLVPDLLSLL 132
Query: 166 GTGDFHIINGVLHTAHSLFKRYRHEFKSQKLWTEIKFVLDNFAKPFTELFKATINLVGEH 225
D L H +FKR R F+S L+ EI VL + PF ++
Sbjct: 133 SEKDMVTNENSLRVLHHIFKRLRRLFRSDALFLEIAPVLLSILCPFLFSSAYFWSMS--E 190
Query: 226 KDNPTALKVIYNSLVVSCKIFYSLNFQDLPEYFEDNMVVWMPALHNLLVTDVPCLRTD 283
+ + L ++ + + +Y L FQD+PE+FEDN+ +M LL P L+ D
Sbjct: 191 NLDESLLS-LFQVCLKLIRRYYDLGFQDIPEFFEDNLDKFMEHFCKLLSYSNPVLQKD 247
>gnl|CDD|197981 smart00913, IBN_N, Importin-beta N-terminal domain. Members of the
importin-beta (karyopherin-beta) family can bind and
transport cargo by themselves, or can form heterodimers
with importin-alpha. As part of a heterodimer,
importin-beta mediates interactions with the pore
complex, while importin-alpha acts as an adaptor protein
to bind the nuclear localisation signal (NLS) on the
cargo through the classical NLS import of proteins.
Importin-beta is a helicoidal molecule constructed from
19 HEAT repeats. Many nuclear pore proteins contain FG
sequence repeats that can bind to HEAT repeats within
importins.. which is important for importin-beta
mediated transport.
Length = 67
Score = 52.6 bits (127), Expect = 2e-09
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 56 ENFLESVETNQNYPLLILTLVERADVDMTIRIAGAVAFKNYVKRNWPLVEDEPDKIHASD 115
E LE + + + LL+L ++ ++ +R A+ KN + R W + +
Sbjct: 2 EKQLEQFQKSPGFWLLLLEILANSEDQY-VRQLAAITLKNKITRRW-------SSLPEEE 53
Query: 116 REAIKGLILHLMLT 129
+E IK +L L+L+
Sbjct: 54 KEEIKNSLLELLLS 67
>gnl|CDD|217743 pfam03810, IBN_N, Importin-beta N-terminal domain.
Length = 71
Score = 46.9 bits (112), Expect = 3e-07
Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 56 ENFLESVETNQ-NYPLLILTLVERADVDMTIRIAGAVAFKNYVKRNWPLVEDEPDKIHAS 114
E LE E + +L ++ D+ +R A+ KN + R+W +
Sbjct: 2 EKQLEQFEKQDPGFWSKLLQILSDTSSDLQVRQLAALYLKNLITRHW-----NQLSLPPE 56
Query: 115 DREAIKGLILHLMLT 129
++E I+ +L+L+ +
Sbjct: 57 EKEQIRNNLLNLLGS 71
>gnl|CDD|227943 COG5656, SXM1, Importin, protein involved in nuclear import
[Posttranslational modification, protein turnover,
chaperones].
Length = 970
Score = 49.1 bits (117), Expect = 2e-06
Identities = 44/223 (19%), Positives = 90/223 (40%), Gaps = 21/223 (9%)
Query: 43 HDKNIQLESRSPTENFLESVETNQNYPLLILTLVERADVDMTIRIAGAVAFKNYVKRNWP 102
D R+ E L+ +E + + +L + + + D+ ++++ A+ FKN + R+W
Sbjct: 15 ADAGK----RTIAEAMLKDLEKQPGFVMALLHICSKDEGDLNVKLSAAIYFKNKIIRSWS 70
Query: 103 LVEDEPDK--IHASDREAIKGLILHLMLTSPEAIQKQLSDATAIIGKSDFPDKWPSLITD 160
D+ K + ++ + IL + L SPE + L+ I D P L
Sbjct: 71 SKRDDGIKADEKSEAKKYLIENILDVFLYSPEVTRTALNAILVNIFSEDKPSDLWGLFPK 130
Query: 161 MVAKFGTGDFHIINGVLHTAHSLFKRYRHEFKSQKLWTEIKFVLDNFAKPFTELFKATIN 220
+ + + + L LFK YR ++ ++ + T LF
Sbjct: 131 AANLLRSSEANHVYTGLLCLEELFKAYRWKYNDEQ---------VDILMLITALFPILEK 181
Query: 221 LVG--EHKDNPTALKVIYNSLVVSCKIFYSLNFQDLPEYFEDN 261
+ G E + N +++ + L++ K F S+ + LP++
Sbjct: 182 VGGNLESQGNYGSVETLM--LIL--KSFKSVCYYSLPDFLSAI 220
>gnl|CDD|219817 pfam08389, Xpo1, Exportin 1-like protein. The sequences featured
in this family are similar to a region close to the
N-terminus of yeast exportin 1 (Xpo1, Crm1). This region
is found just C-terminal to an importin-beta N-terminal
domain (pfam03810) in many members of this family.
Exportin 1 is a nuclear export receptor that interacts
with leucine-rich nuclear export signal (NES) sequences,
and Ran-GTP, and is involved in translocation of
proteins out of the nucleus.
Length = 147
Score = 33.4 bits (77), Expect = 0.057
Identities = 11/44 (25%), Positives = 22/44 (50%)
Query: 131 PEAIQKQLSDATAIIGKSDFPDKWPSLITDMVAKFGTGDFHIIN 174
P+ I+ +L+ A A + K ++P WP+ D+V+ +
Sbjct: 1 PKFIRNKLALALAELAKQEWPSNWPTFFPDLVSLLSSSPSGCEL 44
>gnl|CDD|234506 TIGR04221, SecA2_Mycobac, accessory Sec system translocase SecA2,
Actinobacterial type. Members of this family are the
SecA2 subunit of the Mycobacterial type of accessory
secretory system. This family is quite different SecA2
of the Staph/Strep type (TIGR03714).
Length = 762
Score = 30.6 bits (69), Expect = 1.6
Identities = 7/31 (22%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 97 VKRNWPLV-EDEPDKIHASDREAIKGLILHL 126
+ N P + DE D+++A+ E ++ +
Sbjct: 388 IPPNTPNIRFDEADRVYATAAEKNDAIVEEI 418
>gnl|CDD|191733 pfam07369, DUF1488, Protein of unknown function (DUF1488). This
family consists of several hypothetical bacterial
proteins of around 85 residues in length. The function
of this family is unknown.
Length = 81
Score = 28.0 bits (63), Expect = 1.8
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 248 SLNFQDLPEYFEDNMVVWMPALHN 271
++ F D P Y + V PAL +
Sbjct: 1 AILFPDRPSYDAARLAVRFPALVD 24
>gnl|CDD|152134 pfam11698, V-ATPase_H_C, V-ATPase subunit H. The yeast
Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase)
is a multisubunit complex responsible for acidifying
organelles. It functions as an ATP dependent proton pump
that transports protons across a lipid bilayer. This
domain corresponds to the C terminal domain of the H
subunit of V-ATPase. The N-terminal domain is required
for the activation of the complex whereas the C-terminal
domain is required for coupling ATP hydrolysis to proton
translocation.
Length = 119
Score = 28.7 bits (65), Expect = 2.0
Identities = 17/64 (26%), Positives = 22/64 (34%), Gaps = 19/64 (29%)
Query: 184 FKRYRHEFKSQKL-----------WTE--IKFVLDNFAKPFTELFKATINLVGEHKDNPT 230
F Y E S L W E +KF +N+ EL K ++ D P
Sbjct: 6 FDEYVAELNSGHLEWSPVHTSEKFWKENAMKFEENNY-----ELLKKLAKILETSDD-PL 59
Query: 231 ALKV 234
L V
Sbjct: 60 TLAV 63
>gnl|CDD|227432 COG5101, CRM1, Importin beta-related nuclear transport receptor
[Nuclear structure / Intracellular trafficking and
secretion].
Length = 1053
Score = 29.5 bits (66), Expect = 2.9
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 16/75 (21%)
Query: 97 VKRNWPLVEDEPDKIHASDREAIKGLILHLML---TSPEAIQKQ-----LSDATAI-IGK 147
+ W L+ + R+ I+ ++ L++ + KQ D T + I K
Sbjct: 75 ITTKWKLLPEG-------MRQGIRNYVVQLVIEKSQDDKVRDKQKYVLNKLDLTLVQILK 127
Query: 148 SDFPDKWPSLITDMV 162
++P WP+ I +++
Sbjct: 128 QEWPRNWPTFIPELI 142
>gnl|CDD|241158 cd12714, RRM1_MATR3, RNA recognition motif 1 in vertebrate
matrin-3. This subgroup corresponds to the RRM1 of
Matrin 3 (MATR3 or P130), a highly conserved inner
nuclear matrix protein with a bipartite nuclear
localization signal (NLS), two zinc finger domains
predicted to bind DNA, and two RNA recognition motifs
(RRM), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that are known to interact
with RNA. MATR3 has been implicated in various
biological processes. It is involved in RNA processing
by interacting with other nuclear proteins to anchor
hyperedited RNAs to the nuclear matrix. It plays a role
in mRNA stabilization through maintaining the stability
of certain mRNA species. Besides, it modulates the
activity of proximal promoters by binding to highly
repetitive sequences of matrix/scaffold attachment
region (MAR/SAR). The phosphorylation of MATR3 is
assumed to cause neuronal death. It is phosphorylated by
the protein kinase ATM, which activates the cellular
response to double strand breaks in the DNA. Its
phosphorylation by protein kinase A (PKA) is responsible
for the activation of the N-methyl-d-aspartic acid
(NMDA) receptor. Furthermore, MATR3 has been identified
as both a Ca2+-dependent CaM-binding protein and a
downstream substrate of caspases. Additional research
indicates that matrin 3 also binds Rev/Rev responsive
element (RRE)-containing viral RNA and functions as a
cofactor that mediates the post-transcriptional
regulation of HIV-1. .
Length = 76
Score = 26.7 bits (59), Expect = 4.9
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 71 LILTLVERADVDMTIRIAGAVAFKNYVKRNWPLVEDEPDKIHASDR 116
LIL + A ++M+ AVA NY + LV +P +++ S +
Sbjct: 32 LILNKINEAFLEMSTH-EEAVAMVNYYQTKPALVFGKPVRVYLSQK 76
>gnl|CDD|235407 PRK05322, PRK05322, galactokinase; Provisional.
Length = 387
Score = 28.3 bits (64), Expect = 7.1
Identities = 21/79 (26%), Positives = 25/79 (31%), Gaps = 36/79 (45%)
Query: 204 LDNFAKPFTELFKAT----------INLVGEHKDNPTALKVIYN-SLVVSCKI------- 245
+ K F E+F INL+GEH D YN V I
Sbjct: 3 KEELKKKFAEVFGEEAEDVFFSPGRINLIGEHTD--------YNGGHVFPAAITLGTYGA 54
Query: 246 ----------FYSLNFQDL 254
YS NF+DL
Sbjct: 55 ARKRDDKKVRLYSANFEDL 73
>gnl|CDD|211984 TIGR04261, rSAM_GlyRichRpt, radical SAM/SPASM domain protein, GRRM
system. Members of this protein family are radical
SAM/SPASM domain proteins (see pfam04055 and TIGR04085)
related to anaeroboic sulfatase maturating enzymes and
the peptide modification enzyme PqqE. Members are found
primarily in Cyanobacteria adjacent to a short protein,
~150 residues, in which the last ~60 residues tends to
be repetitive and highly glycine-rich (see TIGR04260).
The arrangement suggests modifications to the repetitive
C-terminal region by this radical SAM domain enzyme, but
the purpose of this system on the whole is unknown.
Length = 363
Score = 28.1 bits (63), Expect = 8.2
Identities = 27/112 (24%), Positives = 49/112 (43%), Gaps = 13/112 (11%)
Query: 93 FKNYVKRNWPLVEDEPDKIHASDREAIKGLILHLMLTSPEAIQKQLSDATAIIG---KSD 149
++ +++R W L ++ + E I LI T +Q ++ AI+ + +
Sbjct: 206 YRAFLQRFWELTAQAGGELRLREFEDICSLI----YTGQRLLQTDMNRPFAIVSVDHQGN 261
Query: 150 FPDKWPSLITDMVAKFGTGDFHIINGVLHTAHSLFKRYRHEFKSQKLWTEIK 201
F P L++ + GDF I+ VL SL + E K QKL+ ++
Sbjct: 262 FSTFDPELLSVKTDHY--GDF-ILGNVLT--DSLESACQTE-KFQKLYQDMT 307
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
0.323 0.138 0.417
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,218,236
Number of extensions: 1650458
Number of successful extensions: 1198
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1191
Number of HSP's successfully gapped: 22
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.4 bits)