RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18049
(204 letters)
>gnl|CDD|216424 pfam01302, CAP_GLY, CAP-Gly domain. Cytoskeleton-associated
proteins (CAPs) are involved in the organisation of
microtubules and transportation of vesicles and
organelles along the cytoskeletal network. A conserved
motif, CAP-Gly, has been identified in a number of CAPs,
including CLIP-170 and dynactins. The crystal structure
of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain
was recently solved. The domain contains three
beta-strands. The most conserved sequence, GKNDG, is
located in two consecutive sharp turns on the surface,
forming the entrance to a groove.
Length = 67
Score = 90.7 bits (226), Expect = 2e-24
Identities = 35/67 (52%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 40 IGDRVYV-GGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPKHGIF 98
+GDRV V GG + G + ++G FAPG W GV LD+P GKNDG V RYF+C PK+GIF
Sbjct: 1 VGDRVEVLGGGRRGTVRYVGPVPFAPGLWVGVELDEPRGKNDGSVDGVRYFECPPKYGIF 60
Query: 99 SRLTRLT 105
R +++
Sbjct: 61 VRPSKVE 67
Score = 63.7 bits (156), Expect = 5e-14
Identities = 25/48 (52%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 156 LGDRVIVMSAQGSKTGVLRFKGTTQFAQGEWCGVELDEPIGKNDGNLG 203
+GDRV V G + G +R+ G FA G W GVELDEP GKNDG++
Sbjct: 1 VGDRVEV--LGGGRRGTVRYVGPVPFAPGLWVGVELDEPRGKNDGSVD 46
>gnl|CDD|214997 smart01052, CAP_GLY, Cytoskeleton-associated proteins (CAPs) are
involved in the organisation of microtubules and
transportation of vesicles and organelles along the
cytoskeletal network. A conserved motif, CAP-Gly, has
been identified in a number of CAPs, including CLIP-170
and dynactins. The crystal structure of Caenorhabditis
elegans F53F4.3 protein CAP-Gly domain was recently
solved. The domain contains three beta-strands. The most
conserved sequence, GKNDG, is located in two consecutive
sharp turns on the surface, forming the entrance to a
groove.
Length = 68
Score = 84.9 bits (211), Expect = 4e-22
Identities = 37/68 (54%), Positives = 48/68 (70%), Gaps = 2/68 (2%)
Query: 40 IGDRVYVGGT-KSGRIAFIGETKFAPGDWAGVVLDDPV-GKNDGQVGQARYFQCEPKHGI 97
+GDRV VGG + G + ++G T FAPG W GV LD+P+ GKNDG V RYF+C PKHGI
Sbjct: 1 VGDRVEVGGGGRRGTVRYVGPTPFAPGVWVGVELDEPLRGKNDGSVKGVRYFECPPKHGI 60
Query: 98 FSRLTRLT 105
F R +++
Sbjct: 61 FVRPSKVE 68
Score = 60.7 bits (148), Expect = 7e-13
Identities = 26/46 (56%), Positives = 30/46 (65%), Gaps = 3/46 (6%)
Query: 156 LGDRVIVMSAQGSKTGVLRFKGTTQFAQGEWCGVELDEP-IGKNDG 200
+GDRV V G + G +R+ G T FA G W GVELDEP GKNDG
Sbjct: 1 VGDRVEV--GGGGRRGTVRYVGPTPFAPGVWVGVELDEPLRGKNDG 44
>gnl|CDD|227569 COG5244, NIP100, Dynactin complex subunit involved in mitotic
spindle partitioning in anaphase B [Cell division and
chromosome partitioning].
Length = 669
Score = 85.9 bits (212), Expect = 1e-19
Identities = 34/61 (55%), Positives = 41/61 (67%), Gaps = 1/61 (1%)
Query: 40 IGDRVYVGGTKSGRIAFIGETKFAPGDWAGVVLDDPVGKNDGQVGQARYFQCEPKHGIFS 99
+ DRV +G G + FIG+TKF G W G+ LDDPVGKNDG V RYF C+ +HGIF
Sbjct: 6 VNDRVLLGDKF-GTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKRHGIFI 64
Query: 100 R 100
R
Sbjct: 65 R 65
Score = 60.5 bits (146), Expect = 6e-11
Identities = 23/48 (47%), Positives = 33/48 (68%), Gaps = 4/48 (8%)
Query: 154 IRLGDRVIVMSAQGSKTGVLRFKGTTQFAQGEWCGVELDEPIGKNDGN 201
+ + DRV++ G K G +RF G T+F G W G+ELD+P+GKNDG+
Sbjct: 4 LSVNDRVLL----GDKFGTVRFIGKTKFKDGIWIGLELDDPVGKNDGS 47
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 31.6 bits (72), Expect = 0.25
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 9/78 (11%)
Query: 100 RLTRLTRTPLDLPPPATPTPGARGDGFISPTGSARSLSFSTPGPGLSTPAKGG---DIRL 156
R+ + + + P GA G G PT R LS PG + P G D+
Sbjct: 306 RIVEVLDAAGPVAEGSAPAAGAVGLG--KPTLELRDLSAGYPG---APPVLDGVSLDLPP 360
Query: 157 GDRVIVMSAQGS-KTGVL 173
G+RV ++ GS K+ +L
Sbjct: 361 GERVAILGPSGSGKSTLL 378
>gnl|CDD|234195 TIGR03396, PC_PLC, phospholipase C, phosphocholine-specific,
Pseudomonas-type. Members of this protein family are
bacterial, phosphatidylcholine-hydrolyzing phospholipase
C enzymes, with a characteristic domain architecture as
found in hemolytyic (PlcH) and nonhemolytic (PlcN)
secreted enzymes of Pseudomonas aeruginosa. PlcH
hydrolyzes phosphatidylcholine to diacylglycerol and
phosphocholine, but unlike PlcN can also hydrolyze
sphingomyelin to ceramide ((N-acylsphingosine)) and
phosphocholine. Members of this family share the
twin-arginine signal sequence for Sec-independent
transport across the plasma membrane. PlcH is secreted
as a heterodimer with a small chaperone, PlcR, encoded
immediately downstream [Cellular processes,
Pathogenesis].
Length = 689
Score = 30.8 bits (70), Expect = 0.51
Identities = 25/77 (32%), Positives = 32/77 (41%), Gaps = 15/77 (19%)
Query: 111 LPPPATPTPGARGDGFISPTGSARSLSFSTPGPGLSTPAKGGDIRLGDRV--IVMS--AQ 166
+PPP P+ A G T F+ P P A+G I LG RV V+S ++
Sbjct: 345 VPPPVPPSYNADGTSAGKSTLDTAGEYFTVPDP---AGARGRPIGLGPRVPMYVISPWSK 401
Query: 167 GSK--------TGVLRF 175
G T VLRF
Sbjct: 402 GGWVNSQVFDHTSVLRF 418
>gnl|CDD|165468 PHA03201, PHA03201, uracil DNA glycosylase; Provisional.
Length = 318
Score = 29.9 bits (67), Expect = 0.96
Identities = 12/40 (30%), Positives = 12/40 (30%)
Query: 112 PPPATPTPGARGDGFISPTGSARSLSFSTPGPGLSTPAKG 151
P P R SP S S PGPG P
Sbjct: 9 PSPPRRPSPPRPTPPRSPDASPEETPPSPPGPGAEPPPGR 48
>gnl|CDD|177556 PHA03195, PHA03195, tegument protein VP11/12; Provisional.
Length = 746
Score = 29.6 bits (66), Expect = 1.1
Identities = 22/84 (26%), Positives = 24/84 (28%), Gaps = 12/84 (14%)
Query: 81 GQVGQARYFQCEPKHGIFSRLTRLTRTPLDLPP----PATPTPGARGDGFISPTGSARS- 135
+ R C P+ F R PP PA P RG GS R
Sbjct: 409 ESIASKRTGSCPPQGATFGRNPSGFPGQFCCPPQGPLPAPPNSKTRGTFRRPRPGSVRGS 468
Query: 136 --LSFSTP----GPGLSTPAKGGD 153
L S P P PA G
Sbjct: 469 RQLPASPPSNIVSPRT-NPAAEGS 491
>gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein;
Provisional.
Length = 352
Score = 28.7 bits (65), Expect = 1.9
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 144 GLSTPAKGGDIRLGDRVIVMSAQG 167
GL+ P KG I L RV+ + +G
Sbjct: 46 GLTRPQKG-RIVLNGRVLFDAEKG 68
>gnl|CDD|151322 pfam10873, DUF2668, Protein of unknown function (DUF2668). Members
in this family of proteins are annotated as Cysteine and
tyrosine-rich protein 1, however currently no function
is known.
Length = 154
Score = 28.3 bits (63), Expect = 2.0
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 108 PLDLPPPATPTPGA 121
P DLPPP +P P A
Sbjct: 125 PTDLPPPYSPAPQA 138
>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 = 28.9 bits (64), Expect = 2.1
Identities = 14/43 (32%), Positives = 15/43 (34%)
Query: 107 TPLDLPPPATPTPGARGDGFISPTGSARSLSFSTPGPGLSTPA 149
P P +TP R P GSA S GPG P
Sbjct: 466 GPPPSLPTSTPAAPPRASSGSQPPGSALPSSGGCAGPGPPLPP 508
>gnl|CDD|221143 pfam11593, Med3, Mediator complex subunit 3 fungal. Mediator is a
large complex of up to 33 proteins that is conserved
from plants to fungi to humans - the number and
representation of individual subunits varying with
species. It is arranged into four different sections, a
core, a head, a tail and a kinase-activity part, and the
number of subunits within each of these is what varies
with species. Overall, Mediator regulates the
transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Mediator subunit
Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast
transcriptional co-repressor.
Length = 381
Score = 28.4 bits (63), Expect = 3.1
Identities = 7/48 (14%), Positives = 12/48 (25%), Gaps = 6/48 (12%)
Query: 105 TRTPLDLPPPATPTPGARGDGFISPTGSARSLSFSTPGPGLSTPAKGG 152
+ TP A + A + S G+ + A
Sbjct: 136 NGSDAATTSSTANTPAA------AKVLKANAASAPNTTTGVGSAATTA 177
>gnl|CDD|234982 PRK01777, PRK01777, hypothetical protein; Validated.
Length = 95
Score = 26.5 bits (59), Expect = 3.8
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 92 EPKHGIFSRLTRLTRTPLD 110
+ K GI+SR +LT D
Sbjct: 49 KNKVGIYSRPAKLTDVLRD 67
>gnl|CDD|216206 pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane
region. There are also some members in this family that
do not match the Prosite motif, and belong to the
subfamily SODIT1.
Length = 471
Score = 28.1 bits (63), Expect = 4.1
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 6/58 (10%)
Query: 114 PATPTPGARGDGFISPTGSARSLSFSTPGPGLSTPAKGGDIRLGDRVIVMSAQGSKTG 171
PA P+ AR G + P + +F STP KG ++G ++ Q +
Sbjct: 135 PAIPSNTARAGGIVFPIIMSLPPAFG------STPEKGSPRKIGAYLMWTVYQSTSIT 186
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits.
Length = 83
Score = 25.7 bits (57), Expect = 7.4
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 154 IRLGDRVIVMSAQGSKTG----VLRFKGTTQFAQ-GEWCGVELDE 193
++ GD+V V G G + RFKG A G+ G+ L +
Sbjct: 27 LKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAVAGDIVGIVLKD 71
>gnl|CDD|225265 COG2401, COG2401, ABC-type ATPase fused to a predicted
acetyltransferase domain [General function prediction
only].
Length = 593
Score = 27.1 bits (60), Expect = 7.7
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 154 IRLGDRVIVMSAQGS-KTGVLRFKGTTQFAQGE 185
I+ GD V V+ G+ KT +LR Q +GE
Sbjct: 406 IKPGDVVAVVGQSGAGKTTLLRMILGAQKGRGE 438
>gnl|CDD|177909 PLN02268, PLN02268, probable polyamine oxidase.
Length = 435
Score = 27.0 bits (60), Expect = 8.7
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 143 PGLSTPAKGGDIRLGDRVIVMSAQGSKTGVLRFKGTTQFA 182
P ++T AKG DIRL RV + + + V GTT A
Sbjct: 202 PVINTLAKGLDIRLNHRVTKIVRRYNGVKVTVEDGTTFVA 241
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
0.316 0.137 0.416
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,373,588
Number of extensions: 979823
Number of successful extensions: 999
Number of sequences better than 10.0: 1
Number of HSP's gapped: 995
Number of HSP's successfully gapped: 30
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
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: 57 (25.6 bits)