RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4533
(365 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 = 100 bits (251), Expect = 1e-26
Identities = 38/69 (55%), Positives = 47/69 (68%), Gaps = 2/69 (2%)
Query: 268 LGDRVIIRSSQGSKSGVLKYKGDTYFADGEWCGVELDDPLGKNDGSVDGVRYFYCEPRFG 327
+GDRV + G + G ++Y G FA G W GVELD+P GKNDGSVDGVRYF C P++G
Sbjct: 1 VGDRVEV--LGGGRRGTVRYVGPVPFAPGLWVGVELDEPRGKNDGSVDGVRYFECPPKYG 58
Query: 328 VFAPVSKVS 336
+F SKV
Sbjct: 59 IFVRPSKVE 67
Score = 64.5 bits (158), Expect = 2e-13
Identities = 21/36 (58%), Positives = 28/36 (77%)
Query: 1 IVLDEPTGKNDGTVGGFRYFQCDPKHGIFSRLNRLT 36
+ LDEP GKNDG+V G RYF+C PK+GIF R +++
Sbjct: 32 VELDEPRGKNDGSVDGVRYFECPPKYGIFVRPSKVE 67
Score = 39.8 bits (94), Expect = 8e-05
Identities = 19/38 (50%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 131 IGDRVYV-GGTIPGKIAYIGETKFGPGDWAGKNRLDEP 167
+GDRV V GG G + Y+G F PG W G LDEP
Sbjct: 1 VGDRVEVLGGGRRGTVRYVGPVPFAPGLWVGV-ELDEP 37
>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 = 93.0 bits (232), Expect = 6e-24
Identities = 38/70 (54%), Positives = 46/70 (65%), Gaps = 3/70 (4%)
Query: 268 LGDRVIIRSSQGSKSGVLKYKGDTYFADGEWCGVELDDPL-GKNDGSVDGVRYFYCEPRF 326
+GDRV + + G ++Y G T FA G W GVELD+PL GKNDGSV GVRYF C P+
Sbjct: 1 VGDRVEVGGGG--RRGTVRYVGPTPFAPGVWVGVELDEPLRGKNDGSVKGVRYFECPPKH 58
Query: 327 GVFAPVSKVS 336
G+F SKV
Sbjct: 59 GIFVRPSKVE 68
Score = 57.6 bits (140), Expect = 5e-11
Identities = 22/37 (59%), Positives = 28/37 (75%), Gaps = 1/37 (2%)
Query: 1 IVLDEPT-GKNDGTVGGFRYFQCDPKHGIFSRLNRLT 36
+ LDEP GKNDG+V G RYF+C PKHGIF R +++
Sbjct: 32 VELDEPLRGKNDGSVKGVRYFECPPKHGIFVRPSKVE 68
Score = 41.4 bits (98), Expect = 3e-05
Identities = 21/40 (52%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 131 IGDRVYVGGTI-PGKIAYIGETKFGPGDWAGKNRLDEPDR 169
+GDRV VGG G + Y+G T F PG W G LDEP R
Sbjct: 1 VGDRVEVGGGGRRGTVRYVGPTPFAPGVWVGVE-LDEPLR 39
>gnl|CDD|227569 COG5244, NIP100, Dynactin complex subunit involved in mitotic
spindle partitioning in anaphase B [Cell division and
chromosome partitioning].
Length = 669
Score = 88.2 bits (218), Expect = 5e-19
Identities = 39/111 (35%), Positives = 57/111 (51%), Gaps = 17/111 (15%)
Query: 266 IRLGDRVIIRSSQGSKSGVLKYKGDTYFADGEWCGVELDDPLGKNDGSVDGVRYFYCEPR 325
+ + DRV++ K G +++ G T F DG W G+ELDDP+GKNDGSV+GVRYF+C+ R
Sbjct: 4 LSVNDRVLLGD----KFGTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKR 59
Query: 326 FGVF------------APVSKVSKSPVQASGHASK-NCVVHPSKDIPTYFY 363
G+F A K+ V S K + + + +F
Sbjct: 60 HGIFIRPDDDSLLNGNAAYEKIKGGLVCESKGMDKDGEIKQENHEDRIHFE 110
Score = 49.7 bits (118), Expect = 2e-06
Identities = 19/31 (61%), Positives = 23/31 (74%)
Query: 1 IVLDEPTGKNDGTVGGFRYFQCDPKHGIFSR 31
+ LD+P GKNDG+V G RYF C +HGIF R
Sbjct: 35 LELDDPVGKNDGSVNGVRYFHCKKRHGIFIR 65
Score = 34.3 bits (78), Expect = 0.12
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 131 IGDRVYVGGTIPGKIAYIGETKFGPGDWAGKNRLDEP 167
+ DRV +G G + +IG+TKF G W G LD+P
Sbjct: 6 VNDRVLLGDKF-GTVRFIGKTKFKDGIWIGL-ELDDP 40
>gnl|CDD|218107 pfam04484, DUF566, Family of unknown function (DUF566). Family of
related proteins that is plant specific.
Length = 313
Score = 34.9 bits (80), Expect = 0.057
Identities = 25/93 (26%), Positives = 32/93 (34%), Gaps = 5/93 (5%)
Query: 30 SRLNRLTRSPLLHLSDRPTSRNSSVDEGRYSPFKKSSFDGLYSRKSSDGGLFSRTSPEDI 89
SR RL S + +SS G S G S + SR SP
Sbjct: 36 SRPRRLNAPASPPSSSPARNTSSSSSFGLSKQRPSSLSRGRLSSRFVS---PSRGSP--S 90
Query: 90 STASPVSECSPLSAKYPSPPCKPQATHSSPLYS 122
+ AS + S S P + + T SS L S
Sbjct: 91 AAASLNGSLATASTSGSSSPSRSRRTTSSDLSS 123
>gnl|CDD|233599 TIGR01853, lipid_A_lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine
N-acyltransferase. This model describes LpxD, an enzyme
for the biosynthesis of lipid A, a component
oflipopolysaccharide (LPS) in the outer membrane outer
leaflet of most Gram-negative bacteria. Some differences
are found between lipid A of different species. This
protein represents the third step from
UDP-N-acetyl-D-glucosamine. The group added at this step
generally is 14:0(3-OH) (myristate) but may vary; in
Aquifex it appears to be 16:0(3-OH) (palmitate) [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 324
Score = 33.0 bits (76), Expect = 0.19
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 252 DEIRLGDRVIIRNEIRLGDRVIIRSS 277
D R+ V+I ++LG VII S
Sbjct: 144 DGSRIHPNVVIYERVQLGKNVIIHSG 169
>gnl|CDD|148635 pfam07139, DUF1387, Protein of unknown function (DUF1387). This
family represents a conserved region approximately 300
residues long within a number of hypothetical proteins
of unknown function that seem to be restricted to
mammals.
Length = 301
Score = 32.7 bits (74), Expect = 0.26
Identities = 19/82 (23%), Positives = 27/82 (32%), Gaps = 15/82 (18%)
Query: 37 RSPLLHLSDRPTSRNSSVDEGRYSPFKKSSFDGLYSRKSSDGGLFSRTSPEDISTASPVS 96
R P D P S +SS+ G K SP + P S
Sbjct: 75 REPEAVTLDAPPSPSSSLTNGLSDLQSKLELQS---------------SPHSSAKPHPSS 119
Query: 97 ECSPLSAKYPSPPCKPQATHSS 118
+ + KY S P +P ++S
Sbjct: 120 DQHKNAKKYVSKPSQPVTPNNS 141
>gnl|CDD|182451 PRK10427, PRK10427, putative PTS system fructose-like transporter
subunit EIIB; Provisional.
Length = 114
Score = 30.2 bits (68), Expect = 0.60
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 225 LTIQEVPHLMVSTQGNPSHGRLPTLSEDEIRLGDRVIIRNEIRLGDRVIIRSSQGSKSGV 284
L E + + TQG + G L++++IR D V++ +I L + + +
Sbjct: 28 LCQLEKWGVKIETQG--ALGTENRLTDEDIRRADVVLLITDIELAGAERFEHCRYVQCSI 85
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 30.9 bits (70), Expect = 1.0
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 254 IRLGDRVIIRNEIRLGDRVIIRSSQGSKS---GVLKYKGDTY 292
+R G R I EI +GD V++ +S GV+ G +
Sbjct: 46 VRFGRRKAIATEISVGDIVLVSRGNPLQSDLTGVVTRVGKRF 87
>gnl|CDD|100043 cd03352, LbH_LpxD, UDP-3-O-acyl-glucosamine N-acyltransferase
(LpxD): The enzyme catalyzes the transfer of
3-hydroxymyristic acid or 3-hydroxy-arachidic acid,
depending on the organism, from the acyl carrier protein
(ACP) to UDP-3-O-acyl-glucosamine to produce
UDP-2,3-diacyl-GlcNAc. This constitutes the third step
in the lipid A biosynthetic pathway in Gram-negative
bacteria. LpxD is a homotrimer, with each subunit
consisting of a novel combination of an N-terminal
uridine-binding domain, a core lipid-binding left-handed
parallel beta helix (LbH) domain, and a C-terminal
alpha-helical extension. The LbH domain contains 9
turns, each containing three imperfect tandem repeats of
a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
Length = 205
Score = 30.5 bits (70), Expect = 1.2
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 252 DEIRLGDRVIIRNEIRLGDRVIIRS 276
D+ + V I +GDRVII S
Sbjct: 42 DDCVIHPNVTIYEGCIIGDRVIIHS 66
>gnl|CDD|213273 cd05905, Dip2, Disco-interacting protein 2 (Dip2). Dip2 proteins
show sequence similarity to other members of the
adenylate forming enzyme family, including insect
luciferase, acetyl CoA ligases and the adenylation
domain of nonribosomal peptide synthetases (NRPS).
However, its function may have diverged from other
members of the superfamily. In mouse embryo, Dip2
homolog A plays an important role in the development of
both vertebrate and invertebrate nervous systems. Dip2A
appears to regulate cell growth and the arrangement of
cells in organs. Biochemically, Dip2A functions as a
receptor of FSTL1, an extracellular glycoprotein, and
may play a role as a cardiovascular protective agent.
Length = 556
Score = 30.6 bits (69), Expect = 1.5
Identities = 15/77 (19%), Positives = 19/77 (24%), Gaps = 24/77 (31%)
Query: 175 CPRASAISNAIRSTAIFSRLNALTRSPSPTSLGPPPHPRQFFSRPKAATH---------- 224
P AS ST + N R P R A H
Sbjct: 298 SPCAS-------STEASTVAN---RRIGTRGYSGPIPGRGVLDM-AALRHGVVRVDSEDK 346
Query: 225 ---LTIQEVPHLMVSTQ 238
L +Q+ +M Q
Sbjct: 347 PSSLPLQDSGMVMPGAQ 363
>gnl|CDD|133468 cd00476, SAICAR_synt, 5-aminoimidazole-4-(N-succinylcarboxamide)
ribonucleotide (SAICAR) synthase. SAICAR synthetase
(the PurC gene product) catalyzes the seventh step of
the de novo biosynthesis of purine nucleotides (also
reported as eighth step). It converts
5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP,
and L-aspartate into
5-aminoimidazole-4-(N-succinylcarboxamide)
ribonucleotide (SAICAR), ADP, and phosphate.
Length = 230
Score = 29.7 bits (67), Expect = 1.9
Identities = 16/76 (21%), Positives = 22/76 (28%), Gaps = 7/76 (9%)
Query: 143 GKIAYIGETKFGPGDWAGKNRLDEPDRARIRHCPRASAISNAIRSTAIFSRL------NA 196
GK + ETK G K+ + D AR I+ + IF L
Sbjct: 5 GKTKIVYETKDGVLLLEFKDDISAGDGARRNFLDEKGDITAKLTLF-IFKYLSEAGIPTH 63
Query: 197 LTRSPSPTSLGPPPHP 212
P +L
Sbjct: 64 FVERLGPRTLLVDKLK 79
>gnl|CDD|220749 pfam10428, SOG2, RAM signalling pathway protein. SOG2 proteins in
Saccharomyces cerevisiae are involved in cell separation
and cytokinesis.
Length = 419
Score = 30.1 bits (68), Expect = 2.1
Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 164 LDEPDRARIRHCPRASAISNAIRSTAIFSRLNALTRSPSPTSLGPPPHPRQFFSRPKAAT 223
L P + R R AS S R+T I RL RS +PT P + S P
Sbjct: 148 LGPPLQHRKRDAVTASPSSMIARNTPISDRLR--PRSVTPTRGRRPSSSPRSLSNPTTLE 205
Query: 224 HLTIQEVPHLMVSTQGNPSH 243
+ +L V+T P +
Sbjct: 206 SPS-----NLQVTTDVPPPY 220
>gnl|CDD|114140 pfam05399, EVI2A, Ectropic viral integration site 2A protein
(EVI2A). This family contains several mammalian
ectropic viral integration site 2A (EVI2A) proteins. The
function of this protein is unknown although it is
thought to be a membrane protein and may function as an
oncogene in retrovirus induced myeloid tumours.
Length = 227
Score = 29.3 bits (65), Expect = 2.5
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 75 SSDGGLFSRTSPEDISTASPVSECSPLSAKYPSPPCKPQATHSSPLYSMDSTDSFI 130
S L SR PE +T P E + S +P +PQ + PLYS ++ F
Sbjct: 41 SICQNLTSRNIPETNNTNPPTPEVNGKS----TPTAEPQTSTPVPLYSTSGSNFFT 92
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 30.0 bits (67), Expect = 2.8
Identities = 18/79 (22%), Positives = 26/79 (32%), Gaps = 2/79 (2%)
Query: 39 PLLHLSDRPTSRNSSVDEG-RYSPFKKSSFDGLYSRKSSDGGLFSRTSPEDISTASPVSE 97
L S P N +V + + +K + D S S S S +S
Sbjct: 93 DLNERSKTPIKNNDNVTTPIKANKKEKHNLDSSSSSSISSSLTNISFFSSPTSIYSCLSN 152
Query: 98 CSPLSAKYPSPPCKPQATH 116
S S P + Q+TH
Sbjct: 153 -SLSSKHSPKVIKENQSTH 170
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 29.3 bits (67), Expect = 3.6
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 14/34 (41%)
Query: 251 EDEI-RLGDRVIIRNEIRLGDRVIIRSSQGSKSG 283
DEI R IR+GD V++R ++G
Sbjct: 360 ADEIERKD--------IRIGDTVVVR-----RAG 380
>gnl|CDD|132946 cd06615, PKc_MEK, Catalytic domain of the dual-specificity Protein
Kinase, MAP/ERK Kinase. Protein kinases (PKs), MAP/ERK
kinase (MEK) subfamily, catalytic (c) domain. PKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine or tyrosine residues on protein
substrates. The MEK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein serine/threonine kinases, protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
mitogen-activated protein (MAP) kinase signaling
pathways are important mediators of cellular responses
to extracellular signals. The pathways involve a triple
kinase core cascade comprising the MAP kinase (MAPK),
which is phosphorylated and activated by a MAPK kinase
(MAPKK or MKK), which itself is phosphorylated and
activated by a MAPK kinase kinase (MAPKKK or MKKK). MEK1
and MEK2 are dual-specificity PKs that phosphorylate and
activate the downstream targets, ERK(extracellular
signal-regulated kinase) 1 and ERK2, on specific
threonine and tyrosine residues. The ERK cascade starts
with extracellular signals including growth factors,
hormones, and neurotransmitters, which act through
receptors and ion channels to initiate intracellular
signaling that leads to the activation at the MAPKKK
(Raf-1 or MOS) level, which leads to the transmission of
signals to MEK1/2, and finally to ERK1/2. The ERK
cascade plays an important role in cell proliferation,
differentiation, oncogenic transformation, and cell
cycle control, as well as in apoptosis and cell survival
under certain conditions. This cascade has also been
implicated in synaptic plasticity, migration,
morphological determination, and stress response
immunological reactions. Gain-of-function mutations in
genes encoding ERK cascade proteins, including MEK1/2,
cause cardiofaciocutaneous (CFC) syndrome, a condition
leading to multiple congenital anomalies and mental
retardation in patients.
Length = 308
Score = 28.9 bits (65), Expect = 4.3
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 6/56 (10%)
Query: 162 NRLDEPDRARIRHCPRASAISNAIRSTAIFSRLNALTRSPSPTSLGPPPHPRQFFS 217
R A+ H P + ++ R AIF L+ + P PP P FS
Sbjct: 211 GRPVSEGEAKESHRPVSGHPPDSPRPMAIFELLDYIVNEP------PPKLPSGAFS 260
>gnl|CDD|239761 cd04094, selB_III, This family represents the domain of elongation
factor SelB, homologous to domain III of EF-Tu. SelB may
function by replacing EF-Tu. In prokaryotes, the
incorporation of selenocysteine as the 21st amino acid,
encoded by TGA, requires several elements: SelC is the
tRNA itself, SelD acts as a donor of reduced selenium,
SelA modifies a serine residue on SelC into
selenocysteine, and SelB is a selenocysteine-specific
translation elongation factor. 3' or 5' non-coding
elements of mRNA have been found as probable structures
for directing selenocysteine incorporation.
Length = 97
Score = 26.8 bits (60), Expect = 6.3
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 244 GRLPTLSEDEIRLGDRVIIRNEIRL--------GDRVIIRS 276
R+ L DE+ G+ + ++RL GDR I+RS
Sbjct: 47 ARVVLLDRDELAPGEEALA--QLRLEEPLVALRGDRFILRS 85
>gnl|CDD|215628 PLN03196, PLN03196, MOC1-like protein; Provisional.
Length = 487
Score = 28.5 bits (64), Expect = 6.8
Identities = 9/51 (17%), Positives = 18/51 (35%)
Query: 84 TSPEDISTASPVSECSPLSAKYPSPPCKPQATHSSPLYSMDSTDSFIIGDR 134
++ S S S S + P + + + S LY S ++ +
Sbjct: 6 SASASRSLPSSGSSRSSRPGRSQRAPLRAKQSSSPSLYERPSVTWGLLEMK 56
>gnl|CDD|164824 PHA00653, mtd, major tropism determinant.
Length = 381
Score = 28.2 bits (62), Expect = 7.0
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 42 HLSDRPTSRNSSVDEGRYSPFKKSSFDGLYSRKSSDGGLFS 82
HL+D + N ++ +G SP K + F G S SDG ++
Sbjct: 200 HLTDGTSKYNVTIADGSASPKKSTKFGGDGSAAYSDGAWYN 240
>gnl|CDD|234858 PRK00892, lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine
N-acyltransferase; Provisional.
Length = 343
Score = 28.2 bits (64), Expect = 8.0
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 255 RLGDRVIIRNEIRLGDRVIIRS 276
RL V I + +R+G+RVII S
Sbjct: 156 RLHANVTIYHAVRIGNRVIIHS 177
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 0.414
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: 18,645,986
Number of extensions: 1762448
Number of successful extensions: 1594
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1589
Number of HSP's successfully gapped: 36
Length of query: 365
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 267
Effective length of database: 6,590,910
Effective search space: 1759772970
Effective search space used: 1759772970
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: 60 (26.8 bits)