RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6084
(106 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 = 101 bits (255), Expect = 4e-30
Identities = 36/67 (53%), Positives = 44/67 (65%)
Query: 18 LGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIF 77
+G+ V + G + Y+GP FA G WVGVELD P GKNDG+V G RYFE PK+GIF
Sbjct: 1 VGDRVEVLGGGRRGTVRYVGPVPFAPGLWVGVELDEPRGKNDGSVDGVRYFECPPKYGIF 60
Query: 78 VRADKLI 84
VR K+
Sbjct: 61 VRPSKVE 67
>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 = 94.2 bits (235), Expect = 4e-27
Identities = 38/67 (56%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 18 LGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPT-GKNDGTVQGTRYFESRPKHGI 76
+G+ V + G + Y+GPT FA G WVGVELD P GKNDG+V+G RYFE PKHGI
Sbjct: 1 VGDRVEVGGGGRRGTVRYVGPTPFAPGVWVGVELDEPLRGKNDGSVKGVRYFECPPKHGI 60
Query: 77 FVRADKL 83
FVR K+
Sbjct: 61 FVRPSKV 67
>gnl|CDD|227569 COG5244, NIP100, Dynactin complex subunit involved in mitotic
spindle partitioning in anaphase B [Cell division and
chromosome partitioning].
Length = 669
Score = 83.6 bits (206), Expect = 3e-20
Identities = 30/64 (46%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
Query: 18 LGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIF 77
+ + VL+ + G + +IG T+F G W+G+ELD P GKNDG+V G RYF + +HGIF
Sbjct: 6 VNDRVLLG--DKFGTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKRHGIF 63
Query: 78 VRAD 81
+R D
Sbjct: 64 IRPD 67
>gnl|CDD|217887 pfam04090, RNA_pol_I_TF, RNA polymerase I specific initiation
factor.
Length = 192
Score = 27.3 bits (61), Expect = 1.2
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 18 LGESVLIRPYNSSGVIAYI 36
L E VL PY G I +I
Sbjct: 158 LSELVLEPPYMDDGEIWFI 176
>gnl|CDD|197612 smart00263, LYZ1, Alpha-lactalbumin / lysozyme C.
Length = 127
Score = 26.9 bits (60), Expect = 1.6
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 7 FDDVTLPEWVCL 18
+ ++L WVCL
Sbjct: 20 YRGISLANWVCL 31
>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 = 27.1 bits (60), Expect = 1.7
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 26 PYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGT--VQGTRYFES 70
PY +G++ ++GPT + G V + L G D T V G R+
Sbjct: 420 PYVRTGLLGFVGPTSHSMGPVVDMGLLFVVGSIDETLEVSGLRHNPD 466
>gnl|CDD|238066 cd00119, LYZ1, C-type lysozyme (1, 4-beta-N-acetylmuramidase,
LYZ) and alpha-lactalbumin (lactose synthase B protein,
LA). They have a close evolutionary relationship and
similar tertiary structure, however, functionally they
are quite different. Lysozymes have primarily
bacteriolytic function; hydrolysis of peptidoglycan of
prokaryotic cell walls and transglycosylation. LA is a
calcium-binding metalloprotein that is expressed
exclusively in the mammary gland during lactation. LA
is the regulatory subunit of the enzyme lactose
synthase. The association of LA with the catalytic
component of lactose synthase, galactosyltransferase,
alters the acceptor substrate specificity of this
glycosyltransferase, facilitating biosynthesis of
lactose.
Length = 123
Score = 26.8 bits (60), Expect = 1.7
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 7 FDDVTLPEWVCLGE 20
+ ++L WVCL E
Sbjct: 18 YPGISLANWVCLAE 31
>gnl|CDD|200968 pfam00062, Lys, C-type lysozyme/alpha-lactalbumin family.
Alpha-lactalbumin is the regulatory subunit of lactose
synthase, changing the substrate specificity of
galactosyltransferase from N-acetylglucosamine to
glucose. C-type lysozymes are secreted bacteriolytic
enzymes that cleave the peptidoglycan of bacterial cell
walls. Structure is a multi-domain, mixed alpha and
beta fold, containing four conserved disulfide bonds.
Length = 125
Score = 25.8 bits (57), Expect = 3.5
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 7 FDDVTLPEWVCL 18
+ ++L WVCL
Sbjct: 20 YRGISLANWVCL 31
>gnl|CDD|198349 cd07771, FGGY_RhuK, L-rhamnulose kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of bacterial L-rhamnulose kinases
(RhuK, also known as rhamnulokinase; EC 2.7.1.5), which
are encoded by the rhaB gene and catalyze the
ATP-dependent phosphorylation of L-rhamnulose to produce
L-rhamnulose-1-phosphate and ADP. Some uncharacterized
homologous sequences are also included in this
subfamily. The prototypical member of this subfamily is
Escherichia coli RhuK, which exists as a monomer
composed of two large domains. The ATP binding site is
located in the cleft between the two domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. The presence of divalent Mg2+ or Mn2+
is required for catalysis. Although an intramolecular
disulfide bridge is present in Rhuk, disulfide formation
is not important to the regulation of RhuK enzymatic
activity. Members of this subfamily belong to the FGGY
family of carbohydrate kinases.
Length = 440
Score = 25.5 bits (57), Expect = 5.9
Identities = 9/13 (69%), Positives = 10/13 (76%), Gaps = 2/13 (15%)
Query: 44 GTW--VGVELDAP 54
GTW +GVELD P
Sbjct: 257 GTWSLMGVELDEP 269
>gnl|CDD|224552 COG1637, COG1637, Predicted nuclease of the RecB family [DNA
replication, recombination, and repair].
Length = 253
Score = 25.4 bits (56), Expect = 6.0
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 12/56 (21%)
Query: 44 GTWVGVELDAPTGKNDGTVQGTRYFESRPK------HGIFV------RADKLIQDR 87
G V +EL Q RY E + GI V +A +L++D
Sbjct: 172 GNIVIIELKRRKAGLSAVSQLKRYVELLREDTGDKVRGILVAPSITEQARRLLEDE 227
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
0.318 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: 5,485,731
Number of extensions: 464634
Number of successful extensions: 326
Number of sequences better than 10.0: 1
Number of HSP's gapped: 325
Number of HSP's successfully gapped: 18
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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 (21.7 bits)
S2: 53 (24.1 bits)