RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3317
(173 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 = 112 bits (282), Expect = 3e-33
Identities = 36/67 (53%), Positives = 44/67 (65%)
Query: 85 IGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIF 144
+G+ V + G + Y+GP FA G WVGVELD P GKNDG+V G RYFE PK+GIF
Sbjct: 1 VGDRVEVLGGGRRGTVRYVGPVPFAPGLWVGVELDEPRGKNDGSVDGVRYFECPPKYGIF 60
Query: 145 VRADKLI 151
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 = 104 bits (263), Expect = 2e-30
Identities = 38/67 (56%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 85 IGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPT-GKNDGTVQGTRYFESRPKHGI 143
+G+ V + G + Y+GPT FA G WVGVELD P GKNDG+V+G RYFE PKHGI
Sbjct: 1 VGDRVEVGGGGRRGTVRYVGPTPFAPGVWVGVELDEPLRGKNDGSVKGVRYFECPPKHGI 60
Query: 144 FVRADKL 150
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 = 75.9 bits (186), Expect = 2e-16
Identities = 30/64 (46%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
Query: 85 IGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIF 144
+ + VL+ + G + +IG T+F G W+G+ELD P GKNDG+V G RYF + +HGIF
Sbjct: 6 VNDRVLLG--DKFGTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKRHGIF 63
Query: 145 VRAD 148
+R D
Sbjct: 64 IRPD 67
>gnl|CDD|215138 PLN02248, PLN02248, cellulose synthase-like protein.
Length = 1135
Score = 29.2 bits (66), Expect = 1.3
Identities = 24/64 (37%), Positives = 29/64 (45%)
Query: 15 MASSSLTVSSEMDSCSDLDKRSSSSSLSSHDENKVVRRKSSTRRSSQSRASYPMSGDQSF 74
MASSS S + S S S++ SS K RR SS R S SR +SG+ S
Sbjct: 1 MASSSSKPSRKSLSSSSSSAGPPSNNSSSPQSVKFARRTSSGRYVSLSRDDLDLSGELSS 60
Query: 75 DDVT 78
D
Sbjct: 61 SDYL 64
>gnl|CDD|219184 pfam06807, Clp1, Pre-mRNA cleavage complex II protein Clp1. This
family consists of several pre-mRNA cleavage complex II
Clp1 (or HeaB) proteins. Six different protein factors
are required in vitro for 3' end formation of mammalian
pre-mRNAs by endonucleolytic cleavage and
polyadenylation. Clp1 is a subunit of cleavage complex
IIA, which is required for cleavage, but not for
polyadenylation of pre-mRNA.
Length = 188
Score = 27.3 bits (61), Expect = 3.2
Identities = 11/48 (22%), Positives = 11/48 (22%), Gaps = 12/48 (25%)
Query: 44 HDENKVVRRKSSTRRSS------------QSRASYPMSGDQSFDDVTL 79
VV R RR P S F DVT
Sbjct: 51 PKSGGVVERSKKYRRIIRDLRILEYFYGTLPMPLSPHSFLVKFSDVTP 98
>gnl|CDD|220776 pfam10483, Hap2_elong, Histone acetylation protein 2. Hap2 is one
of three histone acetyltransferases proteins that, in
yeasts, are found associated with elongating forms of
RNA polymerase II (Elongator). The Haps can be isolated
in two forms, as a six-subunit complex with Elongator
and as a complex of the three proteins on their own. The
role of the Hap complex in transcription is still
speculative, being possibly to keep the HAT activity of
free Elongator in check, allowing histone acetylation
only in the presence of a transcribing polymerase, or
the interaction with Haps might render Elongator
susceptible to modifications thereby altering its
activity.
Length = 280
Score = 27.3 bits (61), Expect = 4.6
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 11/59 (18%)
Query: 7 SSLTISSDMASSSLTVSSEMDSCSDLDKRSSS------SSLSSHDENKVV-----RRKS 54
S LT+ S +A++ + V +D + S + +V RRKS
Sbjct: 141 SPLTLLSYLATTIIEVEPFSHESADKEALDRSLSEPVFPLNEGLNGVGIVLELENRRKS 199
>gnl|CDD|100060 cd05636, LbH_G1P_TT_C_like, Putative glucose-1-phosphate
thymidylyltransferase, C-terminal Left-handed parallel
beta-Helix (LbH) domain: Proteins in this family show
simlarity to glucose-1-phosphate adenylyltransferases in
that they contain N-terminal catalytic domains that
resemble a dinucleotide-binding Rossmann fold and
C-terminal LbH fold domains. Members in this family are
predicted to be glucose-1-phosphate
thymidylyltransferases, which are involved in the
dTDP-L-rhamnose biosynthetic pathway.
Glucose-1-phosphate thymidylyltransferase catalyzes the
synthesis of deoxy-thymidine di-phosphate
(dTDP)-L-rhamnose, an important component of the cell
wall of many microorganisms. The C-terminal LbH domain
contains multiple turns, each containing three imperfect
tandem repeats of a hexapeptide repeat motif
(X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing
hexapeptide repeats are often enzymes showing
acyltransferase activity.
Length = 163
Score = 26.8 bits (60), Expect = 4.7
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 75 DDVTLPEWVCIGESVLIRPYNSSGVIAYI-GPTEFAAGTWVG 115
+ VT+ V IGE ++R AYI GP G +G
Sbjct: 10 EGVTIKGPVWIGEGAIVRSG------AYIEGPVIIGKGCEIG 45
>gnl|CDD|234433 TIGR03992, Arch_glmU, UDP-N-acetylglucosamine
diphosphorylase/glucosamine-1-phosphate
N-acetyltransferase. The MJ_1101 protein from
Methanococcus jannaschii has been characterized as the
GlmU enzyme catalyzing the final two steps of UDP-GlcNAc
biosynthesis. Many of the genes identified by this model
are in proximity to the GlmS and GlmM genes and are also
presumed to be GlmU. However, some archaeal genomes
contain multiple closely-related homologs from this
family and it is not clear what the substrate
specificity is for each of them.
Length = 393
Score = 27.2 bits (61), Expect = 5.0
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 7/42 (16%)
Query: 75 DDVTLPEWVCIGESVLIRPYNSSGVIAYI-GPTEFAAGTWVG 115
++VT+ V IGE +IR YI GP +G
Sbjct: 241 ENVTIKGPVVIGEGAVIRSG------TYIEGPVYIGKNCDIG 276
>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 = 5.2
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 58 RSSQSRASY---PMSGDQSFDDVTLPEWVCIGESVLIRPYNSSGVIAYIGPTEFAAGTWV 114
SS + SY +F+ IGE+ PY +G++ ++GPT + G V
Sbjct: 386 NSSANATSYYGLTGMTKNTFEVFPNSSSDGIGEN----PYVRTGLLGFVGPTSHSMGPVV 441
Query: 115 GVELDAPTGKNDGT--VQGTRYFES 137
+ L G D T V G R+
Sbjct: 442 DMGLLFVVGSIDETLEVSGLRHNPD 466
>gnl|CDD|227604 COG5279, CYK3, Uncharacterized protein involved in cytokinesis,
contains TGc (transglutaminase/protease-like) domain
[Cell division and chromosome partitioning].
Length = 521
Score = 27.2 bits (60), Expect = 5.7
Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 2 KSSMSSSLTISSDMASSSLTVSSEMDSCSDLDKRSSSSSLSSHDENKVVRRKSSTRRSSQ 61
M +S++ ++ SS +++ S D S L S +N + + ++SS
Sbjct: 54 SHPMLNSMSRTNLDLSSRWDNTADNFSEIDALSPLPPSPLRSAMDNVLQSLNAKGKKSSL 113
Query: 62 SRASYPMSGDQSFDDVTLPE 81
R + + + FD + +PE
Sbjct: 114 -RLTNSTTDNTKFDFIPIPE 132
>gnl|CDD|224552 COG1637, COG1637, Predicted nuclease of the RecB family [DNA
replication, recombination, and repair].
Length = 253
Score = 26.9 bits (60), Expect = 5.8
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 12/56 (21%)
Query: 111 GTWVGVELDAPTGKNDGTVQGTRYFESRPK------HGIFV------RADKLIQDR 154
G V +EL Q RY E + GI V +A +L++D
Sbjct: 172 GNIVIIELKRRKAGLSAVSQLKRYVELLREDTGDKVRGILVAPSITEQARRLLEDE 227
>gnl|CDD|220710 pfam10351, Apt1, Golgi-body localisation protein domain. This is
the C-terminus of a family of proteins conserved from
plants to humans. The plant members are localised to the
Golgi proteins and appear to regulate membrane
trafficking, as they are required for rapid vesicle
accumulation at the tip of the pollen tube. The
C-terminus probably contains the Golgi localisation
signal and it is well-conserved.
Length = 451
Score = 26.9 bits (60), Expect = 6.7
Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 2 KSSMSSSLTISSDMASSSLTVSSEMDSCSDLDKRSSSSSLSSHDENKVVRRKSSTRRSS- 60
S +SSS + S +SS+ SS S S SS S D+ ++ S + S
Sbjct: 313 DSDISSSSSSGSRRSSSTSRSSSSSSSLLSSSSILSKSSDKSKDKRFSLKLSKSEKEESD 372
Query: 61 -----QSRAS 65
SR+S
Sbjct: 373 DLEEMISRSS 382
>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 = 26.1 bits (58), Expect = 6.9
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 74 FDDVTLPEWVCIGE 87
+ ++L WVC+ E
Sbjct: 18 YPGISLANWVCLAE 31
>gnl|CDD|197612 smart00263, LYZ1, Alpha-lactalbumin / lysozyme C.
Length = 127
Score = 25.7 bits (57), Expect = 8.0
Identities = 4/12 (33%), Positives = 8/12 (66%)
Query: 74 FDDVTLPEWVCI 85
+ ++L WVC+
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 = 26.7 bits (60), Expect = 8.0
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 7/23 (30%)
Query: 101 AYIGPTEFAAGTW--VGVELDAP 121
AYI ++GTW +GVELD P
Sbjct: 252 AYI-----SSGTWSLMGVELDEP 269
>gnl|CDD|217887 pfam04090, RNA_pol_I_TF, RNA polymerase I specific initiation
factor.
Length = 192
Score = 26.2 bits (58), Expect = 8.7
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 85 IGESVLIRPYNSSGVIAYI 103
+ E VL PY G I +I
Sbjct: 158 LSELVLEPPYMDDGEIWFI 176
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 26.4 bits (58), Expect = 9.3
Identities = 22/88 (25%), Positives = 32/88 (36%), Gaps = 9/88 (10%)
Query: 2 KSSMSSSLTISSDMASSSLTVSSEM-------DSCSDLDKRSSSSSLSSHDENKVVRRKS 54
KS SSS T S +S+ + ++ S ++ S+SS SH S
Sbjct: 299 KSRPSSSSTNGSKETTSNSSSAAAGSIGSKSSKSAKHSNRNKSNSSPKSHSSANGSVPSS 358
Query: 55 STRRSS--QSRASYPMSGDQSFDDVTLP 80
S + Q RAS SG +
Sbjct: 359 SVSDNESKQKRASKSSSGARDSKKDASG 386
>gnl|CDD|220815 pfam10577, UPF0560, Uncharacterized protein family UPF0560. This
family of proteins has no known function.
Length = 805
Score = 26.4 bits (58), Expect = 9.7
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 3 SSMSSSLTISSDMASSSLTVSSEMDSCSDLDKRSSSSSLSSHDENKVVRRKSSTRRSSQS 62
+SMS IS+ + S ++M + SSS +S E + + + QS
Sbjct: 327 TSMSHINLISTHLEMVSSAGEADMHTPMLKSAFSSSRDFTSS-EELLAHKAEDKSQLPQS 385
Query: 63 RASYPM 68
S+P+
Sbjct: 386 GESFPL 391
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
0.311 0.124 0.345
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: 8,017,955
Number of extensions: 693992
Number of successful extensions: 516
Number of sequences better than 10.0: 1
Number of HSP's gapped: 509
Number of HSP's successfully gapped: 37
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
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 (21.8 bits)
S2: 55 (24.9 bits)