RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16788
(423 letters)
>gnl|CDD|214556 smart00204, TGFB, Transforming growth factor-beta (TGF-beta)
family. Family members are active as disulphide-linked
homo- or heterodimers. TGFB is a multifunctional peptide
that controls proliferation, differentiation, and other
functions in many cell types.
Length = 102
Score = 184 bits (469), Expect = 7e-58
Identities = 62/100 (62%), Positives = 78/100 (78%)
Query: 322 RHPLYVDFADVGWNDWIVAPPGYDAFVCKGDCPFPLAEHLNSTNHAIVQTLMNSVQPETV 381
R LYVDF D+GW+DWI+AP GY+A+ C+G+CPFPL+ LN+TNHAIVQTL++ + P V
Sbjct: 3 RRQLYVDFKDLGWDDWIIAPKGYNAYYCEGECPFPLSTSLNATNHAIVQTLVHLLGPNPV 62
Query: 382 PKACCVPTALSAISMLYLDEDNKVVLKTYQDMAVTGCGCR 421
PK CCVPT LS +SMLY D+D VVL+ Y +M V CGCR
Sbjct: 63 PKPCCVPTKLSPLSMLYYDDDGNVVLRNYPNMVVEECGCR 102
>gnl|CDD|215660 pfam00019, TGF_beta, Transforming growth factor beta like domain.
Length = 105
Score = 169 bits (430), Expect = 5e-52
Identities = 61/100 (61%), Positives = 73/100 (73%)
Query: 322 RHPLYVDFADVGWNDWIVAPPGYDAFVCKGDCPFPLAEHLNSTNHAIVQTLMNSVQPETV 381
LYVDF D+GW DWI+AP GY A C G+CPFPLA+ LN TNHAI+QTL+ + P V
Sbjct: 6 LRELYVDFRDLGWGDWIIAPEGYIANYCAGECPFPLADDLNLTNHAILQTLVRLLNPRAV 65
Query: 382 PKACCVPTALSAISMLYLDEDNKVVLKTYQDMAVTGCGCR 421
PK CCVPT LS +SMLYLD+ + VVL+ Y +M V CGCR
Sbjct: 66 PKPCCVPTKLSPLSMLYLDDSSNVVLRLYPNMVVKECGCR 105
>gnl|CDD|216062 pfam00688, TGFb_propeptide, TGF-beta propeptide. This propeptide
is known as latency associated peptide (LAP) in
TGF-beta. LAP is a homodimer which is disulfide linked
to TGF-beta binding protein.
Length = 229
Score = 142 bits (359), Expect = 7e-40
Identities = 77/241 (31%), Positives = 113/241 (46%), Gaps = 17/241 (7%)
Query: 17 ITISTTSAEDSVQLDKKALQQVESNLLSLFGLNRRPRP-NRKNVRIPKAMLDLYKLQTGQ 75
S L ++ L+ +ES LLS GL RRP P +P+ MLDLY Q+
Sbjct: 3 KDNSCCQCVLLEALKQERLEAIESQLLSKLGLKRRPNPSQSLPKSVPQYMLDLYNSQSAD 62
Query: 76 DVDTS-MLPLPGRHTRSANTVRTFTHQVTNIDKRFKYLNKFRLHFDVTSLPDTERVQSAE 134
D S L ANTVR+F + ++ K RL F+++S+P+ E + +AE
Sbjct: 63 DSGASADLEELETLADRANTVRSFADEEEFELEQVDGHRK-RLFFNLSSIPEDELLTAAE 121
Query: 135 LRLSRPMNYEEDKHEQIQRIIVKDILQPGIKGISKPVLRIVDSVLVDSTSGENG-VSLDV 193
LRL E + R+ V +L+P G +P+ R++DS V E+G +S DV
Sbjct: 122 LRLYLEPVEESSRSTT-VRVSVYRVLKPSGSG--EPITRLLDSRSV--KISESGWLSFDV 176
Query: 194 LPAVQRWTKSPEHNHGLLIEVTNRDGVLLDRNIRPLVVMKRDQEEYNDLEWTSLEPILFL 253
PAVQRW + PE N GL +EV + +G L + W+ L P L +
Sbjct: 177 TPAVQRWLRQPETNLGLELEVLDSEGSDLAPTSAGPGGERHV--------WSQLRPFLVV 228
Query: 254 Y 254
+
Sbjct: 229 F 229
>gnl|CDD|177497 PHA02913, PHA02913, TGF-beta-like protein; Provisional.
Length = 172
Score = 46.6 bits (110), Expect = 3e-06
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 7/97 (7%)
Query: 325 LYVDF-ADVGWNDWIVAPPGYDAFVCKGDCPFPLAEHLNSTNHAIVQTLMNSVQPETVPK 383
+DF AD+G WI+ P G A +C G C + +N + + + T+P
Sbjct: 82 FNIDFKADMGMK-WILKPEGTHANLCIGICSISNHKKINLMYGTAFK---HHMPDNTIPF 137
Query: 384 ACCVPTALSAISMLYLDEDNKVVLKTYQDMAVTGCGC 420
CC P + + Y E K+ ++ + C C
Sbjct: 138 -CCAPIKMKNFIIAY-KEGRKIKTDNIKNFKILECAC 172
>gnl|CDD|171510 PRK12452, PRK12452, cardiolipin synthetase; Reviewed.
Length = 509
Score = 32.6 bits (74), Expect = 0.40
Identities = 23/99 (23%), Positives = 45/99 (45%), Gaps = 6/99 (6%)
Query: 4 LLMVVTVLATLNSITISTTSAEDSVQ--LDKKALQQVESNLLSLFGLNRRPRPNRKNVRI 61
+L +T++ I I S + ++ L L V L S+FG +R R +K++
Sbjct: 35 VLWSITIVGISFVIFIENRSPQSTLAWFLVLALLPVVGVLLYSIFGRSRWRR--KKHLHR 92
Query: 62 PKAMLDLYK-LQTGQDVDTSM-LPLPGRHTRSANTVRTF 98
+ L++ + G+ ++ S+ +PL R V+ F
Sbjct: 93 SEEQRKLFREILEGRRLELSLKVPLSERSVHLTEVVQKF 131
>gnl|CDD|212686 cd11736, HSPA12B_like_NBD, Nucleotide-binding domain of HSPA12B and
similar proteins. Human HSPA12B (also known as 70-kDa
heat shock protein-12B, chromosome 20 open reading frame
60/C20orf60, dJ1009E24.2; the gene encoding HSPA12B maps
to 20p13) belongs to the heat shock protein 70 (HSP70)
family of chaperones that assist in protein folding and
assembly, and can direct incompetent "client" proteins
towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). No
co-chaperones have yet been identified for HSPA12B.
HSPA12B is predominantly expressed in endothelial cells,
is required for angiogenesis, and may interact with
known angiogenesis mediators. HSPA12B may be important
for host defense in microglia-mediated immune response.
HSPA12B expression is up-regulated in lipopolysaccharide
(LPS)-induced inflammatory response in the spinal cord,
and mostly located in active microglia; this induced
expression may be regulated by activation of MAPK-p38,
ERK1/2 and SAPK/JNK signaling pathways. Overexpression
of HSPA12B also protects against LPS-induced cardiac
dysfunction and involves the preserved activation of the
PI3K/Akt signaling pathway.
Length = 468
Score = 30.3 bits (68), Expect = 2.2
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 53 RPNRKNVRIPKAMLDLYKLQTGQDVDTSM 81
R N N+ +P + +D Y+ GQ+V+T++
Sbjct: 342 RANTLNISLPFSFIDFYRKHRGQNVETAL 370
>gnl|CDD|197264 cd09167, PLDc_EcPPK1_C2_like, Catalytic C-terminal domain, second
repeat, of Escherichia coli polyphosphate kinase 1 and
similar proteins. Catalytic C-terminal domain, second
repeat (C2 domain), of Escherichia coli polyphosphate
kinase 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and
similar proteins. Inorganic polyphosphate (Poly P) plays
an important role in bacterial stress responses and
stationary-phase survival. PPK1 is the key enzyme
responsible for the synthesis of Poly P in bacteria. It
can catalyze the reversible conversion of the
terminal-phosphate of ATP to Poly P. Therefore, PPK1 is
essential for bacterial motility, quorum sensing,
biofilm formation, and the production of virulence
factors and may serve as an attractive antimicrobial
drug target. Dimerization is crucial for the enzymatic
activity of PPK1. The prototype of this subfamily is
Escherichia coli polyphosphate kinase (EcPPK), which
forms a homotetramer in solution, and becomes a
homodimer upon the binding of AMPPNP, a non-hydrolysable
ATP analogue. Each EcPPK monomer includes four
structural domains, the N-terminal (N) domain, the head
(H) domain, and two closely related C-terminal (C1 and
C2)domains. The N domain provides the upper binding
interface for the adenine ring of the ATP. The H domain
is involved in dimerization, while both the C1 and C2
domains contain residues crucial for catalytic activity.
The intersection of the N, C1, and C2 domains forms a
structural tunnel in which the PPK catalytic reactions
are carried out. In spite of the lack of sequence
homology, the C1 and C2 domains of EcPPK are
structurally similar to the two repetitive catalytic
domains of phospholipase D (PLD). Moreover, some
residues in the HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) of the PLD
superfamily are spatially conserved in the active site
of EcPPK. It is possible that the bacterial PPK1 family
and the PLD family have a common ancestor and diverged
early in evolution.
Length = 165
Score = 29.5 bits (67), Expect = 2.3
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 153 RIIVKDI--LQPGIKGISK--PVLRIVDSVL 179
+IV+ I L PGI GIS+ V+ IVD L
Sbjct: 61 DLIVRGICSLIPGIPGISENIRVISIVDRYL 91
>gnl|CDD|225280 COG2423, COG2423, Predicted ornithine cyclodeaminase, mu-crystallin
homolog [Amino acid transport and metabolism].
Length = 330
Score = 29.6 bits (67), Expect = 2.9
Identities = 16/53 (30%), Positives = 23/53 (43%)
Query: 162 PGIKGISKPVLRIVDSVLVDSTSGENGVSLDVLPAVQRWTKSPEHNHGLLIEV 214
PG + + VL D V+VDS S ++ AV SP+ L +V
Sbjct: 229 PGKRELDPEVLARADRVVVDSLEQTRKESGEISQAVAAGVLSPDAIVAELGDV 281
>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional.
Length = 332
Score = 29.3 bits (66), Expect = 4.1
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 356 PLAEHLNSTNHAIVQTLMNSVQPETVPKACCVPTALSAISMLYL 399
LA + S V+ N ++P+ +A P A + MLY+
Sbjct: 168 ELAAEIYSDASHRVELAKNFMEPQAETEA--QPEATTNFIMLYV 209
>gnl|CDD|219693 pfam08007, Cupin_4, Cupin superfamily protein. This family
contains many hypothetical proteins that belong to the
cupin superfamily.
Length = 319
Score = 29.2 bits (66), Expect = 4.4
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 4/68 (5%)
Query: 267 DLLKRPRRTPNDNAPRKHKKN-TYSICKRHPLYVDFADVGWNDWIVENIRKILIPYRHPL 325
D+L PR + + YS+ R P + + D++++ + I YR PL
Sbjct: 184 DMLYLPRGFIHQ--GVALDDSLHYSVGFRAPTAAELLS-SFLDYLLDKLPGIDERYRDPL 240
Query: 326 YVDFADVG 333
G
Sbjct: 241 LRAVQAPG 248
>gnl|CDD|238403 cd00780, NTF2, Nuclear transport factor 2 (NTF2) domain plays an
important role in the trafficking of macromolecules,
ions and small molecules between the cytoplasm and
nucleus. This bi-directional transport of macromolecules
across the nuclear envelope requires many soluble
factors that includes GDP-binding protein Ran (RanGDP).
RanGDP is required for both import and export of
proteins and poly(A) RNA. RanGDP also has been
implicated in cell cycle control, specifically in
mitotic spindle assembly. In interphase cells, RanGDP is
predominately nuclear and thought to be GTP bound, but
it is also present in the cytoplasm, probably in the
GDP-bound state. NTF2 mediates the nuclear import of
RanGDP. NTF2 binds to both RanGDP and FxFG
repeat-containing nucleoporins.
Length = 119
Score = 28.0 bits (63), Expect = 4.7
Identities = 12/63 (19%), Positives = 20/63 (31%), Gaps = 16/63 (25%)
Query: 62 PKAMLDLYKLQTGQDVDTSMLPLPGRHTRSANTVRTFTHQVTNIDKRFKYLNKFRLHFDV 121
+ + LY DTSML G V I ++ L + +
Sbjct: 21 REGLHRLYG-------DTSMLSREGM-----KQVTG----RDAIVEKLSSLPFQKTKHKI 64
Query: 122 TSL 124
T++
Sbjct: 65 TTV 67
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
0.320 0.136 0.410
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,400,713
Number of extensions: 2067263
Number of successful extensions: 1680
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1676
Number of HSP's successfully gapped: 17
Length of query: 423
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 323
Effective length of database: 6,502,202
Effective search space: 2100211246
Effective search space used: 2100211246
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 (21.8 bits)
S2: 60 (26.9 bits)