RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18161
(209 letters)
>gnl|CDD|218802 pfam05903, DUF862, PPPDE putative peptidase domain. The PPPDE
superfamily (after Permuted Papain fold Peptidases of
DsRNA viruses and Eukaryotes), consists of predicted
thiol peptidases with a circularly permuted papain-like
fold. The inference of the likely DUB function of the
PPPDE superfamily proteins is based on the fusions of
the catalytic domain to Ub-binding PUG (PUB)/UBA domains
and a novel alpha-helical Ub-associated domain (the PUL
domain, after PLAP, Ufd3p and Lub1p).
Length = 151
Score = 158 bits (401), Expect = 1e-49
Identities = 67/191 (35%), Positives = 89/191 (46%), Gaps = 49/191 (25%)
Query: 4 EPILLNVYDMLWTND------YTSTLGL---GVFHSGIEVYGVEYAYGGHQYPFSGIFRI 54
P+ LNVYD+ N LG G+FH+G+EVYGVEY +G H Y SGIF
Sbjct: 1 HPVKLNVYDLSPINGGLARRYSPLLLGKQIEGIFHTGVEVYGVEYFFGAHTYEGSGIFEC 60
Query: 55 SPRDAKELGEQFAFRESIQIGSTDFTESDVKRIVTELGKEYRGDRYHLMNKGESIQIGST 114
P G R ESI++G T
Sbjct: 61 PPGRTCP------------------------------GFTPR----------ESIELGET 80
Query: 115 DFTESDVKRIVTELGKEYRGDRYHLMNKNCNHFSNELTKILCGQEIPGWVNRLAYFSSCV 174
+ TE + + I+ L +EY GD Y+L++KNCNHF++EL + L G++IP W+NRL
Sbjct: 81 ELTEEEFREILNSLSEEYTGDTYNLISKNCNHFTDELCQFLTGKKIPSWINRLPREVLST 140
Query: 175 PFLQRCLPKEW 185
PF Q LP W
Sbjct: 141 PFGQCLLPMLW 151
>gnl|CDD|215749 pfam00148, Oxidored_nitro, Nitrogenase component 1 type
Oxidoreductase.
Length = 397
Score = 29.9 bits (68), Expect = 0.89
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 14/73 (19%)
Query: 68 FRESIQIGSTDFTESDV--------KRIVTELGKEYRGDRYHLMNKGESIQIGSTDFTES 119
FRE I I STD TE DV + + E+ K Y+ + S IG
Sbjct: 38 FREPIPIFSTDLTEKDVVFGGEEKLEEAIREIDKRYKPKAIFVYTTCVSELIG------D 91
Query: 120 DVKRIVTELGKEY 132
D++ + E +E
Sbjct: 92 DIEAVAREAEEEL 104
>gnl|CDD|224543 COG1628, COG1628, Endonuclease V homolog [Replication,
recombination, and repair].
Length = 185
Score = 28.4 bits (64), Expect = 1.7
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 69 RESIQIGSTDFTESDVKRIVTELGKEYRGDRYHLMNKGESIQIGSTDFTESDVKRIVTEL 128
RE +G D S VT +G RGDR I + D T+ + +V
Sbjct: 7 REIRVLGIDDGPFSRGDDKVTLVGVVMRGDRVVDGVAFSLITVDGLDVTD-AISDMVNRS 65
Query: 129 G 129
Sbjct: 66 K 66
>gnl|CDD|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH. The
third LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 51
Score = 26.2 bits (58), Expect = 2.3
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 132 YRGDRYHLMNKNCNHFSNELT 152
++GD YH + NC + ELT
Sbjct: 15 FKGDPYHPYHFNCANCGKELT 35
>gnl|CDD|234217 TIGR03458, YgfH_subfam, succinate CoA transferase. This family of
CoA transferases includes enzymes catalyzing at least
two related but distinct activities. The E. coli YgfH
protein has been characterized as a
propionyl-CoA:succinate CoA transferase where it appears
to be involved in a pathway for the decarboxylation of
succinate to propionate. The Clostridium kluyveri CAT1
protein has been characterized as a acetyl-CoA:succinate
CoA transferase and is believed to be involved in
anaerobic succinate degradation. The
propionate:succinate transferase activity has been
reported in the propionic acid fermentation of
propionibacterium species where it is distinct from the
coupled activities of distinct nucleotide-triphosphate
dependent succinate and propionate/acetate CoA
transferases (as inferred from activity in the absence
of NTPs). The family represented by this model includes
a member from Propionibacterium acnes KPA171202 which is
likely to be responsible for this activity. A closely
related clade not included in this family are the Ach1p
proteins of fungi which are acetyl-CoA hydrolases. This
name has been applied to many of the proteins modeled by
This model, possibly erroneously.
Length = 485
Score = 28.4 bits (64), Expect = 3.2
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 115 DFTESDVKRIVTELG-KEYRG----DRYHLMNKNCNH 146
D TE DV IVTE G + RG +R + NC H
Sbjct: 409 DHTEHDVMVIVTEQGLADLRGLSPRERARAIIDNCAH 445
>gnl|CDD|131514 TIGR02461, osmo_MPG_phos, mannosyl-3-phosphoglycerate phosphatase.
Members of this family are mannosyl-3-phosphoglycerate
phosphatase (EC 3.1.3.70). It acts sequentially after
mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) in a
two-step pathway of biosynthesis of the compatible
solute mannosylglycerate, a typical osmolyte of
thermophiles.
Length = 225
Score = 27.8 bits (62), Expect = 4.0
Identities = 21/102 (20%), Positives = 37/102 (36%), Gaps = 24/102 (23%)
Query: 52 FRISPRDAKELGEQFAFRESIQI--------GSTDF---------TESDVKR---IVTEL 91
F I +K EQ +RE + + G + + + V EL
Sbjct: 32 FPIVFVSSKTRAEQEYYREELGVEPPFIVENGGAIYIPRGYFPFPVGAGREVGNYEVIEL 91
Query: 92 GKEYRGDRYHLMNKGESIQIGSTDFTESDVKRI--VTELGKE 131
GK Y R + + E+ G + +S + + +T L +E
Sbjct: 92 GKPYAKIR-AALKEAENE-AGIKGYGDSTAEEVARLTGLPRE 131
>gnl|CDD|203136 pfam04970, LRAT, Lecithin retinol acyltransferase. The full-length
members of this family are representatives of a novel
class II tumour-suppressor family, designated as
H-REV107-like. This domain is the catalytic N-terminal
proline-rich region of the protein. The downstream
region is a putative C-terminal transmembrane domain
which is found to be crucial for cellular localisation,
but not necessary for the enzyme activity. H-REV107-like
proteins are homologous to lecithin retinol
acyltransferase (LRAT), an enzyme that catalyzes the
transfer of the sn-1 acyl group of phosphatidylcholine
to all-trans-retinol and forming a retinyl ester.
Length = 125
Score = 26.9 bits (60), Expect = 4.0
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 133 RGDRYHLMNKNCNHFSNEL 151
+ Y L++ NC HF
Sbjct: 102 QEVPYSLLSNNCEHFVTYC 120
>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an tRNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required.
TruC makes psi65 in tRNAs. This psi residue is not
universally conserved.
Length = 223
Score = 27.7 bits (62), Expect = 4.5
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 47 PFSGI--FRISPRDAKELGEQFAFRE 70
P SG+ F +S A++LGEQF
Sbjct: 55 PTSGVLLFALSSEVARKLGEQFTEHR 80
>gnl|CDD|240523 cd13150, DAXX_histone_binding, Histone binding domain of the
death-domain associated protein (DAXX). DAXX is a
nuclear protein that modulates transcription of various
genes and is involved in cell death and/or the
suppression of growth. DAXX is also a histone chaperone
conserved in Metazoa that acts specifically on histone
H3.3. This alignment models a functional domain of DAXX
that interacts with the histone H3.3-H4 dimer, and in
doing so competes with DNA binding and interactions
between the histone chaperone ASF1/CIA and the H3-H4
dimer.
Length = 198
Score = 27.2 bits (61), Expect = 4.6
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 11/59 (18%)
Query: 81 ESDVKRIVTELGKEYRGDRYHLMNKGESIQ------IGSTDFTESDVKRIVTELGKEYR 133
D RIV E + G RY +N+ I+ DF D+ +IV + ++
Sbjct: 62 SPDTGRIV-EKKIHFSGTRYPEVNR--KIEKFVNRNKTFPDFH--DILKIVQKANRKKN 115
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 27.5 bits (61), Expect = 5.7
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 18/82 (21%)
Query: 49 SGIFRIS-PRD-AKELGEQFAFRESIQIGSTDFTESDVKRIVTE----LGKEYRGDRYHL 102
+G F ++ P D EL +F R ++ T D +RI+TE L K+Y+
Sbjct: 305 AGAFHLAKPSDLIPELQGRFPIRVELK----ALTIDDFERILTEPKNSLIKQYQA----- 355
Query: 103 MNKGESIQIGSTDFTESDVKRI 124
+ K E + I F++ +KRI
Sbjct: 356 LLKTEGVNI---AFSDEAIKRI 374
>gnl|CDD|212680 cd10238, HSPA14-like_NBD, Nucleotide-binding domain of human HSPA14
and similar proteins. Human HSPA14 (also known as
70-kDa heat shock protein 14, HSP70L1, HSP70-4; the gene
encoding HSPA14 maps to 10p13), is ribosome-associated
and 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). HSPA14
interacts with the J-protein MPP11 to form the mammalian
ribosome-associated complex (mRAC). HSPA14 participates
in a pathway along with Nijmegen breakage syndrome 1
(NBS1, also known as p85 or nibrin), heat shock
transcription factor 4b (HSF4b), and HSPA4 (belonging to
a different subfamily), that induces tumor migration,
invasion, and transformation. HSPA14 is a potent T
helper cell (Th1) polarizing adjuvant that contributes
to antitumor immune responses.
Length = 375
Score = 27.3 bits (61), Expect = 6.0
Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 16/88 (18%)
Query: 110 QIGSTDFTESDVKRIVTELGKEYRGD-------RYHLMN--KNCNHFSNELTKILC---- 156
+G FTE+ + + E ++++ D L N + + L C
Sbjct: 224 NLGGESFTETLSQYLANEFKRKWKQDVRGNARAMMKLNNAAEVAKQILSTLPSANCFVES 283
Query: 157 ---GQEIPGWVNRLAYFSSCVPFLQRCL 181
G + V+R + S C +CL
Sbjct: 284 LYEGIDFQCSVSRARFESLCSSLFPKCL 311
>gnl|CDD|131779 TIGR02732, zeta_caro_desat, 9,9'-di-cis-zeta-carotene desaturase.
Carotene 7,8-desaturase, also called zeta-carotene
desaturase, catalyzes multiple steps in the pathway from
geranylgeranyl-PP to all-trans-lycopene in plants and
cyanobacteria. A similar enzyme and pathway is found in
the green sulfur bacterium Chlorobium tepidum.
Length = 474
Score = 27.1 bits (60), Expect = 7.3
Identities = 10/19 (52%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 168 AYFSSC-VPFLQRCLPKEW 185
AY ++C VP ++R LP+EW
Sbjct: 275 AYVAACDVPGIKRLLPQEW 293
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 27.0 bits (60), Expect = 8.6
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 69 RESIQIGSTDFTESDVKRIVTELGKEYRGDRY---HLMNKGESIQIGSTDFTES 119
R++ + F + V ++ E+ K++ D Y L K S + ES
Sbjct: 95 RKAREQIIKFFDDDTVLGVLKEIQKDFPSDEYSLDLLAEKFLSFCKPNMSEGES 148
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 0.412
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,561,922
Number of extensions: 964868
Number of successful extensions: 879
Number of sequences better than 10.0: 1
Number of HSP's gapped: 875
Number of HSP's successfully gapped: 20
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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: 57 (25.8 bits)