RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3819
(122 letters)
>gnl|CDD|176361 cd01766, Ufm1, Urm1-like ubiquitin domain. Ufm1 (ubiquitin-fold
modifier 1) is a post-translational UBL (ubiquitin-like)
modifier with a tertiary structure similar to that of
ubiquitin. Ufm1 is initially expressed as a precursor
which undergoes C-terminal cleavage to expose a
conserved glycine residue that is required for the
conjugation reactions involving Ufm1.
Length = 82
Score = 78.9 bits (194), Expect = 1e-20
Identities = 34/41 (82%), Positives = 36/41 (87%)
Query: 80 PLVTSAIITDDGIGINPQQTAGTVFMKHGCELRLIPRDRVG 120
P TSAIIT+DGIGINP QTAG VF+KHG ELRLIPRDRVG
Sbjct: 42 PAATSAIITNDGIGINPAQTAGNVFLKHGSELRLIPRDRVG 82
>gnl|CDD|202722 pfam03671, Ufm1, Ubiquitin fold modifier 1 protein. This is a
family of short ubiquitin-like proteins, that is like
neither type-1 or type-2. It is a ubiquitin-fold
modifier 1 (Ufm1) that is synthesised in a precursor
form of 85 amino-acid residues. In humans the enzyme for
Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior
to activation by Uba5 the extra two amino acids at the
C-terminal region of the human pro-Ufm1 protein are
removed to expose Gly whose residue is necessary for
conjugation to target molecule(s). The mature Ufm1 is
conjugated to yet unidentified endogenous proteins.
While Ubiquitin and many Ubls possess the conserved
C-terminal di-glycine that is adenylated by each
specific E1 or E1-like enzyme, respectively, in an
ATP-dependent manner, Ufm1(1-83) possesses a single
glycine at its C-terminus, which is followed by a
Ser-Cys dipeptide in the precursor form of Ufm1. The
C-terminally processed Ufm1(1-83) is specifically
activated by Uba5, an E1-like enzyme, and then
transferred to its cognate Ufc1, an E2-like enzyme.
Length = 76
Score = 61.3 bits (148), Expect = 7e-14
Identities = 27/35 (77%), Positives = 30/35 (85%)
Query: 80 PLVTSAIITDDGIGINPQQTAGTVFMKHGCELRLI 114
P TSAIIT+DGIGINP QTAG VF+KHG ELR+I
Sbjct: 42 PAATSAIITNDGIGINPAQTAGNVFLKHGSELRII 76
>gnl|CDD|188239 TIGR02650, RNase_Z_T_toga, ribonuclease Z, Thermotoga type.
Members of this protein family are ribonuclease Z as
found in the genus Thermotoga, where the enzyme cleaves
after the CCA, in contrast to the activities
characterized for other enzymes also designated
ribonuclease Z. In other systems, cleavage occurs
5-prime to the location of the CCA sequence, and CCA is
added subsequently. A species may lack ribonuclease Z if
all tRNA genes encode the CCA sequence, or if the CCA is
exposed by exonuclease activity rather than endonuclease
activity. Note that members of this sequence family
differ considerably from the majority of RNase Z
sequences [Transcription, RNA processing].
Length = 277
Score = 28.4 bits (63), Expect = 0.74
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 87 ITDDGIGINPQQTAGTVFMKHGCELRLIPRDR 118
I+ D + ++P++ GT + H C L RDR
Sbjct: 186 ISGDSLALDPEEIEGTELLIHECTF-LDARDR 216
>gnl|CDD|132835 cd00147, cPLA2_like, Cytosolic phospholipase A2, catalytic domain;
hydrolyses arachidonyl phospholipids. Catalytic domain
of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4)
hydrolyzes the sn-2-acyl ester bond of phospholipids to
release arachidonic acid. At the active site, cPLA2
contains a serine nucleophile through which the
catalytic mechanism is initiated. The active site is
partially covered by a solvent-accessible flexible lid.
cPLA2 displays interfacial activation as it exists in
both "closed lid" and "open lid" forms. Movement of the
cPLA2 lid possibly exposes a greater hydrophobic surface
and the active site. cPLA2 belongs to the alpha-beta
hydrolase family which is identified by a characteristic
nucleophile elbow with a consensus sequence of
Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu =
nucleophile). Calcium is required for cPLA2 to bind with
membranes or phospholipids. Group IV cPLA2 includes six
intercellular enzymes: cPLA2alpha, cPLA2beta,
cPLA2gamma, cPLA2delta, cPLA2epsilon, and cPLA2zeta.
Length = 438
Score = 26.4 bits (59), Expect = 4.3
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 5/28 (17%)
Query: 18 EDCECPRVGLGECPLVVYLPYFTKQVRR 45
C+ P + PLVVY P R+
Sbjct: 370 FGCDDP-----DAPLVVYFPLVNDTFRK 392
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 25.6 bits (57), Expect = 8.8
Identities = 5/21 (23%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 87 ITDDGIGINPQQTAGTVFMKH 107
+ D+G GI+ + +H
Sbjct: 56 VRDNGCGISKED-LALALARH 75
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
0.322 0.144 0.473
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,042,486
Number of extensions: 493621
Number of successful extensions: 301
Number of sequences better than 10.0: 1
Number of HSP's gapped: 301
Number of HSP's successfully gapped: 11
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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 (21.9 bits)
S2: 53 (24.1 bits)