RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13817
(164 letters)
>gnl|CDD|204429 pfam10276, zf-CHCC, Zinc-finger domain. This is a short
zinc-finger domain conserved from fungi to humans. It
is Cx8Hx14Cx2C.
Length = 40
Score = 41.5 bits (98), Expect = 4e-06
Identities = 17/25 (68%), Positives = 18/25 (72%)
Query: 38 ERVVWCDGGSGPTGHPKVYINLRPE 62
R V CDGG GP GHP+VYINL E
Sbjct: 2 GRRVSCDGGGGPLGHPRVYINLDDE 26
Score = 41.1 bits (97), Expect = 5e-06
Identities = 16/22 (72%), Positives = 17/22 (77%)
Query: 143 ERVVWCDGGSGPTGHPKVYINL 164
R V CDGG GP GHP+VYINL
Sbjct: 2 GRRVSCDGGGGPLGHPRVYINL 23
>gnl|CDD|226826 COG4391, COG4391, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 62
Score = 28.2 bits (63), Expect = 0.46
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 43 CDGGSGPTGHPKVYINLRPE 62
C G P HP+V++++ E
Sbjct: 27 CPGPEPPNDHPRVFLDMGDE 46
Score = 27.1 bits (60), Expect = 1.00
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 148 CDGGSGPTGHPKVYINL 164
C G P HP+V++++
Sbjct: 27 CPGPEPPNDHPRVFLDM 43
>gnl|CDD|218701 pfam05698, Trigger_C, Bacterial trigger factor protein (TF)
C-terminus. In the E. coli cytosol, a fraction of the
newly synthesised proteins requires the activity of
molecular chaperones for folding to the native state.
The major chaperones implicated in this folding process
are the ribosome-associated Trigger Factor (TF), and the
DnaK and GroEL chaperones with their respective
co-chaperones. Trigger Factor is an ATP-independent
chaperone and displays chaperone and
peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
in vitro. It is composed of at least three domains, an
N-terminal domain which mediates association with the
large ribosomal subunit, a central substrate binding and
PPIase domain with homology to FKBP proteins, and a
C-terminal domain of unknown function. The positioning
of TF at the peptide exit channel, together with its
ability to interact with nascent chains as short as 57
residues renders TF a prime candidate for being the
first chaperone that binds to the nascent polypeptide
chains. This family represents the C-terminal region of
the protein.
Length = 162
Score = 29.5 bits (67), Expect = 0.47
Identities = 12/68 (17%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 71 SLLKQTRVNRLIVPLTRTLAKDVAPFNDIETHTGQKFEK--DDYRPVRFVDKEKHVNTQF 128
SL+++ ++RL+ + L + + +G E+ ++++ + EK V
Sbjct: 44 SLVEE-EIDRLLRQFLQQLQGQGLDLEEYLSLSGSSEEELREEFKE----EAEKRVKLGL 98
Query: 129 AIDLIAEV 136
++ IA+
Sbjct: 99 ILEEIAKE 106
>gnl|CDD|164599 MTH00026, COX1, cytochrome c oxidase subunit I; Provisional.
Length = 534
Score = 28.1 bits (62), Expect = 2.3
Identities = 15/28 (53%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 51 GHPKVYINLRPE---ISYIMSLLSLLKQ 75
GHP+VYI + P IS I+SL S KQ
Sbjct: 240 GHPEVYILILPGFGIISQILSLFSYKKQ 267
>gnl|CDD|212673 cd10231, YegD_like, Escherichia coli YegD, a putative chaperone
protein, and related proteins. This bacterial subfamily
includes the uncharacterized Escherichia coli YegD. It
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. YegD lacks the SBD. HSP70
chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). Some family members are not chaperones
but instead, function as NEFs for their Hsp70 partners,
other family members function as both chaperones and
NEFs.
Length = 415
Score = 27.1 bits (61), Expect = 4.9
Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 23/79 (29%)
Query: 56 YINLRPEISYIMSLLSLL-----KQTRVNRLIVPLTRTLA------KDVAPFNDIETHTG 104
Y+ E + SL S L ++TR+ + +A K A E G
Sbjct: 59 YLEGPGEGRLMRSLKSFLGSSLFRETRIFGRRLTFEDLVARFLAELKQRA-----EAALG 113
Query: 105 QKFEK----DDYRPVRFVD 119
+ ++ RPV FV
Sbjct: 114 AEIDRVVIG---RPVHFVG 129
>gnl|CDD|183983 PRK13339, PRK13339, malate:quinone oxidoreductase; Reviewed.
Length = 497
Score = 26.6 bits (59), Expect = 8.3
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 13/56 (23%)
Query: 13 VDKEKHVNTQFAIDLIAEVPPKPCKERVVWCD-GGSGPTGHPKVYINLRPEISYIM 67
++K K +N QF I + W SG G+P+ +IN P IS++
Sbjct: 77 IEKAKEINEQFEI------------SKQFWGHLVKSGTIGNPREFINPLPHISFVR 120
>gnl|CDD|218606 pfam05488, PAAR_motif, PAAR motif. This motif is found usually
in pairs in a family of bacterial membrane proteins. It
is also found as a triplet of tandem repeats comprising
the entire length in a another family of hypothetical
proteins.
Length = 75
Score = 24.9 bits (55), Expect = 8.6
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 4/25 (16%)
Query: 41 VWCDGGSGP----TGHPKVYINLRP 61
V C GP G P V+IN +P
Sbjct: 34 VTCPKCGGPGPIVEGSPTVFINGKP 58
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 0.140 0.440
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,581,264
Number of extensions: 771515
Number of successful extensions: 667
Number of sequences better than 10.0: 1
Number of HSP's gapped: 666
Number of HSP's successfully gapped: 19
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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: 55 (24.9 bits)