RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13444
(129 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 34.3 bits (79), Expect = 0.001
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 86 DMKRHLQTHTGEKPYKCSHCGYETLR 111
+++RH++THTGEKPYKC CG
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR
transcriptional regulator proteins. The ros chromosomal
gene is present in octopine and nopaline strains of
Agrobacterium tumefaciens as well as in Rhizobium
meliloti. This gene encodes a 15.5-kDa protein that
specifically represses the virC and virD operons in the
virulence region of the Ti plasmid and is necessary for
succinoglycan production. Sinorhizobium meliloti can
produce two types of acidic exopolysaccharides,
succinoglycan and galactoglucan, that are
interchangeable for infection of alfalfa nodules. MucR
from Sinorhizobium meliloti acts as a transcriptional
repressor that blocks the expression of the exp genes
responsible for galactoglucan production therefore
allowing the exclusive production of succinoglycan.
Length = 130
Score = 29.8 bits (68), Expect = 0.17
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 8/36 (22%)
Query: 68 KSF--NYVCCLCDYNVNGRT--DMKRHLQTHTGEKP 99
KS +Y+ CL D G+ +KRHL+TH G P
Sbjct: 64 KSVTPDYIICLED----GKKFKTLKRHLRTHHGLTP 95
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional.
Length = 257
Score = 29.6 bits (67), Expect = 0.37
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 108 ETLRSHDLKRHMR-IKHKIVGKS 129
+T R H L+RHM ++H I+G +
Sbjct: 157 KTGRKHQLRRHMAHLRHPIIGDT 179
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 26.4 bits (59), Expect = 0.73
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 100 YKCSHCGYETLRSHDLKRHMRIKHK 124
YKCSHC Y + L+RH+++ H
Sbjct: 1 YKCSHCPYSS-TPKKLERHLKLHHG 24
>gnl|CDD|236983 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
Length = 389
Score = 28.6 bits (65), Expect = 0.84
Identities = 6/24 (25%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 87 MKRHLQTHTGEKP-YKCSHCGYET 109
++ + KP Y+C +CG+
Sbjct: 341 LRDLVGEQLKRKPRYRCRNCGFTA 364
>gnl|CDD|219641 pfam07919, Gryzun, Gryzun, putative trafficking through Golgi.
The proteins featured in this family are all
eukaryotic, and many of them are annotated as being
Gryzun. Gryzun is distantly related to, but distinct
from, the Trs130 subunit of the TRAPP complex but is
absent from S. cerevisiae. RNAi of human Gryzun blocks
Golgi exit. Thus the family is likely to be involved
with trafficking of proteins through membranes, perhaps
as part of the TRAPP complex.
Length = 333
Score = 28.5 bits (64), Expect = 0.86
Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 5/69 (7%)
Query: 8 HCNLTLPSSTEALILHSKICSAVNRPDNKLKCYHCKQVLSSSMDDLLFHSRKCAVVWRPG 67
++L S+ A I S + + D + H +Q S+S +L + PG
Sbjct: 30 QLQVSLRSNAPAPIRLSSLKVQFSGSDYPIVLSHDQQDASASGLEL---EGAEDLTLVPG 86
Query: 68 --KSFNYVC 74
K F +
Sbjct: 87 KTKVFTFTF 95
>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 = 28.5 bits (64), Expect = 0.91
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 108 ETLRSHDLKRHM-RIKHKIVG 127
T R H L+RH+ I+H I+G
Sbjct: 156 HTGRKHQLRRHLAHIRHPIIG 176
>gnl|CDD|238948 cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily. Adenine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins probably binds ATP. This
domain is about 200 amino acids long with a strongly
conserved motif SGGKD at the N terminus.
Length = 202
Score = 27.6 bits (62), Expect = 1.7
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 15/48 (31%)
Query: 31 NRPDNKLKCYHCKQVLSSSMDDLLFHSRKCAVV-----------WRPG 67
N PD +CY CK+ L ++ ++ VV +RPG
Sbjct: 71 NPPD---RCYLCKKALYEALKEIA-EELGLDVVLDGTNADDLGDYRPG 114
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 27.4 bits (60), Expect = 2.2
Identities = 17/40 (42%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 87 MKRHLQTHTGEKPYKCSHCGYETLRS--HDLKRHMRIKHK 124
+ RH+++HTGEKP +CS+ G + S +L RH+R H
Sbjct: 49 LTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHN 88
>gnl|CDD|178497 PLN02909, PLN02909, Endoglucanase.
Length = 486
Score = 27.5 bits (61), Expect = 2.5
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 88 KRHLQTHTGEKPYKCSHCGY 107
K H T+ GE P+ CS+ GY
Sbjct: 219 KAHKGTYDGECPFYCSYSGY 238
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.7 bits (54), Expect = 2.9
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 100 YKCSHCGYETLRSHDLKRHMRI 121
Y+C CG L+ HMR
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|222929 PHA02779, PHA02779, E6 protein; Provisional.
Length = 150
Score = 26.4 bits (58), Expect = 3.4
Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 22/89 (24%)
Query: 3 DVFCYHCNLTLPSSTEALILHSKICSAVNRPDNKLKCYHCKQVLSSSMDDLLFHSRKCAV 62
D C CNLT+ + ++ C CK +L ++ + F ++ V
Sbjct: 14 DQLCKQCNLTMHTL-------------------QINCVFCKSILQTA-EVYSFAYKELYV 53
Query: 63 VWRPGKSFNYVCCLCDYNVNGRTDMKRHL 91
VWR F + C G+ + RH
Sbjct: 54 VWRGD--FPFAACAKCLEFYGKVNQYRHF 80
>gnl|CDD|233316 TIGR01217, ac_ac_CoA_syn, acetoacetyl-CoA synthase. This enzyme
catalyzes the first step of the mevalonate pathway of
IPP biosynthesis. Most bacteria do not use this
pathway, but rather the deoxyxylulose pathway [Central
intermediary metabolism, Other].
Length = 652
Score = 27.2 bits (60), Expect = 3.4
Identities = 6/32 (18%), Positives = 9/32 (28%)
Query: 41 HCKQVLSSSMDDLLFHSRKCAVVWRPGKSFNY 72
S+ ++ W PG NY
Sbjct: 58 WFDVRFSTPCARVVDDRTMPGAQWFPGARLNY 89
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 27.0 bits (61), Expect = 3.6
Identities = 5/12 (41%), Positives = 7/12 (58%)
Query: 100 YKCSHCGYETLR 111
Y C CG E+ +
Sbjct: 8 YVCQECGAESPK 19
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 24.5 bits (53), Expect = 3.8
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 100 YKCSHCGYETLRSHDLKRHMRIKH 123
+KC CG LKRH+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|241286 cd01255, PH2_Tiam1_2, T-lymphoma invasion and metastasis 1 and 2
Pleckstrin Homology (PH) domain, C-terminal domain.
Tiam1 activates Rac GTPases to induce membrane ruffling
and cell motility while Tiam2 (also called STEF (SIF
(still life) and Tiam1 like-exchange factor)
contributes to neurite growth. Tiam1/2 are Dbl-family
of GEFs that possess a Dbl(DH) domain with a PH domain
in tandem. DH-PH domain catalyzes the GDP/GTP exchange
reaction in the GTPase cycle and facillitating the
switch between inactive GDP-bound and active GTP-bound
states. The DH domain of Tiam1 interacts with Switch
regions 1 and 2 of Rac1 which blocks magnesium binding
and GDP is released. Tiam1/2 possess two PH domains,
which are often referred to as PHn and PHc domains. The
DH-PH tandem domain is made up of the PHc domain while
the PHn is part of a novel N-terminal PHCCEx domain
which is made up of the PHn domain, a coiled coil
region(CC), and an extra region (Ex). PHCCEx mediates
binding to plasma membranes and signalling proteins in
the activation of Rac GTPases. The PH domain resembles
the beta-spectrin PH domain, suggesting non-canonical
phosphatidylinositol binding. CC and Ex form a
positively charged surface for protein binding. There
are 2 motifs in Tiam1/2-interacting proteins that bind
to the PHCCEx domain: Motif-I in CD44, ephrinBs, and
the NMDA receptor and Motif-II in Par3 and JIP2. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from
other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 172
Score = 26.2 bits (58), Expect = 5.2
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 3/25 (12%)
Query: 40 YHCKQVLSSSMDDLLFHSRKCAVVW 64
K+V SM DLL + V W
Sbjct: 20 GTKKEVADLSMGDLLLYG---TVEW 41
>gnl|CDD|235487 PRK05474, PRK05474, xylose isomerase; Provisional.
Length = 437
Score = 25.9 bits (58), Expect = 6.9
Identities = 14/31 (45%), Positives = 16/31 (51%), Gaps = 11/31 (35%)
Query: 106 GYETLRSHDLKR---------HMRI--KHKI 125
GYETL + DLKR M + KHKI
Sbjct: 191 GYETLLNTDLKREREQLARFLQMVVDYKHKI 221
>gnl|CDD|179886 PRK04860, PRK04860, hypothetical protein; Provisional.
Length = 160
Score = 25.3 bits (56), Expect = 8.6
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 67 GKSFNYVCCLCDYNVNGRTDMKRHLQTHTGEKPYKCSHCGYETLR 111
GK+F Y C ++ + R RH + GE Y+C CG ETL
Sbjct: 115 GKTFPYRCKCQEHQLTVR----RHNRVVRGEAVYRCRRCG-ETLV 154
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 24.7 bits (54), Expect = 8.7
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 100 YKCSHCGYETLRSHDLKRHMRIKH 123
+KC CG+ T+ LK+H R H
Sbjct: 2 FKCPICGFTTVTLFALKQHARRNH 25
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
0.325 0.136 0.456
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,021,724
Number of extensions: 467829
Number of successful extensions: 679
Number of sequences better than 10.0: 1
Number of HSP's gapped: 678
Number of HSP's successfully gapped: 61
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.3 bits)