RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15834
(175 letters)
>gnl|CDD|221996 pfam13232, Complex1_LYR_1, Complex1_LYR-like. This is a family of
proteins carrying the LYR motif of family Complex1_LYR,
pfam05347, likely to be involved in Fe-S cluster
biogenesis in mitochondria.
Length = 61
Score = 42.9 bits (102), Expect = 2e-06
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 8/58 (13%)
Query: 105 FLHLGKDYPKGFD--YFRLRLKNAFMKNAQVQDPEKIDQMIKHGEFVVKEIQALYMLK 160
L + +P Y R R+++ F KN + DPEKI++++K G+ + L +LK
Sbjct: 10 LLRAARKFPDYNFREYIRRRIRDEFRKNKDLTDPEKIEKLLKEGK------KQLELLK 61
>gnl|CDD|203236 pfam05347, Complex1_LYR, Complex 1 protein (LYR family). Proteins
in this family have been identified as a component of
the higher eukaryotic NADH complex. In Saccharomyces
cerevisiae, the Isd11 protein has been shown to play a
role in Fe/S cluster biogenesis in mitochondria. We have
named this family LYR after a highly conserved
tripeptide motif close to the N-terminus of these
proteins.
Length = 59
Score = 39.5 bits (93), Expect = 3e-05
Identities = 14/36 (38%), Positives = 25/36 (69%)
Query: 117 DYFRLRLKNAFMKNAQVQDPEKIDQMIKHGEFVVKE 152
+YFR R+++ F KN + DPEKI+ ++K G+ ++
Sbjct: 24 EYFRRRIRDEFRKNKNLTDPEKIEALLKEGKKQLEV 59
>gnl|CDD|226744 COG4294, Uve, UV damage repair endonuclease [DNA replication,
recombination, and repair].
Length = 347
Score = 31.3 bits (71), Expect = 0.21
Identities = 13/82 (15%), Positives = 23/82 (28%), Gaps = 1/82 (1%)
Query: 86 WILGLLRYWENPTMLSTKVFLHLGKDYPKGFDYFRLRLKNAFMKNAQVQDPEKIDQMIKH 145
I + W P L KV L + + P I+ K
Sbjct: 257 LIPRIRETWTRPG-LQQKVHLSSPASGTADRRHSDYIHADRVFPFLYRDPPWDIEVEAKA 315
Query: 146 GEFVVKEIQALYMLKKYRTLKQ 167
E + ++ +Y L+ +
Sbjct: 316 KEKAIALLRLMYELQNPPCPLE 337
>gnl|CDD|117364 pfam08794, Lipoprot_C, Lipoprotein GNA1870 C terminal like.
GNA1870 is a surface exposed lipoprotein in Neisseria
meningitidis that and is a potent antigen of
Meningococcus. The structure of the C terminal domain
consists of an anti-parallel beta barrel overlaid by a
short alpha helical region.
Length = 155
Score = 28.8 bits (64), Expect = 1.1
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 132 QVQDPEKIDQMIKHGEFVVKEI 153
Q+QD E +M+ +F + +I
Sbjct: 13 QIQDSEHSGKMVAKRQFRIGDI 34
>gnl|CDD|212579 cd11706, DHR2_DOCK2, Dock Homology Region 2, a GEF domain, of Class
A Dedicator of Cytokinesis 2. Dock2 is a hematopoietic
cell-specific, class A DOCK and is an atypical guanine
nucleotide exchange factor (GEF) that lacks the
conventional Dbl homology (DH) domain. As a GEF, it
activates small GTPases by exchanging bound GDP for free
GTP. It plays an important role in lymphocyte migration
and activation, T-cell differentiation, neutrophil
chemotaxis, and type I interferon induction. DOCK
proteins are divided into four classes (A-D) based on
sequence similarity and domain architecture; class A
includes Dock1, 2 and 5. All DOCKs contain two homology
domains: the DHR-1 (Dock homology region-1), also called
CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and
DHR-2 (also called CZH2 or Docker). The DHR-1 domain
binds phosphatidylinositol-3,4,5-triphosphate. This
alignment model represents the DHR-2 domain of Dock2,
which contains the catalytic GEF activity for Rac and/or
Cdc42. Class A DOCKs, like Dock2, are specific GEFs for
Rac and they contain an SH3 domain at the N-terminal
region and a PxxP motif at the C-terminus.
Length = 421
Score = 28.8 bits (64), Expect = 1.4
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 97 PTMLSTKVFLHLGKDYPKGFDYFRLRLKNAF 127
P+ L KVF++ GK+Y + D F+++L + F
Sbjct: 154 PSFLRNKVFIYRGKEYERRED-FQMQLMSQF 183
>gnl|CDD|178740 PLN03199, PLN03199, delta6-acyl-lipid desaturase-like protein;
Provisional.
Length = 485
Score = 27.7 bits (61), Expect = 4.0
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 11/71 (15%)
Query: 104 VFLHLGKDYPKGFDYFRLRLKNAFMKNAQVQD--PEKIDQMIKHGEFVVKEIQALYMLKK 161
+F H G D F F A MK + D PE + K+ Q + K
Sbjct: 63 IFTHAGDDMTDIFAAFHAPGSQALMKKFYIGDLIPESTEH---------KDPQQIAFEKG 113
Query: 162 YRTLKQRLVLI 172
YR L+ +L+++
Sbjct: 114 YRDLRAKLIMM 124
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 27.4 bits (61), Expect = 5.1
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 2/55 (3%)
Query: 102 TKVFLHLGKDYPKGFDYFRLRLKNAFMKNAQVQDPEKIDQMIKHGEFVVKEIQAL 156
K L + + +AF + V D Q I G+ V+++ L
Sbjct: 712 LKALLEAYQSPTR--AEALRDFADAFGRFPLVMDKWFALQAISPGDTVLEQDIGL 764
>gnl|CDD|217031 pfam02435, Glyco_hydro_68, Levansucrase/Invertase. This Pfam
family consists of the glycosyl hydrolase 68 family,
including several bacterial levansucrase enzymes, and
invertase from zymomonas.
Length = 424
Score = 27.0 bits (60), Expect = 5.9
Identities = 12/43 (27%), Positives = 18/43 (41%)
Query: 20 DGDYQLGFPMSDMKTTAINQFLHNKILNFIVMTQQGLWVNSFN 62
DG +L + D T NQ L + IV + +W+ F
Sbjct: 141 DGSVRLFYTDVDTGTPGGNQALITATVGLIVADDKTVWIKGFE 183
>gnl|CDD|241469 cd13315, PH_Sec3, Sec 3 Pleckstrin homology-like domain. The Sec3
subunit of the exocyst, a complex involved in polarized
exocytosis, bind phospholipids and GTPase Cdc42 and
therefore functions as a coincidence detector at the
plasma membrane. Unlike most PH domains, Sec3 contains
an additional alpha-helix at its N-terminus and two
beta-strands at its C-terminus that mediate dimerization
through domain swapping. 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 = 160
Score = 26.2 bits (58), Expect = 7.0
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 76 STGASMVGKHWILGLLRYWENPTMLSTKVFLHLGKDY 112
+ G+ +G+ W L L E S L LGK Y
Sbjct: 80 NDGSFQIGRTWDLDELTAIEKDLAGSEGFILTLGKPY 116
>gnl|CDD|212578 cd11705, DHR2_DOCK4, Dock Homology Region 2, a GEF domain, of Class
B Dedicator of Cytokinesis 4. Dock4 is an atypical
guanine nucleotide exchange factor (GEF) that lacks the
conventional Dbl homology (DH) domain. As a GEF, it
activates small GTPases by exchanging bound GDP for free
GTP. It plays a role in regulating dendritic growth and
branching in hippocampal neurons, where it is highly
expressed. It may also regulate spine morphology and
synapse formation. Dock4 activates the Ras family GTPase
Rap1, probably indirectly through interaction with Rap
regulatory proteins. DOCK proteins are divided into four
classes (A-D) based on sequence similarity and domain
architecture; class B includes Dock3 and 4. All DOCKs
contain two homology domains: the DHR-1 (Dock homology
region-1), also called CZH1 (CED-5, Dock180, and
MBC-zizimin homology 1), and DHR-2 (also called CZH2 or
Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock4, which
contains the catalytic GEF activity for Rac and/or
Cdc42. Class B DOCKs also contain an SH3 domain at the
N-terminal region and a PxxP motif at the C-terminus.
Length = 391
Score = 26.9 bits (59), Expect = 7.3
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 97 PTMLSTKVFLHLGKDYPKGFDYFRLRLKNAFMKNAQVQDPEKIDQMIKHGEFVVKEIQAL 156
P L K F+ G DY + + F+ R+ N F +Q + D+ I E +I A+
Sbjct: 131 PFFLRNKEFVCRGHDYER-LEAFQQRMLNEFPHAIAMQHANQPDETIFQAEAQYLQIYAV 189
Query: 157 YMLKKYRTLKQR 168
+ + + + QR
Sbjct: 190 TPIPESQEVLQR 201
>gnl|CDD|212581 cd11708, DHR2_DOCK5, Dock Homology Region 2, a GEF domain, of Class
A Dedicator of Cytokinesis 5. Dock5 is an atypical
guanine nucleotide exchange factor (GEF) that lacks the
conventional Dbl homology (DH) domain. As a GEF, it
activates small GTPases by exchanging bound GDP for free
GTP. It functions upstream of Rac1 to regulate
osteoclast function. DOCK proteins are divided into four
classes (A-D) based on sequence similarity and domain
architecture; class A includes Dock1, 2 and 5. All DOCKs
contain two homology domains: the DHR-1 (Dock homology
region-1), also called CZH1 (CED-5, Dock180, and
MBC-zizimin homology 1), and DHR-2 (also called CZH2 or
Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock5, which
contains the catalytic GEF activity for Rac and/or
Cdc42. Class A DOCKs, like Dock5, are specific GEFs for
Rac and they contain an SH3 domain at the N-terminal
region and a PxxP motif at the C-terminus.
Length = 400
Score = 26.4 bits (58), Expect = 9.2
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 97 PTMLSTKVFLHLGKDYPKGFDYFRLRLKNAF 127
P+ L K+F++ GK+Y + D F L+L F
Sbjct: 136 PSFLRNKIFIYRGKEYERLED-FSLKLLTQF 165
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 0.137 0.416
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,803,632
Number of extensions: 782963
Number of successful extensions: 895
Number of sequences better than 10.0: 1
Number of HSP's gapped: 895
Number of HSP's successfully gapped: 21
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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 (21.6 bits)
S2: 56 (25.2 bits)