RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2945
(134 letters)
>gnl|CDD|238464 cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase subunit Vb.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Subunits I, II,
and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Found only in
eukaryotes, subunit Vb is one of three mammalian
subunits that lacks a transmembrane region. Subunit Vb
is located on the matrix side of the membrane and binds
the regulatory subunit of protein kinase A. The
abnormally extended conformation is stable only in the
CcO assembly.
Length = 97
Score = 139 bits (353), Expect = 3e-44
Identities = 54/94 (57%), Positives = 65/94 (69%), Gaps = 2/94 (2%)
Query: 42 ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
E+P L+ ATGLE++ELLA+L G D F++K K GTK P VPSAF+ RIVGCICE
Sbjct: 5 EVPTDLEQATGLERKELLAKLEGI-DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICE 63
Query: 102 EESPSINWMWLYEGKPKRC-MCGHWFKLVYKAPI 134
+S + WMWL +GKPKRC CGH FKLV P
Sbjct: 64 PDSHDVIWMWLEKGKPKRCPECGHVFKLVDVGPP 97
>gnl|CDD|201667 pfam01215, COX5B, Cytochrome c oxidase subunit Vb.
Length = 136
Score = 86.5 bits (214), Expect = 9e-23
Identities = 37/91 (40%), Positives = 49/91 (53%), Gaps = 3/91 (3%)
Query: 42 ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
+P L+ ATGLE+ ELLA L G DPF++K GT P V S RIVGC
Sbjct: 37 GVPTDLEQATGLEREELLAALKGR-DPFDIKPLDASKGTLKDPIIVESIDNYRIVGCTGS 95
Query: 102 E-ESPSINWMWLYEGKPKRCM-CGHWFKLVY 130
S +I W +++G+ +RC CG +KL
Sbjct: 96 PDGSHTIIWFTVHKGEAQRCPECGSVYKLKP 126
>gnl|CDD|177931 PLN02294, PLN02294, cytochrome c oxidase subunit Vb.
Length = 174
Score = 56.4 bits (136), Expect = 7e-11
Identities = 45/139 (32%), Positives = 67/139 (48%), Gaps = 25/139 (17%)
Query: 6 RSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLD-----ELPDPLDLATGLEKRELLA 60
R++V + YL+RS ++ S S ++ ++ D + D + +ATG E+ EL A
Sbjct: 24 RTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAVKKRVEDVMPIATGHEREELEA 83
Query: 61 ELAG----DPD----PFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC--EEESPSINWM 110
EL G D D PF GTK P V S ++ RIVGC E+ + W
Sbjct: 84 ELEGRKLLDIDFPEGPF---------GTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWF 134
Query: 111 WLYEGKPKRC-MCGHWFKL 128
WL +GK C +C +F+L
Sbjct: 135 WLEKGKSFECPVCTQYFEL 153
>gnl|CDD|233595 TIGR01845, outer_NodT, efflux transporter, outer membrane factor
(OMF) lipoprotein, NodT family. Members of This model
comprise a subfamily of the Outer Membrane Factor (TCDB
1.B.17) porins. OMF proteins operate in conjunction with
a primary transporter of the RND, MFS, ABC, or PET
systems, and a MFP (membrane fusion protein) to tranport
substrates across membranes. The complex thus formed
allows transport (export) of various solutes (heavy
metal cations; drugs, oligosaccharides, proteins, etc.)
across the two envelopes of the Gram-negative bacterial
cell envelope in a single energy-coupled step. Current
data suggest that the OMF (and not the MFP) is largely
responsible for the formation of both the trans-outer
membrane and trans-periplasmic channels. The roles
played by the MFP have yet to be determined [Cellular
processes, Detoxification, Transport and binding
proteins, Porins].
Length = 454
Score = 28.1 bits (63), Expect = 1.4
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 56 RELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVG 97
R LA L G + I R L P ++P + + ++
Sbjct: 235 RNALAALLGKGPSRGLAI-ARPLLLDQLPPDLPLSLPSDLLR 275
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 27.5 bits (62), Expect = 2.2
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 47 LDLATGLEKRELL-AELAG-----DPDPFNVKIRKRGLG 79
LD +RE+L EL G + P NV I+K+ G
Sbjct: 85 LDATKPEGQREILERELEGVGIRLNKKPPNVTIKKKKKG 123
>gnl|CDD|192187 pfam08964, DUF1881, Protein of unkown function (DUF1881). This
domain is found in a set of hypothetical bacterial and
eukaryotic proteins, as well as in various
calcium-dependent cell adhesion molecules.
Length = 200
Score = 26.7 bits (59), Expect = 3.3
Identities = 9/83 (10%), Positives = 25/83 (30%), Gaps = 5/83 (6%)
Query: 5 FRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPD-----PLDLATGLEKRELL 59
FRS+ + +++ A T T + ++ D+ + +
Sbjct: 37 FRSVKVGASSKVNAWRHTPTPGKYQQREWGSSQPDITSIGGLSKFQVAPKDFQAVDIRFV 96
Query: 60 AELAGDPDPFNVKIRKRGLGTKT 82
GD +++ + +
Sbjct: 97 DNTGGDDGKYSMTVIPYQVNPVE 119
>gnl|CDD|147852 pfam05925, IpgD, Enterobacterial virulence protein IpgD. This
family consists of several enterobacterial IpgD like
virulence factor proteins. In the Gram-negative pathogen
Shigella flexneri, the virulence factor IpgD is
translocated directly into eukaryotic cells and acts as
a potent inositol 4-phosphatase that specifically
dephosphorylates phosphatidylinositol 4,5-bisphosphate
[PtdIns(4,5)P(2)] into phosphatidylinositol
5-monophosphate [PtdIns(5)P] that then accumulates.
Transformation of PtdIns(4,5)P(2) into PtdIns(5)P by
IpgD is responsible for dramatic morphological changes
of the host cell, leading to a decrease in membrane
tether force associated with membrane blebbing and actin
filament remodelling.
Length = 569
Score = 27.0 bits (59), Expect = 3.9
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 88 PSAFEARIVGCICEEESPSINWMWLY------EGKPKRCMCG 123
P A+E + + C +E +WL +GK K CG
Sbjct: 212 PKAYEGKGICCADTKEIHHAANLWLSKVSVDDDGKDKTIFCG 253
>gnl|CDD|224556 COG1641, COG1641, Uncharacterized conserved protein [Function
unknown].
Length = 387
Score = 26.5 bits (59), Expect = 4.7
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 6/64 (9%)
Query: 41 DELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC 100
+ L TG L + D P +K + G G T+ +P+ R++ +
Sbjct: 178 RGVNGELLTPTGAAILRHLVKEFKDFPPGRIK--EVGYGAGTKDLPIPNV--LRVI--LG 231
Query: 101 EEES 104
EE S
Sbjct: 232 EEAS 235
>gnl|CDD|143262 cd05854, Ig6_Contactin-2, Sixth Ig domain of contactin-2.
Ig6_Contactin-2: Sixth Ig domain of the neural cell
adhesion molecule contactin-2-like. Contactins are
comprised of six Ig domains followed by four
fibronectin type III (FnIII) domains anchored to the
membrane by glycosylphosphatidylinositol. Contactin-2
(TAG-1, axonin-1) facilitates cell adhesion by
homophilic binding between molecules in apposed
membranes. It may play a part in the neuronal processes
of neurite outgrowth, axon guidance and fasciculation,
and neuronal migration. The first four Ig domains form
the intermolecular binding fragment, which arranges as
a compact U-shaped module by contacts between IG
domains 1 and 4, and domains 2 and 3. The different
contactins show different expression patterns in the
central nervous system. During development and in
adulthood, contactin-2 is transiently expressed in
subsets of central and peripheral neurons. Contactin-2
is also expressed in retinal amacrine cells in the
developing chick retina, corresponding to the period of
formation and maturation of AC proce sses.
Length = 85
Score = 25.4 bits (55), Expect = 4.7
Identities = 18/54 (33%), Positives = 24/54 (44%)
Query: 40 LDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEA 93
LD+ P LD G +R + E GD N ++ G T T T V SA +
Sbjct: 23 LDDFPIDLDKPNGHYRRMEVKETIGDLVIVNAQLSHAGTYTCTAQTVVDSASAS 76
>gnl|CDD|236782 PRK10871, nlpD, lipoprotein NlpD; Provisional.
Length = 319
Score = 26.3 bits (58), Expect = 5.2
Identities = 10/37 (27%), Positives = 13/37 (35%)
Query: 80 TKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGK 116
T T P P+A +P W W +GK
Sbjct: 171 TVTAPVTAPTASTTEPTASSTSTSTPISTWRWPTDGK 207
>gnl|CDD|240240 PTZ00043, PTZ00043, cytochrome c oxidase subunit; Provisional.
Length = 268
Score = 26.3 bits (58), Expect = 5.5
Identities = 21/55 (38%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 79 GTKTQPTEVPSAFEARIVGC---ICEEESPSINWMWLYEGKPKRC-MCGHWFKLV 129
GT P VPS R+VGC E E + W EG RC C F LV
Sbjct: 141 GTIENPVLVPSVGTERVVGCTGGTGEHEHVPL-WFRCREGFLYRCGECDQIFMLV 194
>gnl|CDD|216465 pfam01379, Porphobil_deam, Porphobilinogen deaminase, dipyromethane
cofactor binding domain.
Length = 213
Score = 26.1 bits (58), Expect = 5.5
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 81 KTQPTEVPSAFEARIVGCICEEESP 105
K PTE+P +G I + E P
Sbjct: 79 KDVPTELPEGLV---LGAIPKREDP 100
>gnl|CDD|239987 cd04614, CBS_pair_1, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa
(IMP dehydrogenase-1), and homocystinuria
(cystathionine beta-synthase).
Length = 96
Score = 25.0 bits (55), Expect = 7.4
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 18 ARSVTATGN-SFSTCAQRWNKNDLDELP 44
+ VTAT + S CAQ+ +N ++++P
Sbjct: 49 SEVVTATKRTTVSECAQKMKRNRIEQIP 76
>gnl|CDD|238276 cd00494, HMBS, Hydroxymethylbilane synthase (HMBS), also known as
porphobilinogen deaminase (PBGD), is an intermediate
enzyme in the biosynthetic pathway of tetrapyrrolic ring
systems, such as heme, chlorophylls, and vitamin B12.
HMBS catalyzes the conversion of porphobilinogen (PBG)
into hydroxymethylbilane (HMB). HMBS consists of three
domains, and is believed to bind substrate through a
hinge-bending motion of domains I and II. HMBS is found
in all organisms except viruses.
Length = 292
Score = 25.7 bits (57), Expect = 8.1
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 81 KTQPTEVPSAFEARIVGCICEEESP 105
K PTE+P +G I + E P
Sbjct: 78 KDVPTELPEGLV---LGAIPKREDP 99
>gnl|CDD|217319 pfam03013, Pyr_excise, Pyrimidine dimer DNA glycosylase.
Pyrimidine dimer DNA glycosylases excise pyrimidine
dimers by hydrolysis of the glycosylic bond of the 5'
pyrimidine, followed by the intra-pyrimidine
phosphodiester bond. Pyrimidine dimers are the major
UV-lesions of DNA.
Length = 121
Score = 25.4 bits (56), Expect = 8.2
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 34 RWNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKR 76
W+ + + ELP LA + REL A L + N I K
Sbjct: 3 LWHLDLISELPRQQLLA---QHRELPA-LFNERG--NGWIPKH 39
>gnl|CDD|176747 cd08336, DED_FADD, Death Effector Domain found in Fas-Associated
via Death Domain. Death Effector Domain (DED) found in
Fas-Associated via Death Domain (FADD). DEDs comprise a
subfamily of the Death Domain (DD) superfamily. FADD is
a component of the death-inducing signaling complex
(DISC) and serves as an adaptor in the signaling
pathway of death receptor proteins. It modulates
apoptosis as well as non-apoptotic processes such as
cell cycle progression, survival, innate immune
signaling, and hematopoiesis. FADD contains an
N-terminal DED and a C-terminal DD. Its DD interacts
with the DD of the activated death receptor and its DED
recruits the initiator caspases 8 and 10 to the DISC
complex via a homotypic interaction with the N-terminal
DED of the caspase. DDs are protein-protein interaction
domains found in a variety of domain architectures.
Their common feature is that they form homodimers by
self-association or heterodimers by associating with
other members of the DD superfamily including PYRIN and
CARD (Caspase activation and recruitment domain). They
serve as adaptors in signaling pathways and they can
recruit other proteins into signaling complexes.
Length = 82
Score = 24.9 bits (55), Expect = 8.4
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 31 CAQRWNKNDLDELPDPLDLATGLEKRELLAE 61
C + K L+++ L L + L +R L++
Sbjct: 26 CRDKIGKRKLEKVQSGLQLFSALMERNLISP 56
>gnl|CDD|219969 pfam08687, ASD2, Apx/Shroom domain ASD2. This region is found in
the actin binding protein Shroom which mediates apical
contriction in epithelial cells and is required for
neural tube closure.
Length = 274
Score = 25.8 bits (57), Expect = 8.4
Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 14/55 (25%)
Query: 7 SLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPDPLDLATGLEKRELLAE 61
SL+LS + R LAR N+ S LDE DP + A+ LEKR+LL
Sbjct: 164 SLLLSLSGR-LAR----VENALSR---------LDEDADPEERASLLEKRKLLTR 204
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 25.7 bits (57), Expect = 10.0
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 9/44 (20%)
Query: 39 DLDELPDPLDLATGLEKRELLAELAG---DPDPFNVKIRKRGLG 79
D+ E P D+ +REL E G + P +V I+K+ G
Sbjct: 149 DVFEDPHHRDII----EREL--EDVGIRLNKRPPDVTIKKKESG 186
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 0.136 0.439
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,964,531
Number of extensions: 612629
Number of successful extensions: 499
Number of sequences better than 10.0: 1
Number of HSP's gapped: 492
Number of HSP's successfully gapped: 28
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
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: 54 (24.7 bits)