RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18026
(246 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan
signaling molecules, often in tandem arrangements. May
be responsible for specific protein-protein
interactions, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of PDZ domains an N-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in proteases.
Length = 82
Score = 81.1 bits (201), Expect = 5e-20
Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 6/88 (6%)
Query: 36 IITVTLNMDTVNFLGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDIN 95
+ TVTL D LG S+ G K GGI+V + GG G + GD IL+VN ++
Sbjct: 1 VRTVTLRKDPGGGLGFSLRG--GKDSGGGIFVSRVEPGGPAER-GGLRVGDRILEVNGVS 57
Query: 96 FENMSNDEAVRVLREVVQKPGPIKLVVA 123
E ++++EAV +L+ + L V
Sbjct: 58 VEGLTHEEAVELLKNS---GDEVTLTVR 82
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 76.9 bits (190), Expect = 2e-18
Identities = 33/86 (38%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 38 TVTLNMDTVNFLGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFE 97
VTL LG S+VG S+ GD GI+V ++ GGA G ++ GD IL +N + E
Sbjct: 1 EVTLEKSGRGGLGFSLVGGSD--GDPGIFVSEVLPGGAAEAGG-LQEGDRILSINGQDLE 57
Query: 98 NMSNDEAVRVLREVVQKPGPIKLVVA 123
N+S+DEAV L+ G + L +
Sbjct: 58 NLSHDEAVLALKG---SGGEVTLTIL 80
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some PDZs
have been shown to bind C-terminal polypeptides; others
appear to bind internal (non-C-terminal) polypeptides.
Different PDZs possess different binding specificities.
Length = 85
Score = 71.6 bits (176), Expect = 2e-16
Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 35 NIITVTLNMDTVNFLGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDI 94
V L LG S+VG K GG+ V S++ G A G + GD+IL+VN
Sbjct: 1 EPRLVELEKGG-GGLGFSLVG--GKDEGGGVVVSSVVPGSPAAKAG-LRVGDVILEVNGT 56
Query: 95 NFENMSNDEAVRVLREVVQKPGPIKLVV 122
+ E +++ EAV +L++ G + L V
Sbjct: 57 SVEGLTHLEAVDLLKKA---GGKVTLTV 81
>gnl|CDD|239885 cd04438, DEP_dishevelled, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain found in dishevelled-like proteins.
Dishevelled-like proteins play a key role in the
transduction of the Wnt signal from the cell surface to
the nucleus, which in turn is an important regulatory
pathway for cellular development and growth. They
contain an N-terminal DIX domain, a central PDZ domain,
and a C-terminal DEP domain.
Length = 84
Score = 66.6 bits (163), Expect = 1e-14
Identities = 25/33 (75%), Positives = 28/33 (84%)
Query: 202 ATIVRVMARPESGLEIRDRMWLKITIPNAFIGK 234
I RVM RP+SGLEI+DRMWLKITIPN+FIG
Sbjct: 1 NGIPRVMRRPDSGLEIKDRMWLKITIPNSFIGS 33
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization through
PDZ-PDZ domain interactions adds to the domain's
versatility, and PDZ domain-mediated interactions may be
modulated dynamically through target phosphorylation.
Some PDZ domains play a role in scaffolding
supramolecular complexes. PDZ domains are found in
diverse signaling proteins in bacteria, archebacteria,
and eurkayotes. This CD contains two distinct structural
subgroups with either a N- or C-terminal beta-strand
forming the peptide-binding groove base. The circular
permutation placing the strand on the N-terminus appears
to be found in Eumetazoa only, while the C-terminal
variant is found in all three kingdoms of life, and
seems to co-occur with protease domains. PDZ domains
have been named after PSD95(post synaptic density
protein), DlgA (Drosophila disc large tumor suppressor),
and ZO1, a mammalian tight junction protein.
Length = 70
Score = 54.2 bits (131), Expect = 4e-10
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 49 LGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVL 108
LG SI G G +GG+ V S+ G A ++ GD+IL VN + +N++ ++ +L
Sbjct: 3 LGFSIRG----GTEGGVVVLSVEPGSP-AERAGLQAGDVILAVNGTDVKNLTLEDVAELL 57
Query: 109 REVVQKPGPIKLVV 122
++ V + + L V
Sbjct: 58 KKEVGE--KVTLTV 69
>gnl|CDD|239836 cd04371, DEP, DEP domain, named after Dishevelled, Egl-10, and
Pleckstrin, where this domain was first discovered. The
function of this domain is still not clear, but it is
believed to be important for the membrane association of
the signaling proteins in which it is present. New
studies show that the DEP domain of Sst2, a yeast RGS
protein is necessary and sufficient for receptor
interaction.
Length = 81
Score = 42.7 bits (101), Expect = 7e-06
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 203 TIVRVMARPESGLEIRDRMWLKITIPNAFIGK 234
+VR+M +SG+ I+DR + T PN F G
Sbjct: 1 DLVRIMLDSDSGVPIKDRKYHLKTYPNCFTGS 32
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 43.5 bits (103), Expect = 5e-05
Identities = 31/103 (30%), Positives = 50/103 (48%), Gaps = 10/103 (9%)
Query: 50 GISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLR 109
GI I Q GG+ V S + G A G I+PGD+I++++ + +S DEAV+++R
Sbjct: 101 GIGIELQMED--IGGVKVVSPIDGSPAAKAG-IKPGDVIIKIDGKSVGGVSLDEAVKLIR 157
Query: 110 EVVQKPG-PIKLVVAKCWDPNPKGYFTIPRTEPVRPIDPGAWV 151
KPG + L + + P T+ R E ++ A
Sbjct: 158 G---KPGTKVTLTILRAGGGKPF-TVTLTREE--IELEDVAAK 194
>gnl|CDD|214489 smart00049, DEP, Domain found in Dishevelled, Egl-10, and
Pleckstrin. Domain of unknown function present in
signalling proteins that contain PH, rasGEF, rhoGEF,
rhoGAP, RGS, PDZ domains. DEP domain in Drosophila
dishevelled is essential to rescue planar polarity
defects and induce JNK signalling (Cell 94, 109-118).
Length = 77
Score = 38.4 bits (90), Expect = 2e-04
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 211 PESGLEIRDRMWLKITIPNAFIGKC 235
PE+GL++RDR + T PN F G
Sbjct: 1 PETGLKLRDRKYFLKTYPNCFTGSE 25
>gnl|CDD|216020 pfam00610, DEP, Domain found in Dishevelled, Egl-10, and Pleckstrin
(DEP). The DEP domain is responsible for mediating
intracellular protein targeting and regulation of
protein stability in the cell. The DEP domain is present
in a number of signaling molecules, including Regulator
of G protein Signaling (RGS) proteins, and has been
implicated in membrane targeting. New findings in yeast,
however, demonstrate a major role for a DEP domain in
mediating the interaction of an RGS protein to the
C-terminal tail of a GPCR, thus placing RGS in close
proximity with its substrate G protein alpha subunit.
Length = 74
Score = 37.6 bits (88), Expect = 5e-04
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 214 GLEIRDRMWLKITIPNAFIGK 234
G++++DR T PN F G
Sbjct: 1 GVKLKDRKKHLKTYPNCFTGS 21
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function in
posttranslational protein processing, maturation, and
disassembly or degradation, in Bacteria, Archaea, and
plant chloroplasts. May be responsible for substrate
recognition and/or binding, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 85
Score = 37.2 bits (87), Expect = 8e-04
Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 62 DGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLR 109
DGG+ + S++ G A I+ GD+I+ ++ + +S ++ V++LR
Sbjct: 12 DGGLVITSVLPGS-PAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLR 58
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 90
Score = 34.9 bits (81), Expect = 0.005
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 11/82 (13%)
Query: 48 FLGISIV-------GQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMS 100
+LG+++ + G+ V S+ G A G ++PGD+IL VN +++
Sbjct: 2 WLGVTVQDLTPDLAEELGLKDTKGVLVASVDPGSPAAKAG-LKPGDVILAVNGKPVKSV- 59
Query: 101 NDEAVRVLREVVQKPGPIKLVV 122
+ R L E ++ + L V
Sbjct: 60 -ADLRRALAE-LKPGDKVTLTV 79
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 34.1 bits (79), Expect = 0.009
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 12/76 (15%)
Query: 48 FLGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRV 107
LG G + +G ++ G A G ++ GD IL +N ++ + +
Sbjct: 2 ILGFVPGGPPIE-----PVIGEVVPGSPAAKAG-LKAGDRILAINGQKIKSWED-----L 50
Query: 108 LREVVQKPG-PIKLVV 122
+ V + PG P+ L V
Sbjct: 51 VDAVQENPGKPLTLTV 66
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 34.3 bits (79), Expect = 0.046
Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 11/101 (10%)
Query: 48 FLGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRV 107
GI I + DG I + S +G A I+PGD I+++N + MS D+AV +
Sbjct: 50 LEGIGIQVGMD---DGEIVIVSPFEGSP-AEKAGIKPGDKIIKINGKSVAGMSLDDAVAL 105
Query: 108 LREVVQKPG-PIKLVVAKCWDPNPKGYFTIPRTEPVRPIDP 147
+R K G + L + + T +
Sbjct: 106 IR---GKKGTKVSLEILR---AGKSKPLTFTLKRDRIELQT 140
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 33.2 bits (76), Expect = 0.10
Identities = 28/101 (27%), Positives = 46/101 (45%), Gaps = 24/101 (23%)
Query: 22 SSFSSI--------TDSSMSLNII--------TVTL------NMDTVN-FLGISIVGQSN 58
SSF+++ S ++L ++ V L +D+ N F GI SN
Sbjct: 344 SSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIEGAELSN 403
Query: 59 KGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENM 99
KGGD G+ V ++ G A G ++ GD+I+ N +N+
Sbjct: 404 KGGDKGVVVDNVKPGTPAAQIG-LKKGDVIIGANQQPVKNI 443
>gnl|CDD|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing
protease, deltaproteobacterial. This model describes a
multidomain protein of about 1070 residues, restricted
to the order Myxococcales in the Deltaproteobacteria.
Members contain a PDZ domain (pfam00595), an S41 family
peptidase domain (pfam03572), and an SH3 domain
(pfam06347). A core region of this family, including PDZ
and S41 regions, is described by TIGR00225, C-terminal
processing peptidase, which recognizes the Prc protease.
The species distribution of this family approximates
that of largely Deltaproteobacterial C-terminal putative
protein-sorting domain, TIGR03901, analogous to LPXTG
and PEP-CTERM, but the co-occurrence may reflect shared
restriction to the Myxococcales rather than a
substrate/target relationship.
Length = 973
Score = 32.1 bits (73), Expect = 0.33
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 49 LGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVL 108
LGI I + D + V ++ G A G ++ D+I++++D + NM+ ++AV L
Sbjct: 142 LGIVIGMR-----DRNLTVVRVIPGTPAARAG-LQRNDVIVKIDDESTVNMTLNDAVGRL 195
Query: 109 R 109
R
Sbjct: 196 R 196
>gnl|CDD|70841 pfam07390, P30, Mycoplasma P30 protein. This family consists of
several P30 proteins which seem to be specific to
Mycoplasma agalactiae. P30 is a 30-kDa immunodominant
antigen and is known to be a transmembrane protein.
Length = 266
Score = 30.9 bits (69), Expect = 0.43
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 118 IKLVVAKCWDPNPKGYFTIPRTEPVRPIDPGAWVAHTAAIRGDGFPLRPPSVSTLTSTSS 177
I V AKC + + K T P+ EP +P+D ++ + G+ T+ S+
Sbjct: 19 IPFVAAKCSEDDKKEKVTKPKNEPTKPVDNSKTNDNSNEMVGE------------TNLSN 66
Query: 178 SLTSSIAETEKAF 190
S+ SS + T+ F
Sbjct: 67 SINSSNSSTQNHF 79
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 30.6 bits (70), Expect = 0.72
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 56 QSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVND 93
KG G+ V ++ G A G ++PGD+IL VN
Sbjct: 355 LRLKGDVKGVVVTKVVSGSPAARAG-LQPGDVILSVNQ 391
Score = 29.9 bits (68), Expect = 1.3
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 63 GGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMS 100
G V ++ G G ++ GD+I VN + +
Sbjct: 257 RGALVAQVLPGSPAEKAG-LKAGDVITSVNGKPISSFA 293
>gnl|CDD|201816 pfam01472, PUA, PUA domain. The PUA domain named after
Pseudouridine synthase and Archaeosine transglycosylase,
was detected in archaeal and eukaryotic pseudouridine
synthases, archaeal archaeosine synthases, a family of
predicted ATPases that may be involved in RNA
modification, a family of predicted archaeal and
bacterial rRNA methylases. Additionally, the PUA domain
was detected in a family of eukaryotic proteins that
also contain a domain homologous to the translation
initiation factor eIF1/SUI1; these proteins may comprise
a novel type of translation factors. Unexpectedly, the
PUA domain was detected also in bacterial and yeast
glutamate kinases; this is compatible with the
demonstrated role of these enzymes in the regulation of
the expression of other genes. It is predicted that the
PUA domain is an RNA binding domain.
Length = 74
Score = 28.6 bits (65), Expect = 0.72
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 6/53 (11%)
Query: 69 SIMKGGAVALDGRIEPGDMILQVNDINFE------NMSNDEAVRVLREVVQKP 115
S++ G V +DG GD ++ V + N S++E ++ K
Sbjct: 18 SLLAPGVVEVDGDFRRGDEVVVVTEKGELVAVGLANYSSEEMAKIKGGKAVKV 70
>gnl|CDD|234035 TIGR02860, spore_IV_B, stage IV sporulation protein B. SpoIVB, the
stage IV sporulation protein B of endospore-forming
bacteria such as Bacillus subtilis, is a serine
proteinase, expressed in the spore (rather than mother
cell) compartment, that participates in a proteolytic
activation cascade for Sigma-K. It appears to be
universal among endospore-forming bacteria and occurs
nowhere else [Cellular processes, Sporulation and
germination].
Length = 402
Score = 30.4 bits (69), Expect = 0.94
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 20/88 (22%)
Query: 37 ITVTLNMDTVNFLGISIVGQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINF 96
I V LN V +G S + + G I+ + + I+ GD IL++N
Sbjct: 98 IGVKLNTKGVLVVGFSDI----ETEKGKIH--------SPGEEAGIQIGDRILKINGEKI 145
Query: 97 ENMSNDEAVRVLREVVQKPG--PIKLVV 122
+NM + L ++ K G + L +
Sbjct: 146 KNMDD------LANLINKAGGEKLTLTI 167
>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1. TT virus (TTV), isolated
initially from a Japanese patient with hepatitis of
unknown aetiology, has since been found to infect both
healthy and diseased individuals and numerous
prevalence studies have raised questions about its role
in unexplained hepatitis. ORF1 is a large 750 residue
protein. The N-terminal half of this protein
corresponds to the capsid protein.
Length = 525
Score = 30.3 bits (69), Expect = 1.1
Identities = 10/18 (55%), Positives = 10/18 (55%)
Query: 3 RRRRPQRRRRHRPPALSR 20
RRRR RRRR R R
Sbjct: 20 RRRRRARRRRRRRRVRRR 37
Score = 27.6 bits (62), Expect = 7.4
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 3 RRRRPQRRRRHRPPALSR 20
RRRR + RRR R R
Sbjct: 28 RRRRRRVRRRRRGRRRRR 45
>gnl|CDD|113681 pfam04917, Shufflon_N, Bacterial shufflon protein, N-terminal
constant region. This family represents the
high-similarity N-terminal 'constant region' shared by
shufflon proteins.
Length = 356
Score = 30.0 bits (67), Expect = 1.2
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 64 GIYVGSIMKGGAVALDGRIEPGDMILQVNDIN 95
GIY G +KGG V DGR+ G+ LQ+
Sbjct: 300 GIYTGGQVKGGTVRADGRLYTGE-YLQLEKTA 330
>gnl|CDD|226011 COG3480, SdrC, Predicted secreted protein containing a PDZ domain
[Signal transduction mechanisms].
Length = 342
Score = 29.3 bits (66), Expect = 2.0
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 64 GIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPG 116
G+YV S++ G++E GD I+ V+ F S+DE + + +KPG
Sbjct: 131 GVYVLSVIDNSPFK--GKLEAGDTIIAVDGEPFT--SSDELIDYVSS--KKPG 177
>gnl|CDD|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine
synthase and Archaeosine transglycosylase.
Length = 76
Score = 27.2 bits (61), Expect = 2.1
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 8/52 (15%)
Query: 68 GSIMKGGAVALDGRIEPGDMILQVNDINFE-------NMSNDEAVRVLREVV 112
S++ G V +DG I+ GD ++ + D E NMS++E R+ + +
Sbjct: 17 ASLLAPGVVRVDGDIKEGD-VVVIVDEKGEPLGIGLANMSSEEIARIKGKGL 67
>gnl|CDD|132166 TIGR03122, one_C_dehyd_C, formylmethanofuran dehydrogenase subunit
C. Members of this largely archaeal protein family are
subunit C of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit C. Note
that this model does not distinguish tungsten (FwdC)
from molybdenum-containing (FmdC) forms of this enzyme.
Length = 260
Score = 28.8 bits (65), Expect = 2.3
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 61 GDGGIYVGSIMKGGAVALDGRIEP---GDM 87
G+ GI+ G M GG + +DG + G+M
Sbjct: 170 GNAGIFAGIHMNGGTIIIDGDVGRRPGGEM 199
>gnl|CDD|238486 cd00986, PDZ_LON_protease, PDZ domain of ATP-dependent LON serine
proteases. Most PDZ domains bind C-terminal
polypeptides, though binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this bacterial subfamily of
protease-associated PDZ domains a C-terminal
beta-strand is thought to form the peptide-binding
groove base, a circular permutation with respect to PDZ
domains found in Eumetazoan signaling proteins.
Length = 79
Score = 27.0 bits (60), Expect = 2.6
Identities = 11/34 (32%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 64 GIYVGSIMKGGAVALDGRIEPGDMILQVNDINFE 97
G+YV S+++G + G+++ GD I+ V+ F+
Sbjct: 9 GVYVTSVVEG--MPAAGKLKAGDHIIAVDGKPFK 40
>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW;
Provisional.
Length = 223
Score = 28.3 bits (63), Expect = 3.1
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 80 GRIEPGDMIL-QVNDINFENMSN--DEAVRVLREVVQKPGPIKLV 121
G I P +I ++ INF++ +N D A+R LR V P P KL+
Sbjct: 164 GEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDDPFPEKLI 208
>gnl|CDD|215036 PLN00034, PLN00034, mitogen-activated protein kinase kinase;
Provisional.
Length = 353
Score = 28.3 bits (63), Expect = 3.6
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 163 PLRPPSVSTLTSTSSSLTSSIAETEKAFEEL 193
PL PPS S+ +S+SSS + S K+ EL
Sbjct: 46 PLPPPSSSSSSSSSSSASGSAPSAAKSLSEL 76
>gnl|CDD|225128 COG2218, FwdC, Formylmethanofuran dehydrogenase subunit C [Energy
production and conversion].
Length = 264
Score = 28.1 bits (63), Expect = 4.4
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 61 GDGGIYVGSIMKGGAVALDGRIE 83
GD G +VG MKGG + +DG+
Sbjct: 194 GDAGDFVGGEMKGGTIVVDGKAG 216
>gnl|CDD|238480 cd00980, FwdC/FmdC, FwdC/FmdC. This domain of unknown function is
found in the subunit C of formylmethanofuran
dehydrogenase, an enzyme that catalyzes the first step
in methane formation from CO2 in methanogenic archaea,
hyperthermophiles and bacteria. There are two
isoenzymes, a tungsten-containing isoenzyme (Fwd) and a
molybdenum-containing isoenzyme (Fmd). The subunits C of
both isoenzymes (FwdC/FmdC) are characterized by a
repeated GXXGXXXG motif.
Length = 203
Score = 27.3 bits (61), Expect = 5.5
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 60 GGDGGIYVGSIMKGGAVALDGRI 82
GD GI+ G M GG + + G
Sbjct: 128 KGDAGIFAGIRMNGGTIIVRGDA 150
>gnl|CDD|238481 cd00981, arch_gltB, Archaeal-type gltB domain. This domain shares
sequence similarity with a region of unknown function
found in the large subunit of glutamate synthase, which
is encoded by gltB and found in most bacteria and
eukaryotes. It is predicted to be homologous to the
C-terminal domain of glutamate synthase based upon
sequence similarity coupled with genome organization
data, showing that this domain is found in a gene
cluster with other domains of Glts, which are annotated.
This domain is found primarily in archaea, but is also
present in a few bacteria, likely as a result of lateral
gene transfer.
Length = 232
Score = 27.3 bits (61), Expect = 7.1
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 50 GISIV-GQSNKGGDGGIYVGSIMKGGAVALDGRIEPGDMILQVNDINFENMSNDEA 104
G+ IV G G Y+G+ M GG + + G++E + +V FE D
Sbjct: 147 GVIIVLGLGTDEEPVGRYIGTGMHGGVIYIRGKVERSKLGKEV--PKFELTEEDLE 200
>gnl|CDD|222616 pfam14239, RRXRR, RRXRR protein. This domain is found in bacteria,
eukaryotes and viruses, and is approximately 180 amino
acids in length. It contains a conserved RRXRR motif. It
is often found in association with pfam01844.
Length = 174
Score = 26.8 bits (60), Expect = 8.5
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 1 MSRRRRPQRRRRHRPP 16
RRRR R+ R+R P
Sbjct: 95 RLRRRRRNRKTRYRKP 110
>gnl|CDD|133178 cd05046, PTK_CCK4, Pseudokinase domain of the Protein Tyrosine
Kinase, Colon Carcinoma Kinase 4. Protein Tyrosine
Kinase (PTK) family; Colon Carcinoma Kinase 4 (CCK4);
pseudokinase domain. The PTKc (catalytic domain) family,
to which this subfamily belongs, includes the catalytic
domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. CCK4,
also called protein tyrosine kinase 7 (PTK7), is an
orphan receptor tyr kinase (RTK) containing an
extracellular region with seven immunoglobulin domains,
a transmembrane segment, and an intracellular inactive
pseudokinase domain. Studies in mice reveal that CCK4 is
essential for neural development. Mouse embryos
containing a truncated CCK4 die perinatally and display
craniorachischisis, a severe form of neural tube defect.
The mechanism of action of the CCK4 pseudokinase is
still unknown. Other pseudokinases such as HER3 rely on
the activity of partner RTKs.
Length = 275
Score = 27.0 bits (60), Expect = 9.2
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 96 FENMSNDEAVRVLREVVQK-------PGPIKLVVAKCWDPNPK 131
F +S++E + L+ + P + ++ +CW NPK
Sbjct: 219 FYGLSDEEVLNRLQAGKLELPVPEGCPSRLYKLMTRCWAVNPK 261
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
0.319 0.135 0.398
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,664,650
Number of extensions: 1191692
Number of successful extensions: 1580
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1556
Number of HSP's successfully gapped: 53
Length of query: 246
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 152
Effective length of database: 6,768,326
Effective search space: 1028785552
Effective search space used: 1028785552
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 (21.7 bits)
S2: 58 (26.1 bits)