RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4897
(774 letters)
>gnl|CDD|241289 cd01258, PHsplit_syntrophin, Syntrophin Split Pleckstrin homology
(PH) domain. Syntrophins are scaffold proteins that
associate with associate with the Duchenne muscular
dystrophy protein dystrophin and the dystrophin-related
proteins, utrophin and dystrobrevin to form the
dystrophin glycoprotein complex (DGC). There are 5
members: alpha, beta1, beta2, gamma1, and gamma2) all of
which contains a split (also called joined) PH domain
and a PDZ domain (PHN-PDZ-PHC). The split PH domain of
alpha-syntrophin adopts a canonical PH domain fold and
together with PDZ forms a supramodule functioning
synergistically in binding to inositol phospholipids.
The alpha-syntrophin PH-PDZ supramodule showed strong
binding to phosphoinositides PI(3,5)P2 and PI(5)P,
modest binding to PI(3,4)P2 and PI(4,5)P2, and weak
binding to PI(3)P, PI(4)P, and PI(3,4,5)P. There are a
large number of signaling proteins that bind to the PDZ
domain of syntrophins: nitric oxide synthase (nNOS),
aquaporin-4, voltage-gated sodium channels, potassium
channels, serine/threonine protein kinases, and the
ATP-binding cassette transporter A1. 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 = 89
Score = 96.2 bits (240), Expect = 5e-24
Identities = 31/54 (57%), Positives = 39/54 (72%)
Query: 302 RYLPLQLCYLVRNYKHYDSENRTLELHSPDGVHSCILRASDASEASLWFNTLHS 355
+ +PL++CY+ RN D ENR LELHSPDG HSCILR D++ A WFN +HS
Sbjct: 32 KSIPLKMCYVTRNLTPPDPENRLLELHSPDGRHSCILRCKDSATAQSWFNAIHS 85
Score = 43.0 bits (102), Expect = 2e-05
Identities = 13/31 (41%), Positives = 24/31 (77%)
Query: 108 RCGTLETYVRGQWYKVFVSLEEDYISITLDE 138
R G LE VRG+W++V +LEED +++++++
Sbjct: 2 RSGLLEVLVRGRWHRVLATLEEDALTLSIEK 32
>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 = 94.6 bits (236), Expect = 2e-23
Identities = 33/82 (40%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 176 RIIRVKKSENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLRE 235
R + ++K GLG S++GGK++ I +S++ G A++ L VGD IL VNG +
Sbjct: 2 RTVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVEG 60
Query: 236 ATHDEAVKALKRAGKLVELEVK 257
TH+EAV+ LK +G V L V+
Sbjct: 61 LTHEEAVELLKNSGDEVTLTVR 82
Score = 86.5 bits (215), Expect = 1e-20
Identities = 31/74 (41%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 29 TENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAV 88
GLG S++GGK++ I +S++ G A++ L VGD IL VNG + TH+EAV
Sbjct: 9 DPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVEGLTHEEAV 67
Query: 89 KALKRAGKVVELEV 102
+ LK +G V L V
Sbjct: 68 ELLKNSGDEVTLTV 81
>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 = 79.7 bits (197), Expect = 3e-18
Identities = 33/85 (38%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 174 QKRIIRVKKSENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDL 233
+ R++ ++K GLG S+ GGK+ +++S + G A + L VGD IL VNG +
Sbjct: 1 EPRLVELEKGGG-GLGFSLVGGKDEGGGVVVSSVVPGSPAAKA-GLRVGDVILEVNGTSV 58
Query: 234 REATHDEAVKALKRAGKLVELEVKY 258
TH EAV LK+AG V L V
Sbjct: 59 EGLTHLEAVDLLKKAGGKVTLTVLR 83
Score = 78.2 bits (193), Expect = 1e-17
Identities = 31/73 (42%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 30 ENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVK 89
GLG S+ GGK+ +++S + G A + L VGD IL VNG + TH EAV
Sbjct: 10 GGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKA-GLRVGDVILEVNGTSVEGLTHLEAVD 68
Query: 90 ALKRAGKVVELEV 102
LK+AG V L V
Sbjct: 69 LLKKAGGKVTLTV 81
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 77.7 bits (192), Expect = 1e-17
Identities = 34/80 (42%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 178 IRVKKSENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREAT 237
+ ++KS GLG S+ GG + I +S++ G AA+ L GD ILS+NG+DL +
Sbjct: 2 VTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAG-GLQEGDRILSINGQDLENLS 60
Query: 238 HDEAVKALKRAGKLVELEVK 257
HDEAV ALK +G V L +
Sbjct: 61 HDEAVLALKGSGGEVTLTIL 80
Score = 74.6 bits (184), Expect = 2e-16
Identities = 32/73 (43%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 30 ENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVK 89
GLG S+ GG + I +S++ G AA+ L GD ILS+NG+DL +HDEAV
Sbjct: 8 GRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAG-GLQEGDRILSINGQDLENLSHDEAVL 66
Query: 90 ALKRAGKVVELEV 102
ALK +G V L +
Sbjct: 67 ALKGSGGEVTLTI 79
>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 = 55.4 bits (134), Expect = 6e-10
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 32 NGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKAL 91
GLG SI+GG E +++ + G A++ L GD IL+VNG D++ T ++ + L
Sbjct: 1 GGLGFSIRGGTEG--GVVVLSVEPGSPAER-AGLQAGDVILAVNGTDVKNLTLEDVAELL 57
Query: 92 KRA-GKVVELEV 102
K+ G+ V L V
Sbjct: 58 KKEVGEKVTLTV 69
Score = 53.1 bits (128), Expect = 4e-09
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 186 NGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKAL 245
GLG SI+GG E +++ + G A++ L GD IL+VNG D++ T ++ + L
Sbjct: 1 GGLGFSIRGGTEG--GVVVLSVEPGSPAER-AGLQAGDVILAVNGTDVKNLTLEDVAELL 57
Query: 246 KRA-GKLVELEVK 257
K+ G+ V L V+
Sbjct: 58 KKEVGEKVTLTVR 70
>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 = 48.0 bits (115), Expect = 3e-07
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 9/74 (12%)
Query: 187 GLGISIK--GGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKA 244
G+G+ +K G ++I+ + G A + + GD I++++GE + + ++ VK
Sbjct: 3 GIGLELKYDDGG-----LVITSVLPGSPAAKA-GIKAGDIIVAIDGEPVDGLSLEDVVKL 56
Query: 245 LK-RAGKLVELEVK 257
L+ +AG V L +K
Sbjct: 57 LRGKAGTKVRLTLK 70
Score = 46.8 bits (112), Expect = 9e-07
Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 11/88 (12%)
Query: 33 GLGISIK--GGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKA 90
G+G+ +K G ++I+ + G A + + GD I++++GE + + ++ VK
Sbjct: 3 GIGLELKYDDGG-----LVITSVLPGSPAAKA-GIKAGDIIVAIDGEPVDGLSLEDVVKL 56
Query: 91 LK-RAGKVVELEVGVGYGRCGTLETYVR 117
L+ +AG V L + G G E +
Sbjct: 57 LRGKAGTKVRLTLKRGDG--EPREVTLT 82
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 44.2 bits (105), Expect = 2e-04
Identities = 24/106 (22%), Positives = 48/106 (45%), Gaps = 11/106 (10%)
Query: 152 SNTVDSISSFMDTVDIPDSVENQKRIIRVKKSENNGLGISIKGGKENKMPILISKIFKGM 211
S+ D S+++D D + + E G+GI ++ E+ + + G
Sbjct: 73 SSLGDPHSTYLDPEDAAEFRTDTS-------GEFGGIGIELQ--MEDIGGVKVVSPIDGS 123
Query: 212 AADQTEQLYVGDAILSVNGEDLREATHDEAVKALK-RAGKLVELEV 256
A + + GD I+ ++G+ + + DEAVK ++ + G V L +
Sbjct: 124 PAAKA-GIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTI 168
Score = 41.5 bits (98), Expect = 0.001
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 10/93 (10%)
Query: 18 SRDFYSENYKYTENN------GLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAI 71
S E+ + G+GI ++ E+ + + G A + + GD I
Sbjct: 80 STYLDPEDAAEFRTDTSGEFGGIGIELQ--MEDIGGVKVVSPIDGSPAAKA-GIKPGDVI 136
Query: 72 LSVNGEDLREATHDEAVKALK-RAGKVVELEVG 103
+ ++G+ + + DEAVK ++ + G V L +
Sbjct: 137 IKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTIL 169
>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 = 39.5 bits (93), Expect = 0.006
Identities = 42/202 (20%), Positives = 73/202 (36%), Gaps = 52/202 (25%)
Query: 49 LISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKALKRAGKVVELEVGVGYGR 108
L++++ G A++ L GD I SVNG+ + + GK V L +
Sbjct: 260 LVAQVLPGSPAEKA-GLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGI------ 312
Query: 109 CGTLETYVRGQWYKVFVSLEEDYISITLDENYDNSTVLNGTLNSNTVDSISSFMDTVDIP 168
+R +E I++TL + + + TV ++
Sbjct: 313 -------LRKG--------KEKTITVTLGASPEEQASSSNPFLGLTV---------ANLS 348
Query: 169 DSVENQKRIIRVKKSENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSV 228
+ + R+ K + G ++++K+ G A + L GD ILSV
Sbjct: 349 PEIRKELRL----KGDVKG--------------VVVTKVVSGSPAARA-GLQPGDVILSV 389
Query: 229 NGEDLREATHDEAVKALKRAGK 250
N + + E K L RA K
Sbjct: 390 NQQPVSSV--AELRKVLARAKK 409
Score = 34.9 bits (81), Expect = 0.17
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 203 LISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKALKRAGKLVELEV 256
L++++ G A++ L GD I SVNG+ + + GK V L +
Sbjct: 260 LVAQVLPGSPAEKA-GLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGI 312
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 36.7 bits (85), Expect = 0.006
Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 13/92 (14%)
Query: 459 DRWVSIFGAVTERELRLYESAPWSPEAWSTPAHVFPLVSTRLVSSSRHSDV---IVFSVR 515
R+ +F V L Y+ S ++ S P PL ++ D F +R
Sbjct: 20 KRYFVLFDGV----LLYYKD---SKKSSSRPKGSIPLSGCQVTKVPDSEDGKRKNCFEIR 72
Query: 516 CGTPQGVATHHLRAETHRDLANWARTLVQATH 547
G + T L+AE+ + W + + A
Sbjct: 73 TGDRE---TFLLQAESEEERKEWVKAIRSAIR 101
>gnl|CDD|214574 smart00233, PH, Pleckstrin homology domain. Domain commonly found
in eukaryotic signalling proteins. The domain family
possesses multiple functions including the abilities to
bind inositol phosphates, and various proteins. PH
domains have been found to possess inserted domains
(such as in PLC gamma, syntrophins) and to be inserted
within other domains. Mutations in Brutons tyrosine
kinase (Btk) within its PH domain cause X-linked
agammaglobulinaemia (XLA) in patients. Point mutations
cluster into the positively charged end of the molecule
around the predicted binding site for
phosphatidylinositol lipids.
Length = 102
Score = 36.0 bits (83), Expect = 0.012
Identities = 14/97 (14%), Positives = 25/97 (25%), Gaps = 8/97 (8%)
Query: 454 GDDSTDRWVSIFGAVTERELRLYESAPWSPEAWSTPAHVFPLVSTRLV---SSSRHSDVI 510
W + + L Y+S P L +
Sbjct: 11 SGGGKKSWKKRYFVLFNSTLLYYKSKKDKKS--YKPKGSIDLSGCTVREAPDPDSSKKPH 68
Query: 511 VFSVRCGTPQGVATHHLRAETHRDLANWARTLVQATH 547
F ++ + T L+AE+ + W L +A
Sbjct: 69 CFEIKTSDRK---TLLLQAESEEEREKWVEALRKAIA 102
Score = 28.7 bits (64), Expect = 3.7
Identities = 9/57 (15%), Positives = 18/57 (31%), Gaps = 2/57 (3%)
Query: 303 YLPLQLCYLVRNYKH-YDSENRTLELHSPDGVHSCILRASDASEASLWFNTLHSTLH 358
+ L C + + E+ + D + +L+A E W L +
Sbjct: 47 SIDLSGCTVREAPDPDSSKKPHCFEIKTSDR-KTLLLQAESEEEREKWVEALRKAIA 102
>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 = 34.0 bits (78), Expect = 0.028
Identities = 18/58 (31%), Positives = 35/58 (60%), Gaps = 6/58 (10%)
Query: 202 ILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKAL--KRAGKLVELEVK 257
+ ++ + +GM A +L GD I++V+G+ +EA +E + + K+ G V+L+VK
Sbjct: 10 VYVTSVVEGMPAA--GKLKAGDHIIAVDGKPFKEA--EELIDYIQSKKEGDTVKLKVK 63
Score = 32.8 bits (75), Expect = 0.094
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 48 ILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKAL--KRAGKVVELEV 102
+ ++ + +GM A +L GD I++V+G+ +EA +E + + K+ G V+L+V
Sbjct: 10 VYVTSVVEGMPAA--GKLKAGDHIIAVDGKPFKEA--EELIDYIQSKKEGDTVKLKV 62
>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 = 31.8 bits (73), Expect = 0.20
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 204 ISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKAL-KRAGKLVELEVK 257
I ++ G A + L GD IL++NG+ ++ ++ V A+ + GK + L V+
Sbjct: 16 IGEVVPGSPAAKA-GLKAGDRILAINGQKIKSW--EDLVDAVQENPGKPLTLTVE 67
Score = 30.7 bits (70), Expect = 0.46
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 50 ISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKAL-KRAGKVVELEV 102
I ++ G A + L GD IL++NG+ ++ ++ V A+ + GK + L V
Sbjct: 16 IGEVVPGSPAAKA-GLKAGDRILAINGQKIKSW--EDLVDAVQENPGKPLTLTV 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 = 0.23
Identities = 30/129 (23%), Positives = 55/129 (42%), Gaps = 13/129 (10%)
Query: 129 EDYISITLDENYDNSTVLNGTLNSNTVDSISSFMDTVDIPDSVENQKRIIRVKKSENNGL 188
+Y+ LDE + + G L S D + ++ E K G+
Sbjct: 2 SEYVKRVLDETEEIYGAIKGMLASL-NDPYTRYLSP-------ETAKSFSETTSGSLEGI 53
Query: 189 GISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKALK-R 247
GI + + I+I F+G A++ + GD I+ +NG+ + + D+AV ++ +
Sbjct: 54 GIQVG---MDDGEIVIVSPFEGSPAEKA-GIKPGDKIIKINGKSVAGMSLDDAVALIRGK 109
Query: 248 AGKLVELEV 256
G V LE+
Sbjct: 110 KGTKVSLEI 118
Score = 31.2 bits (71), Expect = 2.0
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 33 GLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKALK 92
G+GI + + I+I F+G A++ + GD I+ +NG+ + + D+AV ++
Sbjct: 52 GIGIQVG---MDDGEIVIVSPFEGSPAEKA-GIKPGDKIIKINGKSVAGMSLDDAVALIR 107
Query: 93 -RAGKVVELEV 102
+ G V LE+
Sbjct: 108 GKKGTKVSLEI 118
>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 = 31.1 bits (71), Expect = 0.39
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 10/78 (12%)
Query: 34 LGISI---------KGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATH 84
LG+++ + G ++ +L++ + G A + L GD IL+VNG+ ++
Sbjct: 3 LGVTVQDLTPDLAEELGLKDTKGVLVASVDPGSPAAKAG-LKPGDVILAVNGKPVKSVAD 61
Query: 85 DEAVKALKRAGKVVELEV 102
A + G V L V
Sbjct: 62 LRRALAELKPGDKVTLTV 79
Score = 30.7 bits (70), Expect = 0.66
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 10/79 (12%)
Query: 188 LGISI---------KGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATH 238
LG+++ + G ++ +L++ + G A + L GD IL+VNG+ ++
Sbjct: 3 LGVTVQDLTPDLAEELGLKDTKGVLVASVDPGSPAAKAG-LKPGDVILAVNGKPVKSVAD 61
Query: 239 DEAVKALKRAGKLVELEVK 257
A + G V L V
Sbjct: 62 LRRALAELKPGDKVTLTVL 80
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 29.9 bits (68), Expect = 0.96
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 33 GLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKALK 92
+G+ + + + + +G A + L GD ILS++G+ + T V
Sbjct: 2 DIGVRVVQ--NEGTGVTVVSVKEGSPAAK-AGLKPGDIILSIDGKKVNSLTELIEVILNG 58
Query: 93 RAGKVVELEV 102
+ G V+L V
Sbjct: 59 KPGDTVKLTV 68
Score = 29.5 bits (67), Expect = 1.1
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 187 GLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKALK 246
+G+ + + + + +G A + L GD ILS++G+ + T V
Sbjct: 2 DIGVRVVQ--NEGTGVTVVSVKEGSPAAK-AGLKPGDIILSIDGKKVNSLTELIEVILNG 58
Query: 247 RAGKLVELEVK 257
+ G V+L V
Sbjct: 59 KPGDTVKLTVY 69
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 32.0 bits (73), Expect = 1.5
Identities = 24/112 (21%), Positives = 44/112 (39%), Gaps = 7/112 (6%)
Query: 163 DTVDIPDSVENQKRIIRVKKSENNGLGISIKGGKENKMPILISKIFKGMAADQTEQLYVG 222
+ + +E K E LG+ + E I+ +F G A L G
Sbjct: 428 EPPPLNPLLERFGLTFTPKPREAYYLGLKV--KSEGGH-EKITFVFPGGPA-YKAGLSPG 483
Query: 223 DAILSVNGEDLREATH--DEAVK-ALKRAGKLVELEVKYLREVTPYFRKASI 271
D I+++NG + + ++ ++ + R G+L E VK + T + I
Sbjct: 484 DKIVAINGISDQLDRYKVNDKIQVHVFREGRLREFLVKLGGDPTAQYIILPI 535
>gnl|CDD|212676 cd10234, HSPA9-Ssq1-like_NBD, Nucleotide-binding domain of human
HSPA9 and similar proteins. This subfamily includes
human mitochondrial HSPA9 (also known as 70-kDa heat
shock protein 9, CSA; MOT; MOT2; GRP75; PBP74; GRP-75;
HSPA9B; MTHSP75; the gene encoding HSPA9 maps to
5q31.1), Escherichia coli DnaK, Saccharomyces cerevisiae
Stress-seventy subfamily Q protein 1/Ssq1p (also called
Ssc2p, Ssh1p, mtHSP70 homolog), and S. cerevisiae
Stress-Seventy subfamily C/Ssc1p (also called mtHSP70,
Endonuclease SceI 75 kDa subunit). 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.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs); for Escherichia coli DnaK, these are the
DnaJ and GrpE, respectively.
Length = 376
Score = 31.5 bits (72), Expect = 1.6
Identities = 29/113 (25%), Positives = 40/113 (35%), Gaps = 19/113 (16%)
Query: 153 NTVDSISSFMDTVDIPDSVENQKRIIRVKKSENNGLGISIKGGKENKMPILIS-KIFKGM 211
NT+ SI FM E + V N + I ++ P IS I + +
Sbjct: 64 NTIFSIKRFMGRKFDEVEEERKVPYKVVVDEGGNY-KVEIDSNGKDYTPQEISAMILQKL 122
Query: 212 AADQTEQLYVGDAILSVNGEDLREAT-------HDEAVKALKRAGKLVELEVK 257
D L GE + EA +D +A K AGK+ LEV
Sbjct: 123 KEDAEAYL----------GEKVTEAVITVPAYFNDSQRQATKDAGKIAGLEVL 165
>gnl|CDD|184552 PRK14175, PRK14175, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 286
Score = 31.4 bits (71), Expect = 1.7
Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 7/101 (6%)
Query: 77 EDLREATHDEAVKALKRAGKVVELEVGVGYGRCGTLETYVRGQWYKVFVSLEEDYIS--I 134
+D R+ D+ V+ALK G +L V + G G ++YVR K + + IS +
Sbjct: 13 KDYRQGLQDQ-VEALKEKGFTPKLSV-ILVGNDGASQSYVRS---KKKAAEKIGMISEIV 67
Query: 135 TLDENYDNSTVLNGTLNSNTVDSISSFMDTVDIPDSVENQK 175
L+E VLN N DS+S + V +P V QK
Sbjct: 68 HLEETATEEEVLNELNRLNNDDSVSGILVQVPLPKQVSEQK 108
>gnl|CDD|213947 TIGR04334, rSAM_Clo7bot, radical SAM/SPASM domain Clo7bot peptide
maturase. In multiple strains of Clostridium botulinum,
this single radical SAM domain protein occurs next to a
tandem array of seven homologous Cys-rich small peptides
(see TIGR04333). Because this radical SAM enzyme
contains the SPASM domain, associated with peptide
modification, it is proposed to modify all seven C.
botulinum targets, hence the name Clo7bot for this
system. Suggested gene symbol is ctpM (Clostridial
Tandem Peptide Maturase) [Protein fate, Protein
modification and repair].
Length = 440
Score = 31.4 bits (71), Expect = 2.0
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 19/74 (25%)
Query: 139 NYDNSTVLNGTL-NSNTVDS-----ISSFMDTVDIPDSVENQKRIIR------------- 179
NY V NG L + + I+ T+D P ++ N++R ++
Sbjct: 171 NYSAYIVTNGYLIDDVVISKLNDLKINGAQITLDGPPNIHNKRRKLKNSDEGTFEVILSN 230
Query: 180 VKKSENNGLGISIK 193
VKK + NG+ I I+
Sbjct: 231 VKKLKKNGINIIIR 244
>gnl|CDD|227488 COG5159, RPN6, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 421
Score = 31.4 bits (71), Expect = 2.1
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 33 GLGISIKGGKENKMPILISKIFKGMAADQTEQLYVGDAILSVNGEDLREATHDEAVKALK 92
GL + GK ++M ++ KIF G DQ GD L V GE ++ T+DEA++ ++
Sbjct: 354 GLDTNQVEGKLSQM--ILDKIFYGTL-DQ------GDGCLIVYGEPAQDNTYDEALEQVE 404
Query: 93 RAGKVVEL 100
VV+
Sbjct: 405 ALDCVVDS 412
>gnl|CDD|173155 PRK14692, PRK14692, lagellar hook-associated protein FlgL;
Provisional.
Length = 749
Score = 31.1 bits (70), Expect = 2.8
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 130 DYISITLDENYDNSTVL--NGTLNSNTVDSISSFMD----TVDIPDSVENQKRI-IRVKK 182
D I + +N +T+ NG +N+N I M TVD+ S++ + RI + K
Sbjct: 523 DIIGMFAADNIPTATIQANNGQINNNDYTQIQQLMKDSQATVDV--SMDYKGRISVTDKL 580
Query: 183 SENNGLGISIKGGKENKMP 201
S + IS+ + + P
Sbjct: 581 SSGTNIEISLSDSQSGQFP 599
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 30.4 bits (70), Expect = 4.1
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 69 DAILSVNGEDLREATHDEAVKALKRAGKVVELEVGVGYGR 108
DAI G D + T +EA K G +E+E G G+
Sbjct: 319 DAIKEYTGVDFDDMTDEEARALAKELG--IEVEKSWGLGK 356
>gnl|CDD|241519 cd13365, PH_PLC_plant-like, Plant-like Phospholipase C (PLC)
pleckstrin homology (PH) domain. PLC-gamma (PLCgamma)
was the second class of PLC discovered. PLC-gamma
consists of an N-terminal PH domain, a EF hand domain, a
catalytic domain split into X and Y halves internal to
which is a PH domain split by two SH2 domains and a
single SH3 domain, and a C-terminal C2 domain. PLCs (EC
3.1.4.3) play a role in the initiation of cellular
activation, proliferation, differentiation and
apoptosis. They are central to inositol lipid signalling
pathways, facilitating intracellular Ca2+ release and
protein kinase C (PKC) activation. Specificaly, PLCs
catalyze the cleavage of
phosphatidylinositol-4,5-bisphosphate (PIP2) and result
in the release of 1,2-diacylglycerol (DAG) and inositol
1,4,5-triphosphate (IP3). These products trigger the
activation of protein kinase C (PKC) and the release of
Ca2+ from intracellular stores. There are fourteen kinds
of mammalian phospholipase C proteins which are are
classified into six isotypes (beta, gamma, delta,
epsilon, zeta, eta). This cd contains PLC members from
fungi and plants. 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 = 115
Score = 28.8 bits (65), Expect = 4.4
Identities = 17/68 (25%), Positives = 24/68 (35%), Gaps = 4/68 (5%)
Query: 290 SPSPQSSQRAD----TRYLPLQLCYLVRNYKHYDSENRTLELHSPDGVHSCILRASDASE 345
SP S +R +R +P Q + E ++ + DG S L D E
Sbjct: 43 SPKKGSEKRVRLSSVSRIIPGQRTVVFERPPPPGLEEQSFSIIYADGERSLDLTCKDRQE 102
Query: 346 ASLWFNTL 353
WF L
Sbjct: 103 FDTWFTGL 110
>gnl|CDD|224446 COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large
subunit CoxL/CutL homologs [Energy production and
conversion].
Length = 731
Score = 30.4 bits (69), Expect = 4.7
Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 13/94 (13%)
Query: 175 KRIIRVKKSENNGL--GISIKGGKENKMPILISKIFKGMAAD--QTEQLYVGDAILSVNG 230
RI+ + SE GL +++ +E + + + Y G+ + +V
Sbjct: 47 ARIVSIDVSEAQGLPGVLAVITAEELPAWSPVRVELAPADEVLARGKVRYTGEPVAAVVA 106
Query: 231 EDLREATHDEAVKALKRAGKLVELEVKYLREVTP 264
ED +A A +LV +E + L V
Sbjct: 107 EDEYQARA---------AAELVLVEYEALPPVVD 131
>gnl|CDD|223601 COG0527, LysC, Aspartokinases [Amino acid transport and
metabolism].
Length = 447
Score = 29.9 bits (68), Expect = 5.2
Identities = 23/133 (17%), Positives = 50/133 (37%), Gaps = 23/133 (17%)
Query: 151 NSNTVDSISSFMDTVDIPDSVENQKRIIRVKKSENNGLGISIKGGKENKMPILISKIFKG 210
N+ D+ T+ I E+ + +++ ++N I++ G N M +++F
Sbjct: 276 NTFNPDAPG----TL-ITAETESDEPVVKGIALDDNVALITVSGPGMNGMVGFAARVFGI 330
Query: 211 MAADQTEQLYVGDAI------LSVNGEDLREATHDEAVKALKRAGKLVELEVKYLREVTP 264
+A + +I +V D A++AL + EV+ +
Sbjct: 331 LAEAGINVDLITQSISEVSISFTVPESDA-----PRALRALLEEKLELLAEVEVEEGL-- 383
Query: 265 YFRKASIISEVGW 277
+++S VG
Sbjct: 384 -----ALVSIVGA 391
>gnl|CDD|220913 pfam10949, DUF2777, Protein of unknown function (DUF2777). This
family of proteins with unknown function appears to be
restricted to Bacillus cereus.
Length = 184
Score = 29.2 bits (66), Expect = 5.7
Identities = 10/54 (18%), Positives = 16/54 (29%), Gaps = 3/54 (5%)
Query: 576 GFRLLEATAGSMGREPKILWTYPFERLRMSSDDGVKLLWLDF--GSDLSLQDKI 627
+ G R K L + L +D L +L S+ D +
Sbjct: 71 AGEQIPLRGGESIRYEKSL-LFSLLELLDELEDSAFLQFLSQLNSLGFSVYDCV 123
>gnl|CDD|241448 cd13294, PH_ORP_plant, Plant Oxysterol binding protein related
protein Pleckstrin homology (PH) domain. Plant ORPs
contain a N-terminal PH domain and a C-terminal
OSBP-related domain. Not much is known about its
specific function in plants to date. Members here
include: Arabidopsis, spruce, and petunia. Oxysterol
binding proteins are a multigene family that is
conserved in yeast, flies, worms, mammals and plants. In
general OSBPs and ORPs have been found to be involved in
the transport and metabolism of cholesterol and related
lipids in eukaryotes. They all contain a C-terminal
oxysterol binding domain, and most contain an N-terminal
PH domain. OSBP PH domains bind to membrane
phosphoinositides and thus likely play an important role
in intracellular targeting. They are members of the
oxysterol binding protein (OSBP) family which includes
OSBP, OSBP-related proteins (ORP), Goodpasture antigen
binding protein (GPBP), and Four phosphate adaptor
protein 1 (FAPP1). They have a wide range of purported
functions including sterol transport, cell cycle
control, pollen development and vessicle transport from
Golgi recognize both PI lipids and ARF proteins. 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 = 100
Score = 28.2 bits (63), Expect = 5.8
Identities = 21/48 (43%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 501 VSSSRHS--DVIVFSVRCGTPQGVATHHLRAETHRDLANWARTLVQAT 546
VSS R S D F + GT T HLRAE+ D A W L QA
Sbjct: 48 VSSIRESRSDDKKFYIFTGT----KTLHLRAESREDRAAWLEAL-QAA 90
>gnl|CDD|132240 TIGR03196, pucD, xanthine dehydrogenase D subunit. This gene has
been characterized in B. subtilis as the molybdopterin
binding-subunit of xanthine dehydrogenase (pucD), acting
in conjunction with pucC, the FAD-binding subunit and
pucE, the FeS-binding subunit. The more common XDH
complex (GenProp0640) includes the xdhB gene which is
related to pucD. It appears that most of the relatives
of pucD outside of this narrow clade are involved in
other processes as they are found in unrelated genomic
contexts, contain the more common XDH complex and/or do
not appear to process purines to allantoin.
Length = 768
Score = 29.6 bits (66), Expect = 7.9
Identities = 21/100 (21%), Positives = 32/100 (32%), Gaps = 15/100 (15%)
Query: 215 QTEQLYVGDAILSVNGEDLREATHDEAVKALKRAGKLVELEVKYLREVTPYFR----KAS 270
E Y GDAI +V ED A + A +E++ + L + + A
Sbjct: 88 ADEIRYAGDAIAAVAAEDEEIA---------EAALAAIEVDYEELAPMDDPDKALQPDAE 138
Query: 271 IISEVGWELQRGFLSDSPPSPSPQSSQRA--DTRYLPLQL 308
+ E G L P + D L +Q
Sbjct: 139 PLHEAGNILHEAEFRHGDPDEGFAAGDTVFEDQYELGMQD 178
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
0.316 0.133 0.392
Gapped
Lambda K H
0.267 0.0618 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,960,163
Number of extensions: 3794875
Number of successful extensions: 3476
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3469
Number of HSP's successfully gapped: 46
Length of query: 774
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 670
Effective length of database: 6,324,786
Effective search space: 4237606620
Effective search space used: 4237606620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 63 (28.3 bits)