RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11003
(96 letters)
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 40.6 bits (96), Expect = 3e-06
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 44 KRFRKLDLDNSGALSIDEFM----SLPELQQNPLVQRVIDIFDEDGNGEVDFK 92
+ FR D D G +S DE SL E + +I D+DG+G++DF+
Sbjct: 4 EAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFE 56
Score = 24.0 bits (53), Expect = 6.5
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 13/46 (28%)
Query: 33 KIDADEIRRLGKR-------------FRKLDLDNSGALSIDEFMSL 65
I ADE++ K R++D D G + +EF+ L
Sbjct: 16 TISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLEL 61
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 36.9 bits (86), Expect = 4e-04
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 32 NKIDADEIRRLGKRFRKLDLDNSGALSIDEFMSLP-ELQQNP---LVQRVIDIFDEDGNG 87
++ ++I+ L + F+ D D+ G + +E + L NP + ++ + D GN
Sbjct: 12 TQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEID-AGNE 70
Query: 88 EVDFK 92
VDF
Sbjct: 71 TVDFP 75
Score = 30.0 bits (68), Expect = 0.099
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 46 FRKLDLDNSGALSIDE-FMSLPELQQNPLVQRV---IDIFDEDGNGEVDFK 92
F+ D D+ G +SI E L L + + V + +DEDG+GE+D++
Sbjct: 98 FKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYE 148
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 30.8 bits (70), Expect = 0.017
Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 47 RKLDLDNSGALSIDEFMSL--------PELQQNPLVQRVIDIFDEDGNGEVDFK 92
+ LD D G + ++E L + + L++ + D+DG+G + F+
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFE 54
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 28.6 bits (65), Expect = 0.12
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 33 KIDADEIRRLGKRFRKLDLDNSGALSIDEFMSL 65
+ +E+ L FR+ D D G +S +EF L
Sbjct: 20 SLSEEEVDIL---FREFDTDGDGKISFEEFCVL 49
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 26.9 bits (61), Expect = 0.25
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 44 KRFRKLDLDNSGALSIDEFMSL 65
FR+ D + G +S +E L
Sbjct: 3 DLFRQFDTNGDGKISKEELKRL 24
>gnl|CDD|182323 PRK10236, PRK10236, hypothetical protein; Provisional.
Length = 237
Score = 28.4 bits (63), Expect = 0.44
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 36 ADEIRRLGKRFRKLDLDNSGALSI--DEFMSLPELQQNPLVQ 75
A+++R GK +R + LD S L + D+ MS E++Q L Q
Sbjct: 79 ANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQ 120
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 26.3 bits (59), Expect = 0.57
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 46 FRKLDLDNSGALSIDEFMSL 65
F++ D D G +S +EF L
Sbjct: 6 FKEFDKDGDGKISFEEFKEL 25
Score = 24.3 bits (54), Expect = 2.7
Identities = 6/19 (31%), Positives = 13/19 (68%)
Query: 74 VQRVIDIFDEDGNGEVDFK 92
++ FD+DG+G++ F+
Sbjct: 2 LKEAFKEFDKDGDGKISFE 20
>gnl|CDD|173961 cd08551, Fe-ADH, iron-containing alcohol dehydrogenases
(Fe-ADH)-like. Large metal-containing alcohol
dehydrogenases (ADH), known as iron-containing alcohol
dehydrogenases. They contain a dehydroquinate
synthase-like protein structural fold and mostly
contain iron. They are distinct from other alcohol
dehydrogenases which contains different protein
domains. There are several distinct families of alcohol
dehydrogenases: Zinc-containing long-chain alcohol
dehydrogenases; insect-type, or short-chain alcohol
dehydrogenases; iron-containing alcohol dehydrogenases,
and others. The iron-containing family has a Rossmann
fold-like topology that resembles the fold of the
zinc-dependent alcohol dehydrogenases, but lacks
sequence homology, and differs in strand arrangement.
ADH catalyzes the reversible oxidation of alcohol to
acetaldehyde with the simultaneous reduction of NAD(P)+
to NAD(P)H.
Length = 370
Score = 27.6 bits (62), Expect = 1.0
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 14/64 (21%)
Query: 30 SLNKIDADEIRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNPLVQRVIDIFDEDGNGEV 89
++ K+ +EI+ LG R AL ++ P L + ++ +VID E G V
Sbjct: 10 AIEKL-GEEIKNLGGRK---------AL----IVTDPGLVKTGVLDKVIDSLKEAGIEVV 55
Query: 90 DFKG 93
F G
Sbjct: 56 IFDG 59
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 25.2 bits (56), Expect = 1.2
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 41 RLGKRFRKLDLDNSGALSIDEFMSL 65
L + F+ D D G +S +E
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKA 25
>gnl|CDD|197382 cd10016, EcoRII_N, N-terminal domain of type IIE restriction
endonuclease EcoRII and similar proteins. N-terminal
domain of type IIE restriction endonuclease EcoRII and
similar proteins. Type II restriction endonucleases are
components of restriction modification (RM) systems that
protect bacteria and archaea against invading foreign
DNA. They usually function as homodimers or
homotetramers that cleave DNA at defined sites of 4 to 8
bp in length, and they require Mg2+, not ATP or GTP,
for catalysis. EcoRII is specific for the 5'-CCWGG
sequence (W stands for A or T). EcoRII consists of 2
domains, the C-terminal catalytic/dimerization domain
(EcoRII-C), and the N-terminal effector DNA binding
domain (EcoRII-N). To be catalytically active, EcoRII
has to form a dimer.
Length = 142
Score = 27.0 bits (60), Expect = 1.3
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 39 IRRLGKRFRKLDLDNSGALSI 59
I R GK F LD DN+GAL +
Sbjct: 83 ITRFGKGFPFLDPDNTGALLV 103
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 25.0 bits (56), Expect = 1.5
Identities = 7/19 (36%), Positives = 15/19 (78%)
Query: 74 VQRVIDIFDEDGNGEVDFK 92
++ +FD+DG+G++DF+
Sbjct: 2 LKEAFRLFDKDGDGKIDFE 20
Score = 23.9 bits (53), Expect = 4.5
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 46 FRKLDLDNSGALSIDEFMSL 65
FR D D G + +EF L
Sbjct: 6 FRLFDKDGDGKIDFEEFKDL 25
>gnl|CDD|240154 cd05027, S-100B, S-100B: S-100B domain found in proteins similar
to S100B. S100B is a calcium-binding protein belonging
to a large S100 vertebrate-specific protein family
within the EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100B group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately.
S100B is most abundant in glial cells of the central
nervous system, predominately in astrocytes. S100B is
involved in signal transduction via the inhibition of
protein phoshorylation, regulation of enzyme activity
and by affecting the calcium homeostasis. Upon calcium
binding the S100B homodimer changes conformation to
expose a hydrophobic cleft, which represents the
interaction site of S100B with its more than 20 known
target proteins. These target proteins include several
cellular architecture proteins such as tubulin and
GFAP; S100B can inhibit polymerization of these
oligomeric molecules. Furthermore, S100B inhibits the
phosphorylation of multiple kinase substrates including
the Alzheimer protein tau and neuromodulin (GAP-43)
through a calcium-sensitive interaction with the
protein substrates.
Length = 88
Score = 26.0 bits (57), Expect = 1.7
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 65 LPELQQNPLVQRVIDIFDEDGNGEVDFK 92
L E+++ +V +V++ D DG+GE DF+
Sbjct: 44 LEEIKEQEVVDKVMETLDSDGDGECDFQ 71
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 26.4 bits (58), Expect = 2.5
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 32 NKIDADEIRRLGKRFRKLDLDNSGALSIDEFMSLPELQQ 70
N + A++ L F+ DL+ G ++IDE +L LQQ
Sbjct: 210 NLVAANKKEEL---FKAADLNGDGVVTIDELAALLALQQ 245
>gnl|CDD|219141 pfam06697, DUF1191, Protein of unknown function (DUF1191). This
family contains hypothetical plant proteins of unknown
function.
Length = 278
Score = 26.3 bits (58), Expect = 3.0
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 30 SLNKIDADEIRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNPLVQRVIDIFDEDGN 86
+L+ I A +R R L G EF P L P +RV+ + GN
Sbjct: 42 NLSGIAASAVR-----LRSGSLRRYGVRKFGEFAIPPGLVVEPYAERVVLVRQNLGN 93
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 25.9 bits (57), Expect = 3.2
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 32 NKIDADEIRRLGKRFRKLDLDNSGALSIDEF-MSLPELQQNPL---VQRVIDIFDEDGNG 87
+++ ++I + F D D G ++ E + L QNP +Q +I+ D DGNG
Sbjct: 3 DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG 62
Query: 88 EVDFK 92
+DF
Sbjct: 63 TIDFP 67
>gnl|CDD|204173 pfam09231, RDV-p3, Rice dwarf virus p3. Members of this family are
core structural proteins found in the double-stranded
RNA virus Phytoreovirus. They are large proteins without
apparent domain division, with a number of all-alpha
regions and one all beta domain near the C-terminal end.
Length = 967
Score = 26.1 bits (57), Expect = 3.5
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 21 IKPSTELNLSLNKI-----DADEIRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNPLVQ 75
I ++ LN + K D + L + ++DL++S L EF L E+ N V+
Sbjct: 747 ILAASSLNENQIKTTHIIADFEAANALRLQQERVDLNSSHDLFEAEFNGLREIASNEFVR 806
Query: 76 RVIDIFDEDGNGEVDF 91
E G GE F
Sbjct: 807 SN-----ERGEGEPHF 817
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 25.8 bits (57), Expect = 3.8
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 34 IDADEIRRLGKRFRKLDLDNSGALSIDEF----MSLPELQQNPLVQRVIDIFDEDGNGEV 89
+ D+ + + + F D D SG + E SL + ++++I D+DG+G++
Sbjct: 11 LTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKI 70
Query: 90 DF 91
DF
Sbjct: 71 DF 72
>gnl|CDD|176023 cd08377, C2C_MCTP_PRT, C2 domain third repeat found in Multiple
C2 domain and Transmembrane region Proteins (MCTP).
MCTPs are involved in Ca2+ signaling at the membrane.
The cds in this family contain multiple C2 domains as
well as a C-terminal PRT domain. It is one of four
protein classes that are anchored to membranes via a
transmembrane region; the others being synaptotagmins,
extended synaptotagmins, and ferlins. MCTPs are the
only membrane-bound C2 domain proteins that contain two
functional TMRs. MCTPs are unique in that they bind
Ca2+ but not phospholipids. C2 domains fold into an
8-standed beta-sandwich that can adopt 2 structural
arrangements: Type I and Type II, distinguished by a
circular permutation involving their N- and C-terminal
beta strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of
piccolo/aczonin and intersectin which only have a
single C2 domain. C2 domains with a calcium binding
region have negatively charged residues, primarily
aspartates, that serve as ligands for calcium ions.
This cd contains the third C2 repeat, C2C, and has a
type-II topology.
Length = 119
Score = 25.3 bits (56), Expect = 4.2
Identities = 6/18 (33%), Positives = 13/18 (72%)
Query: 78 IDIFDEDGNGEVDFKGKL 95
+ ++DED + + +F GK+
Sbjct: 65 VTVYDEDKDKKPEFLGKV 82
>gnl|CDD|131034 TIGR01979, sufS, cysteine desulfurases, SufSfamily. This model
represents a subfamily of NifS-related cysteine
desulfurases involved in FeS cluster formation needed
for nitrogen fixation among other vital functions. Many
cysteine desulfurases are also active as selenocysteine
lyase and/or cysteine sulfinate desulfinase. This
subfamily is associated with the six-gene SUF system
described in E. coli and Erwinia as an FeS cluster
formation system during oxidative stress. The active
site Cys is this subfamily resembles GHHC with one or
both His conserved [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 403
Score = 25.7 bits (57), Expect = 4.6
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 40 RRLGKRFRKLDLDNSGALSIDEFMSL 65
R G + + LD+ G L +D+ L
Sbjct: 130 ERTGATLKFIPLDDDGTLDLDDLEKL 155
>gnl|CDD|202832 pfam03960, ArsC, ArsC family. This family is related to
glutaredoxins pfam00462.
Length = 109
Score = 24.9 bits (55), Expect = 5.4
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 39 IRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNP-LVQRVIDIFDEDG 85
+ G +R+L+LD LS DE + L + +NP L++R I + D
Sbjct: 53 LNTRGTTYRELNLDVE-ELSEDELIEL--MLENPSLIRRPI-VVDGKR 96
>gnl|CDD|240156 cd05030, calgranulins, Calgranulins: S-100 domain found in
proteins belonging to the Calgranulin subgroup of the
S100 family of EF-hand calcium-modulated proteins,
including S100A8, S100A9, and S100A12 . Note that the
S-100 hierarchy, to which this Calgranulin group
belongs, contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. These proteins
are expressed mainly in granulocytes, and are involved
in inflammation, allergy, and neuritogenesis, as well
as in host-parasite response. Calgranulins are
modulated not only by calcium, but also by other metals
such as zinc and copper. Structural data suggested that
calgranulins may exist in multiple structural forms,
homodimers, as well as hetero-oligomers. For example,
the S100A8/S100A9 complex called calprotectin plays
important roles in the regulation of inflammatory
processes, wound repair, and regulating zinc-dependent
enzymes as well as microbial growth.
Length = 88
Score = 24.6 bits (54), Expect = 5.6
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 32 NKIDADEIRRLGKRFRKLDLDNSGALSIDEFMSL 65
N+ D+I F LD + G LS +EF+ L
Sbjct: 49 NQKAIDKI------FEDLDTNQDGQLSFEEFLVL 76
>gnl|CDD|173415 PTZ00124, PTZ00124, adenosine deaminase; Provisional.
Length = 362
Score = 25.2 bits (55), Expect = 6.3
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 23 PSTELNLSLNKIDADEIRRLGKRFRKLDLDNSG--ALSIDEFMSLP---ELQQNPLVQRV 77
ELN+ L+++D E ++ KR K +L S+D F+S LQ N + +
Sbjct: 12 KKDELNIDLSQMDKKERYKIWKRIPKCELHCHLDLCFSVDFFLSCIRKYNLQPNLSDEEI 71
Query: 78 ID--IFDEDGNGEVDFKGK 94
+D +F + G +F K
Sbjct: 72 LDYYLFAKGGKSLGEFVEK 90
>gnl|CDD|233798 TIGR02244, HAD-IG-Ncltidse, HAD superfamily (subfamily IG)
hydrolase, 5'-nucleotidase. This model includes a
5'-nucleotidase specific for purines (IMP and GMP).
These enzymes are members of the Haloacid Dehalogenase
(HAD) superfamily. HAD members are recognized by three
short motifs {hhhhDxDx(T/V)}, {hhhh(T/S)}, and either
{hhhh(D/E)(D/E)x(3-4)(G/N)} or
{hhhh(G/N)(D/E)x(3-4)(D/E)} (where "h" stands for a
hydrophobic residue). Crystal structures of many HAD
enzymes has verified PSI-PRED predictions of secondary
structural elements which show each of the "hhhh"
sequences of the motifs as part of beta sheets. This
subfamily of enzymes is part of "Subfamily I" of the HAD
superfamily by virtue of a "cap" domain in between
motifs 1 and 2. This subfamily's cap domain has a
different predicted secondary structure than all other
known HAD enzymes and thus has been designated
"subfamily IG". This domain appears to consist of a
mixed alpha/beta fold. A Pfam model (pfam05761) detects
an identical range of sequences above the trusted
cutoff, but does not model the N-terminal motif 1
region. A TIGRFAMs model (TIGR01993) represents a
(putative) family of _pyrimidine_ 5'-nucleotidases which
are also subfamily I HAD's, which should not be confused
with the current model.
Length = 343
Score = 25.4 bits (56), Expect = 6.3
Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 31 LNKIDADEIRRLGKRFRKLDLDNSGALS-IDEFMSLPELQQNPLVQRVIDIFDEDGNGEV 89
L + E++ + + + N +D SLPE L+ +++D FD+ G +
Sbjct: 92 LRPLSDKEVQEIYGN-KYISRSNGDRYYLLDTLFSLPEAC---LIAQLVDYFDDHPKGPL 147
Query: 90 DF 91
F
Sbjct: 148 AF 149
>gnl|CDD|218059 pfam04391, DUF533, Protein of unknown function (DUF533). Some
family members may be secreted or integral membrane
proteins.
Length = 187
Score = 24.9 bits (55), Expect = 6.4
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 34 IDADEIRRLGKRFRKLDLDNSGALSIDEFMSLP 66
ID +E R+ + +L LD +++ + P
Sbjct: 95 IDEEERARIEQELGELGLDAEERAWLEQELRAP 127
>gnl|CDD|131310 TIGR02257, cobalto_cobN, cobaltochelatase, CobN subunit.
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 1122
Score = 25.1 bits (55), Expect = 7.3
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 22 KPSTELNLSLNKIDADEIRRLGKRFRKLDLDNSGAL 57
P ELN L+ + D RL K R+ +N G
Sbjct: 119 DPDLELN-ELSTVPLDLSDRLWKYLREGGPENMGRF 153
>gnl|CDD|234575 PRK00016, PRK00016, metal-binding heat shock protein;
Provisional.
Length = 159
Score = 24.8 bits (55), Expect = 7.3
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 20 SIKPSTELNLSLNKIDADEIRRLGKRFRKLD 50
++P EL++ L +D +EIR L +R D
Sbjct: 33 GVQPEAELSIRL--VDNEEIRELNLEYRGKD 61
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 24.9 bits (55), Expect = 7.7
Identities = 23/99 (23%), Positives = 38/99 (38%), Gaps = 14/99 (14%)
Query: 6 YIHEVSNDIKNDWSSIKPSTELNLSLNKI--DADEIRRLGKRFRKL-------DLDNSGA 56
Y +++ D++ D E + DE L ++F L LD G
Sbjct: 198 YYVKIAKDLEED---PGNDEEEAREEVEKLESGDEEAELWRKFVDLSLEGIKETLDRLG- 253
Query: 57 LSIDEFMSLPELQQNPLVQRVIDIFDEDGNGEVDFKGKL 95
+ D + S E N V++V++ +E G D G L
Sbjct: 254 VKFDVYDSEGESFYNGKVEKVVEDLEEKGLLYED-DGAL 291
>gnl|CDD|221489 pfam12252, SidE, Dot/Icm substrate protein. This family of
proteins is found in bacteria. Proteins in this family
are typically between 397 and 1543 amino acids in
length. This family is the SidE protein in the Dot/Icm
pathway of Legionella pneumophila bacteria. There is
little literature describing the family.
Length = 1443
Score = 25.2 bits (55), Expect = 7.8
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 52 DNSGALSIDEFMSLPELQQ 70
+N + +DEF+ LPE+Q
Sbjct: 509 ENERFMRVDEFLKLPEVQS 527
>gnl|CDD|238131 cd00213, S-100, S-100: S-100 domain, which represents the largest
family within the superfamily of proteins carrying the
Ca-binding EF-hand motif. Note that this S-100
hierarchy contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100 proteins
are expressed exclusively in vertebrates, and are
implicated in intracellular and extracellular
regulatory activities. Intracellularly, S100 proteins
act as Ca-signaling or Ca-buffering proteins. The most
unusual characteristic of certain S100 proteins is
their occurrence in extracellular space, where they act
in a cytokine-like manner through RAGE, the receptor
for advanced glycation products. Structural data
suggest that many S100 members exist within cells as
homo- or heterodimers and even oligomers;
oligomerization contributes to their functional
diversification. Upon binding calcium, most S100
proteins change conformation to a more open structure
exposing a hydrophobic cleft. This hydrophobic surface
represents the interaction site of S100 proteins with
their target proteins. There is experimental evidence
showing that many S100 proteins have multiple binding
partners with diverse mode of interaction with
different targets. In addition to S100 proteins (such
as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group
includes the ''fused'' gene family, a group of calcium
binding S100-related proteins. The ''fused'' gene
family includes multifunctional epidermal
differentiation proteins - profilaggrin, trichohyalin,
repetin, hornerin, and cornulin; functionally these
proteins are associated with keratin intermediate
filaments and partially crosslinked to the cell
envelope. These ''fused'' gene proteins contain
N-terminal sequence with two Ca-binding EF-hands motif,
which may be associated with calcium signaling in
epidermal cells and autoprocessing in a
calcium-dependent manner. In contrast to S100 proteins,
"fused" gene family proteins contain an extraordinary
high number of almost perfect peptide repeats with
regular array of polar and charged residues similar to
many known cell envelope proteins.
Length = 88
Score = 24.4 bits (54), Expect = 7.9
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 42 LGKRFRKLDLDNSGALSIDEFMSL 65
+ K + LD++ G + EF+ L
Sbjct: 53 VDKIMKDLDVNKDGKVDFQEFLVL 76
>gnl|CDD|239275 cd02977, ArsC_family, Arsenate Reductase (ArsC) family; composed of
TRX-fold arsenic reductases and similar proteins
including the transcriptional regulator, Spx. ArsC
catalyzes the reduction of arsenate [As(V)] to arsenite
[As(III)], using reducing equivalents derived from
glutathione (GSH) via glutaredoxin (GRX), through a
single catalytic cysteine. This family of predominantly
bacterial enzymes is unrelated to two other families of
arsenate reductases which show similarity to
low-molecular-weight acid phosphatases and
phosphotyrosyl phosphatases. Spx is a general regulator
that exerts negative and positive control over
transcription initiation by binding to the C-terminal
domain of the alpha subunit of RNA polymerase.
Length = 105
Score = 24.4 bits (54), Expect = 8.7
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 39 IRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNP-LVQRVIDIFDEDG 85
G +RKL L + LS +E + L + ++P L++R I + D D
Sbjct: 56 FNTRGTPYRKLGLADKDELSDEEALEL--MAEHPKLIKRPI-VVDGDR 100
>gnl|CDD|215346 PLN02643, PLN02643, ADP-glucose phosphorylase.
Length = 336
Score = 24.7 bits (54), Expect = 9.4
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 66 PELQQNPLVQRVIDIFDEDGNGEVDFKGK 94
EL+++P+ R + G DFK K
Sbjct: 2 AELRKDPVTNRWVIFSPARGKRPTDFKSK 30
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA
polymerase I (RNAP I), C-terminal domain. RNA
polymerase I (RNAP I) is a multi-subunit protein
complex responsible for the synthesis of rRNA
precursor. It consists of at least 14 different
subunits, and the largest one is homologous to subunit
Rpb1 of yeast RNAP II and subunit beta' of bacterial
RNAP. Rpa1 is also known as Rpa190 in yeast. Structure
studies suggest that different RNAP complexes share a
similar crab-claw-shape structure. The C-terminal
domain of Rpb1, the largest subunit of RNAP II, makes
up part of the foot and jaw structures of RNAP II. The
similarity between this domain and the C-terminal
domain of Rpb1, its counterpart in RNAP II, suggests a
similar functional and structural role.
Length = 309
Score = 24.5 bits (54), Expect = 9.7
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 11 SNDIKNDWSSIKPSTELNLSLNKIDADEIRRLGKRFRKLDL 51
S +IK PS L L N A+ L KR ++ L
Sbjct: 58 SKNIKT------PSMTLPL-KNGKSAERAETLKKRLSRVTL 91
>gnl|CDD|131168 TIGR02113, coaC_strep, phosphopantothenoylcysteine decarboxylase,
streptococcal. In most bacteria, a single bifunctional
protein catalyses phosphopantothenoylcysteine
decarboxylase and phosphopantothenate--cysteine ligase
activities, sequential steps in coenzyme A biosynthesis
(see TIGR00521). These activities reside in separate
proteins encoded by tandem genes in some bacterial
lineages. This model describes proteins from the genera
Streptococcus and Enterococcus homologous to the
N-terminal region of TIGR00521, corresponding to
phosphopantothenoylcysteine decarboxylase activity
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 177
Score = 24.4 bits (53), Expect = 10.0
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 70 QNPLVQRVIDIFDEDGNGEVDFKGKLL 96
QNP+ QR I I + G E+ K LL
Sbjct: 127 QNPITQRNIKILKKIGYQEIQPKESLL 153
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
0.317 0.138 0.390
Gapped
Lambda K H
0.267 0.0908 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,123,185
Number of extensions: 447474
Number of successful extensions: 593
Number of sequences better than 10.0: 1
Number of HSP's gapped: 585
Number of HSP's successfully gapped: 61
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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: 53 (23.9 bits)