RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4132
(473 letters)
>gnl|CDD|241380 cd13226, PH-like_Eap45_GLUE, Eap45 GLUE (GRAM-like
ubiquitin-binding in Eap45) Pleckstrin homology-like
domain. ESCRT complexes form the main machinery driving
protein sorting from endosomes to lysosomes. Human/yeast
ESCRT-I consists of Tsg101/Vps23, Vps28/Vps28, and a
Vps37 homolog/Vps37. Human/yeast ESCRT-II is composed of
EAP20/Vps25, EAP30/Vps22, and EAP45/Vps36. Yeast
ESCRT-III consists Vps2, Vps20, Vps24, and Snf7
subunits. In contrast, there are three Human paralogs of
Snf7 (hSnf7-1/CHMP4A, hSnf7-2/CHMP4B, and
hSnf7-3/CHMP4C) and two paralogs of Vps2 (CHMP2A and
CHMP2B). Yeast ESCRT-I links directly to ESCRT-II,
through a tight interaction of Vps28 (ESCRT-I) with the
yeast-specific zinc-finger insertion within the GLUE
domain of Vps36. The Vps36 subunit (ESCRT-II) binds
ubiquitin using one of its two NZF zinc fingers in its
N-terminal region. Human Vps36, EAP45, also binds
ubiquitin despite having no NZF domain. Instead,
mammalian ESCRT-II interacts with Ub through the Eap45
GLUE domain directly. While yeast Vps36 GLUE shows a
preference for the singly phosphorylated PI(3)P, while
Eap45 GLUE preferentially binds the triply
phosphorylated phosphatidylinositol PI(3,4,5)P3.
Structurally, Eap45 GLUE only has a PH-like fold since
it lacks the secondary structure element corresponding
to the 4 strand, unlike that of yeast Vps36 GLUE.
ESCRT-II also interacts with ESCRT-III via a
EAP20(Vps25)/CHMP6(Vps20) interaction. The interactions
of ESCRT-II GLUE domain with membranes, ESCRT-I, and
ubiquitin are critical for ubiquitinated cargo
progression from early to late endosomes. 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 = 128
Score = 137 bits (346), Expect = 6e-39
Identities = 58/128 (45%), Positives = 80/128 (62%), Gaps = 5/128 (3%)
Query: 1 MDRFEYCSFELSPDESPVLKHSNVRLYDGENKSQFQRGELILTSHRLFW--QKDITLCLA 58
MDRF + + L P+E+ V++ VR+YDG+ K+ F GEL+LTSHRL W QK+I CL+
Sbjct: 1 MDRFMWTNGLLEPNETLVIQQRGVRIYDGDEKTNFDSGELVLTSHRLIWRDQKNIERCLS 60
Query: 59 LSYIQNA-VEEAKSMFNLTAGRKIILYLSKAVPGKNLGPSATSAYDYVKLSFREGIQNEF 117
L Q +EE + F +A KI+L+L A P K GP +S Y Y+KLSF+EG Q+EF
Sbjct: 61 LPLSQIVFIEEEAAGFGKSA--KIVLHLHPAPPNKEPGPVQSSPYSYIKLSFKEGGQSEF 118
Query: 118 LDALKSTV 125
L +
Sbjct: 119 YRRLSEEL 126
>gnl|CDD|217934 pfam04157, EAP30, EAP30/Vps36 family. This family includes EAP30
as well as the Vps36 protein. Vps36 is involved in Golgi
to endosome trafficking. EAP30 is a subunit of the ELL
complex. The ELL is an 80-kDa RNA polymerase II
transcription factor. ELL interacts with three other
proteins to form the complex known as ELL complex. The
ELL complex is capable of increasing that catalytic rate
of transcription elongation, but is unable to repress
initiation of transcription by RNA polymerase II as is
the case of ELL. EAP30 is thought to lead to the
derepression of ELL's transcriptional inhibitory
activity.
Length = 219
Score = 111 bits (280), Expect = 2e-28
Identities = 47/136 (34%), Positives = 63/136 (46%), Gaps = 3/136 (2%)
Query: 322 NDDDYYQALGNELIAALIEPLTSAGGTMLLTDAYCRINRAR-GLELLSPEDLLNSCLALD 380
D+Y L +++ + L GG + L D Y NRAR G EL+SPEDLL +C L+
Sbjct: 85 GVGDFYYELAVQIVEICLATLKENGGIISLQDLYALYNRARGGTELVSPEDLLKACKKLE 144
Query: 381 KLPDSPIYLKTYSSGVKVLQLKS-CEDASFVEKTYEIVSQNVFVTVEQFSRLASVSLVIA 439
KL L SGV V+Q E + K E+ + VT + + S+ A
Sbjct: 145 KL-GLGFKLVKIGSGVLVVQSVPKSELSEDQTKILELAEELGGVTASELAEKLGWSIGRA 203
Query: 440 KHRLLLAETHGKLCRD 455
K L AE G L RD
Sbjct: 204 KEVLEKAEKEGLLWRD 219
Score = 60.7 bits (148), Expect = 1e-10
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 150 GIVGIERNIVEKQKETSSNINNAFKDLNQLMSMAKEMVEISKNISNKIINRQGEITEDDS 209
GI GIER+ E++K + AF+DL LM AK+ VE+ ++ + K + E +
Sbjct: 2 GIAGIERSREEQRKYNDLGLQLAFEDLEALMKQAKDFVELLESFAKKHKSEIKANPEFRA 61
Query: 210 NKDRDGKINFQEFCSIVG 227
FQ C+ +G
Sbjct: 62 --------QFQSMCASLG 71
>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 = 69.3 bits (170), Expect = 5e-14
Identities = 27/90 (30%), Positives = 48/90 (53%), Gaps = 5/90 (5%)
Query: 238 DIRRLGKRFRKLDLDNSGALSIDEFMSLP-ELQQNP---LVQRVIDIFDEDRNGEVDFKE 293
I+ L + F+ D D+ G + +E + L NP + ++ + D N VDF E
Sbjct: 18 QIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDAG-NETVDFPE 76
Query: 294 FIQGVSQFSVKGDRESKLKFAFRIYDIDND 323
F+ +S +GD+E +L+ AF+++D D+D
Sbjct: 77 FLTVMSVKLKRGDKEEELREAFKLFDKDHD 106
Score = 47.3 bits (113), Expect = 2e-06
Identities = 31/129 (24%), Positives = 57/129 (44%), Gaps = 15/129 (11%)
Query: 175 DLNQLMSMAKEMVEISKNISNKIINRQGEITEDDSNKDRDGKINFQEFCSIVGNTDIHKK 234
D N+L + + + N S IN+ E D+ ++F EF +++
Sbjct: 38 DRNELGKI---LRSLGFNPSEAEINKL--FEEIDAGN---ETVDFPEFLTVMSVKLKRGD 89
Query: 235 MVVDIRRLGKRFRKLDLDNSGALSIDE-FMSLPELQQNPLVQRV---IDIFDEDRNGEVD 290
++R F+ D D+ G +SI E L L + + V + +DED +GE+D
Sbjct: 90 KEEELREA---FKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEID 146
Query: 291 FKEFIQGVS 299
++EF + +
Sbjct: 147 YEEFKKLIK 155
>gnl|CDD|221148 pfam11605, Vps36_ESCRT-II, Vacuolar protein sorting protein 36
Vps36. Vps36 is a subunit of ESCRT-II, a protein
involved in driving protein sorting from endosomes to
lysosomes. The GLUE domain of Vps36 allows for a tight
interaction to occur between the protein and Vps28, a
subunit of ESCRT-I. This interaction is critical for
ubiquitinated cargo progression from early to late
endosomes.
Length = 93
Score = 59.7 bits (145), Expect = 3e-11
Identities = 30/93 (32%), Positives = 45/93 (48%), Gaps = 9/93 (9%)
Query: 3 RFEYCSFELSPDESPVLKHSNVRLYDGENKS-QFQRGELILTSHRLFWQKD-------IT 54
R L +E + NV LYDG+ K+ Q G L LT+HRL + ++
Sbjct: 2 RTTSGRPVLRENEVDIYVQDNVGLYDGDEKTLNRQNGRLYLTTHRLIYVDSADPKKVSLS 61
Query: 55 LCLALSYIQNAVEEAKSMFNLTAGRKIILYLSK 87
L L+L + ++ +E S F L + KIIL+L
Sbjct: 62 LPLSLVLVISSSKEYSSGF-LRSSPKIILFLKP 93
>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 = 52.9 bits (128), Expect = 2e-09
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 244 KRFRKLDLDNSGALSIDEFM----SLPELQQNPLVQRVIDIFDEDRNGEVDFKEFIQGVS 299
+ FR D D G +S DE SL E + +I D+D +G++DF+EF++ ++
Sbjct: 4 EAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELMA 63
Score = 35.2 bits (82), Expect = 0.004
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 274 VQRVIDIFDEDRNGEVDFKEFIQGVSQFSVKGDRESKLKFAFRIYDIDND 323
++ +FD+D +G + E + E ++ R D D D
Sbjct: 2 LREAFRLFDKDGDGTISADELKAALKSLGEGLSEE-EIDEMIREVDKDGD 50
Score = 28.7 bits (65), Expect = 0.90
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 211 KDRDGKINFQEFCSIV 226
KD DGKI+F+EF ++
Sbjct: 47 KDGDGKIDFEEFLELM 62
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 45.1 bits (107), Expect = 1e-05
Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 4/90 (4%)
Query: 238 DIRRLGKRFRKLDLDNSGALSIDEF-MSLPELQQNPL---VQRVIDIFDEDRNGEVDFKE 293
I + F D D G ++ E + L QNP +Q +I+ D D NG +DF E
Sbjct: 9 QIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPE 68
Query: 294 FIQGVSQFSVKGDRESKLKFAFRIYDIDND 323
F+ +++ D E ++K AF+++D D +
Sbjct: 69 FLTLMARKMKDTDSEEEIKEAFKVFDRDGN 98
Score = 28.2 bits (63), Expect = 5.4
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 161 KQKETSSNINNAFK----DLNQLMSMAKEMVEISKNISNKIINRQGEITEDDSNKDRDGK 216
K ++ I AFK D N +S A E+ + N+ K+ + + + +++ D DG+
Sbjct: 78 KDTDSEEEIKEAFKVFDRDGNGFIS-AAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQ 136
Query: 217 INFQEFCSIV 226
IN++EF ++
Sbjct: 137 INYEEFVKMM 146
>gnl|CDD|241381 cd13227, PH-like_Vps36_GLUE, Vps36 GLUE (GRAM-like
ubiquitin-binding in Eap45) Pleckstrin homology-like
domain. ESCRT complexes form the main machinery driving
protein sorting from endosomes to lysosomes. Yeast/human
ESCRT-I consists of Vps23/Tsg101, Vps28/Vps28, and
Vps37/Vps37 homolog. Yeast/human ESCRT-II is composed of
Vps25/EAP20, Vps22/EAP30, and Vps36/EAP45. Yeast
ESCRT-III consists Vps2, Vps20, Vps24, and Snf7
subunits. In contrast, there are three human paralogs of
Snf7 (hSnf7-1/CHMP4A, hSnf7-2/CHMP4B, and
hSnf7-3/CHMP4C) and two paralogs of Vps2 (CHMP2A and
CHMP2B). Yeast ESCRT-I links directly to ESCRT-II,
through a tight interaction of Vps28 (ESCRT-I) with the
yeast-specific zinc-finger insertion within the GLUE
domain of Vps36. The Vps36 subunit (ESCRT-II) binds
ubiquitin using one of its two NZF zinc fingers in its
N-terminal region. Human Vps36, EAP45, also binds
ubiquitin despite having no NZF domain. Instead,
mammalian ESCRT-II interacts with Ub through the Eap45
GLUE domain itself. The yeast Vps36 GLUE has a complete
PH domain, wherease Eap45 GLUE only has a PH-like fold
since it lacks the secondary structure element
corresponding to the 4 strand. ESCRT-II also interacts
with ESCRT-III via a Vps25(EAP20)/Vps20(CHMP6)
interaction. Structure 2CAY is missing this insertion
that contains 2 NZF zinc fingers. It is a split PH
domain, with a noncanonical lipid binding pocket that
binds PI(3)P. The interactions of ESCRT-II GLUE domain
with membranes, ESCRT-I, and ubiquitin are critical for
ubiquitinated cargo progression from early to late
endosomes. 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 = 126
Score = 42.7 bits (101), Expect = 4e-05
Identities = 31/105 (29%), Positives = 45/105 (42%), Gaps = 10/105 (9%)
Query: 11 LSPDESPVLKHSNVRLYDGENKS-QFQRGELILTSHRLFWQKDI-----TLCLALSYIQN 64
L +E + NV LY G++K Q G + LTS R+ + D ++ + L I +
Sbjct: 12 LRENEKDIYVDDNVGLYHGKSKILNRQNGRIYLTSQRIIYVDDEDPKKNSVAIELDDIDS 71
Query: 65 AVEEAKSMFNLTAGRKIILYLSKAVPGK-NLGPSATSAYDYVKLS 108
E S F L KIIL+L + K LG S+ S
Sbjct: 72 V--EYSSGF-LKRSPKIILFLKDEINSKSGLGQSSNKTGSQNVTS 113
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 40.4 bits (95), Expect = 6e-05
Identities = 13/60 (21%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 247 RKLDLDNSGALSIDEFMSL--------PELQQNPLVQRVIDIFDEDRNGEVDFKEFIQGV 298
+ LD D G + ++E L + + L++ + D+D +G + F+EF++ +
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
Score = 32.7 bits (75), Expect = 0.038
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 211 KDRDGKIN---FQEFCSIVGNTDIHKKMVVDIRRLGKRFRKLDLDNSGALSIDEFMSL 265
KD DG I+ ++ +G +++ I F ++D D G +S +EF+
Sbjct: 5 KDGDGYIDVEELRKLLKALGLKLTDEEVEELIEAD---FNEIDKDGDGRISFEEFLEA 59
Score = 27.7 bits (62), Expect = 1.9
Identities = 9/60 (15%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 279 DIFDEDRNGEV---DFKEFIQGVSQFSVKGDRESKLKFAFRIYDIDND-----DDYYQAL 330
+ D+D +G + + ++ ++ + + E ++ F D D D +++ +A+
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
Score = 26.2 bits (58), Expect = 7.5
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 211 KDRDGKINFQEFCSIV 226
KD DG+I+F+EF +
Sbjct: 45 KDGDGRISFEEFLEAM 60
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 36.6 bits (85), Expect = 0.009
Identities = 31/100 (31%), Positives = 47/100 (47%), Gaps = 23/100 (23%)
Query: 208 DSNKDRDGKINFQEFCSIVGNTDIHKKMVVDIRRLG--KRFRKLDLDNSGALS------- 258
D +KD GKI+F+EF I + KK+ R K FR D D +G +S
Sbjct: 61 DVDKDGSGKIDFEEFLDI-----MTKKLGERDPREEILKAFRLFDDDKTGKISLKNLKRV 115
Query: 259 ---IDEFMSLPELQQNPLVQRVIDIFDEDRNGEVDFKEFI 295
+ E ++ ELQ+ +ID D + +GE+ +EF
Sbjct: 116 AKELGETITDEELQE------MIDEADRNGDGEISEEEFY 149
Score = 32.4 bits (74), Expect = 0.27
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 246 FRKLDLDNSGALSIDEF----MSLPELQQNPLVQRVIDIFDEDRNGEVDFKEFIQGVSQF 301
F D D SG + E SL + ++++I D+D +G++DF+EF+ +++
Sbjct: 23 FDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKIDFEEFLDIMTKK 82
Query: 302 SVKGDRESKLKFAFRIYDIDN 322
+ D ++ AFR++D D
Sbjct: 83 LGERDPREEILKAFRLFDDDK 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 = 33.1 bits (77), Expect = 0.010
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 274 VQRVIDIFDEDRNGEVDFKEFIQGVSQF 301
++ +FD+D +G++DF+EF +
Sbjct: 2 LKEAFRLFDKDGDGKIDFEEFKDLLKAL 29
Score = 29.3 bits (67), Expect = 0.27
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 211 KDRDGKINFQEFCSIV 226
KD DGKI+F+EF ++
Sbjct: 11 KDGDGKIDFEEFKDLL 26
Score = 25.8 bits (58), Expect = 4.9
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 246 FRKLDLDNSGALSIDEFMSL 265
FR D D G + +EF L
Sbjct: 6 FRLFDKDGDGKIDFEEFKDL 25
>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 = 32.0 bits (74), Expect = 0.029
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 274 VQRVIDIFDEDRNGEVDFKEFIQGVSQF 301
++ FD+D +G++ F+EF + + +
Sbjct: 2 LKEAFKEFDKDGDGKISFEEFKELLKKL 29
Score = 28.2 bits (64), Expect = 0.61
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 246 FRKLDLDNSGALSIDEFMSL 265
F++ D D G +S +EF L
Sbjct: 6 FKEFDKDGDGKISFEEFKEL 25
Score = 27.8 bits (63), Expect = 0.87
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 211 KDRDGKINFQEFCSIV 226
KD DGKI+F+EF ++
Sbjct: 11 KDGDGKISFEEFKELL 26
>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 = 32.1 bits (74), Expect = 0.097
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 210 NKDRDGKINFQEFCSIVGN--TDIHKKM 235
+ ++DGK++FQEF ++G H+
Sbjct: 61 DVNKDGKVDFQEFLVLIGKLAVACHEFF 88
Score = 30.2 bits (69), Expect = 0.53
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 253 NSGALSIDEFMSL-----PELQQNPLVQRVIDIF----DEDRNGEVDFKEFI 295
+ LS E L P +N +D D +++G+VDF+EF+
Sbjct: 23 DKDTLSKKELKELLETELPNFLKNQKDPEAVDKIMKDLDVNKDGKVDFQEFL 74
>gnl|CDD|240152 cd05025, S-100A1, S-100A1: S-100A1 domain found in proteins similar
to S100A1. S100A1 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-100A1 group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately. As
is the case with many other members of S100 protein
family, S100A1 is implicated in intracellular and
extracellular regulatory activities, including
interaction with myosin-associated twitchin kinase,
actin-capping protein CapZ, sinapsin I, and tubulin.
Structural data suggests that S100A1 proteins exist
within cells as antiparallel homodimers, while
heterodimers with S100A4 and S100B also has been
reported. Upon binding calcium S100A1 changes
conformation to expose a hydrophobic cleft which is the
interaction site of S100A1 with its more that 20 known
target proteins.
Length = 92
Score = 31.8 bits (72), Expect = 0.18
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 265 LPELQQNPLVQRVIDIFDEDRNGEVDFKEFIQGVSQFSV 303
L + V +++ DE+ +GEVDF+EF+ V+ +V
Sbjct: 45 LDAQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTV 83
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 34.1 bits (78), Expect = 0.18
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 10/62 (16%)
Query: 212 DRDGKINFQEFCSIV---GNTDIHKKMVVDIRRLGKRFRKLDLDNSGALSIDEFMSLPEL 268
D DG+++F EF ++ GN +V + + F+ DL+ G ++IDE +L L
Sbjct: 191 DEDGQLSFSEFSDLIKAFGN-------LVAANKKEELFKAADLNGDGVVTIDELAALLAL 243
Query: 269 QQ 270
QQ
Sbjct: 244 QQ 245
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 29.2 bits (67), Expect = 0.29
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 244 KRFRKLDLDNSGALSIDEFMSL 265
FR+ D + G +S +E L
Sbjct: 3 DLFRQFDTNGDGKISKEELKRL 24
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 29.4 bits (67), Expect = 0.46
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 214 DGKINFQEFCSIVGNTDIHKKMVVDIRRLGKRFRKLDLDNSGALSIDEFMSL 265
G I +E + I ++ L FR+ D D G +S +EF L
Sbjct: 2 KGLITREELKRALALLGISLS-EEEVDIL---FREFDTDGDGKISFEEFCVL 49
Score = 28.2 bits (64), Expect = 0.97
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 274 VQRVIDIFDEDRNGEVDFKEFIQ 296
V + FD D +G++ F+EF
Sbjct: 26 VDILFREFDTDGDGKISFEEFCV 48
>gnl|CDD|238009 cd00052, EH, Eps15 homology domain; found in proteins implicated in
endocytosis, vesicle transport, and signal transduction.
The alignment contains a pair of EF-hand motifs,
typically one of them is canonical and binds to Ca2+,
while the other may not bind to Ca2+. A hydrophobic
binding pocket is formed by residues from both EF-hand
motifs. The EH domain binds to proteins containing NPF
(class I), [WF]W or SWG (class II), or H[TS]F (class
III) sequence motifs.
Length = 67
Score = 29.5 bits (67), Expect = 0.55
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 10/56 (17%)
Query: 246 FRKLDLDNSGALSIDE----FMS--LPELQQNPLVQRVIDIFDEDRNGEVDFKEFI 295
FR LD D G +S DE LP ++ ++ D+ D D++G++D +EF
Sbjct: 5 FRSLDPDGDGLISGDEARPFLGKSGLP----RSVLAQIWDLADTDKDGKLDKEEFA 56
Score = 27.2 bits (61), Expect = 4.3
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 207 DDSNKDRDGKINFQEFCSIVGNTDIHKKMVVDIRRLGKRFRKLDLDNSGALSIDEF---M 263
+ D DG I+ E +G + + + + L + + D D G L +EF M
Sbjct: 6 RSLDPDGDGLISGDEARPFLGKSGLPRSV------LAQIWDLADTDKDGKLDKEEFAIAM 59
Query: 264 SLPELQQN 271
L L N
Sbjct: 60 HLIALALN 67
>gnl|CDD|240157 cd05031, S-100A10_like, S-100A10_like: S-100A10 domain found in
proteins similar to S100A10. S100A10 is a member of the
S100 family of EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100A1_like group belongs, 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. A unique feature of S100A10 is
that it contains mutation in both of the calcium binding
sites, making it calcium insensitive. S100A10 has been
detected in brain, heart, gastrointestinal tract,
kidney, liver, lung, spleen, testes, epidermis, aorta,
and thymus. Structural data supports the homo- and
hetero-dimeric as well as hetero-tetrameric nature of
the protein. S100A10 has multiple binding partners in
its calcium free state and is therefore involved in many
diverse biological functions.
Length = 94
Score = 29.7 bits (67), Expect = 0.86
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 15/58 (25%)
Query: 174 KDLNQLMSMAKEMVEISKNISN-----KIINRQGEITEDDSNKDRDGKINFQEFCSIV 226
K+L +LM KE+ E KN + KI+ D +++RDGK+NF+EF S+V
Sbjct: 30 KELKKLME--KELSEFLKNQKDPMAVDKIMK--------DLDQNRDGKVNFEEFVSLV 77
Score = 27.8 bits (62), Expect = 4.1
Identities = 11/36 (30%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 261 EFMSLPELQQNPL-VQRVIDIFDEDRNGEVDFKEFI 295
E + Q++P+ V +++ D++R+G+V+F+EF+
Sbjct: 39 ELSEFLKNQKDPMAVDKIMKDLDQNRDGKVNFEEFV 74
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 27.2 bits (61), Expect = 1.6
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 241 RLGKRFRKLDLDNSGALSIDEFMSL 265
L + F+ D D G +S +E
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKA 25
Score = 26.0 bits (58), Expect = 4.5
Identities = 5/28 (17%), Positives = 14/28 (50%)
Query: 274 VQRVIDIFDEDRNGEVDFKEFIQGVSQF 301
++ +FD+D +G + +E + +
Sbjct: 2 LREAFKLFDKDGDGYISAEELRKALRSL 29
>gnl|CDD|240153 cd05026, S-100Z, S-100Z: S-100Z domain found in proteins similar to
S100Z. S100Z is a member of the S100 domain family
within the EF-hand Ca2+-binding proteins superfamily.
Note that the S-100 hierarchy, to which this S-100Z
group belongs, contains only S-100 EF-hand domains,
other EF-hands have been modeled separately.S100
proteins exhibit unique patterns of tissue- and cell
type-specific expression and have been implicated in the
Ca2+-dependent regulation of diverse physiological
processes, including cell cycle regulation,
differentiation, growth, and metabolic control. S100Z is
normally expressed in various tissues, with its highest
level of expression being in spleen and leukocytes. The
function of S100Z remains unclear. Preliminary
structural data suggests that S100Z is homodimer,
however a heterodimer with S100P has been reported.
S100Z is capable of binding calcium ions. When calcium
binds to S110Z, the protein experiences a
conformational change, which exposes hydrophobic
surfaces on the protein. In comparison with their normal
tissue counterparts, S100Z gene expression appears to be
deregulated in some tumor tissues.
Length = 93
Score = 28.3 bits (63), Expect = 2.3
Identities = 13/36 (36%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 269 QQNP-LVQRVIDIFDEDRNGEVDFKEFIQGVSQFSV 303
Q++P LV ++++ D +++ EVDF EF+ V+ +V
Sbjct: 49 QKDPMLVDKIMNDLDSNKDNEVDFNEFVVLVAALTV 84
>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 = 28.3 bits (63), Expect = 2.3
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 265 LPELQQNPLVQRVIDIFDEDRNGEVDFKEFIQGVS 299
L E+++ +V +V++ D D +GE DF+EF+ V+
Sbjct: 44 LEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVA 78
>gnl|CDD|240155 cd05029, S-100A6, S-100A6: S-100A6 domain found in proteins similar
to S100A6. S100A6 is a member of the S100 domain family
within EF-hand Ca2+-binding proteins superfamily. Note
that the S-100 hierarchy, to which this S-100A6 group
belongs, contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100 proteins
exhibit unique patterns of tissue- and cell
type-specific expression and have been implicated in the
Ca2+-dependent regulation of diverse physiological
processes, including cell cycle regulation,
differentiation, growth, and metabolic control . S100A6
is normally expressed in the G1 phase of the cell cycle
in neuronal cells. The function of S100A6 remains
unclear, but evidence suggests that it is involved in
cell cycle regulation and exocytosis. S100A6 may also be
involved in tumorigenesis; the protein is overexpressed
in several tumors. Ca2+ binding to S100A6 leads to a
conformational change in the protein, which exposes a
hydrophobic surface for interaction with target
proteins. Several such proteins have been identified:
glyceraldehyde-3-phosphate dehydrogenase , annexins 2,
6 and 11 and Calcyclin-Binding Protein (CacyBP).
Length = 88
Score = 27.9 bits (62), Expect = 2.9
Identities = 13/46 (28%), Positives = 30/46 (65%), Gaps = 4/46 (8%)
Query: 184 KEMVEISKNISNKIINRQGEITE--DDSNKDRDGKINFQEFCSIVG 227
KE+++ I +K+ + EI + +D ++++D ++NFQE+ + +G
Sbjct: 35 KELIQKELTIGSKL--QDAEIAKLMEDLDRNKDQEVNFQEYVTFLG 78
>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 = 28.9 bits (65), Expect = 2.9
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 239 IRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNPLVQRVIDIFDEDRNGEV 289
I R GK F LD DN+GAL + F S + V R + +ED
Sbjct: 83 ITRFGKGFPFLDPDNTGALLVLAFQSSDCDLYSVWVCRSDE--EEDEFEAE 131
>gnl|CDD|226661 COG4198, COG4198, Uncharacterized conserved protein [Function
unknown].
Length = 405
Score = 29.8 bits (67), Expect = 3.3
Identities = 20/97 (20%), Positives = 41/97 (42%), Gaps = 9/97 (9%)
Query: 229 TDIHK-KMVVDIRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNPLVQRVIDIFDEDRNG 287
+ H+ M VD + +++ D +L +D + Q+ +++ + I D +
Sbjct: 285 SKPHEIGMYVDGKWYALTPKRVPEDVVYSLDVD-------ILQDFVLEPIFGISDPREDN 337
Query: 288 EVDFKEFIQGVSQFSVKGDRESKLKFAFRIYDIDNDD 324
+DF I G+ + + S AF +Y D +D
Sbjct: 338 RIDFVGGIHGLEELERLVNSGS-FSVAFAMYPWDIED 373
>gnl|CDD|132264 TIGR03220, catechol_dmpE, 2-oxopent-4-enoate hydratase. Members of
this protein family are 2-oxopent-4-enoate hydratase,
which is also called 2-hydroxypent-2,4-dienoate
hydratase. It is closely related to another gene found
in the same operon, 4-oxalocrotonate decarboxylase, with
which it interacts closely.
Length = 255
Score = 29.3 bits (66), Expect = 3.6
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 328 QALGNELIAAL-----IEPLTSAGGTMLLTDAY 355
LG+EL AL + PLTS G + + DAY
Sbjct: 3 TQLGDELYQALVTRTPVAPLTSRGPDISIEDAY 35
>gnl|CDD|197477 smart00027, EH, Eps15 homology domain. Pair of EF hand motifs that
recognise proteins containing Asn-Pro-Phe (NPF)
sequences.
Length = 96
Score = 26.9 bits (60), Expect = 7.6
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 246 FRKLDLDNSGALSIDE----FMS--LPELQQNPLVQRVIDIFDEDRNGEVDFKEFI 295
FR LD + G ++ + + LP L+ ++ ++ D D +GE+D EF
Sbjct: 16 FRSLDKNQDGTVTGAQAKPILLKSGLP----QTLLAKIWNLADIDNDGELDKDEFA 67
>gnl|CDD|182175 PRK09971, PRK09971, xanthine dehydrogenase subunit XdhB;
Provisional.
Length = 291
Score = 28.5 bits (64), Expect = 8.6
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 10/68 (14%)
Query: 225 IVGNTDI-----HKKM----VVDIRRLGKRFRKLDLDNSGALSIDEFMSLPELQQNPLVQ 275
I G TD+ H +V I + R + L G++ I + ++ ++P++Q
Sbjct: 29 IAGGTDVLIQLHHHNDRYRHLVSIHNI-AELRGITLAEDGSIRIGAATTFTQIIEDPIIQ 87
Query: 276 RVIDIFDE 283
+ + E
Sbjct: 88 KHLPALAE 95
>gnl|CDD|180650 PRK06665, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 627
Score = 28.5 bits (64), Expect = 8.6
Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 155 ERNIV-EKQKETSSNINNAFKDLNQLMSMAKEMVEIS----KNISNKIINRQGEITEDDS 209
ER +V E+ + I++ ++ L ++ MA + +EI+ NI I + +I + +
Sbjct: 140 ERQVVLERAQSLGERIHDRYRSLERIRDMANDEIEITVEEINNILRNIADLNEQIVKSQA 199
Query: 210 NKDR 213
D
Sbjct: 200 MGDN 203
>gnl|CDD|240151 cd05024, S-100A10, S-100A10: A subgroup of the S-100A10 domain
found in proteins similar to S100A10. S100A10 is a
member of the S100 family of EF-hand superfamily of
calcium-binding proteins. Note that the S-100 hierarchy,
to which this S-100A10 group belongs, 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. A unique feature of
S100A10 is that it contains mutation in both of the
calcium binding sites, making it calcium insensitive.
S100A10 has been detected in brain, heart,
gastrointestinal tract, kidney, liver, lung, spleen,
testes, epidermis, aorta, and thymus. Structural data
supports the homo- and hetero-dimeric as well as
hetero-tetrameric nature of the protein. S100A10 has
multiple binding partners in its calcium free state and
is therefore involved in many diverse biological
functions.
Length = 91
Score = 26.7 bits (59), Expect = 8.9
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 13/56 (23%)
Query: 175 DLNQLMSMAKEMVEISKNISNKIINRQGEITEDDSNKD----RDGKINFQEFCSIV 226
DL +LM KE E KN + + D KD RDGK+ FQ F S++
Sbjct: 28 DLQKLME--KEFSEFLKN-------QNDPMAVDKIMKDLDDCRDGKVGFQSFFSLI 74
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
0.318 0.135 0.374
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: 23,922,730
Number of extensions: 2365222
Number of successful extensions: 2279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2255
Number of HSP's successfully gapped: 89
Length of query: 473
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 373
Effective length of database: 6,502,202
Effective search space: 2425321346
Effective search space used: 2425321346
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 (21.7 bits)
S2: 61 (27.0 bits)