RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2054
(75 letters)
>gnl|CDD|238099 cd00170, SEC14, Sec14p-like lipid-binding domain. Found in
secretory proteins, such as S. cerevisiae
phosphatidylinositol transfer protein (Sec14p), and in
lipid regulated proteins such as RhoGAPs, RhoGEFs and
neurofibromin (NF1). SEC14 domain of Dbl is known to
associate with G protein beta/gamma subunits.
Length = 157
Score = 52.0 bits (125), Expect = 4e-10
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 1 MDFSKISLEEAFQLGTSVFEIALLDPRLQISGAEKIPLRVKAIHIVNQPFYFNALYAIFK 60
+D +SL + + +I + + P R+KA++I+N P++F L+ I K
Sbjct: 68 IDLKGLSLSHLLPDPSLLKKILKILQ-------DNYPERLKAVYIINPPWFFKVLWKIVK 120
Query: 61 PFLKQKLRRRW 71
PFL +K R++
Sbjct: 121 PFLSEKTRKKI 131
>gnl|CDD|216042 pfam00650, CRAL_TRIO, CRAL/TRIO domain.
Length = 152
Score = 48.0 bits (115), Expect = 1e-08
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 36 IPLRVKAIHIVNQPFYFNALYAIFKPFLKQKLRRR 70
P R+ I IVN P+ FN ++ + KPFL K R +
Sbjct: 90 YPERLGKILIVNAPWIFNVIWKLIKPFLDPKTREK 124
>gnl|CDD|214706 smart00516, SEC14, Domain in homologues of a S. cerevisiae
phosphatidylinositol transfer protein (Sec14p). Domain
in homologues of a S. cerevisiae phosphatidylinositol
transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and
the RasGAP, neurofibromin (NF1). Lipid-binding domain.
The SEC14 domain of Dbl is known to associate with G
protein beta/gamma subunits.
Length = 158
Score = 45.8 bits (109), Expect = 9e-08
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 37 PLRVKAIHIVNQPFYFNALYAIFKPFLKQKLRRRW 71
P R+ ++I+N P++F L+ I KPFL +K R +
Sbjct: 95 PERLGKVYIINPPWFFRVLWKIIKPFLDEKTREKI 129
>gnl|CDD|132839 cd07200, cPLA2_Grp-IVA, Group IVA cytosolic phospholipase A2;
catalytic domain; Ca-dependent. Group IVA cPLA2, an 85
kDa protein, consists of two domains: the regulatory C2
domain and the alpha/beta hydrolase PLA2 domain. Group
IVA cPLA2 is also referred to as cPLA2-alpha. The
catalytic domain of cytosolic phospholipase A2 (cPLA2;
EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of
phospholipids to release arachidonic acid. At the active
site, cPLA2 contains a serine nucleophile through which
the catalytic mechanism is initiated. The active site is
partially covered by a solvent-accessible flexible lid.
cPLA2 displays interfacial activation as it exists in
both "closed lid" and "open lid" forms. Movement of the
cPLA2 lid possibly exposes a greater hydrophobic surface
and the active site. cPLA2 belongs to the alpha-beta
hydrolase family which is identified by a characteristic
nucleophile elbow with a consensus sequence of
Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu =
nucleophile). Calcium is required for cPLA2 to bind with
membranes or phospholipids. A calcium-dependent
phospholipid binding domain resides in the N-terminal
region of cPLA2; it is homologous to the C2 domain
superfamily which is not included in this hierarchy.
Includes PLA2G4A from chicken, human, and frog.
Length = 505
Score = 26.3 bits (58), Expect = 1.4
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 14 LGTSVFEIALLDPRLQISGAEKIPLRVKAIHIVNQPFYFNALY-AIFKPF 62
L T E A+ D E + + K IH+V+ FN Y I +P
Sbjct: 294 LATDEPEAAVADADEFERIYEPLDTKSKKIHVVDSGLTFNLPYPLILRPQ 343
>gnl|CDD|215615 PLN03180, PLN03180, reversibly glycosylated polypeptide;
Provisional.
Length = 346
Score = 25.1 bits (55), Expect = 3.9
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 5/23 (21%)
Query: 44 HIVN-----QPFYFNALYAIFKP 61
HI N PF+FN LY ++
Sbjct: 121 HIKNLLSPSTPFFFNTLYDPYRE 143
>gnl|CDD|187847 cd09716, Cas5_I, CRISPR/Cas system-associated RAMP superfamily
protein Cas5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas5 is a RAMP superfamily protein; Subunit of the
Cascade complex.
Length = 220
Score = 25.0 bits (54), Expect = 3.9
Identities = 6/65 (9%), Positives = 18/65 (27%), Gaps = 3/65 (4%)
Query: 5 KISLEEAFQLGTSVFEIALLDPRLQISGAEKIPLRVKAIHIVNQPFYFNALYAIFKPFLK 64
+ + + + ++ + + IPL + + + K
Sbjct: 50 REIITKEIK---NIRKKTKKGYIPPTIRSIFIPLLSDFFELDSVRIVSTDSPFFYNDLWK 106
Query: 65 QKLRR 69
+ RR
Sbjct: 107 RAFRR 111
>gnl|CDD|176019 cd08373, C2A_Ferlin, C2 domain first repeat in Ferlin. Ferlins are
involved in vesicle fusion events. Ferlins and other
proteins, such as Synaptotagmins, are implicated in
facilitating the fusion process when cell membranes fuse
together. There are six known human Ferlins: Dysferlin
(Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3),
Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can
lead to a wide range of diseases including muscular
dystrophy (dysferlin), deafness (otoferlin), and
infertility (fer-1, fertilization factor-1).
Structurally they have 6 tandem C2 domains, designated
as (C2A-C2F) and a single C-terminal transmembrane
domain, though there is a new study that disputes this
and claims that there are actually 7 tandem C2 domains
with another C2 domain inserted between C2D and C2E.
In a subset of them (Dysferlin, Myoferlin, and Fer1)
there is an additional conserved domain called DysF. 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 first C2
repeat, C2A, and has a type-II topology.
Length = 127
Score = 24.9 bits (55), Expect = 4.2
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 5 KISLEEAFQLGTSVFEIALLDPRLQISGAEKIPLRVK 41
+SL++ G LLD + +GA I L V
Sbjct: 79 TVSLQDLVSEGLLEVTEPLLDSNGRPTGAT-ISLEVS 114
>gnl|CDD|235773 PRK06291, PRK06291, aspartate kinase; Provisional.
Length = 465
Score = 24.9 bits (55), Expect = 4.7
Identities = 18/39 (46%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 4 SKISLEEAFQLGTSVFEIALLDPRLQISGAEK-IPLRVK 41
KIS EA +L S F +L PR EK IP+RVK
Sbjct: 253 PKISYIEAMEL--SYFGAKVLHPRTIEPAMEKGIPVRVK 289
>gnl|CDD|178419 PLN02824, PLN02824, hydrolase, alpha/beta fold family protein.
Length = 294
Score = 24.7 bits (54), Expect = 5.1
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 9 EEAFQLGTSV-----FEIALLDPRLQISGAEKIPLRVKAIHIVNQPFYFNALYAIFKPFL 63
+ AF + SV + A+ P L + G I + ++ +HI QP+ F+ L
Sbjct: 102 DPAFVICNSVGGVVGLQAAVDAPEL-VRGVMLINISLRGLHIKKQPWLGRPFIKAFQNLL 160
Query: 64 KQ 65
++
Sbjct: 161 RE 162
>gnl|CDD|147056 pfam04705, TSNR_N, Thiostrepton-resistance methylase, N terminus.
This region is found in some members of the SpoU-type
rRNA methylase family (pfam00588).
Length = 115
Score = 24.5 bits (53), Expect = 5.3
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 10 EAFQLGTSVFEIALLDPRLQISGAEKIPLRVKAIHIVNQPF 50
E + T F LLD + IP+R+ IVNQ F
Sbjct: 52 EVYGSDTVPFPGDLLD----LCEKRGIPVRLIDASIVNQLF 88
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 24.6 bits (54), Expect = 5.5
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 28 LQISGAEKIPLRVKAIHIVNQP 49
L ++G K P+RV+ +H NQP
Sbjct: 207 LWLTGVNK-PMRVRGLHAQNQP 227
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 24.7 bits (54), Expect = 5.6
Identities = 17/70 (24%), Positives = 23/70 (32%), Gaps = 5/70 (7%)
Query: 9 EEAFQLGTSVFEIALLDPR-----LQISGAEKIPLRVKAIHIVNQPFYFNALYAIFKPFL 63
F L +ALL+ L I G +K L +N F L IF
Sbjct: 264 TGKFILQEPNVTVALLEVGKWEYWLYIEGKDKRWLGTPVSPEMNPTFNLENLSFIFNYTT 323
Query: 64 KQKLRRRWCL 73
+ + W L
Sbjct: 324 EDGIALSWLL 333
>gnl|CDD|190568 pfam03214, RGP, Reversibly glycosylated polypeptide.
Length = 348
Score = 24.4 bits (53), Expect = 6.6
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 37 PLRVKAIHIVN-----QPFYFNALYAIFK 60
P+ A HI N PF+FN LY ++
Sbjct: 112 PVDAVAQHIKNLKTPATPFFFNTLYDPYR 140
>gnl|CDD|149946 pfam09069, efhand_2, EF-hand. Members of this family adopt a
helix-loop-helix motif, as per other EF hand domains.
However, since they do not contain the canonical
pattern of calcium binding residues found in many EF
hand domains, they do not bind calcium ions. The main
function of this domain is the provision of specificity
in beta-dystroglycan recognition, though in dystrophin
it serves an additional role: stabilisation of the WW
domain (pfam00397), enhancing dystroglycan binding.
Length = 89
Score = 23.4 bits (51), Expect = 9.9
Identities = 11/24 (45%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 1 MDFSKIS--LEEAFQLGTSVFEIA 22
MD K+ L EA QL V E A
Sbjct: 19 MDQRKLGLLLHEALQLPRQVGEGA 42
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
0.329 0.144 0.435
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,964,962
Number of extensions: 310939
Number of successful extensions: 335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 19
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)