RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10209
(106 letters)
>gnl|CDD|218397 pfam05044, Prox1, Homeobox prospero-like protein (PROX1). The
homeobox gene Prox1 is expressed in a subpopulation of
endothelial cells that, after budding from veins, gives
rise to the mammalian lymphatic system. Prox1 has been
found to be an early specific marker for the developing
liver and pancreas in the mammalian foregut endoderm.
This family contains an atypical homeobox domain.
Length = 908
Score = 190 bits (484), Expect = 6e-58
Identities = 82/106 (77%), Positives = 91/106 (85%), Gaps = 5/106 (4%)
Query: 1 MEKYARQAVSEGVLHAEDLHVSGECEIYRVLNLHYNRNNHIEVCGPQVPTNFRFVIEQTL 60
MEKYARQA++EGV ++DL VS + E+YRVLNLHYNRNNHIEV P NFRFV+EQTL
Sbjct: 808 MEKYARQAINEGVKTSDDLSVSRDSELYRVLNLHYNRNNHIEV-----PENFRFVVEQTL 862
Query: 61 REFFKAIQDGKDQEPSWKKSIYKIISRMDDPVPEYFKSPNFLEQLE 106
REFF+AI GKD E SWKKSIYKIISR+DDPVPEYFKSPNFLEQLE
Sbjct: 863 REFFRAIIAGKDSEQSWKKSIYKIISRLDDPVPEYFKSPNFLEQLE 908
>gnl|CDD|147335 pfam05105, Phage_holin_4, Holin family. Phage holins and lytic
enzymes are both necessary for bacterial lysis and virus
dissemination.This family also includes TcdE/UtxA
involved in toxin secretion in Clostridium difficile.
Length = 118
Score = 28.7 bits (65), Expect = 0.32
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 80 SIYKIISRMDDPVPEYFKSPNFLEQL 105
SI + + RM P+PE K + LEQL
Sbjct: 91 SILENLGRMGVPIPEKLK--DALEQL 114
>gnl|CDD|240396 PTZ00388, PTZ00388, 40S ribosomal protein S8-like; Provisional.
Length = 223
Score = 28.1 bits (63), Expect = 0.65
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 7/42 (16%)
Query: 62 EFFKAIQDGKDQEPSWKKSIYKIISRMDDPVPEYF--KSPNF 101
E FK ++ GK ++ SWK+ + K+ V E F K P +
Sbjct: 94 EMFKVVKSGKRKKKSWKRLVNKVTF-----VGEDFTRKPPKY 130
>gnl|CDD|240127 cd04823, ALAD_PBGS_aspartate_rich, Porphobilinogen synthase
(PBGS), which is also called delta-aminolevulinic acid
dehydratase (ALAD), catalyzes the condensation of two
5-aminolevulinic acid (ALA) molecules to form the
pyrrole porphobilinogen (PBG), which is the second step
in the biosynthesis of tetrapyrroles, such as heme,
vitamin B12 and chlorophyll. This reaction involves the
formation of a Schiff base link between the substrate
and the enzyme. PBGSs are metalloenzymes, some of which
have a second, allosteric metal binding site, beside
the metal ion binding site in their active site.
Although PBGS is a family of homologous enzymes, its
metal ion utilization at catalytic site varies between
zinc and magnesium and/or potassium. PBGS can be
classified into two groups based on differences in
their active site metal binding site. All of
PBGS_aspartate_rich contain an aspartate rich metal
binding site with the general sequence
DXALDX(Y/F)X3G(H/Q)DG. They also contain an allosteric
magnesium binding sequence RX~164DX~65EXXXD and are
activated by magnesium and/or potassium, but not by
zinc. PBGSs_aspartate_rich are found in some bacterial
species and photosynthetic organisms such as vascular
plants, mosses and algae, but not in archaea.
Length = 320
Score = 27.5 bits (62), Expect = 1.3
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 6 RQAVSEGVLHAEDLHVSGECEIYRVLNLHYNRNNHIEVCGPQVPTNFRFVIEQTLREFFK 65
R+ V E L +DL I + +H N + P +P FR I++ L+E +
Sbjct: 13 RRLVRETTLSPDDL-------ILPLF-VHEGENQREPI--PSMPGVFRLSIDELLKEAEE 62
Query: 66 AIQDG 70
A+ G
Sbjct: 63 AVDLG 67
>gnl|CDD|220663 pfam10266, Strumpellin, Hereditary spastic paraplegia protein
strumpellin. This is a family of proteins conserved
from plants to humans, in which two closely situated
point mutations in the human protein lead to the
condition of hereditary spastic paraplegia. Strumpellin
contains one known domain called a spectrin repeat that
consists of three alpha-helices of a characteristic
length wrapped in a left-handed coiled coil. The
spectrin proteins have multiple copies of this repeat,
which can then form multimers in the cell. Spectrin
associates with the cell membrane via spectrin repeats
in the ankyrin protein. The spectrin repeat is a
structural platform for cytoskeletal protein assemblies.
Length = 1077
Score = 26.5 bits (59), Expect = 2.9
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 57 EQTLREFFKAIQDGKDQEPSWKKSIYKIISRMDDPVPEYF 96
E TLR F + KD+ W++S + + RM + + E+F
Sbjct: 392 EFTLRNMFTTLLQEKDER--WEESKKEAVERMQE-LAEFF 428
>gnl|CDD|235019 PRK02259, PRK02259, aspartoacylase; Provisional.
Length = 288
Score = 26.4 bits (59), Expect = 3.0
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 10/62 (16%)
Query: 41 IEVCGPQVPTNFR--FVIEQT------LREFFKAIQDGKDQEPSWKKSIYKIISRMDDPV 92
IEV GP VP + EQT + ++ + GK P+ + +Y+ + +D P
Sbjct: 161 IEV-GP-VPQGVLDAEIFEQTELLIESILDYLEKYNQGKLPLPNEQLVVYRHLGSIDYPR 218
Query: 93 PE 94
E
Sbjct: 219 DE 220
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 26.1 bits (58), Expect = 3.9
Identities = 27/80 (33%), Positives = 36/80 (45%), Gaps = 19/80 (23%)
Query: 28 YRVL-NLHYNRNNHIEVCGPQVPTNFRFVIEQTLREFFKAIQDGKDQEPSWKKSIYKIIS 86
YR L + NR+ +EV P VP + FVI +A+ D+E I + +S
Sbjct: 192 YRALVTVERNRDGLLEVSFPSVPGSIPFVI------LMRALGLETDEE------IVEAVS 239
Query: 87 RMDDPVPEYFKSPNFLEQLE 106
DD PE K LE LE
Sbjct: 240 --DD--PEIVK--FMLENLE 253
>gnl|CDD|153248 cd07986, LPLAT_ACT14924-like, Lysophospholipid Acyltransferases
(LPLATs) of Glycerophospholipid Biosynthesis: Unknown
ACT14924. Lysophospholipid acyltransferase (LPLAT)
superfamily member: acyltransferases of de novo and
remodeling pathways of glycerophospholipid biosynthesis
which catalyze the incorporation of an acyl group from
either acylCoAs or acyl-acyl carrier proteins (acylACPs)
into acceptors such as glycerol 3-phosphate,
dihydroxyacetone phosphate or lyso-phosphatidic acid.
Included in this subgroup are uncharacterized
phospholipid/glycerol acyltransferases such as the
Pectobacterium carotovorum subsp. carotovorum PC1 locus
ACT14924 putative acyltransferase, and similar proteins.
Length = 210
Score = 26.1 bits (58), Expect = 3.9
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 70 GKDQEPSWKKSIYKIISRMDDP-VPEYFKSPN 100
G+ + W + ++ + P VP YF N
Sbjct: 117 GRVSDRPWNPFVARLARKAKAPVVPVYFSGRN 148
>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23. RAD23 belongs to
a family of adaptor molecules having affinity for both
the proteasome and ubiquitinylated proteins and thought
to shuttle these ubiquitinylated proteins to the
proteasome for destruction. RAD23 interacts with
ubiquitin through its C-terminal ubiquitin-associated
domains (UBA) and with the proteasome through its
N-terminal ubiquitin-like domain (UBL).
Length = 77
Score = 25.0 bits (55), Expect = 5.0
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 53 RFVIE----QTLREFFKAIQD--GKDQEPSWKKSIY--KIISRMDDPVPEY-FKSPNFL 102
F IE T+ E + I++ G D P +K IY KI+ D + EY +F+
Sbjct: 12 TFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKD-DTTLEEYKIDEKDFV 69
>gnl|CDD|241425 cd13271, PH2_TAPP1_2, Tandem PH-domain-containing proteins 1 and 2
Pleckstrin homology (PH) domain, C-terminal repeat. The
binding of TAPP1 (also called PLEKHA1/pleckstrin
homology domain containing, family A (phosphoinositide
binding specific) member 1) and TAPP2 (also called
PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4,
5)P3, function as negative regulators of insulin and
PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin
complex). TAPP1 and TAPP2 contain two sequential PH
domains in which the C-terminal PH domain specifically
binds PtdIns(3,4)P2 with high affinity. The N-terminal
PH domain does not interact with any phosphoinositide
tested. They also contain a C-terminal PDZ-binding motif
that interacts with several PDZ-binding proteins,
including PTPN13 (known previously as PTPL1 or FAP-1) as
well as the scaffolding proteins MUPP1 (multiple
PDZ-domain-containing protein 1), syntrophin and
utrophin. 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 = 114
Score = 25.0 bits (55), Expect = 5.7
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 54 FVIEQTLREFFKAIQDGKDQE-PSWKKSIYKIISRMDDPVPE 94
F I T R F+ IQ ++ SW K+I I P
Sbjct: 74 FEIITTSRTFY--IQADSPEDMHSWIKAISGAIVARRGPYRS 113
>gnl|CDD|211393 cd11381, NSA2, pre-ribosomal protein NSA2 (Nop seven-associated 2).
NSA2 appears to be a protein required for the
maturation of 27S pre-rRNA in yeast; it has been
characterized in mammalian cells as a nucleolar protein
that might play a role in the regulation of the cell
cycle and in cell proliferation.
Length = 257
Score = 24.9 bits (55), Expect = 8.9
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 62 EFFKAIQDGKDQEPSWKKSIYKI 84
E FK ++ GK ++ SWK+ + K+
Sbjct: 128 EMFKVVKTGKRKKKSWKRMVTKV 150
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 25.1 bits (56), Expect = 9.3
Identities = 8/31 (25%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 64 FKAIQDGKDQEPSWKKSIYKIISRMDDPVPE 94
KA++ D + W+K I +++ +D +P
Sbjct: 176 LKALEG--DDDEEWEKKILELMDAVDSYIPT 204
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.137 0.412
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,502,777
Number of extensions: 455291
Number of successful extensions: 409
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 27
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)