RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14481
(179 letters)
>gnl|CDD|201378 pfam00658, PABP, Poly-adenylate binding protein, unique domain.
The region featured in this family is found towards the
C-terminus of poly(A)-binding proteins (PABPs). These
are eukaryotic proteins that, through their binding of
the 3' poly(A) tail on mRNA, have very important roles
in the pathways of gene expression. They seem to provide
a scaffold on which other proteins can bind and mediate
processes such as export, translation and turnover of
the transcripts. Moreover, they may act as antagonists
to the binding of factors that allow mRNA degradation,
regulating mRNA longevity. PABPs are also involved in
nuclear transport. PABPs interact with poly(A) tails via
RNA-recognition motifs (pfam00076). Note that the PABP
C-terminal region is also found in members of the
hyperplastic discs protein (HYD) family of ubiquitin
ligases that contain HECT domains - these are also
included in this family.
Length = 72
Score = 128 bits (324), Expect = 2e-39
Identities = 55/72 (76%), Positives = 68/72 (94%)
Query: 95 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 154
EPLT++ LAAA PQEQKQMLGERL+PLIQ M+PELAGKITGMLLE+DN+ELL++LE +E+
Sbjct: 1 EPLTASALAAAPPQEQKQMLGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEA 60
Query: 155 LKSKVEEAVAVL 166
LK+KV+EA+AVL
Sbjct: 61 LKAKVDEALAVL 72
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 124 bits (312), Expect = 1e-33
Identities = 46/81 (56%), Positives = 60/81 (74%)
Query: 87 RAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELL 146
GQ + +LA+A PQ QKQ+LGERLFPL++ + P LA KITGMLLE+DN+ELL
Sbjct: 482 STASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELL 541
Query: 147 YMLEHNESLKSKVEEAVAVLQ 167
++LE E LKSKV+EA+ VL+
Sbjct: 542 HLLESPELLKSKVDEALEVLK 562
>gnl|CDD|197769 smart00517, PolyA, C-terminal domain of Poly(A)-binding protein.
Present also in Drosophila hyperplastics discs protein.
Involved in homodimerisation (either directly or
indirectly).
Length = 64
Score = 103 bits (258), Expect = 1e-29
Identities = 42/63 (66%), Positives = 55/63 (87%)
Query: 107 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVL 166
PQEQKQ LGERL+P +Q + PELAGKITGMLLE+DN+ELL++LE E L++KV+EA+ VL
Sbjct: 2 PQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRAKVDEALEVL 61
Query: 167 QAH 169
++H
Sbjct: 62 KSH 64
>gnl|CDD|238324 cd00580, CHMI, 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI)
is a trimeric enzyme catalyzing the isomerization of the
unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate
to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is
one step in the homoprotocatechuate pathway, one of the
microbial meta-fission pathways that degrade aromatic
carbon sources to citric acid cycle intermediates.
Despite the structural similarity of CHMI with
4-oxalocrotonate tautomerase (4-OT) and macrophage
migration inhibitory factor (MIF), there is no
significant sequence similarity among these protein
families, and therefore, they are not combined in one
hierarchy.
Length = 113
Score = 29.5 bits (67), Expect = 0.41
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 102 LAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGML-LEID 141
+ A + +EQKQ L E L ++ + K L +EI
Sbjct: 67 ILAGRSEEQKQELSEALLAALRAHLAPVFAKRYLSLSVEIR 107
>gnl|CDD|182407 PRK10359, PRK10359, lipopolysaccharide core biosynthesis protein;
Provisional.
Length = 232
Score = 29.3 bits (66), Expect = 0.76
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 136 MLLE-IDNAELLYMLEHNESLKSKVEEAVAVLQAH 169
ML+E I+ EL M E +E +K+K++ ++ L H
Sbjct: 120 MLIEYIEGVELNDMPEISEDVKAKIKASIESLHQH 154
>gnl|CDD|114869 pfam06176, WaaY, Lipopolysaccharide core biosynthesis protein
(WaaY). This family consists of several bacterial
lipopolysaccharide core biosynthesis proteins (WaaY or
RfaY). The waaY, waaQ, and waaP genes are located in the
central operon of the waa (formerly rfa) locus on the
chromosome of Escherichia coli. This locus contains
genes whose products are involved in the assembly of the
core region of the lipopolysaccharide molecule. WaaY is
the enzyme that phosphorylates HepII in this system.
Length = 229
Score = 29.4 bits (66), Expect = 0.79
Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 136 MLLE-IDNAELLYMLEHNESLKSKVEEAVAVLQAH 169
ML+E I+ EL M E +E +K+K+++++ L H
Sbjct: 120 MLIEYIEGVELNDMPEISEDVKAKIKQSIESLHQH 154
>gnl|CDD|177576 PHA03286, PHA03286, envelope glycoprotein E; Provisional.
Length = 492
Score = 29.9 bits (67), Expect = 0.85
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 33 AMISGISFGALALVTLFGAVSFIMYRRYR 61
++S ++ GA+ +V LF +YRR R
Sbjct: 391 LLVSSMAAGAILVVLLFALCIAGLYRRRR 419
>gnl|CDD|115715 pfam07079, DUF1347, Protein of unknown function (DUF1347). This
family consists of several hypothetical bacterial
proteins of around 610 residues in length. Members of
this family are highly conserved and seem to be specific
to Chlamydia species. The function of this family is
unknown.
Length = 550
Score = 29.3 bits (66), Expect = 1.1
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 144 ELLYMLEHNESL-KSKVEEAVAVLQAHQAKQ 173
E L+ L NE SKV++A+ + Q H K
Sbjct: 516 EYLHSLPLNERTYDSKVQKALLLCQKHLPKD 546
>gnl|CDD|233780 TIGR02210, rodA_shape, rod shape-determining protein RodA. This
protein is a member of the FtsW/RodA/SpoVE family
(pfam01098). It is found only in species with rod (or
spiral) shapes. In many species, mutation of rodA has
been shown to correlate with loss of the normal rod
shape. Note that RodA homologs are found, scoring below
the cutoffs for this model, in a number of both
rod-shaped and coccoid bacteria, including four proteins
in Bacillus anthracis, for example [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan, Cellular processes, Cell division].
Length = 352
Score = 28.6 bits (65), Expect = 1.6
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 14/45 (31%)
Query: 30 VNVAMISGI-----------SFGALALVTLFGAVSFIM---YRRY 60
VN+ M+ G+ S+G +L+TL +M R
Sbjct: 308 VNIGMVIGLLPVVGIPLPLVSYGGSSLLTLMIGFGLLMSIHTHRR 352
>gnl|CDD|236674 PRK10364, PRK10364, sensor protein ZraS; Provisional.
Length = 457
Score = 28.6 bits (64), Expect = 1.8
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 31 NVAMISGISFGALALVTLFGAVSFIMYRRYR 61
N +I ALA V L ++F YRRY
Sbjct: 192 NTLIILF----ALATVLLASLLAFFWYRRYL 218
>gnl|CDD|218739 pfam05767, Pox_A14, Poxvirus virion envelope protein A14. This
family consists of several Poxvirus virion envelope
protein A14 like sequences. A14 is a component of the
virion membrane and has been found to be an H1
phosphatase substrate in vivo and in vitro. A14 is
hyperphosphorylated on serine residues in the absence
of H1 expression.
Length = 92
Score = 27.0 bits (60), Expect = 2.1
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 35 ISGISFGALALVTLFGAVSFIMYRRY 60
+S I F L +V L G V F MY RY
Sbjct: 47 LSIICF-ILGIVLLLGIVLFSMYGRY 71
>gnl|CDD|223843 COG0772, FtsW, Bacterial cell division membrane protein [Cell
division and chromosome partitioning].
Length = 381
Score = 27.6 bits (62), Expect = 4.1
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 14/49 (28%)
Query: 30 VNVAMISG-----------ISFGALALVTLFGAVSFIM---YRRYRWNK 64
+N+ M+ G IS+G +L+ A+ ++ R R
Sbjct: 329 INIGMVLGLLPVTGVPLPFISYGGSSLLANSIALGILLNISRHRRRKLS 377
>gnl|CDD|216018 pfam00606, Glycoprotein_B, Herpesvirus Glycoprotein B. This family
of proteins contains a transmembrane region.
Length = 711
Score = 27.5 bits (62), Expect = 4.6
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 25 SGEGGVNVAMISGIS------FGALALVTLFGAV---SFIMYRRYR 61
SG G +++SG+ FG L ++ L A F+ YRR R
Sbjct: 644 SGVAGAVGSIVSGVVSFLKNPFGGLLIILLVLAGLVAVFLAYRRVR 689
>gnl|CDD|172743 PRK14255, PRK14255, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 252
Score = 26.9 bits (59), Expect = 5.8
Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 127 PELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVA-VLQAHQAKQAAVKK 178
P + +I MLLE+ + + ++ H+ S++ + A L + + A K+
Sbjct: 181 PISSTQIENMLLELRDQYTIILVTHSMHQASRISDKTAFFLTGNLIEFADTKQ 233
>gnl|CDD|220692 pfam10324, 7TM_GPCR_Srw, Serpentine type 7TM GPCR chemoreceptor
Srw. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of
proteins which are of the serpentine type. Srw is a
solo family amongst the superfamilies of
chemoreceptors. Chemoperception is one of the central
senses of soil nematodes like C. elegans which are
otherwise 'blind' and 'deaf'. The genes encoding Srw do
not appear to be under as strong an adaptive
evolutionary pressure as those of Srz.
Length = 317
Score = 26.8 bits (60), Expect = 6.0
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 30 VNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDKCSNPDS 77
+N+ MI GI+ ++T+ +Y + +C PDS
Sbjct: 31 INIIMI-GIAI--CDIITML----LTIYNFIPEFIISYENSECIPPDS 71
>gnl|CDD|240598 cd10546, VKOR, Vitamin K epoxide reductase (VKOR) family. VKOR
(also named VKORC1) is an integral membrane protein
that catalyzes the reduction of vitamin K 2,3-epoxide
and vitamin K to vitamin K hydroquinone, an essential
co-factor subsequently used in the gamma-carboxylation
of glutamic acid residues in blood coagulation enzymes.
This family includes enzymes that are present in
vertebrates, Drosophila, plants, bacteria, and archaea.
All homologs of VKOR contain an active site CXXC motif,
which is switched between reduced and disulfide-bonded
states during the reaction cycle. In some plant and
bacterial homologs, the VKOR domain is fused with
domains of the thioredoxin family of oxidoreductases
which may function as redox partners in initiating the
reduction cascade. Warfarin, a widely used oral
anticoagulant used in medicine as well as rodenticides,
inhibits the activity of VKOR, resulting in decreased
levels of reduced vitamin K, which is required for the
function of several clotting factors. However,
anticoagulation effect of warfarin is significantly
associated with polymorphism of certain genes,
including VKORC1. Interestingly, in rodents, an
adaptive trait appears to have evolved convergently by
selection on new or standing genetic polymorphisms in
VKORC1 as well as by adaptive introgressive
hybridization between species, likely brought about by
human-mediated dispersal.
Length = 126
Score = 26.2 bits (58), Expect = 6.5
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 20 LSNPWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWN 63
L++ WS GV ++++ + + LV L +S R RW
Sbjct: 42 LTSRWSRIFGVPLSLLGALYY----LVVLGLLLSPPAGARLRWT 81
>gnl|CDD|171610 PRK12615, PRK12615, galactose-6-phosphate isomerase subunit LacB;
Reviewed.
Length = 171
Score = 26.5 bits (58), Expect = 6.5
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 129 LAGKITGMLLEIDNAELLYMLEHNESLKSKVEEA-VAVLQAHQAKQA 174
GKITG LL D + E+ E+ ++K A +A L++H A Q
Sbjct: 106 FGGKITGELLMCDIIDAFIKAEYKETEENKKLIAKIAHLESHHANQE 152
>gnl|CDD|182453 PRK10429, PRK10429, melibiose:sodium symporter; Provisional.
Length = 473
Score = 27.0 bits (60), Expect = 7.1
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 31 NVAMISGISFGALALVTLFGAVSFIMYRRY 60
+ + G+ F + L TLF ++ ++Y RY
Sbjct: 403 SAQTLLGMQFIMIGLPTLFFMITLVLYFRY 432
>gnl|CDD|218594 pfam05450, Nicastrin, Nicastrin. Nicastrin and presenilin are two
major components of the gamma-secretase complex, which
executes the intramembrane proteolysis of type I
integral membrane proteins such as the amyloid precursor
protein (APP) and Notch. Nicastrin is synthesised in
fibroblasts and neurons as an
endoglycosidase-H-sensitive glycosylated precursor
protein (immature nicastrin) and is then modified by
complex glycosylation in the Golgi apparatus and by
sialylation in the trans-Golgi network (mature
nicastrin). A region featured in this family has a fold
similar to human transferrin receptor (TfR) and a
bacterial aminopeptidase. It is implicated in the
pathogenesis of Alzheimer's disease.
Length = 227
Score = 26.7 bits (59), Expect = 7.3
Identities = 26/141 (18%), Positives = 48/141 (34%), Gaps = 25/141 (17%)
Query: 34 MISGISFGALALVTLFGAVSFIMYRRYRWNKPQTLSDK-----CSNPDSSGYIDDSTLRA 88
M G+S GA++ ++ F + + + + N +S YI R
Sbjct: 14 MFDGVSLGAMSSLSGFIVLLAAADALSKALPDISNLKRNVLFAFFNGESYDYIGSQ--RF 71
Query: 89 VH--VQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELL 146
V+ G+ P T P ML I ++ GK T L
Sbjct: 72 VYDMENGKFPSDRTHTHPISPDNIDYMLE------IGQV-----GKATSRKF-----YLH 115
Query: 147 YMLEHNESLKSKVEEAVAVLQ 167
N+S+K++ + + ++
Sbjct: 116 VDAARNQSVKTQTLDLLDRIE 136
>gnl|CDD|222907 PHA02611, 51, baseplate hub assembly protein; Provisional.
Length = 249
Score = 26.6 bits (59), Expect = 8.4
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 97 LTSTMLAAAQPQEQKQMLGERLFPLIQRMYPE 128
L + P+EQ+++L E L+ +PE
Sbjct: 29 LVRNDMEGRSPEEQQEILDE----LLDEYFPE 56
>gnl|CDD|217235 pfam02800, Gp_dh_C, Glyceraldehyde 3-phosphate dehydrogenase,
C-terminal domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
C-terminal domain is a mixed alpha/antiparallel beta
fold.
Length = 157
Score = 26.0 bits (58), Expect = 8.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 122 IQRMYPELAGKITGM 136
+ + PEL GK+TGM
Sbjct: 60 VGLVLPELKGKLTGM 74
>gnl|CDD|131561 TIGR02509, type_III_yopR, type III secretion effector, YopR family.
Members of this family are type III secretion system
effectors, named differently in different species and
designated YopR (Yersinia outer protein R), encoded by
the YscH (Yersinia secretion H) gene. This Yops protein
is unusual in that it is released to extracellularly
rather than injected directly into the target cell as
are most Yops [Cellular processes, Pathogenesis].
Length = 131
Score = 25.9 bits (57), Expect = 8.8
Identities = 16/69 (23%), Positives = 27/69 (39%)
Query: 94 QEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNE 153
+E L ++ E L P+ +R+ G+ ++ ID EL ML +
Sbjct: 14 RELLWQQYQQGKPAAGTADLVPELLSPVKERLLGRFGGQQLPVVPPIDRLELRAMLRQFD 73
Query: 154 SLKSKVEEA 162
L + E A
Sbjct: 74 PLGRQQEAA 82
>gnl|CDD|179568 PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiporter;
Provisional.
Length = 504
Score = 26.6 bits (59), Expect = 9.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 38 ISFGALALVTLFGAVSFIM 56
+SF L V + G SFIM
Sbjct: 265 LSFLMLGWVFIVGGTSFIM 283
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
0.315 0.130 0.370
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,137,358
Number of extensions: 839484
Number of successful extensions: 1097
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1094
Number of HSP's successfully gapped: 48
Length of query: 179
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 88
Effective length of database: 6,901,388
Effective search space: 607322144
Effective search space used: 607322144
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: 56 (25.3 bits)