RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7158
(402 letters)
>gnl|CDD|217378 pfam03124, EXS, EXS family. We have named this region the EXS
family after (ERD1, XPR1, and SYG1). This family
includes C-terminus portions from the SYG1 G-protein
associated signal transduction protein from
Saccharomyces cerevisiae, and sequences that are thought
to be murine leukaemia virus (MLV) receptors (XPR1).
N-terminus portions from these proteins are aligned in
the SPX pfam03105 family. The previously noted
similarity between SYG1 and MLV receptors over their
whole sequences is thus borne out in pfam03105 and this
family. While the N-termini aligned in pfam03105 are
thought to be involved in signal transduction, the role
of the C-terminus sequences aligned in this family is
not known. This region of similarity contains several
predicted transmembrane helices. This family also
includes the ERD1 (ERD: ER retention defective) yeast
proteins. ERD1 proteins are involved in the localisation
of endogenous endoplasmic reticulum (ER) proteins. erd1
null mutants secrete such proteins even though they
possess the C-terminal HDEL ER lumen localisation label
sequence. In addition, null mutants also exhibit defects
in the Golgi-dependent processing of several
glycoproteins, which led to the suggestion that the
sorting of luminal ER proteins actually occurs in the
Golgi, with subsequent return of these proteins to the
ER via `salvage' vesicles.
Length = 337
Score = 112 bits (282), Expect = 6e-28
Identities = 47/128 (36%), Positives = 66/128 (51%), Gaps = 8/128 (6%)
Query: 161 MAMRLYRGPLLIIQFIFLMGVNVYGWRSSGVNHVLIFELDPRNHLSEQHLMEISLIMGNV 220
LYRG L+I ++L G+N+Y W+ SG+N+V IFE DPR LS + L+E++ +
Sbjct: 1 TLFPLYRGFFLLILGLWLWGLNLYVWKRSGINYVFIFEFDPRTSLSHRELLELASFFTVL 60
Query: 221 WALSLLCFFFSHVFSIPPYSQ----PVALLLIMLAFLLNPSRTLKYDARFWLLRVTPVAL 276
W LS L + + + P+ LLLI+L L P RFWLLR L
Sbjct: 61 WLLSFLLYLLLEHLELTKPASWVQVPLVLLLIVLLILFLPFNIFYRSGRFWLLRT----L 116
Query: 277 LLIMLAFL 284
I+LA
Sbjct: 117 FRILLAPF 124
Score = 66.5 bits (163), Expect = 3e-12
Identities = 23/50 (46%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 312 DNPFFYPWLAASVISSIYSYIWDIKMDWGLFDKNAPPDNPFLREETVYSS 361
+ + W+ S+I+SIYS+ WD+KMDWGLF KN+ N FLR++ +Y
Sbjct: 228 SDAYRILWIVFSIINSIYSFYWDVKMDWGLFQKNSSK-NRFLRDKLLYPR 276
>gnl|CDD|227696 COG5409, COG5409, EXS domain-containing protein [Signal
transduction mechanisms].
Length = 384
Score = 36.7 bits (85), Expect = 0.019
Identities = 29/151 (19%), Positives = 56/151 (37%), Gaps = 20/151 (13%)
Query: 140 AILFAIILLRVFFDTSQEDFKMAMRLYRGPLLIIQFIFLMGVNVYGWRSSGVNHVLIFEL 199
++ I L + + + L+ G +L+ FL V+ Y + +N+ IF
Sbjct: 14 SLGLYIQNLLNVGEPQSFIVLILLALWGGWILVFFLAFLFDVSCYILTRTPINYRFIFLF 73
Query: 200 D-----PRNHLSEQHLMEISLIMGNVWALSLLCFFFSH--------VFSIPPYSQPVALL 246
+ RN + H + I + SL F F + + + P+ +
Sbjct: 74 EQLSSTARNFNLDFHRIIIPFHF---FTTSL--FIFLNAVEGLKFILLFVYFL--PLLQV 126
Query: 247 LIMLAFLLNPSRTLKYDARFWLLRVTPVALL 277
+ FLL P + + Y +R +L+ L
Sbjct: 127 GTVFWFLLKPFQIIYYWSRRYLIESLIRVFL 157
Score = 35.9 bits (83), Expect = 0.035
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 316 FYPWLAASVISSIYSYIWDIKMDWGL 341
F+ + ++++SIY+ WD+ MDW L
Sbjct: 266 FHLQIWFALLNSIYTSFWDVFMDWSL 291
>gnl|CDD|234485 TIGR04154, archaeo_STT3, oligosaccharyl transferase, archaeosortase
A system-associated. Members of this protein family
occur, one to three members per genome, in the same
species of Euryarchaeota as contain the predicted
protein-sorting enzyme archaeosortase (TIGR04125) and
its cognate protein-sorting signal PGF-CTERM
(TIGR04126).
Length = 815
Score = 35.4 bits (82), Expect = 0.064
Identities = 26/91 (28%), Positives = 39/91 (42%), Gaps = 13/91 (14%)
Query: 202 RNHLSEQHLMEISLIMGNVWALSLLCFFFSHVFSIPPYS--QPVALLLIMLAFLLNPSRT 259
R E +L + + V A+ +L F F FS YS QP+ALL + L +L
Sbjct: 231 RGRSPE-YLAIVGAVTFAVAAVLVLPFGFKLGFSATYYSLFQPLALLGVALGAVL----- 284
Query: 260 LKYDARFWLLR-----VTPVALLLIMLAFLL 285
L +RFW + P A+ + +L
Sbjct: 285 LAGLSRFWERKDLPRYYYPAAVAGLAALGIL 315
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is
functionally equivalent to L7/L12 in bacteria and the
P1 and P2 proteins in eukaryotes. L12p is homologous to
P1 and P2 but is not homologous to bacterial L7/L12. It
is located in the L12 stalk, with proteins L10, L11,
and 23S rRNA. L12p is the only protein in the ribosome
to occur as multimers, always appearing as sets of
dimers. Recent data indicate that most archaeal species
contain six copies of L12p (three homodimers), while
eukaryotes have four copies (two heterodimers), and
bacteria may have four or six copies (two or three
homodimers), depending on the species. The organization
of proteins within the stalk has been characterized
primarily in bacteria, where L7/L12 forms either two or
three homodimers and each homodimer binds to the
extended C-terminal helix of L10. L7/L12 is attached to
the ribosome through L10 and is the only ribosomal
protein that does not directly interact with rRNA.
Archaeal L12p is believed to function in a similar
fashion. However, hybrid ribosomes containing the large
subunit from E. coli with an archaeal stalk are able to
bind archaeal and eukaryotic elongation factors but not
bacterial elongation factors. In several mesophilic and
thermophilic archaeal species, the binding of 23S rRNA
to protein L11 and to the L10/L12p pentameric complex
was found to be temperature-dependent and cooperative.
Length = 106
Score = 32.9 bits (75), Expect = 0.076
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEISM 34
E+K E+EEE+KK ++ EEEEE ++
Sbjct: 73 AAEEKAEEKEEEKKKEEEKEEEEEEAL 99
Score = 27.8 bits (62), Expect = 3.4
Identities = 9/26 (34%), Positives = 21/26 (80%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEIS 33
+E+ ++ EEE+++++ K+ EEEE ++
Sbjct: 75 EEKAEEKEEEKKKEEEKEEEEEEALA 100
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 34.1 bits (79), Expect = 0.14
Identities = 27/123 (21%), Positives = 37/123 (30%), Gaps = 32/123 (26%)
Query: 224 SLLCFFFSHVFSIPP--YSQPVALLLIMLAFLL---------NPSRTLKYDARFW--LLR 270
LL + P S LLL +L FLL + R + LL
Sbjct: 11 LLLAYLLRFGSRGIPDIESYLALLLLAVLLFLLIFALFGLYRSWRRRSRLREMLLRILLA 70
Query: 271 VTPVALLLIMLAFLLNPSRTLKYDARFWLLRVTVKKDQSVMDNPFFYPWLAASVISSIYS 330
T L+L +LAFLL +R W +L A + +
Sbjct: 71 WTLTFLILALLAFLLKYGTEF---SRLW----------------LLLWFLLALALLLLGR 111
Query: 331 YIW 333
I
Sbjct: 112 LIL 114
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 31.8 bits (73), Expect = 0.15
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEIS 33
E+KK EEEEEE +K E EEE +
Sbjct: 76 AAEEKKEEEEEEE---EKEESEEEAA 98
Score = 30.3 bits (69), Expect = 0.49
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEEISM 34
E++EEE++ ++ EE EE +
Sbjct: 73 AAAAAEEKKEEEEEEEEKEESEEEAA 98
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 31.6 bits (72), Expect = 0.22
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEIS 33
+++ EEEEEE++ ++ EEE ++
Sbjct: 73 AAAEEEEEEEEEEEEEEEESEEEAMA 98
Score = 30.8 bits (70), Expect = 0.34
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEEISM 34
+ EEEEEE++ ++ EE EE +M
Sbjct: 72 AAAAEEEEEEEEEEEEEEEESEEEAM 97
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 33.0 bits (76), Expect = 0.32
Identities = 23/134 (17%), Positives = 44/134 (32%), Gaps = 31/134 (23%)
Query: 138 CFAILFAIILLRVFFDTSQEDFKMAMRLYRG-PLLIIQFIFLMGVNVYGWRSSGVNHVLI 196
+L A+ L + +++ L+ G LL I L G+ WR+S + +I
Sbjct: 7 LLLVLVALALALLLR------DELSASLWSGAQLLTICVFILFGLYRAVWRASVSDLFII 60
Query: 197 FELDPRNHLSEQHLMEISLIMGNVWALSLLCFFFSHVFSIPPYSQPVALLLIMLAFLLNP 256
+++ AL L FF + + P S + L++ +
Sbjct: 61 L---------------KAVL---TSALVSLLFFST--RTDLPRSVVLVYWLLLFVLIG-- 98
Query: 257 SRTLKYDARFWLLR 270
+ R
Sbjct: 99 --ASRLLFRALRDA 110
>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex. This
entry is characterized by proteins with alternating
conserved and low-complexity regions. Bud13 together
with Snu17p and a newly identified factor,
Pml1p/Ylr016c, form a novel trimeric complex. called
The RES complex, pre-mRNA retention and splicing
complex. Subunits of this complex are not essential for
viability of yeasts but they are required for efficient
splicing in vitro and in vivo. Furthermore,
inactivation of this complex causes pre-mRNA leakage
from the nucleus. Bud13 contains a unique,
phylogenetically conserved C-terminal region of unknown
function.
Length = 141
Score = 31.5 bits (72), Expect = 0.34
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEISMRLV 37
EEK++ +E E+E+K +K E+E+E LV
Sbjct: 14 IEEKREEKEREKEEKERKEEKEKEWGKGLV 43
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 30.3 bits (68), Expect = 0.47
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEE 31
EE++ E++EEE+ + EE EE
Sbjct: 53 EEEEVDEDDEEEEGEGEEEEGEE 75
>gnl|CDD|206063 pfam13892, DBINO, DNA-binding domain. DBINO is a DNA-binding
domain found on global transcription activator SNF2L1
proteins and chromatin re-modelling proteins.
Length = 140
Score = 31.1 bits (71), Expect = 0.50
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 8/37 (21%)
Query: 2 EPLLKWK-------EEKKKMEEEEEEKKNKKGEEEEE 31
E LL WK E +K+ E+E E+ KK EE E
Sbjct: 73 EMLLFWKKNEKEERELRKRAEKEALEQA-KKEEELRE 108
>gnl|CDD|132966 cd06635, STKc_TAO1, Catalytic domain of the Protein
Serine/Threonine Kinase, Thousand-and-one amino acids 1.
Serine/threonine kinases (STKs), thousand-and-one amino
acids 1 (TAO1) subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The TAO subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. TAO proteins possess mitogen-activated protein
kinase (MAPK) kinase kinase (MAPKKK or MAP3K or MKKK)
activity. MAPK signaling cascades are important in
mediating cellular responses to extracellular signals.
TAO1 is sometimes referred to as prostate-derived
sterile 20-like kinase 2 (PSK2). TAO1 activates the p38
MAPK through direct interaction with and activation of
MEK3. TAO1 is highly expressed in the brain and may play
a role in neuronal apoptosis. TAO1 interacts with the
checkpoint proteins BubR1 and Mad2, and plays an
important role in regulating mitotic progression, which
is required for both chromosome congression and
checkpoint-induced anaphase delay. TAO1 may play a role
in protecting genomic stability.
Length = 317
Score = 31.6 bits (71), Expect = 0.67
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 19/88 (21%)
Query: 319 WLAASVISSIYSYIWDIKMD-WGL------FDKNAPPDNPFLREETVYSSTEMKALLYQA 371
W+A VI ++ +D K+D W L + PP +++ M AL + A
Sbjct: 187 WMAPEVILAMDEGQYDGKVDVWSLGITCIELAERKPP---------LFNMNAMSALYHIA 237
Query: 372 MEEAPSLETTEPEVISRYFRMFDENFFH 399
E+P+L++ E S YFR F ++
Sbjct: 238 QNESPTLQSNE---WSDYFRNFVDSCLQ 262
>gnl|CDD|187737 cd09616, Peptidase_C12_UCH_L1_L3, Cysteine peptidase C12 containing
ubiquitin carboxyl-terminal hydrolase (UCH) families L1
and L3. This ubiquitin C-terminal hydrolase (UCH)
family includes UCH-L1 and UCH-L3, the two members
sharing around 53% sequence identity as well as
conserved catalytic residues. Both enzymes hydrolyze
carboxyl terminal esters and amides of ubiquitin (Ub).
UCH-L1, in dimeric form, has additional enzymatic
activity as a ubiquitin ligase. It is highly abundant in
the brain, constituting up to 2% of total protein, and
is expressed exclusively in neurons and testes. Abnormal
expression of UCH-L1 has been shown to correlate with
several forms of cancer, including several primary lung
tumors, lung tumor cell lines, and colorectal cancers.
Mutations in the UCH-L1 gene have been linked to
susceptibility to and protection from Parkinson's
disease (PD); dysfunction of the hydrolase activity can
lead to an accumulation of alpha-synuclein, which is
linked to Parkinson's disease (PD), while accumulation
of neurofibrillary tangles is linked to Alzheimer's
disease (AD). UCH-L3 hydrolyzes isopeptide bonds at the
C-terminal glycine of either Ub or Nedd8, a
ubiquitin-like protein. It can also interact with
Lys48-linked Ub dimers to protect them from degradation
while inhibiting its hydrolase activity at the same
time. Unlike UCH-L1, neither dimerization nor ligase
activity have been observed for UCH-L3. It has been
shown that levels of Nedd8 and the apoptotic protein p53
and Bax are elevated in UCH-L3 knockout mice upon
cryptorchid injury, possibly contributing to profound
germ cell loss via apoptosis.
Length = 222
Score = 31.1 bits (71), Expect = 0.74
Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 15/78 (19%)
Query: 3 PLLKWKEEKKKMEEEEEEKKNKKGEEEEEI------------SMRLVHSLINVSNAAISL 50
P+ K EE +K EEEEE K K E E + ++ L+H++ N + L
Sbjct: 52 PITKAYEEFRK--EEEEEIKEKGQEVSESVYFMKQTIGNACGTIALIHAVANNEDRINIL 109
Query: 51 TDLGFFASHVKTLLNVDV 68
F ++ +
Sbjct: 110 EG-SFLKKFLEEAKGLSP 126
>gnl|CDD|227448 COG5118, BDP1, Transcription initiation factor TFIIIB, Bdp1 subunit
[Transcription].
Length = 507
Score = 31.6 bits (71), Expect = 0.90
Identities = 15/55 (27%), Positives = 24/55 (43%)
Query: 2 EPLLKWKEEKKKMEEEEEEKKNKKGEEEEEISMRLVHSLINVSNAAISLTDLGFF 56
E L++ + E K +E EE KN EE++ +L + I DL +
Sbjct: 441 EKLIELQNEHKHHMKEIEEAKNTAKEEDQTAQRLNDANLNKKGSGGIMTNDLKVY 495
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 30.9 bits (70), Expect = 1.0
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEISM 34
K+ K+ E+ +E+ K EEEEE
Sbjct: 158 KKLKELEAEDVDEEDEKDEEEEEEEEE 184
Score = 28.6 bits (64), Expect = 5.3
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 5 LKWKEEKKKMEEEEEEKKNKKGEEEEE 31
L E+K K E E+ + + +EEEE
Sbjct: 153 LSMLEKKLKELEAEDVDEEDEKDEEEE 179
Score = 28.6 bits (64), Expect = 5.3
Identities = 9/26 (34%), Positives = 20/26 (76%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEIS 33
+++ K++E E+ +++++K EEEEE
Sbjct: 157 EKKLKELEAEDVDEEDEKDEEEEEEE 182
Score = 27.8 bits (62), Expect = 9.9
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 2 EPLLKWKEEKKKM-----EEEEEEKKNKKGEEEEE 31
+ K +KK+ E+ +EE + + EEEEE
Sbjct: 148 DIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEE 182
>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are approximately 90 amino acids in
length. There are two completely conserved L residues
that may be functionally important.
Length = 70
Score = 28.5 bits (64), Expect = 1.1
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 5 LKWKEEKKKMEEEEEEKKNKKGEEEEEISM 34
LK +EEK++ EEEE K+ ++ E E+ S
Sbjct: 29 LKAEEEKRE-EEEEARKREERKEREKNKSF 57
Score = 27.3 bits (61), Expect = 3.3
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 6 KWKEEKKKMEEEEEEKKNKKGEEEEE 31
K K +KK+++ EEE+++ ++ + E
Sbjct: 21 KLKAKKKELKAEEEKREEEEEARKRE 46
>gnl|CDD|218688 pfam05680, ATP-synt_E, ATP synthase E chain. This family
consists of several ATP synthase E chain sequences
which are components of the CF(0) subunit.
Length = 83
Score = 28.6 bits (64), Expect = 1.3
Identities = 6/29 (20%), Positives = 16/29 (55%)
Query: 7 WKEEKKKMEEEEEEKKNKKGEEEEEISMR 35
++ ++K +E+ + KK ++E S+
Sbjct: 42 YEAQEKLIEKAKAAYAKKKQAKQEAKSLA 70
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 29.3 bits (66), Expect = 1.3
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEEIS 33
E +E EE++ ++ EEE
Sbjct: 77 AEAAAEADEAEEEEKEEEAEEESDD 101
Score = 28.5 bits (64), Expect = 2.7
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEEISM 34
E + +E EEE+K ++ EEE + M
Sbjct: 78 EAAAEADEAEEEEKEEEAEEESDDDM 103
>gnl|CDD|145924 pfam03034, PSS, Phosphatidyl serine synthase. Phosphatidyl serine
synthase is also known as serine exchange enzyme. This
family represents eukaryotic PSS I and II which are
membrane bound proteins which catalyzes the replacement
of the head group of a phospholipid (phosphotidylcholine
or phosphotidylethanolamine) by L-serine.
Length = 278
Score = 30.4 bits (69), Expect = 1.4
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 220 VWALSLL-CFFFSHVFSIPPYSQPVALL-LIMLAFLLNPS 257
+ L+ L FF H+ IPP S P+ L LI+ + P+
Sbjct: 200 LILLAELNTFFLKHILWIPP-SHPLVLYRLILWGLISAPA 238
>gnl|CDD|216292 pfam01086, Clathrin_lg_ch, Clathrin light chain.
Length = 225
Score = 30.5 bits (69), Expect = 1.4
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 2 EPLLKWKEEKKKMEEEEEEKKNKKGEE 28
E + KW+E + EE +E KK EE
Sbjct: 112 ESIRKWRERRDLRIEERDEASEKKKEE 138
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.1 bits (70), Expect = 1.4
Identities = 13/23 (56%), Positives = 20/23 (86%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEE 31
EE+++ EEEEEE++ ++ EEEEE
Sbjct: 866 EEEEEEEEEEEEEEEEEEEEEEE 888
Score = 30.7 bits (69), Expect = 1.6
Identities = 13/24 (54%), Positives = 21/24 (87%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEE 31
+EE+++ EEEEEE++ ++ EEEEE
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEE 887
Score = 30.7 bits (69), Expect = 1.7
Identities = 13/24 (54%), Positives = 21/24 (87%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEE 31
+EE+++ EEEEEE++ ++ EEEEE
Sbjct: 866 EEEEEEEEEEEEEEEEEEEEEEEE 889
Score = 30.3 bits (68), Expect = 2.3
Identities = 12/24 (50%), Positives = 20/24 (83%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEE 31
+EE+++ EEEEEE++ ++ EEEE
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEEN 890
Score = 30.0 bits (67), Expect = 2.6
Identities = 12/27 (44%), Positives = 22/27 (81%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEISM 34
+EE+++ EEEEEE++ ++ E EE +S+
Sbjct: 870 EEEEEEEEEEEEEEEEEEEENEEPLSL 896
Score = 30.0 bits (67), Expect = 3.3
Identities = 13/29 (44%), Positives = 22/29 (75%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEISMRL 36
+EE+++ EEEEEE++ ++ EEE E + L
Sbjct: 868 EEEEEEEEEEEEEEEEEEEEEENEEPLSL 896
>gnl|CDD|218482 pfam05178, Kri1, KRI1-like family. The yeast member of this
family (Kri1p) is found to be required for 40S ribosome
biogenesis in the nucleolus.
Length = 99
Score = 28.8 bits (65), Expect = 1.5
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEE 31
+EEK + EEE + KN K EE EE
Sbjct: 5 EEEKAQREEELKRLKNLKREEIEE 28
>gnl|CDD|238233 cd00400, Voltage_gated_ClC, CLC voltage-gated chloride channel. The
ClC chloride channels catalyse the selective flow of Cl-
ions across cell membranes, thereby regulating
electrical excitation in skeletal muscle and the flow of
salt and water across epithelial barriers. This domain
is found in the halogen ions (Cl-, Br- and I-) transport
proteins of the ClC family. The ClC channels are found
in all three kingdoms of life and perform a variety of
functions including cellular excitability regulation,
cell volume regulation, membrane potential
stabilization, acidification of intracellular
organelles, signal transduction, transepithelial
transport in animals, and the extreme acid resistance
response in eubacteria. They lack any structural or
sequence similarity to other known ion channels and
exhibit unique properties of ion permeation and gating.
Unlike cation-selective ion channels, which form
oligomers containing a single pore along the axis of
symmetry, the ClC channels form two-pore homodimers with
one pore per subunit without axial symmetry. Although
lacking the typical voltage-sensor found in cation
channels, all studied ClC channels are gated (opened and
closed) by transmembrane voltage. The gating is
conferred by the permeating ion itself, acting as the
gating charge. In addition, eukaryotic and some
prokaryotic ClC channels have two additional C-terminal
CBS (cystathionine beta synthase) domains of putative
regulatory function.
Length = 383
Score = 30.2 bits (69), Expect = 1.7
Identities = 21/78 (26%), Positives = 27/78 (34%), Gaps = 16/78 (20%)
Query: 223 LSLLCFFFSHVFS--------------IPPYSQPV--ALLLIMLAFLLNPSRTLKYDARF 266
L LL +F IPP+ +P LLL +L L Y A
Sbjct: 212 LGLLAGLVGVLFVRLLYKIERLFRRLPIPPWLRPALGGLLLGLLGLFLPQVLGSGYGAIL 271
Query: 267 WLLRVTPVALLLIMLAFL 284
L LLL++L L
Sbjct: 272 LALAGELSLLLLLLLLLL 289
>gnl|CDD|191634 pfam06886, TPX2, Targeting protein for Xklp2 (TPX2). This family
represents a conserved region approximately 60 residues
long within the eukaryotic targeting protein for Xklp2
(TPX2). Xklp2 is a kinesin-like protein localised on
centrosomes throughout the cell cycle and on spindle
pole microtubules during metaphase. In Xenopus, it has
been shown that Xklp2 protein is required for
centrosome separation and maintenance of spindle
bi-polarity. TPX2 is a microtubule-associated protein
that mediates the binding of the C-terminal domain of
Xklp2 to microtubules. It is phosphorylated during
mitosis in a microtubule-dependent way.
Length = 57
Score = 27.7 bits (62), Expect = 1.8
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 9 EEKKKMEEEEEEK--KNKKGEEEEEISM---RLVH 38
EEK+K E E+E+ +K EEEE I LV
Sbjct: 18 EEKEKALEAEKEEAEARQKEEEEEAIKQLRKELVP 52
>gnl|CDD|220763 pfam10453, NUFIP1, Nuclear fragile X mental
retardation-interacting protein 1 (NUFIP1). Proteins
in this family have been implicated in the assembly of
the large subunit of the ribosome and in telomere
maintenance. Some proteins in this family contain a
CCCH zinc finger. This family contains a protein called
human fragile X mental retardation-interacting protein
1, which is known to bind RNA and is phosphorylated
upon DNA damage.
Length = 57
Score = 27.3 bits (61), Expect = 2.0
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 7/31 (22%)
Query: 6 KWKEEKKKM-------EEEEEEKKNKKGEEE 29
KW EE+KK E++++ ++ + E
Sbjct: 26 KWIEERKKNYPTKANIEKKKKAEEERIKRGE 56
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 30.2 bits (69), Expect = 2.1
Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEIS 33
+++ EEEEEE+ ++ EEE +
Sbjct: 299 AAAEEEEEEEEEEE--EEEPSEEEAA 322
>gnl|CDD|169428 PRK08404, PRK08404, V-type ATP synthase subunit H; Validated.
Length = 103
Score = 28.6 bits (64), Expect = 2.1
Identities = 19/39 (48%), Positives = 23/39 (58%), Gaps = 11/39 (28%)
Query: 4 LLKWKEEKKKMEEE-----EE------EKKNKKGEEEEE 31
+ K KEE KK+EEE EE EKK K+GEEE +
Sbjct: 30 IRKAKEEAKKIEEEIIKKAEEEAQKLIEKKKKEGEEEAK 68
Score = 27.8 bits (62), Expect = 3.4
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 9 EEKKKMEEEEEEKKNKKGEEE-EEISMRLVHSLINVSNAAISL 50
E+KKK EEE +K ++GE+E EE+ ++ + + AI L
Sbjct: 57 EKKKKEGEEEAKKILEEGEKEIEELKVKAEENFETAVSEAIKL 99
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 28.0 bits (63), Expect = 2.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 15 EEEEEEKKNKKGEEEEEISM 34
EEEKK ++ EEEE+ M
Sbjct: 64 AAAEEEKKEEEEEEEEDDDM 83
Score = 27.6 bits (62), Expect = 3.7
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 8 KEEKKKMEEEEEE 20
+EEKK+ EEEEEE
Sbjct: 67 EEEKKEEEEEEEE 79
>gnl|CDD|224951 COG2040, MHT1, Homocysteine/selenocysteine methylase
(S-methylmethionine-dependent) [Amino acid transport and
metabolism].
Length = 300
Score = 29.6 bits (67), Expect = 2.8
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 213 ISLIMG--NVWALSLLCFFFSHVFSIPPYSQPVALLLIMLAFLLNPSRTLKYDAR 265
+++ G N+ AL + C H IP + ++ LL ++ P+ +YD
Sbjct: 198 AAILAGLPNIAALGVNCCHPDH---IPAAIEELSKLLTGKPIIVYPNSGEQYDPA 249
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 29.3 bits (66), Expect = 2.9
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 8 KEEKKKM----EEEEEEKKNKKGEEEEEISMR 35
KE K+ E EEEEKK KK ++E + +
Sbjct: 137 KETTAKVEKEAEVEEEEKKEKKKKKEVKKEKK 168
>gnl|CDD|220569 pfam10101, DUF2339, Predicted membrane protein (DUF2339). This
domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 738
Score = 29.6 bits (67), Expect = 3.2
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
Query: 195 LIFELDPRNHLSEQHLMEISLIMGN-VWALSLLCFFFSHVFSIPPYSQPVALLLIMLAFL 253
++ L R + ++++L+ GN + A SL +++ + +A L + LAFL
Sbjct: 201 VLPALRWRLPARLRPYVDLTLLFGNPLVAFSLQALLVHDPYALAWSALGLAALYLALAFL 260
Query: 254 LNPSRTLKYDARFWLLRVTPVALLLIMLAFLL 285
L +R + R + +AL + LA L
Sbjct: 261 L--ARRARLSLRLLAYSLLALALAFVTLAIPL 290
>gnl|CDD|216831 pfam01988, VIT1, VIT family. This family includes the vacuolar
Fe2+/Mn2+ uptake transporter, Ccc1 and the vacuolar iron
transporter VIT1.
Length = 209
Score = 29.2 bits (66), Expect = 3.2
Identities = 23/119 (19%), Positives = 41/119 (34%), Gaps = 14/119 (11%)
Query: 74 AEHVDVSHFYVNKDINHLISETEATVTSELEEGDRQKAMKRLRVPPLGEQQSPWTTFKVG 133
E +++ Y + ++ E V EL + D AM R LG + + K
Sbjct: 80 GEREELAEIYRARGLSE---ELARQVARELMKKDALDAMMREE---LGLEPETASPLKAA 133
Query: 134 LFLGCFAILFAIILLRVFFDTSQEDFKMAMRLYRGPLLIIQFIFLMGVNVYGWRSSGVN 192
L G IL +I L + ++ + + + L + R SG +
Sbjct: 134 LASGLSFILGGLIPLLPYLLAPPSALIVS--------IAVTLLALFLLGYVKARLSGRS 184
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 29.2 bits (66), Expect = 3.4
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 4 LLKWKEEKKKM-EEEEEEKKNKKGEEEEE 31
+ KE+KK M +EE++ K +K + EE
Sbjct: 94 FEEEKEKKKAMSKEEKKAIKEEKEKLEEP 122
>gnl|CDD|225105 COG2194, COG2194, Predicted membrane-associated, metal-dependent
hydrolase [General function prediction only].
Length = 555
Score = 29.7 bits (67), Expect = 3.5
Identities = 22/78 (28%), Positives = 30/78 (38%), Gaps = 12/78 (15%)
Query: 210 LMEISLIMGNVWALSLLCFF--FSHVFSIPPYSQPVALLLIMLAFLLNPSRTLKYDARFW 267
L ++SL + W LL F F VF I S ++ L L+ A
Sbjct: 10 LTKLSLSLLLAWYFLLLLNFAFFLQVFLI--NSLDLSFSFSFLLALVF--------AFLL 59
Query: 268 LLRVTPVALLLIMLAFLL 285
LL + LL LA +L
Sbjct: 60 LLLLLSFPRLLKPLAGVL 77
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 29.3 bits (65), Expect = 3.9
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 5 LKWKEEKKKMEEEEEEKKNKKGEEEEEISMRLVHSLINVSNAAIS 49
+K +EE++ + E++K+ KK E+E+ R HSL S+ I+
Sbjct: 82 VKLEEERRHRQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIA 126
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 29.2 bits (66), Expect = 4.2
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 2 EPLLKWKEEKKKMEEEEEEKKNKKGEEEEE 31
E L + KEEK+ ++E++ +K KK EE+++
Sbjct: 551 EELQREKEEKEALKEQKRLRKLKKQEEKKK 580
>gnl|CDD|114219 pfam05483, SCP-1, Synaptonemal complex protein 1 (SCP-1).
Synaptonemal complex protein 1 (SCP-1) is the major
component of the transverse filaments of the
synaptonemal complex. Synaptonemal complexes are
structures that are formed between homologous
chromosomes during meiotic prophase.
Length = 787
Score = 29.3 bits (65), Expect = 4.5
Identities = 27/114 (23%), Positives = 52/114 (45%), Gaps = 9/114 (7%)
Query: 1 MEPLLKWKEEKKKMEEEEEEKKNKKGEEEEEISMRLVHSLINVSNAAISLTDLGFFASHV 60
+E K KE+ +K++ EEE K + ++E+++S+ LI ++ + DL F
Sbjct: 211 LEMHFKLKEDHEKIQHLEEEYKKEINDKEKQVSLL----LIQITEKENKMKDLTFLLEES 266
Query: 61 KTLLN-VDVGAKWRAEHVDVSHFYVNKDINHLISETEATVTSELEEGDRQKAMK 113
+ N ++ K + E++ + +HL E E S QKA++
Sbjct: 267 RDKANQLEEKTKLQDENLKEL----IEKKDHLTKELEDIKMSLQRSMSTQKALE 316
>gnl|CDD|151173 pfam10669, Phage_Gp23, Protein gp23 (Bacteriophage A118). This
is the highly conserved family of the major tail
subunit protein.
Length = 121
Score = 27.8 bits (61), Expect = 4.5
Identities = 12/27 (44%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 5 LKWKEEKKKMEEEEEEKKNKKGEEEEE 31
++ KEE+ KM E E EK++K+ +EE +
Sbjct: 46 VEMKEERDKM-ETEREKRDKESKEERD 71
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 28.5 bits (64), Expect = 4.7
Identities = 9/26 (34%), Positives = 22/26 (84%)
Query: 6 KWKEEKKKMEEEEEEKKNKKGEEEEE 31
KWK +KKK ++++++ K+KK +++++
Sbjct: 83 KWKWKKKKSKKKKDKDKDKKDDKKDD 108
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 309
Score = 28.6 bits (64), Expect = 5.2
Identities = 8/33 (24%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 8 KEEKKK-MEEEEEEKKNKKGEEEEEISMRLVHS 39
+E+++ +++EEEE++ K + ++ + L S
Sbjct: 158 EEQRRLLLQKEEEEQQMNKRKNKQALLDELETS 190
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 28.5 bits (64), Expect = 5.3
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 6 KWKEEKKKMEEEEEEKKNKKGEEEE 30
K K++++K EEE +++ K+ EEEE
Sbjct: 191 KLKQQQQKREEERRKQRKKQQEEEE 215
Score = 28.5 bits (64), Expect = 5.9
Identities = 8/31 (25%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 6 KWKEEKKKMEEEE-EEKKNKKGEEEEEISMR 35
+W+ +K K ++++ EE++ K+ ++++E R
Sbjct: 186 EWELKKLKQQQQKREEERRKQRKKQQEEEER 216
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 28.8 bits (64), Expect = 5.4
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 11/41 (26%)
Query: 2 EPLLKWKEEKKKMEE-----EEEEKKNKKGE------EEEE 31
E L+ +E KKK EE EEEE++ K+ E EEEE
Sbjct: 211 EAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEE 251
>gnl|CDD|198151 smart01083, Cir_N, N-terminal domain of CBF1 interacting
co-repressor CIR. This is a 45 residue conserved
region at the N-terminal end of a family of proteins
referred to as CIRs (CBF1-interacting co-repressors).
CBF1 (centromere-binding factor 1) acts as a
transcription factor that causes repression by binding
specifically to GTGGGAA motifs in responsive promoters,
and it requires CIR as a co-repressor. CIR binds to
histone deacetylase and to SAP30 and serves as a linker
between CBF1 and the histone deacetylase complex.
Length = 37
Score = 25.6 bits (57), Expect = 5.4
Identities = 9/24 (37%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 7 WK-EEKKKMEEEEEEKKNKKGEEE 29
WK E+K + E+++ E++ K+ E+E
Sbjct: 14 WKAEQKAEEEKKKIEERRKEIEKE 37
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 28.8 bits (65), Expect = 5.6
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 5 LKWKEEKKKMEEEEEEKKNKKGEEEEE 31
L+ K E+ + E EK+ K+ +E+E
Sbjct: 239 LEQKAERLRQEAAAYEKQQKELAKEQE 265
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 29.0 bits (65), Expect = 5.6
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEE 31
EE+K+ ++EEEEK K EE +E
Sbjct: 41 EEEKEEKKEEEEKTTDKEEEVDE 63
>gnl|CDD|239575 cd03495, SQR_TypeC_SdhD_like, Succinate:quinone oxidoreductase
(SQR) Type C subfamily, Succinate dehydrogenase D (SdhD)
subunit-like; composed of predominantly uncharacterized
bacterial proteins with similarity to the E. coli SdhD
subunit. One characterized protein is the respiratory
Complex II SdhD subunit of the only eukaryotic member,
Reclinomonas americana. SQR catalyzes the oxidation of
succinate to fumarate coupled to the reduction of
quinone to quinol. It is also called succinate
dehydrogenase or Complex II, and is part of the citric
acid cycle and the aerobic respiratory chain. SQR is
composed of a flavoprotein catalytic subunit, an
iron-sulfur protein and one or two hydrophobic
transmembrane subunits. E. coli SQR is classified as
Type C SQRs because it contains two transmembrane
subunits and one heme group. The SdhD and SdhC subunits
are membrane anchor subunits containing heme and quinone
binding sites. The two-electron oxidation of succinate
in the flavoprotein active site is coupled to the
two-electron reduction of quinone in the membrane anchor
subunits via electron transport through FAD and three
iron-sulfur centers. The reversible reduction of quinone
is an essential feature of respiration, allowing
transfer of electrons between respiratory complexes.
Length = 100
Score = 27.2 bits (61), Expect = 5.6
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 265 RFWLLRVTPVALLLIMLAFLLN 286
+W RVT VAL+ ++L F+ +
Sbjct: 2 HWWAQRVTAVALVPLVLWFVFS 23
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 28.7 bits (65), Expect = 5.9
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 6 KWKEEKKKMEEEEEEK----KNKKGEEEEEI 32
+ KEE+K+ E EEE K + +K E EEE
Sbjct: 139 ERKEEEKEREREEELKILEYQREKAEREEER 169
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.0 bits (64), Expect = 6.0
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 8/37 (21%)
Query: 2 EPLLKWKEEKKKMEE----EEEEKKN----KKGEEEE 30
E K +E++KK E E EE K KK E EE
Sbjct: 1678 EEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEE 1714
Score = 29.0 bits (64), Expect = 7.0
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 2 EPLLKWKEEKKKMEEEEEEKKNKKGEEEEE 31
E +K EE KK EE++++ + K EE+E
Sbjct: 1658 ENKIKAAEEAKKAEEDKKKAEEAKKAEEDE 1687
Score = 28.6 bits (63), Expect = 9.0
Identities = 31/120 (25%), Positives = 47/120 (39%), Gaps = 18/120 (15%)
Query: 2 EPLLKWKEEKKKMEE-----EEEEKKNKKGEEEEEISMRLVHSLINVSNAAISLTDLGFF 56
E L K EE KK EE EE+KK ++ ++ EE + I A +
Sbjct: 1692 EALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENK------IKAEEAKKEAEEDKKK 1745
Query: 57 ASHVKTLLNVDVGAKWRAEHVDVSHFYVNKDINHLISETEATVTSELEEGDRQKAMKRLR 116
A K D K + H+ K + E EA + EL+E D ++ M+ +
Sbjct: 1746 AEEAK----KDEEEKKKIAHLKKEE---EKKAEEIRKEKEAVIEEELDEEDEKRRMEVDK 1798
Score = 28.6 bits (63), Expect = 9.3
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 6/32 (18%)
Query: 6 KWKEEKKKMEE--EEEEKKNKKGE----EEEE 31
K +E+KKK EE + EE + K E E EE
Sbjct: 1669 KAEEDKKKAEEAKKAEEDEKKAAEALKKEAEE 1700
>gnl|CDD|181537 PRK08676, PRK08676, hydrogenase membrane subunit; Validated.
Length = 485
Score = 28.6 bits (64), Expect = 6.5
Identities = 13/33 (39%), Positives = 15/33 (45%)
Query: 125 SPWTTFKVGLFLGCFAILFAIILLRVFFDTSQE 157
S W V L L A FAI LL+ F S+
Sbjct: 404 SVWLVLAVLLLLLLAASSFAIFLLKAFTRVSEG 436
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 27.8 bits (62), Expect = 6.5
Identities = 8/41 (19%), Positives = 19/41 (46%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEISMRLVHSLINVSNAAI 48
++++ E EE+E K E++E+ ++ L +
Sbjct: 98 EQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKT 138
>gnl|CDD|215648 pfam00003, 7tm_3, 7 transmembrane sweet-taste receptor of 3 GCPR.
This is a domain of seven transmembrane regions that
forms the C-terminus of some subclass 3
G-coupled-protein receptors. It is often associated with
a downstream cysteine-rich linker domain, NCD3G
pfam07562, which is the human sweet-taste receptor, and
the N-terminal domain, ANF_receptor pfam01094. The seven
TM regions assemble in such a way as to produce a
docking pocket into which such molecules as cyclamate
and lactisole have been found to bind and consequently
confer the taste of sweetness.
Length = 238
Score = 28.3 bits (64), Expect = 6.6
Identities = 23/115 (20%), Positives = 42/115 (36%), Gaps = 24/115 (20%)
Query: 134 LFLGCFAILFAIILLRVF-----FDTSQEDFKMAMRLYRGPLLIIQFIFLMGV------- 181
LF F + F+ +L++ F S L +G LLI+ + L+ V
Sbjct: 62 LFGLGFTLCFSCLLVKTNRIVRIFKKSSPGRPRLKSLPKGQLLIVLGLTLVQVIICVIWL 121
Query: 182 -----NVYGWRSSGVNHVLIFELDPRNHLSEQHLMEISLIMGNVWALSLLCFFFS 231
+++ ++ ++ L++G V L LLCFF +
Sbjct: 122 VVDPPFPTKDIHPEKGEIIL-------ECNKGSNVDFVLVLGYVGLLLLLCFFLA 169
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
hybrid binding domain (HBD) at the N-terminus.
Ribonuclease H (RNase H) enzymes are divided into two
major families, Type 1 and Type 2, based on amino acid
sequence similarities and biochemical properties. RNase
H is an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner in the
presence of divalent cations. RNase H is involved in
DNA replication, repair and transcription. RNase H is
widely present in various organisms, including
bacteria, archaea and eukaryotes and most prokaryotic
and eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type
1 and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD)
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability. Some bacteria
distinguished from other bacterial RNase HI in the
presence of a hybrid binding domain (HBD) at the
N-terminus which is commonly present at the N-termini
of eukaryotic RNase HI. It has been reported that this
domain is required for dimerization and processivity of
RNase HI upon binding to RNA-DNA hybrids.
Length = 133
Score = 27.5 bits (62), Expect = 6.9
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 14 MEEEEEEKKNKKGEEEEEISMRLV 37
++ EE K + G + E SMR V
Sbjct: 23 LKNGEEIKFSGSGNDPELASMRNV 46
>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 156 to 174 amino acids in length. This domain is
found associated with pfam07780, pfam01728.
Length = 154
Score = 27.6 bits (62), Expect = 7.1
Identities = 10/29 (34%), Positives = 21/29 (72%), Gaps = 1/29 (3%)
Query: 4 LLKWKEE-KKKMEEEEEEKKNKKGEEEEE 31
LLKW+++ +K + +++EK+ ++ EE E
Sbjct: 83 LLKWRKKVRKLLGLDKKEKEEEEEEEVEV 111
>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355). This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 180 and
214 amino acids in length.
Length = 125
Score = 27.2 bits (61), Expect = 7.2
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEIS 33
EEK + E E+ EK+ ++ E E
Sbjct: 43 AEEKAEYELEKLEKELEELEAELARR 68
>gnl|CDD|233951 TIGR02614, ftsW, cell division protein FtsW. This family consists
of FtsW, an integral membrane protein with ten
transmembrane segments. In general, it is one of two
paralogs involved in peptidoglycan biosynthesis, the
other being RodA, and is essential for cell division.
All members of the seed alignment for this model are
encoded in operons for the biosynthesis of
UDP-N-acetylmuramoyl-pentapeptide, a precursor of murein
(peptidoglycan). The FtsW designation is not used in
endospore-forming bacterial (e.g. Bacillus subtilis),
where the member of this family is designated SpoVE and
three or more RodA/FtsW/SpoVE family paralogs are
present. SpoVE acts in spore cortex formation and is
dispensible for growth. Biological rolls for FtsW in
cell division include recruitment of penicillin-binding
protein 3 to the division site [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan, Cellular processes, Cell division].
Length = 356
Score = 28.3 bits (64), Expect = 7.5
Identities = 25/119 (21%), Positives = 52/119 (43%), Gaps = 15/119 (12%)
Query: 141 ILFAIILLRVFFDTSQEDFKMAMRLYRGPLLIIQFIFLMGVNVYGWRSSGVN-----HVL 195
+ +A++ L + F S+ + +L P+L+I + L+ V + G +
Sbjct: 42 LFYALLGLILMFVASRLPLRFWRKLSV-PILLIAIVLLVLVLIPGIGKEVNGARRWIGLG 100
Query: 196 IFELDPRNHLSEQHLMEISLIMGNVWALSLLCFFFSHVFSIPPYSQPVALLLIMLAFLL 254
F + P SE +++LI ++ L V S + +P+A+L +++ LL
Sbjct: 101 GFSIQP----SE--FAKLALI---IYLAWYLARKQKEVKSFLKFLKPLAVLGLLVGLLL 150
>gnl|CDD|234909 PRK01146, PRK01146, DNA-directed RNA polymerase subunit L;
Provisional.
Length = 85
Score = 26.4 bits (59), Expect = 7.5
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 62 TLLNVDVGAKWRAEHVDVSHFYVNKDINH-LISETEATVTSELEEGDRQKAMKR 114
TL+N+ V+ + + DI+H LIS + ++ D +A+K
Sbjct: 23 TLMNLLKEELLEDPGVEAASY----DIDHPLISNPVLKIKTD-GGIDPLEALKE 71
>gnl|CDD|220376 pfam09745, DUF2040, Coiled-coil domain-containing protein 55
(DUF2040). This entry is a conserved domain of
approximately 130 residues of proteins conserved from
fungi to humans. The proteins do contain a coiled-coil
domain, but the function is unknown.
Length = 128
Score = 27.4 bits (61), Expect = 7.6
Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 4/25 (16%)
Query: 11 KKKMEE----EEEEKKNKKGEEEEE 31
KK++EE EEEEK+ ++ EEE +
Sbjct: 96 KKQLEENRKLEEEEKEREELEEEND 120
Score = 27.0 bits (60), Expect = 9.3
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 1 MEPLLKWKEEKKKMEEEEEEKKNKKG 26
+E K +EE+K+ EE EEE KG
Sbjct: 99 LEENRKLEEEEKEREELEEENDVTKG 124
>gnl|CDD|237115 PRK12489, PRK12489, anaerobic C4-dicarboxylate transporter;
Reviewed.
Length = 443
Score = 28.3 bits (64), Expect = 7.7
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 26/82 (31%)
Query: 170 LLIIQFIFLMGVNVYGWRSSGVNHVLIFELDPRNHLSEQHLMEISLIMGNVWALSLLCFF 229
+ IQF+ L+ G R G+ + L+ G L +L F
Sbjct: 1 MFWIQFLILLICLFLGARYGGIG--------------------LGLLGG--IGLVILVF- 37
Query: 230 FSHVFSIPPYSQPVALLLIMLA 251
VF +PP PV ++LI+LA
Sbjct: 38 ---VFGLPPGKPPVDVMLIILA 56
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 27.7 bits (62), Expect = 8.0
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEE 31
EE+KK+EE+ E ++ ++ E EEE
Sbjct: 29 EERKKLEEKREGERKEEEELEEE 51
>gnl|CDD|221099 pfam11377, DUF3180, Protein of unknown function (DUF3180). Some
members in this family of proteins are annotated as
membrane proteins however this cannot be confirmed.
Currently there is no known function.
Length = 137
Score = 27.2 bits (61), Expect = 8.2
Identities = 10/42 (23%), Positives = 20/42 (47%)
Query: 221 WALSLLCFFFSHVFSIPPYSQPVALLLIMLAFLLNPSRTLKY 262
W L+ + + I P++ PV+LL++ L+ R +
Sbjct: 13 WLLASVLERYGGSLPILPWTAPVSLLVLAAIELVLAVRVRRR 54
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 28.2 bits (63), Expect = 8.3
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 1 MEPLLKWKEEKKKMEEEEEEKKNKKGEEEEE 31
+ L K K+E+ EE+E E++ K EEE+
Sbjct: 148 LRELEKIKKER--AEEKEREEEEKAAEEEKA 176
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM).
This family consists of several Plasmodium falciparum
SPAM (secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the
alanine heptad-repeat domain. Heptad repeats in which
the a and d position contain hydrophobic residues
generate amphipathic alpha-helices which give rise to
helical bundles or coiled-coil structures in proteins.
SPAM is an example of a P. falciparum antigen in which
a repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 27.5 bits (61), Expect = 8.3
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 9 EEKKKMEEEEEEKKNKKGEEEEEI 32
E++++ EE+EE+ + K E++ I
Sbjct: 76 EDEEEEEEDEEDNVDLKDIEKKNI 99
>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit
[Energy production and conversion].
Length = 470
Score = 28.2 bits (63), Expect = 8.6
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 6 KWKEEKKKMEEEEEEKKNKKGEEEEE 31
+W EE+++ EEEEEE+ + EE
Sbjct: 400 RWAEEEEEEEEEEEEEAAEAEAPMEE 425
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 28.1 bits (63), Expect = 9.8
Identities = 25/98 (25%), Positives = 38/98 (38%), Gaps = 25/98 (25%)
Query: 8 KEEKKKMEEEEEEKKNKKGEEEEEISMRLVHSLINVSNAAISLTDLGFFASHVKTLLNVD 67
EE K+++E ++ K E +E R + V++ L D G AS +K +
Sbjct: 378 AEELAKLQDELDKIVKTKSELVKEKYHRGI-----VTDL---LKDSGIKASIIKKYIP-- 427
Query: 68 VGAKWRAEHVDVSHFYVNKDINHLISETEATVTSELEE 105
Y NK INH + EA L+E
Sbjct: 428 ---------------YFNKQINHYLQIMEADYNFTLDE 450
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
0.324 0.138 0.422
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,210,679
Number of extensions: 2127259
Number of successful extensions: 6422
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6158
Number of HSP's successfully gapped: 238
Length of query: 402
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 303
Effective length of database: 6,546,556
Effective search space: 1983606468
Effective search space used: 1983606468
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 60 (26.7 bits)