RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1790
(299 letters)
>gnl|CDD|176899 cd08890, SRPBCC_PITPNC1_like, Lipid-binding SRPBCC domain of
mammalian PITPNC1,and related proteins (Class IIB
PITPs). This subgroup includes the N-terminal SRPBCC
(START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain of
mammalian Class IIB phosphatidylinositol transfer
protein (PITP), PITPNC1/RdgBbeta, and related proteins.
These are metazoan proteins belonging to the PITP family
of lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. Mammalian PITPNC1
contains an amino-terminal SRPBCC PITP-like domain and a
short carboxyl-terminal domain. It is a cytoplasmic
protein, and is ubiquitously expressed. It can transfer
phosphatidylinositol (PtdIns) in vitro with a similar
ability to other PITPs.
Length = 250
Score = 419 bits (1078), Expect = e-149
Identities = 173/272 (63%), Positives = 211/272 (77%), Gaps = 23/272 (8%)
Query: 3 LLKEYRIPMPLTVEEYRIGQLYMIARHSHEQSEDGEGVETIVNISCEDEEHGRGQYTEKR 62
LLKEYRI MPLTVEEYRIGQLYMI+RHSHEQSE GEGVE + N CED EHG GQ+TEKR
Sbjct: 1 LLKEYRICMPLTVEEYRIGQLYMISRHSHEQSERGEGVEVVQNEPCEDPEHGNGQFTEKR 60
Query: 63 IHLSNRLPYWIQAIGRGQYTEKRIHLSNRLPYWIQAIIPKVFYITEKAWNYYPYTMTEYT 122
++L++RLP W +A+ +PK+FY+TEKAWNYYPYT+TEYT
Sbjct: 61 VYLNSRLPSWARAV-----------------------VPKIFYVTEKAWNYYPYTITEYT 97
Query: 123 CSFIPKLNIMIRTKFEDNNGSNDNCLGLTEEELLARQVEYLDIAYDEINPKHYKEEEDPK 182
CSF+PK +I I TK+EDN G ++NC+ L+E EL R+V +LDIAYDEI K+YKEEEDPK
Sbjct: 98 CSFLPKFSIHIETKYEDNKGKSENCIFLSEAELSEREVCHLDIAYDEIPEKYYKEEEDPK 157
Query: 183 FFQSKKTGRGPLKEGWRDTFEPIMCSYKVVEGAFEVWGLQTKAEDFIQKAIRDILLVGHR 242
+F+S+KTGRGPLKEGWR+T +PIMCSYK+V FEVWGLQT+ E F+ K +RDILL+GHR
Sbjct: 158 YFKSEKTGRGPLKEGWRETHKPIMCSYKLVTVKFEVWGLQTRVEQFVHKVVRDILLLGHR 217
Query: 243 QAFAWLDEWLDMSLTDVRVYEGEMQRATNVKL 274
QAFAW+DEW DM++ DVR YE +Q TN K+
Sbjct: 218 QAFAWVDEWYDMTMDDVREYERTIQEKTNEKI 249
>gnl|CDD|176857 cd07815, SRPBCC_PITP, Lipid-binding SRPBCC domain of Class I and
Class II Phosphatidylinositol Transfer Proteins. This
family includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the
phosphatidylinositol transfer protein (PITP) family of
lipid transfer proteins. This family of proteins
includes Class 1 PITPs (PITPNA/PITPalpha and
PITPNB/PITPbeta, Drosophila vibrator and related
proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2,
PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related
proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and
related proteins). The PITP family belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket. In vitro, PITPs bind
phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Class III PITPs, exemplified by the Sec14p
family, are found in yeast and plants but are unrelated
in sequence and structure to Class I and II PITPs and
belong to a different superfamily.
Length = 251
Score = 335 bits (862), Expect = e-117
Identities = 126/272 (46%), Positives = 171/272 (62%), Gaps = 22/272 (8%)
Query: 3 LLKEYRIPMPLTVEEYRIGQLYMIARHSHEQSEDGEGVETIVNISCEDEEHGRGQYTEKR 62
L+KE+RI +PLTVEEY+IGQLYM+A+ S E++ GEGVE + N EDE G+GQYT K
Sbjct: 1 LIKEFRIVLPLTVEEYQIGQLYMVAKASKEETGSGEGVEVLKNEPYEDENGGKGQYTHKI 60
Query: 63 IHLSNRLPYWIQAIGRGQYTEKRIHLSNRLPYWIQAIIPKVFYITEKAWNYYPYTMTEYT 122
HL ++LP W++A+ P I EK+WN YPY T Y+
Sbjct: 61 YHLGSKLPSWLRAL---------------AP-------KSALTIEEKSWNAYPYCKTVYS 98
Query: 123 CSFIPKLNIMIRTKFEDNNGSNDNCLGLTEEELLARQVEYLDIAYDEINPKHYKEEEDPK 182
C F K +I I + + + G+ +N L+ E+L R+V +DIA D + K YK EEDPK
Sbjct: 99 CPFFEKFSISIESMHKPDLGTQENAHNLSAEQLAQRKVVVIDIANDSVASKDYKPEEDPK 158
Query: 183 FFQSKKTGRGPLKEGWRDTFEPIMCSYKVVEGAFEVWGLQTKAEDFIQKAIRDILLVGHR 242
F+SKKTGRGPL++GWR + +PIMC+YK+V F WGLQ K E+FIQK RD+ L HR
Sbjct: 159 LFKSKKTGRGPLRKGWRKSTKPIMCAYKLVTVDFPYWGLQNKVENFIQKVERDVFLNYHR 218
Query: 243 QAFAWLDEWLDMSLTDVRVYEGEMQRATNVKL 274
QAF W+DEW D+++ D+R +E E + + K
Sbjct: 219 QAFCWIDEWFDLTMEDIREFEEETKELLDAKR 250
>gnl|CDD|176898 cd08889, SRPBCC_PITPNM1-2_like, Lipid-binding SRPBCC domain of
mammalian PITPNM1-2 and related proteins (Class IIA
PITPs). This subgroup includes an N-terminal SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class II phosphatidylinositol transfer protein
(PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal
domain-interacting receptor2) and
PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related
proteins. These are membrane associated multidomain
proteins belonging to the PITP family of lipid transfer
proteins, and to the SRPBCC domain superfamily of
proteins that bind hydrophobic ligands. SRPBCC domains
have a deep hydrophobic ligand-binding pocket. In vitro,
PITPs bind phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Ablation of the mouse gene encoding PITPNM1
results in early embryonic death. PITPNM1 is localized
chiefly to the Golgi apparatus, and under certain
conditions translocates to the lipid droplets. Targeting
to the latter is dependent on a specific threonine
residue within the SRPBCC domain. PITPNM1 plays a part
in Golgi-mediated transport. It regulates diacylglycerol
(DAG) production at the trans-Golgi network (TGN) via
the CDP-choline pathway. Drosophila RdgB, the founding
member of the PITP family, is implicated in the visual
and olfactory transduction. RdgB is required for
maintenance of ultra structure in photoreceptors and for
sensory transduction. The mouse PITPNM1 gene rescues the
phenotype of Drosophila rdgB mutant flies. In addition
to the SRPBCC domain, PITPNM1 and -2 contain a
Rho-inhibitory domain (Rid), six hydrophobic stretches,
a DDHD calcium binding region, and a C-terminal tyrosine
kinase Pyk2-binding / HAD-like phosphohydrolase domain.
PITPNM1 has a role in regulating cell morphogenesis
through its Rho inhibitory domain (Rid). This
SRPBCC_PITPNM1-2_like domain model includes the first 52
residues of the 224 residues Rid (Rho-inhibitory
domain).
Length = 260
Score = 257 bits (659), Expect = 6e-86
Identities = 117/281 (41%), Positives = 163/281 (58%), Gaps = 32/281 (11%)
Query: 3 LLKEYRIPMPLTVEEYRIGQLYMIARHSHEQSED-GEGVETIVNISCEDEEHGRGQYTEK 61
L+KEYRIP+P++VEEYRI QLYMI + S E+S+ G GVE + N
Sbjct: 2 LIKEYRIPLPMSVEEYRIAQLYMIQKKSREESKGEGSGVEILEN---------------- 45
Query: 62 RIHLSNRLPYWIQAIGRGQYTEKRIHLSNRLPYWIQAIIPK-VFYITEKAWNYYPYTMTE 120
PY G GQYT K H+ + +P W +AI+PK + E+AWN YPYT T
Sbjct: 46 -------RPYTDGPGGSGQYTHKIYHIGSHIPGWFRAILPKSALRVEEEAWNAYPYTRTR 98
Query: 121 YTCSFIPKLNIMIRTKFEDNNGSNDNCLGLTEEELLARQVEYLDIAYDEINPKHYKEEED 180
YTC F+ K ++ I T + D+ G +N L+ EL R ++++DI D + YK EED
Sbjct: 99 YTCPFVEKFSLDIETYYFDDAGEQENVFNLSPAELRQRIIDFIDIVKDPVPGSDYKAEED 158
Query: 181 PKFFQSKKTGRGPLKEGWRDTFE------PIMCSYKVVEGAFEVWGLQTKAEDFIQK-AI 233
PK + S+KTGRGPL + W + ++ PIMC+YK+ + F WG+QTK E FI A+
Sbjct: 159 PKLYVSEKTGRGPLSDDWIEEYKDPPGKGPIMCAYKLCKVEFRYWGMQTKIERFIHDVAL 218
Query: 234 RDILLVGHRQAFAWLDEWLDMSLTDVRVYEGEMQRATNVKL 274
R ++L HRQA+ W DEW +++ D+R E E Q A K+
Sbjct: 219 RKVMLRAHRQAWCWQDEWYGLTMEDIRKLEEETQLALAQKM 259
>gnl|CDD|111058 pfam02121, IP_trans, Phosphatidylinositol transfer protein. Along
with the structurally unrelated Sec14p family (found in
pfam00650), this family can bind/exchange one molecule
of phosphatidylinositol (PI) or phosphatidylcholine (PC)
and thus aids their transfer between different membrane
compartments. There are three sub-families - all share
an N-terminal PITP-like domain, whose sequence is highly
conserved. It is described as consisting of three
regions. The N-terminal region is thought to bind the
lipid and contains two helices and an eight-stranded,
mostly antiparallel beta-sheet. An intervening loop
region, which is thought to play a role in
protein-protein interactions, separates this from the
C-terminal region, which exhibits the greatest sequence
variation and may be involved in membrane binding. PITP
alpha has a 16-fold greater affinity for PI than PC.
Together with PITP beta, it is expressed ubiquitously in
all tissues.
Length = 254
Score = 248 bits (634), Expect = 3e-82
Identities = 107/276 (38%), Positives = 159/276 (57%), Gaps = 31/276 (11%)
Query: 2 VLLKEYRIPMPLTVEEYRIGQLYMIARHSHEQSE-DGEGVETIVNISCEDEEHGRGQYTE 60
+L+KEYRI +P++V+EY++ QLYMIA+ S +S +G GVE + N E E G G
Sbjct: 1 MLIKEYRILLPMSVQEYQVAQLYMIAKKSRNESHGEGSGVEILSN---EPYEDGPG---- 53
Query: 61 KRIHLSNRLPYWIQAIGRGQYTEKRIHLSNRLPYWIQAIIPK-VFYITEKAWNYYPYTMT 119
G+GQYT K HL +++P WI+ ++P+ + E+AWN YPYT T
Sbjct: 54 ----------------GKGQYTHKIYHLGSKVPAWIRTLLPEGALEVHEEAWNAYPYTRT 97
Query: 120 EYTCSFIPKLNIMIRTKFEDNNGSNDNCLGLTEEELLARQVEYLDIAYDEINPKHYKEEE 179
YT ++ +I I T ++ + G+ +N L+ ++ R ++Y+DI D+++ YK EE
Sbjct: 98 RYTNPYMEDFSIKIETWYKPDLGTQENVFNLSPKDWKTRIIDYIDIVRDQVSSGDYKAEE 157
Query: 180 DPKFFQSKKTGRGPLKEGWRDTF-----EPIMCSYKVVEGAFEVWGLQTKAEDFIQK-AI 233
DPK F S KTGRGPL W+ P+MC+YK+ F WG+QTK E+FI A+
Sbjct: 158 DPKLFHSVKTGRGPLGPDWKAELVKTGDCPLMCAYKLCTVEFRYWGMQTKVENFIHDQAL 217
Query: 234 RDILLVGHRQAFAWLDEWLDMSLTDVRVYEGEMQRA 269
R + HRQA+ W DEW +++ D+R E E Q
Sbjct: 218 RRTMTRAHRQAWCWQDEWTGLTMEDIRRLEEETQLH 253
>gnl|CDD|176897 cd08888, SRPBCC_PITPNA-B_like, Lipid-binding SRPBCC domain of
mammalian PITPNA, -B, and related proteins (Class I
PITPs). This subgroup includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class 1 phosphatidylinositol transfer proteins
(PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta,
Drosophila vibrator, and related proteins. These are
single domain proteins belonging to the PITP family of
lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. In addition,
PITPNB transfers sphingomyelin in vitro, with a low
affinity. PITPNA is found chiefly in the nucleus and
cytoplasm; it is enriched in the brain and predominantly
localized in the axons. A reduced expression of PITPNA
contributes to the neurodegenerative phenotype of the
mouse vibrator mutation. The role of PITPNA in vivo may
be to provide PtdIns for localized PI3K-dependent
signaling, thereby controlling the polarized extension
of axonal processes. PITPNA homozygous null mice die
soon after birth from complicated organ failure,
including intestinal and hepatic steatosis,
hypoglycemia, and spinocerebellar disease. PITPNB is
associated with the Golgi and ER, and is highly
expressed in the liver. Deletion of the PITPNB gene
results in embryonic lethality. The PtdIns and PtdCho
exchange activity of PITPNB is required for
COPI-mediated retrograde transport from the Golgi to the
ER. Drosophila vibrator localizes to the ER, and has an
essential role in cytokinesis during mitosis and
meiosis.
Length = 258
Score = 231 bits (590), Expect = 2e-75
Identities = 105/274 (38%), Positives = 155/274 (56%), Gaps = 31/274 (11%)
Query: 3 LLKEYRIPMPLTVEEYRIGQLYMIARHSHEQSEDGEGVETIVNISCEDEEHGRGQYTEKR 62
L+KE+R+ +PL+VEEY++GQLY +A S ++ GEG+E +VN E + + +
Sbjct: 1 LIKEFRVILPLSVEEYQVGQLYSVAEASKNETGGGEGIEVLVN-----EPYEKDDGEK-- 53
Query: 63 IHLSNRLPYWIQAIGRGQYTEKRIHLSNRLPYWIQAIIPK-VFYITEKAWNYYPYTMTEY 121
GQYT K HL +++P +++ + P+ I EKAWN YPY T
Sbjct: 54 ----------------GQYTHKIYHLQSKVPGFVRMLAPEGSLEIHEKAWNAYPYCRTII 97
Query: 122 TCSFIP-KLNIMIRTKFEDNNGSNDNCLGLTEEELLARQVEYLDIAYD-EINPKHYKEEE 179
T ++ I+I T + + G+ +N L EE +V Y+DIA +++PK YK +E
Sbjct: 98 TNEYMKEDFLIIIETWHKPDLGTQENVHNLDPEEWKEVEVVYIDIADRSQVDPKDYKADE 157
Query: 180 DPKFFQSKKTGRGPLKEGWRDTFE-----PIMCSYKVVEGAFEVWGLQTKAEDFIQKAIR 234
DP FQS+KTGRGPL W+ PIMC+YK+V F+ WGLQ K E+FIQK R
Sbjct: 158 DPAKFQSEKTGRGPLGPNWKKELVNQKDCPIMCAYKLVTVEFKWWGLQNKVENFIQKQER 217
Query: 235 DILLVGHRQAFAWLDEWLDMSLTDVRVYEGEMQR 268
+ HRQ F WLD+W +++ D+R E E ++
Sbjct: 218 RLFTNFHRQVFCWLDKWHGLTMDDIRRMEDETKK 251
>gnl|CDD|177445 PHA02662, PHA02662, ORF131 putative membrane protein; Provisional.
Length = 226
Score = 33.5 bits (76), Expect = 0.079
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 277 PPPTLPTP---PTPTPTSPKSWFN 297
PP T PTP P PTP +P S ++
Sbjct: 2 PPRTPPTPPRPPEPTPAAPGSLYD 25
>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA
carboxylase.
Length = 274
Score = 30.6 bits (69), Expect = 0.99
Identities = 10/27 (37%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 269 ATNVKLTPPPPTLPTPPTPTPT-SPKS 294
A P PTP +P P +PKS
Sbjct: 169 AQPAPSAPASSPPPTPASPPPAKAPKS 195
Score = 28.3 bits (63), Expect = 4.2
Identities = 6/20 (30%), Positives = 8/20 (40%)
Query: 275 TPPPPTLPTPPTPTPTSPKS 294
PP P P P + P +
Sbjct: 164 ASPPAAQPAPSAPASSPPPT 183
>gnl|CDD|218219 pfam04707, PRELI, PRELI-like family. This family includes a
conserved region found in the PRELI protein and yeast
YLR168C gene MSF1 product. The function of this protein
is unknown, though it is thought to be involved in
intra-mitochondrial protein sorting. This region is also
found in a number of other eukaryotic proteins.
Length = 157
Score = 29.2 bits (66), Expect = 1.6
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 81 YTEKRIHLSNRLPYWIQAIIPKV--FYITEKAW-NYYPYTMTEYTC 123
+TE+ + RLP W++ +I Y+ E + + T+T T
Sbjct: 36 HTERLLTKQGRLPRWLKKLIGVADTVYVLEVSVVDPKKRTLTLETR 81
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 29.9 bits (68), Expect = 2.0
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 214 GAFEVWGLQTKAEDFIQKAIRDILLVGHRQAFAWL 248
G F WG ED I + ++ L VG FA++
Sbjct: 45 GLFWAWGAD---EDVIARLVKKTLYVG---VFAYI 73
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 29.9 bits (67), Expect = 2.0
Identities = 9/17 (52%), Positives = 9/17 (52%)
Query: 276 PPPPTLPTPPTPTPTSP 292
PP P P PP P P P
Sbjct: 2908 PPQPQAPPPPQPQPQPP 2924
Score = 28.8 bits (64), Expect = 4.5
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 277 PPPTLPTPPTPTPTSP 292
P LP P + PT+P
Sbjct: 2824 PAGPLPPPTSAQPTAP 2839
Score = 28.0 bits (62), Expect = 8.6
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 275 TPPPPTLPTPPTPTPTSPKS 294
PPPP P PP P P P+
Sbjct: 2922 QPPPPPQPQPPPPPPPRPQP 2941
>gnl|CDD|173846 cd01157, MCAD, Medium chain acyl-CoA dehydrogenase. MCADs are
mitochondrial beta-oxidation enzymes, which catalyze the
alpha,beta dehydrogenation of the corresponding medium
chain acyl-CoA by FAD, which becomes reduced. The
reduced form of MCAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. MCAD is a homotetramer.
Length = 378
Score = 29.5 bits (66), Expect = 2.0
Identities = 17/30 (56%), Positives = 22/30 (73%), Gaps = 2/30 (6%)
Query: 199 RDTFEPIMCSYKVVE-GA-FEVWGLQTKAE 226
R T EP+MC+Y V E GA +V G++TKAE
Sbjct: 108 RMTEEPLMCAYCVTEPGAGSDVAGIKTKAE 137
>gnl|CDD|216421 pfam01299, Lamp, Lysosome-associated membrane glycoprotein (Lamp).
Length = 305
Score = 29.3 bits (66), Expect = 2.2
Identities = 8/18 (44%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 275 TPPPPTLPTPPTPTPTSP 292
T P PTP P+SP
Sbjct: 89 TTVATPSP-SPTPVPSSP 105
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
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 = 378
Score = 29.5 bits (66), Expect = 2.2
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 268 RATNVKLTPPPPTLPTPPTPTPTSPKS 294
+ K+ PP T + PTPTP+ P S
Sbjct: 78 KTGTGKVAPPAATPTSAPTPTPSPPAS 104
>gnl|CDD|178744 PLN03205, PLN03205, ATR interacting protein; Provisional.
Length = 652
Score = 29.7 bits (66), Expect = 2.2
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 249 DEWLDMSLTDVRVYEGEMQRATNVKLTPPP--PT-LPTPPTPTPTSPKS 294
DE D + + + E +A +L PPP PT LP PP T+P +
Sbjct: 6 DEDEDDFIKAIDIIEAIEAKADMYRLLPPPSLPTFLPAPPVSEMTTPST 54
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 29.8 bits (67), Expect = 2.3
Identities = 15/51 (29%), Positives = 21/51 (41%)
Query: 243 QAFAWLDEWLDMSLTDVRVYEGEMQRATNVKLTPPPPTLPTPPTPTPTSPK 293
+AF+ LD L + E + A V + P P PT P+P P
Sbjct: 332 KAFSQLDFQLRTTSYGQLPLELAVIEALLVPVPAPQPAKPTAAAPSPVRPT 382
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 468
Score = 29.2 bits (66), Expect = 2.8
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 9/61 (14%)
Query: 170 INPKH-YKEEEDPKFFQSKK--TGRGPLKEGWRDTFEPIMCSYKVVEGAFE-VWGLQTKA 225
I PKH +++ EDP+ F + G GP K + +Y A E WG + K
Sbjct: 136 ILPKHIWEKVEDPEKFTGPEAAIGSGPYKLV---DYNKEQGTYLYE--ANEDYWGGKPKV 190
Query: 226 E 226
+
Sbjct: 191 K 191
>gnl|CDD|171499 PRK12438, PRK12438, hypothetical protein; Provisional.
Length = 991
Score = 29.1 bits (65), Expect = 3.5
Identities = 8/29 (27%), Positives = 9/29 (31%)
Query: 264 GEMQRATNVKLTPPPPTLPTPPTPTPTSP 292
G + A PP PP P P
Sbjct: 900 GRVATAPGGDAASAPPPGAGPPAPPQAVP 928
>gnl|CDD|171806 PRK12897, PRK12897, methionine aminopeptidase; Reviewed.
Length = 248
Score = 28.5 bits (63), Expect = 4.1
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 179 EDPKFFQSKKTGRGP-LKEGWRDTFEPIM 206
E+P F K G+GP L+EG T EPI+
Sbjct: 176 EEPAIFHFGKQGQGPELQEGMVITIEPIV 204
>gnl|CDD|187863 cd09732, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.
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;
Protein of this family often fused to HTH domain; Some
proteins could have an additional fusion with
RecB-family nuclease domain; Core domain appears to have
a Rossmann-like fold; loosely associated with CRISPR/Cas
systems; also known as TM1812 family.
Length = 221
Score = 28.0 bits (63), Expect = 4.5
Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 21/111 (18%)
Query: 73 IQAIGRGQYTEKRIHLSNRLPY---WIQ-AIIPK------VFYITEKAWNYYPYTMTEYT 122
I +G G+Y E +R ++Q A+I + ++T++A
Sbjct: 3 ISFLGTGRYKETTYVFEDREEIKTRFVQEALIEYLKPDEVIVFLTDEAAWSNWEVNQPGL 62
Query: 123 CSFIPKLNIMIRTKFEDNNGSNDNCLGLTEEELLARQVEYLDIAYDEINPK 173
+ KLN ++ + G +E+EL E D +E+
Sbjct: 63 KKHLEKLNEVLPKLVRIPD-------GRSEDEL----WEIFDKITEEVEEG 102
>gnl|CDD|221020 pfam11191, DUF2782, Protein of unknown function (DUF2782). This
is a bacterial family of proteins whose function is
unknown.
Length = 104
Score = 26.9 bits (60), Expect = 4.7
Identities = 11/14 (78%), Positives = 13/14 (92%), Gaps = 1/14 (7%)
Query: 14 TVEEYRI-GQLYMI 26
T+EEYR+ GQLYMI
Sbjct: 50 TIEEYRVNGQLYMI 63
>gnl|CDD|165468 PHA03201, PHA03201, uracil DNA glycosylase; Provisional.
Length = 318
Score = 27.5 bits (61), Expect = 8.1
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 266 MQRATNVKLTPPPPTLPTPPTPT-PTSP 292
M+RA + +P PP P+PP PT P SP
Sbjct: 1 MKRARS--RSPSPPRRPSPPRPTPPRSP 26
>gnl|CDD|217197 pfam02711, Pap_E4, E4 protein. This is is a family of
Papillomavirus proteins, E4, coded for by ORF4. A splice
variant, E1--E4, exists but neither the function of E4
or E1--E4 is known.
Length = 95
Score = 26.1 bits (58), Expect = 9.0
Identities = 7/21 (33%), Positives = 7/21 (33%)
Query: 275 TPPPPTLPTPPTPTPTSPKSW 295
T P P PP P K
Sbjct: 18 TYTTPPRPPPPPPPWAPKKRC 38
>gnl|CDD|177553 PHA03185, PHA03185, UL14 tegument protein; Provisional.
Length = 214
Score = 27.3 bits (60), Expect = 9.6
Identities = 10/16 (62%), Positives = 10/16 (62%)
Query: 279 PTLPTPPTPTPTSPKS 294
P PTPP P PT P S
Sbjct: 187 PAPPTPPRPGPTDPAS 202
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 0.137 0.431
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,041,829
Number of extensions: 1539077
Number of successful extensions: 2160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2123
Number of HSP's successfully gapped: 36
Length of query: 299
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 203
Effective length of database: 6,679,618
Effective search space: 1355962454
Effective search space used: 1355962454
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: 59 (26.6 bits)