RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4655
(595 letters)
>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 = 234 bits (599), Expect = 3e-73
Identities = 132/396 (33%), Positives = 173/396 (43%), Gaps = 154/396 (38%)
Query: 1 MLIKEYRIPLPLTVDEYKIAQLYMIAKKSREESKGAGSGVEILYNEPYDNDEEAPGTKGQ 60
MLIKEYRI LP++V EY++AQLYMIAKKSR ES G GSGVEIL NEPY++ PG KGQ
Sbjct: 1 MLIKEYRILLPMSVQEYQVAQLYMIAKKSRNESHGEGSGVEILSNEPYEDG---PGGKGQ 57
Query: 61 KTVKIYPLEWKIYHVGSHLPGWIKSLLPKSALEV-----------KYRIPLPLTVDEYKI 109
T KIYH+GS +P WI++LLP+ ALEV + R P ++++ I
Sbjct: 58 YT-------HKIYHLGSKVPAWIRTLLPEGALEVHEEAWNAYPYTRTRYTNPY-MEDFSI 109
Query: 110 AQLYMIAVSDLSQGGDISSQHRIKQTFNLRSSLTRLGLKPYSKKLNPRLRCGDCRGKEFQ 169
I + + LG + L+P
Sbjct: 110 ---------------KIETWY-----------KPDLGTQENVFNLSP------------- 130
Query: 170 LSGSDLRSRIVEVIDVVKDQLYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKED 229
D ++RI++ ID+V+DQ+ GDY EEDP ++ S TGRGPL +W +E
Sbjct: 131 ---KDWKTRIIDYIDIVRDQVSSGDYKAEEDPKLFHSVKTGRGPLGPDWKAEL------- 180
Query: 230 PTVSHDNKSMMCAYKLCKIQLNYWGIQSKGHDQPHNGQALMCAYKLCRVQFHYWGMQTKL 289
K D P LMCAYKLC V+F YWGMQTK+
Sbjct: 181 ---------------------------VKTGDCP-----LMCAYKLCTVEFRYWGMQTKV 208
Query: 290 ENPEENHKIYHVGSHLPGWIKSL-LPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEIT 348
EN +I L ++ +AW
Sbjct: 209 EN----------------FIHDQALRRTMTRAHRQAW----------------------- 229
Query: 349 TKYLPESVLAWAWQDEWNGLNIEDIRKIERDTAEAL 384
WQDEW GL +EDIR++E +T L
Sbjct: 230 -----------CWQDEWTGLTMEDIRRLEEETQLHL 254
Score = 183 bits (466), Expect = 7e-54
Identities = 84/218 (38%), Positives = 120/218 (55%), Gaps = 22/218 (10%)
Query: 290 ENPEENHKIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEITT 349
+ HKIYH+GS +P WI++LLP+ ALEV EEAWNAYP+T+T Y+ ++++F ++I T
Sbjct: 54 GKGQYTHKIYHLGSKVPAWIRTLLPEGALEVHEEAWNAYPYTRTRYTNPYMEDFSIKIET 113
Query: 350 KYLPESVLAWAWQDEWNGLNIEDIRKIERDTAEALKLKMSD----ANVDMTAKKSDTTTF 405
Y P+ Q+ L+ +D + D + ++ ++S A D S T
Sbjct: 114 WYKPDL----GTQENVFNLSPKDWKTRIIDYIDIVRDQVSSGDYKAEEDPKLFHSVKTG- 168
Query: 406 RGAFESVIRQHYPSMMGRGHDQPHNGQALMCAYKLCRVQFHYWGMQTKLEKFVHEFGKVA 465
RG + + D P LMCAYKLC V+F YWGMQTK+E F+H A
Sbjct: 169 RGPLGPDWKAEL----VKTGDCP-----LMCAYKLCTVEFRYWGMQTKVENFIH---DQA 216
Query: 466 GKKRGL-ASVLAWAWQDEWNGLNIEDIRKIERDTAEAL 502
++ A AW WQDEW GL +EDIR++E +T L
Sbjct: 217 LRRTMTRAHRQAWCWQDEWTGLTMEDIRRLEEETQLHL 254
>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 = 201 bits (513), Expect = 1e-60
Identities = 95/217 (43%), Positives = 131/217 (60%), Gaps = 21/217 (9%)
Query: 296 HKIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEITTKYLPES 355
HKIYH+GSH+PGW +++LPKSAL V+EEAWNAYP+T+T Y+C FV+ F L+I T Y ++
Sbjct: 60 HKIYHIGSHIPGWFRAILPKSALRVEEEAWNAYPYTRTRYTCPFVEKFSLDIETYYFDDA 119
Query: 356 VLAWAWQDEWNGLNIEDIRKIERDTAEALKLKMSD----ANVDMTAKKSDTTTFRGAFES 411
Q+ L+ ++R+ D + +K + A D S+ T RG
Sbjct: 120 ----GEQENVFNLSPAELRQRIIDFIDIVKDPVPGSDYKAEEDPKLYVSEKTG-RGPLSD 174
Query: 412 VIRQHYPSMMGRGHDQPHNGQALMCAYKLCRVQFHYWGMQTKLEKFVHEFGKVAGKKRGL 471
+ Y G+G +MCAYKLC+V+F YWGMQTK+E+F+H+ VA +K L
Sbjct: 175 DWIEEYKDPPGKG--------PIMCAYKLCKVEFRYWGMQTKIERFIHD---VALRKVML 223
Query: 472 -ASVLAWAWQDEWNGLNIEDIRKIERDTAEALKLKMS 507
A AW WQDEW GL +EDIRK+E +T AL KM+
Sbjct: 224 RAHRQAWCWQDEWYGLTMEDIRKLEEETQLALAQKMA 260
Score = 161 bits (408), Expect = 2e-45
Identities = 76/222 (34%), Positives = 98/222 (44%), Gaps = 87/222 (39%)
Query: 168 FQLSGSDLRSRIVEVIDVVKDQLYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVK 227
F LS ++LR RI++ ID+VKD + G DY EEDP +YVS+ TGRGPLS++WI EY +
Sbjct: 126 FNLSPAELRQRIIDFIDIVKDPVPGSDYKAEEDPKLYVSEKTGRGPLSDDWIEEYKDPPG 185
Query: 228 EDPTVSHDNKSMMCAYKLCKIQLNYWGIQSKGHDQPHNGQALMCAYKLCRVQFHYWGMQT 287
+ P +MCAYKLC+V+F YWGMQT
Sbjct: 186 KGP--------------------------------------IMCAYKLCKVEFRYWGMQT 207
Query: 288 KLENPEENHKIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEI 347
K+E I+ V L K L +A
Sbjct: 208 KIE-----RFIHDVA----------LRKVMLRAHRQA----------------------- 229
Query: 348 TTKYLPESVLAWAWQDEWNGLNIEDIRKIERDTAEALKLKMS 389
W WQDEW GL +EDIRK+E +T AL KM+
Sbjct: 230 -----------WCWQDEWYGLTMEDIRKLEEETQLALAQKMA 260
Score = 157 bits (399), Expect = 4e-44
Identities = 62/94 (65%), Positives = 72/94 (76%), Gaps = 10/94 (10%)
Query: 1 MLIKEYRIPLPLTVDEYKIAQLYMIAKKSREESKGAGSGVEILYNEPYDNDEEAPGTKGQ 60
MLIKEYRIPLP++V+EY+IAQLYMI KKSREESKG GSGVEIL N PY + PG GQ
Sbjct: 1 MLIKEYRIPLPMSVEEYRIAQLYMIQKKSREESKGEGSGVEILENRPY---TDGPGGSGQ 57
Query: 61 KTVKIYPLEWKIYHVGSHLPGWIKSLLPKSALEV 94
T KIYH+GSH+PGW +++LPKSAL V
Sbjct: 58 YT-------HKIYHIGSHIPGWFRAILPKSALRV 84
Score = 50.9 bits (122), Expect = 6e-07
Identities = 16/21 (76%), Positives = 20/21 (95%)
Query: 96 YRIPLPLTVDEYKIAQLYMIA 116
YRIPLP++V+EY+IAQLYMI
Sbjct: 6 YRIPLPMSVEEYRIAQLYMIQ 26
>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 = 195 bits (498), Expect = 2e-58
Identities = 115/390 (29%), Positives = 153/390 (39%), Gaps = 141/390 (36%)
Query: 2 LIKEYRIPLPLTVDEYKIAQLYMIAKKSREESKGAGSGVEILYNEPYDNDEEAPGTKGQK 61
LIKE+RI LPLTV+EY+I QLYM+AK S+EE+ G+G GVE+L NEPY+++ G KGQ
Sbjct: 1 LIKEFRIVLPLTVEEYQIGQLYMVAKASKEET-GSGEGVEVLKNEPYEDE---NGGKGQY 56
Query: 62 TVKIYPLEWKIYHVGSHLPGWIKSLLPKSALEV--KYRIPLPLTVDEYKIAQLYMIAVSD 119
T KIYH+GS LP W+++L PKSAL + K P Y ++S
Sbjct: 57 T-------HKIYHLGSKLPSWLRALAPKSALTIEEKSWNAYPYCKTVYSCPFFEKFSIS- 108
Query: 120 LSQGGDISSQHRIKQTFNLRSSLTRLGLKPYSKKLNPRLRCGDCRGKEFQLSGSDLRSRI 179
I S H+ + LS L R
Sbjct: 109 ------IESMHKPD---------------------------LGTQENAHNLSAEQLAQRK 135
Query: 180 VEVIDVVKDQLYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSM 239
V VID+ D + DY EEDP ++ SK TGRGPL + W
Sbjct: 136 VVVIDIANDSVASKDYKPEEDPKLFKSKKTGRGPLRKGWRK------------------- 176
Query: 240 MCAYKLCKIQLNYWGIQSKGHDQPHNGQALMCAYKLCRVQFHYWGMQTKLENPEENHKIY 299
+ + +MCAYKL V F YWG+Q K+EN
Sbjct: 177 -------------------------STKPIMCAYKLVTVDFPYWGLQNKVEN-------- 203
Query: 300 HVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEITTKYLPESVLAW 359
F++ + ++ Y W
Sbjct: 204 ---------------------------------------FIQKVERDVFLNYH-RQAFCW 223
Query: 360 AWQDEWNGLNIEDIRKIERDTAEALKLKMS 389
DEW L +EDIR+ E +T E L K
Sbjct: 224 --IDEWFDLTMEDIREFEEETKELLDAKRK 251
Score = 157 bits (399), Expect = 3e-44
Identities = 77/222 (34%), Positives = 109/222 (49%), Gaps = 38/222 (17%)
Query: 296 HKIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEITTKYLPES 355
HKIYH+GS LP W+++L PKSAL ++E++WNAYP+ KTVYSC F + F + I + + P+
Sbjct: 58 HKIYHLGSKLPSWLRALAPKSALTIEEKSWNAYPYCKTVYSCPFFEKFSISIESMHKPDL 117
Query: 356 VLAWAWQDEWNGLNIED----IRKIER-DTAE-ALKLKMSDANVDMTAKKSDTTTFRGAF 409
+ N N+ RK+ D A ++ K D KS T
Sbjct: 118 ------GTQENAHNLSAEQLAQRKVVVIDIANDSVASKDYKPEEDPKLFKSKKT------ 165
Query: 410 ESVIRQHYPSMMGRGHDQP---HNGQALMCAYKLCRVQFHYWGMQTKLEKFVHEFGKVAG 466
GRG + + + +MCAYKL V F YWG+Q K+E F+ +
Sbjct: 166 ------------GRGPLRKGWRKSTKPIMCAYKLVTVDFPYWGLQNKVENFIQK----VE 209
Query: 467 KKRGLASV-LAWAWQDEWNGLNIEDIRKIERDTAEALKLKMS 507
+ L A+ W DEW L +EDIR+ E +T E L K
Sbjct: 210 RDVFLNYHRQAFCWIDEWFDLTMEDIREFEEETKELLDAKRK 251
>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 = 126 bits (317), Expect = 1e-32
Identities = 68/219 (31%), Positives = 117/219 (53%), Gaps = 33/219 (15%)
Query: 296 HKIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVK-NFKLEITTKYLP- 353
HKIYH+ S +PG+++ L P+ +LE+ E+AWNAYP+ +T+ + +++K +F + I T + P
Sbjct: 58 HKIYHLQSKVPGFVRMLAPEGSLEIHEKAWNAYPYCRTIITNEYMKEDFLIIIETWHKPD 117
Query: 354 ----ESVLAWAWQDEWNGLNIEDIRKIERDTAEALKLKMSD--ANVDMTAKKSDTTTFRG 407
E+V +EW + + I D A+ ++ D A+ D +S+ T RG
Sbjct: 118 LGTQENVHNLD-PEEWKEVEVVYI-----DIADRSQVDPKDYKADEDPAKFQSEKTG-RG 170
Query: 408 AFESVIRQHYPSMMGRGHDQPHNGQALMCAYKLCRVQFHYWGMQTKLEKFVHEFGKVAGK 467
++ + D P MCAYKL V+F +WG+Q K+E F+ +
Sbjct: 171 PLGPNWKKE----LVNQKDCPI-----MCAYKLVTVEFKWWGLQNKVENFIQ------KQ 215
Query: 468 KRGLASVL---AWAWQDEWNGLNIEDIRKIERDTAEALK 503
+R L + + W D+W+GL ++DIR++E +T + L
Sbjct: 216 ERRLFTNFHRQVFCWLDKWHGLTMDDIRRMEDETKKELD 254
Score = 109 bits (273), Expect = 1e-26
Identities = 43/94 (45%), Positives = 64/94 (68%), Gaps = 11/94 (11%)
Query: 2 LIKEYRIPLPLTVDEYKIAQLYMIAKKSREESKGAGSGVEILYNEPYDNDEEAPGTKGQK 61
LIKE+R+ LPL+V+EY++ QLY +A+ S+ E+ G G G+E+L NEPY+ D G KGQ
Sbjct: 1 LIKEFRVILPLSVEEYQVGQLYSVAEASKNET-GGGEGIEVLVNEPYEKD---DGEKGQY 56
Query: 62 TVKIYPLEWKIYHVGSHLPGWIKSLLPKSALEVK 95
T KIYH+ S +PG+++ L P+ +LE+
Sbjct: 57 T-------HKIYHLQSKVPGFVRMLAPEGSLEIH 83
Score = 77.1 bits (190), Expect = 9e-16
Identities = 31/91 (34%), Positives = 47/91 (51%), Gaps = 10/91 (10%)
Query: 169 QLSGSDLRSRIVEVIDVVKD-QLYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVK 227
L + + V ID+ Q+ DY +EDP+ + S+ TGRGPL NW E +
Sbjct: 126 NLDPEEWKEVEVVYIDIADRSQVDPKDYKADEDPAKFQSEKTGRGPLGPNWKKE--LVNQ 183
Query: 228 EDPTVSHDNKSMMCAYKLCKIQLNYWGIQSK 258
+D +MCAYKL ++ +WG+Q+K
Sbjct: 184 KDC-------PIMCAYKLVTVEFKWWGLQNK 207
Score = 40.9 bits (96), Expect = 0.001
Identities = 11/21 (52%), Positives = 18/21 (85%)
Query: 96 YRIPLPLTVDEYKIAQLYMIA 116
+R+ LPL+V+EY++ QLY +A
Sbjct: 5 FRVILPLSVEEYQVGQLYSVA 25
>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 = 124 bits (312), Expect = 4e-32
Identities = 79/258 (30%), Positives = 122/258 (47%), Gaps = 60/258 (23%)
Query: 2 LIKEYRIPLPLTVDEYKIAQLYMIAKKSREESKGAGSGVEILYNEPYDNDEEAPGTKGQK 61
L+KEYRI +PLTV+EY+I QLYMI++ S E+S+ G GVE++ NEP ++ E GQ
Sbjct: 1 LLKEYRICMPLTVEEYRIGQLYMISRHSHEQSE-RGEGVEVVQNEPCEDPEHG---NGQF 56
Query: 62 TVKIYPLEWKIYHVGSHLPGWIKSLLPKSALEV-KYRIPLPLTVDEYKIAQLYMIAVSDL 120
T K ++Y + S LP W ++++PK K P T+ EY
Sbjct: 57 TEK------RVY-LNSRLPSWARAVVPKIFYVTEKAWNYYPYTITEYTC----------- 98
Query: 121 SQGGDISSQHRIKQTFNLRSSLTRLGLKPYSKKLNPRLRCGDCRGKEFQLSGSDLRSRIV 180
S L + + +K + + + +C LS ++L R V
Sbjct: 99 -------------------SFLPKFSIHIETKYEDNKGKSENC----IFLSEAELSEREV 135
Query: 181 EVIDVVKDQLYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSMM 240
+D+ D++ Y EEDP + S+ TGRGPL E W +K +M
Sbjct: 136 CHLDIAYDEIPEKYYKEEEDPKYFKSEKTGRGPLKEGW--------------RETHKPIM 181
Query: 241 CAYKLCKIQLNYWGIQSK 258
C+YKL ++ WG+Q++
Sbjct: 182 CSYKLVTVKFEVWGLQTR 199
Score = 106 bits (265), Expect = 1e-25
Identities = 64/214 (29%), Positives = 101/214 (47%), Gaps = 27/214 (12%)
Query: 297 KIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEITTKYLPESV 356
K ++ S LP W ++++PK V E+AWN YP+T T Y+C F+ F + I TKY
Sbjct: 59 KRVYLNSRLPSWARAVVPKI-FYVTEKAWNYYPYTITEYTCSFLPKFSIHIETKY----- 112
Query: 357 LAWAWQDEWNGLNIEDIRKIERDTAEALKLKMSDANVDMTAKKSDTTTFRGAFESVIRQH 416
ED + + + ++S+ V D + E ++
Sbjct: 113 --------------EDNKGKSENCIFLSEAELSEREVCHLDIAYDEIPEKYYKEEEDPKY 158
Query: 417 YPSM-MGRGHDQP---HNGQALMCAYKLCRVQFHYWGMQTKLEKFVHEFGKVAGKKRGLA 472
+ S GRG + + +MC+YKL V+F WG+QT++E+FVH KV L
Sbjct: 159 FKSEKTGRGPLKEGWRETHKPIMCSYKLVTVKFEVWGLQTRVEQFVH---KVVRDILLLG 215
Query: 473 SVLAWAWQDEWNGLNIEDIRKIERDTAEALKLKM 506
A+AW DEW + ++D+R+ ER E K+
Sbjct: 216 HRQAFAWVDEWYDMTMDDVREYERTIQEKTNEKI 249
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 34.9 bits (80), Expect = 0.14
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 1/69 (1%)
Query: 522 SASSHSTAPSASTITSAPNPALKT-LADALDSIEKSDSELQQHVSTPKPASVPASASSKH 580
SA + +PSA++ TS+ N + A DS+ + S Q + P
Sbjct: 88 SAGPITHSPSATSSTSSLNSNDGDQFSPASDSLSFNPSSTQSRKDSGPGDGSPVQKRKNP 147
Query: 581 LSSHSSNYS 589
L SS +
Sbjct: 148 LLPSSSTHG 156
>gnl|CDD|225805 COG3266, DamX, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 292
Score = 31.1 bits (70), Expect = 1.7
Identities = 16/70 (22%), Positives = 26/70 (37%)
Query: 526 HSTAPSASTITSAPNPALKTLADALDSIEKSDSELQQHVSTPKPASVPASASSKHLSSHS 585
T P + S P K A + K + PA A+AS + S+ S
Sbjct: 150 AITRPVRAQAVSEPAVEPKAAKTATATEAKVQTASPAQTPATPPAGKGAAASGQLKSAPS 209
Query: 586 SNYSEAILNT 595
S+Y+ + +
Sbjct: 210 SHYTLQLSAS 219
>gnl|CDD|226571 COG4086, COG4086, Predicted secreted protein [Function unknown].
Length = 299
Score = 30.1 bits (68), Expect = 2.8
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 15/60 (25%)
Query: 371 EDIRKIERDTAE---------------ALKLKMSDANVDMTAKKSDTTTFRGAFESVIRQ 415
DIRK+ D A L L MS+ N+D T + + + + +++
Sbjct: 213 ADIRKVVDDVANNYNVNLTDTQVNQIVNLFLAMSNLNIDWTKVQGQLKQAKDSLKWFLQR 272
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 30.5 bits (69), Expect = 2.9
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 3/75 (4%)
Query: 516 PSDGLQSASSHSTAPSASTITSAPNPALKTLADALDSIEKSDSELQQHVSTPKPASVPAS 575
+ L S + APS+ A P A A + S + S+P PA ++
Sbjct: 172 AALPLSSPEETARAPSSP---PAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSA 228
Query: 576 ASSKHLSSHSSNYSE 590
A SS S+ SE
Sbjct: 229 ADDAGASSSDSSSSE 243
>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional.
Length = 566
Score = 30.5 bits (68), Expect = 3.2
Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 5/84 (5%)
Query: 513 TDIPSDGLQSASSHSTAP-----SASTITSAPNPALKTLADALDSIEKSDSELQQHVSTP 567
T P + S AP S + P+ A A + + + + Q P
Sbjct: 37 TQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAP 96
Query: 568 KPASVPASASSKHLSSHSSNYSEA 591
PA P A++ + + S A
Sbjct: 97 DPAVAPQLAAAPKPDAAEAFTSAA 120
>gnl|CDD|227952 COG5665, NOT5, CCR4-NOT transcriptional regulation complex, NOT5
subunit [Transcription].
Length = 548
Score = 30.0 bits (67), Expect = 4.2
Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 518 DGLQSASSHSTAPSASTITSAPNPALKTLADALDSIEKSDSELQQHVSTPKPASVP 573
+Q +SS++ AP ++ + ++++ S +K Q+ VS A+ P
Sbjct: 198 CEIQPSSSNNEAPKEGNNQTSLS-SIRSSKKQERSPKKKAP--QRDVSISDRATTP 250
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 30.1 bits (67), Expect = 4.6
Identities = 23/107 (21%), Positives = 40/107 (37%), Gaps = 22/107 (20%)
Query: 508 GGANGTDIPSDGLQSASSHSTAPSASTITSAPNPALKTLADALDSIEKSDSELQ------ 561
G + Q S +++P A+T T P P+ + + A SI S ++Q
Sbjct: 1212 GMSGTNTFTFKAAQLQLSAASSPPAAT-TPTPPPSSSSSSSA-QSISTSPGQIQIVLNGS 1269
Query: 562 ----------QHVSTPKPASVPAS----ASSKHLSSHSSNYSEAILN 594
+STPK + A +S +S + ++ A N
Sbjct: 1270 TTIHINFLFFPALSTPKIGQILAMPIVNSSGAFISLYVNSAISANFN 1316
>gnl|CDD|144512 pfam00935, Ribosomal_L44, Ribosomal protein L44.
Length = 77
Score = 27.6 bits (62), Expect = 4.8
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 148 KPYSKKLNPRLRCGDCRGKEFQLSG 172
KP +KK+ RLRC +C K Q G
Sbjct: 45 KP-TKKIVLRLRCTEC-KKAHQRPG 67
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 29.7 bits (66), Expect = 5.5
Identities = 19/73 (26%), Positives = 28/73 (38%), Gaps = 8/73 (10%)
Query: 517 SDGLQSASSHSTAPSASTITSAPNPALKTLADALDSIEKSDS-ELQQHVSTPKPASV--P 573
S G Q S + P P ++ + LD E+ +S +P+P V P
Sbjct: 483 SSGSQPPGSALPSSGGCAGPGPPLPPIQIKEEPLDEAEEPESPPPPPRSPSPEPTVVNTP 542
Query: 574 ASASS-----KHL 581
+ AS KHL
Sbjct: 543 SHASQSARFYKHL 555
>gnl|CDD|180247 PRK05767, rpl44e, 50S ribosomal protein L44e; Validated.
Length = 92
Score = 27.6 bits (62), Expect = 5.9
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 146 GLKPYSKKLNPRLRCGDCRGKEFQLSGSDLRSRIVEVIDV 185
G KP +KK++ R RC +C GK G R++ E+++V
Sbjct: 57 GAKP-TKKVDLRYRCTEC-GKAHTREG--FRAKKFELVEV 92
>gnl|CDD|151868 pfam11429, Colicin_D, Colicin D. Colicin D is a tRNase which kills
sensitive E.coli cells via a specific tRNA cleavage. It
targets the four isoaccepting tRNAs for Arg and cleaves
the phosphodiester bond between positions 38 and 39 at
the 3' junction of the anticodon stem and the loop.
Length = 92
Score = 27.4 bits (61), Expect = 6.3
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 171 SGSDLRSRIVEVIDVVKDQLYGGDYVREEDPSIYVSKTTGRG 212
+ ++ I E I K +Y G Y RE+D +Y + TTG
Sbjct: 23 TLTEFEDAIQEHIAD-KPTVYKGTYRREQDSKVYFNPTTGVV 63
>gnl|CDD|219000 pfam06367, Drf_FH3, Diaphanous FH3 Domain. This region is found in
the Formin-like and and diaphanous proteins.
Length = 197
Score = 28.8 bits (65), Expect = 6.5
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 9/50 (18%)
Query: 106 EYKIAQLYMI-AVSDLSQGGDISSQHRIKQTFNLRSSLTRLGLKPYSKKL 154
EYK+A + I A+ ++ D+ R+ +LRS TRLGL KL
Sbjct: 39 EYKVATMQFINAL--VNSPEDL--NFRL----HLRSEFTRLGLDRILDKL 80
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 28.8 bits (65), Expect = 9.1
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 516 PSDGLQSAS-SHSTAPSASTITSAPNPALKTLADALDSIEKSDSELQQHVSTPKPA 570
P D L + +S APS + ++ + AL AL + K + S K A
Sbjct: 178 PQDALPTDRNGNSGAPSKFSFPTSFDNALDRGKKALTRVTKGAPSQSAN-SKEKKA 232
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 0.131 0.397
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,565,671
Number of extensions: 2804200
Number of successful extensions: 1909
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1871
Number of HSP's successfully gapped: 45
Length of query: 595
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 493
Effective length of database: 6,413,494
Effective search space: 3161852542
Effective search space used: 3161852542
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: 42 (22.0 bits)
S2: 62 (27.9 bits)