RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8611
(280 letters)
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 205 bits (524), Expect = 4e-66
Identities = 101/253 (39%), Positives = 143/253 (56%), Gaps = 50/253 (19%)
Query: 15 EDKGLLLDSLESQLSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASVSRVVST 74
E+K +++L+ QL LH+SVE+L R++L++ + AKS A++SN EEH S+SR +S
Sbjct: 15 EEKQQQIENLDQQLRKLHASVESLVNHRKELALNTGSFAKSAAMLSNCEEHTSLSRALSQ 74
Query: 75 LGELYERTEGVYAAEAGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILNK 134
L E+ E+ E ++ +A D ILAEL +DY+ LI A+KD FH R K++Q WQ+ Q L K
Sbjct: 75 LAEVEEKIEQLHGEQADTDFYILAELLKDYIGLIGAIKDVFHERVKVWQNWQNAQQTLTK 134
Query: 135 KREAKVKLELAGRSDKSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTVSGGFR 194
KREAK KLEL+GR+DK QA E+ E
Sbjct: 135 KREAKAKLELSGRTDKLDQAQQEIKE---------------------------------- 160
Query: 195 SDICDEQVRVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGYQ 254
WE KV+R Q++F IS IK+E FE +RV++FKD ++KYLE L+ Q
Sbjct: 161 -----------WEAKVDRGQKEFEEISKTIKKEIERFEKNRVKDFKDIIIKYLESLLNTQ 209
Query: 255 QQEFKDTMVKYLE 267
QQ ++KY E
Sbjct: 210 QQ-----LIKYWE 217
>gnl|CDD|153348 cd07664, BAR_SNX2, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 2. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX2 is a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi. The retromer consists of a cargo-recognition
subcomplex and a subcomplex formed by a dimer of sorting
nexins (SNX1 and/or SNX2), which ensures effcient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 234
Score = 141 bits (356), Expect = 5e-41
Identities = 90/257 (35%), Positives = 134/257 (52%), Gaps = 50/257 (19%)
Query: 14 LEDKGLLLDSLESQLSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASVSRVVS 73
E+K ++L+ QL LH+SVE+L R++LS +A AKS A++ N+E+H ++SR +S
Sbjct: 24 FEEKQQQFENLDQQLRKLHASVESLVCHRKELSANTAAFAKSAAMLGNSEDHTALSRALS 83
Query: 74 TLGELYERTEGVYAAEAGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILN 133
L E+ E+ + ++ +A AD + +EL DY+ LIAAVK F R K +Q WQ Q+ L
Sbjct: 84 QLAEVEEKIDQLHQDQAFADFYLFSELLGDYIRLIAAVKGVFDQRMKCWQKWQDAQVTLQ 143
Query: 134 KKREAKVKLELAGRSDKSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTVSGGF 193
KKREA+ KL+ A + DK QA E+ E
Sbjct: 144 KKREAEAKLQYANKPDKLQQAKDEIKE--------------------------------- 170
Query: 194 RSDICDEQVRVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGY 253
WE KV++ + DF IS I++E FE RV++FK ++KYLE L+
Sbjct: 171 ------------WEAKVQQGERDFEQISKTIRKEVGRFEKERVKDFKTVIIKYLESLVQT 218
Query: 254 QQQEFKDTMVKYLEELM 270
QQQ ++KY E +
Sbjct: 219 QQQ-----LIKYWEAFL 230
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 137 bits (347), Expect = 1e-39
Identities = 79/247 (31%), Positives = 120/247 (48%), Gaps = 47/247 (19%)
Query: 12 PVLEDKGLLLDSLESQLSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASVSRV 71
P EDK +DSLESQL L+ ++E L R++L+ + AKSLA++++ E +SR
Sbjct: 24 PWFEDKRQYIDSLESQLKKLYKALELLVNQRKELASATGEFAKSLAMLASLELSTGLSRA 83
Query: 72 VSTLGELYERTEGVYAAEAGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQII 131
+S L E+ ER + + +A D+ L E +Y+ LI +VK F+ R K +Q WQ+ +
Sbjct: 84 LSQLAEVEERIKELLERQALQDVLTLGETIDEYLRLIGSVKAVFNQRVKAWQQWQNAEQD 143
Query: 132 LNKKREAKVKLELAGRS--DKSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTV 189
L+KKR KL+ AG+S DK QA EV E
Sbjct: 144 LSKKRAQLAKLKGAGKSRQDKLQQAKKEVDE----------------------------- 174
Query: 190 SGGFRSDICDEQVRVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEE 249
E KV++ +++F IS IK+E FE RV +FK+ + YLE
Sbjct: 175 ----------------AERKVQQAKKEFEDISETIKKELERFETERVDDFKNVLEIYLES 218
Query: 250 LMGYQQQ 256
+ Q++
Sbjct: 219 AIESQKE 225
>gnl|CDD|153349 cd07665, BAR_SNX1, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 1. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX1 is a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi. The retromer consists of a cargo-recognition
subcomplex and a subcomplex formed by a dimer of sorting
nexins (SNX1 and/or SNX2), which ensures effcient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. SNX1 is localized to a
microdomain in early endosomes where it regulates
cation-independent mannose-6-phosphate receptor
retrieval to the trans Golgi network. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 234
Score = 122 bits (308), Expect = 7e-34
Identities = 82/257 (31%), Positives = 132/257 (51%), Gaps = 50/257 (19%)
Query: 14 LEDKGLLLDSLESQLSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASVSRVVS 73
E+K ++ E +L LH+ VE L R++L++ +A AKSLA++ ++E++ ++SR +S
Sbjct: 24 FEEKLQEVECEEQRLRKLHAVVETLVNHRKELALNTALFAKSLAMLGSSEDNTALSRALS 83
Query: 74 TLGELYERTEGVYAAEAGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILN 133
L E+ E+ E ++ +A D +LAEL DY+ L++AV+ F R K +Q WQ Q +L
Sbjct: 84 QLAEVEEKIEQLHQEQANNDFFLLAELLADYIRLLSAVRGAFDQRMKTWQRWQDAQAMLQ 143
Query: 134 KKREAKVKLELAGRSDKSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTVSGGF 193
KKREA+ +L A + DK QA E+ E
Sbjct: 144 KKREAEARLLWANKPDKLQQAKDEIAE--------------------------------- 170
Query: 194 RSDICDEQVRVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGY 253
WE +V + + DF ISA +++E FE + ++FK+ ++KYLE L+
Sbjct: 171 ------------WESRVTQYERDFERISATVRKEVIRFEKEKSKDFKNHIIKYLETLLHS 218
Query: 254 QQQEFKDTMVKYLEELM 270
QQQ +VKY E +
Sbjct: 219 QQQ-----LVKYWEAFL 230
>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Vps5p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Vsp5p is the yeast counterpart of human SNX1 and is part
of the retromer complex, which functions in the
endosome-to-Golgi retrieval of vacuolar protein sorting
receptor Vps10p, the Golgi-resident membrane protein
A-ALP, and endopeptidase Kex2. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 216
Score = 75.4 bits (186), Expect = 3e-16
Identities = 57/237 (24%), Positives = 107/237 (45%), Gaps = 47/237 (19%)
Query: 14 LEDKGLLLDSLESQLSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASVSRVVS 73
+K LDSLESQL L+ S+E ++ R++L+ + A++L +S+ E S+S +++
Sbjct: 6 FIEKKQYLDSLESQLKQLYKSLELVSSQRKELASATEEFAETLEALSSLELSKSLSDLLA 65
Query: 74 TLGELYERTEGVYAAEAGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILN 133
L E+ +R + +A D+ L +Y+ I +V+ F R K++Q WQS + L+
Sbjct: 66 ALAEVQKRIKESLERQALQDVLTLGVTLDEYIRSIGSVRAAFAQRQKLWQYWQSAESELS 125
Query: 134 KKRE--AKVKLELAGRSDKSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTVSG 191
KK+ K+K + + +K E+ E +
Sbjct: 126 KKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRAS------------------------- 160
Query: 192 GFRSDICDEQVRVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLE 248
+++ ++E +S +IK E FE RV++F++++ YLE
Sbjct: 161 ---------ELKKEFEE-----------VSELIKSELERFERERVEDFRNSVEIYLE 197
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 69.3 bits (170), Expect = 4e-14
Identities = 49/247 (19%), Positives = 86/247 (34%), Gaps = 45/247 (18%)
Query: 12 PVLEDKGLLLDSLESQLSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASV--S 69
E+ + LE QL L + L RR+L K+L ++ EE
Sbjct: 4 QEFEEAKDYILKLEEQLKKLSKQAQRLVKRRRELGSALGEFGKALIKLAKCEEEVGGELG 63
Query: 70 RVVSTLGELYERTEGVYAAEAGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQ 129
+S LG+ E + A+A +L L E ++Y+ AVK+T R T QS +
Sbjct: 64 EALSKLGKAAEELSSLSEAQANQELVKLLEPLKEYLRYCQAVKETLDDRADALLTLQSLK 123
Query: 130 IILNKKREAKVKLELAGRSDKSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTV 189
L K+ KL+ A +++ L + L
Sbjct: 124 KDLASKKAQLEKLKAAPGI----------KPAKVEELEEEL------------------- 154
Query: 190 SGGFRSDICDEQVRVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEE 249
+ E +E ++ + IS +K E F R ++ K + ++
Sbjct: 155 --------------EEAESALEEARKRYEEISERLKEELKRFHEERARDLKAALKEFARL 200
Query: 250 LMGYQQQ 256
+ Y ++
Sbjct: 201 QVQYAEK 207
>gnl|CDD|153347 cd07663, BAR_SNX5, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 5. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX5, abundantly expressed in
macrophages, regulates macropinocytosis, a process that
enables cells to internalize large amounts of external
solutes. It may also be a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi, acting as a mammalian equivalent of yeast
Vsp17p. It also binds the Fanconi anaemia
complementation group A protein (FANCA). SNX5 is
localized to a subdomain of early endosome and is
recruited to the plasma membrane following EGF
stimulation and elevation of PI(3,4)P2 levels. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 218
Score = 29.9 bits (67), Expect = 1.1
Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 1/105 (0%)
Query: 33 SSVEALALARRDLSVYSAHLAKSLALVS-NTEEHASVSRVVSTLGELYERTEGVYAAEAG 91
S +A + R +V ++ S AL S EE + + + + EL+E+ V A
Sbjct: 42 SCAKADKMTRSHKNVADDYIHISAALNSVAAEEPTVIKKYLLKVAELFEKLRKVEDRVAS 101
Query: 92 ADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILNKKR 136
L EL R Y+ I A KD + R + +++ L+K R
Sbjct: 102 DQDLKLTELLRYYMLNIEAAKDLLYRRARALADYENSNKALDKAR 146
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 30.0 bits (68), Expect = 1.5
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 146 GRSDKSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTVS 190
GR +++A+ EV E R LL LFN S +V T T +
Sbjct: 34 GRYRLALRASREVEETR--QLLAKLFNA--PSSAHVVFTNNATTA 74
>gnl|CDD|216810 pfam01959, DHQS, 3-dehydroquinate synthase (EC 4.6.1.3).
3-Dehydroquinate synthase is an enzyme in the common
pathway of aromatic amino acid biosynthesis that
catalyzes the conversion of
3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP)
into 3-dehydroquinic acid. This synthesis of aromatic
amino acids is an essential metabolic function for most
prokaryotic as well as lower eukaryotic cells, including
plants. The pathway is absent in humans; therefore, DHQS
represents a potential target for the development of
novel and selective antimicrobial agents. Owing to the
threat posed by the spread of pathogenic bacteria
resistant to many currently used antimicrobial drugs,
there is clearly a need to develop new anti-infective
drugs acting at novel targets. A further potential use
for DHQS inhibitors is as herbicides.
Length = 347
Score = 28.4 bits (64), Expect = 4.8
Identities = 37/183 (20%), Positives = 62/183 (33%), Gaps = 33/183 (18%)
Query: 5 LKQLGGWPVLEDKGLLLDSLESQLSHLHSSVEALALARR--DLSVYSAHLAKSLALVSNT 62
LK G W E K + +LES + + E + R ++V + L +
Sbjct: 5 LKADGPWD--ERKERITTALESGVDAVLVDEEDVERVRELGRITVAADGTDDLPDLETLK 62
Query: 63 EEHASVSRVVSTLGELYERTEGVYAAEAGADL----------------NILAELFRDYVC 106
E V V L + E +AAEA + N++A L
Sbjct: 63 ESGKDVGAYVEILDKEDEE----FAAEAAKEADYVIVEGRDWTIIPLENLIARLQGSETK 118
Query: 107 LIAAVKDTFHARGKIYQTWQ--SWQIILNKK-----REAKVKLELAGRSDKSIQAAHEVT 159
+IA V+ A+ +T + ++L+ + +E + A VT
Sbjct: 119 VIAVVRSAEEAK-LALETLEKGVDGVLLDSDDPNEIKAIVAVVEEKSSESLDLVPA-TVT 176
Query: 160 EVR 162
EV
Sbjct: 177 EVE 179
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 28.5 bits (64), Expect = 5.4
Identities = 12/63 (19%), Positives = 24/63 (38%)
Query: 92 ADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILNKKREAKVKLELAGRSDKS 151
ILA+LF ++ A+K + + + Q + +L + E + + D
Sbjct: 723 RGNKILAKLFGRFLKAFNALKKLYEFAYTLEEEIQYLEDLLKARLEKDYQSKYLDLIDNL 782
Query: 152 IQA 154
A
Sbjct: 783 NDA 785
>gnl|CDD|150393 pfam09712, PHA_synth_III_E, Poly(R)-hydroxyalkanoic acid synthase
subunit (PHA_synth_III_E). This entry represents the
PhaE subunit of the heterodimeric class (class III) of
polymerase for poly(R)-hydroxyalkanoic acids (PHAs),
carbon and energy storage polymers of many bacteria. The
most common PHA is polyhydroxybutyrate but about 150
different constituent hydroxyalkanoic acids (HAs) have
been identified in various species.
Length = 293
Score = 27.9 bits (62), Expect = 6.0
Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 14/102 (13%)
Query: 185 QGRTVSGGFRSDICDEQVRVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMV 244
G +G SD + W+ ++ Q F+++S M G Q+F+ +
Sbjct: 94 AGSLDTGDTTSD----RAAQAWQLPLDGWQRMFSSLSPM---PGDGLRNMPHQQFRSQLD 146
Query: 245 KYLE-ELMGY------QQQEFKDTMVKYLEELMGYQQQVSRI 279
+L +GY Q Q ++Y + L Y Q S+
Sbjct: 147 PFLSMPALGYTREHQAQYQALIRAQMEYQQALQEYTGQYSQA 188
>gnl|CDD|151783 pfam11342, DUF3144, Protein of unknown function (DUF3144). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 78
Score = 26.1 bits (58), Expect = 6.3
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 228 YAGFEASRVQEFKDTMVKYLEELMGYQQQEFKDTMVKYLEE 268
+ F A+ E + +E + Y +++K + LE+
Sbjct: 36 FNAFVAANSFESGADLAADKDEAVEYFSEQYKKMLRDNLED 76
>gnl|CDD|233227 TIGR00996, Mtu_fam_mce, virulence factor Mce family protein.
Members of this paralogous family are found as six
tandem homologous proteins in the same orientation per
cassette, in four separate cassettes in Mycobacterium
tuberculosis. The six members of each cassette represent
six subfamilies. One subfamily includes the protein mce
(mycobacterial cell entry), a virulence protein required
for invasion of non-phagocytic cells [Cellular
processes, Pathogenesis].
Length = 291
Score = 27.6 bits (62), Expect = 6.3
Identities = 19/91 (20%), Positives = 32/91 (35%), Gaps = 3/91 (3%)
Query: 14 LEDKGLLLDSLESQLSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASVSRVVS 73
D G L+D+L L L + L +L+ +A LA + + S +
Sbjct: 187 DGDIGALIDNLNRVLDVLADRSDQLDRLLDNLATLTAQLADRDDALDDALAAL--SGASA 244
Query: 74 TLGELYERTEGVYAAEAGADLNILAELFRDY 104
+ +L A+L + L DY
Sbjct: 245 QVRDLLAENRPNLPQAL-ANLAPVLTLLVDY 274
>gnl|CDD|153314 cd07630, BAR_SNX_like, The Bin/Amphiphysin/Rvs (BAR) domain of
uncharacterized Sorting Nexins. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions. This subfamily is composed of uncharacterized
proteins with similarity to sorting nexins (SNXs), which
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 198
Score = 27.5 bits (61), Expect = 6.4
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 214 QEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLE 248
+ +F IS++ K+E F RV E + +V Y E
Sbjct: 145 ETEFEEISSLAKKELERFHRQRVLELQSALVCYAE 179
>gnl|CDD|239571 cd03489, Topoisomer_IB_N_LdtopoI_like,
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the 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 topo I play putative roles in
organizing the kinetoplast DNA network unique to these
parasites. This family may represent more than one
structural domain.
Length = 212
Score = 27.1 bits (60), Expect = 8.2
Identities = 12/40 (30%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 107 LIAAVKDTFHARGKIYQT--WQSWQIILNKKREAKVKLEL 144
+ A +K+ + R ++++ ++SW+ IL+K+ KLEL
Sbjct: 42 MFAVMKEHDYYRKEVFRRNFFESWREILDKRHHPIRKLEL 81
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 0.132 0.372
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,001,030
Number of extensions: 1322638
Number of successful extensions: 1271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1264
Number of HSP's successfully gapped: 45
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
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: 58 (26.2 bits)