RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5854
(392 letters)
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 185 bits (471), Expect = 4e-54
Identities = 72/164 (43%), Positives = 107/164 (65%), Gaps = 3/164 (1%)
Query: 6 RLTLKLSCAMNFMIYPHDTQECSLQMESLSHTTDDLIFQWDPEMPLAVDEK--IELPQLQ 63
R+TL L+C M+ +P D Q CSL+ ES +TT+D+ +W + + VD+ I LP+ +
Sbjct: 149 RITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQGAVQVDDSLFISLPEFE 208
Query: 64 LVKNK-TADCSQVYSTGNFTCLEVIFVLKRRLGYYLFHTYIPTCLIVIMSWVSFWIKPEA 122
L+ T C+ +TG + CL FVL+RR YYL YIP+ LIVI+SWVSFW+ +A
Sbjct: 209 LLGVYGTRYCTSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADA 268
Query: 123 APARVTLGVTSLLTLSTQHAKSQASLPPVSYLKAVDAFMSACTV 166
+ ARV+LG+T+LLT++T + + SLP VSY+KA+D + + C
Sbjct: 269 SGARVSLGITTLLTMTTFSSGVRESLPAVSYVKAIDVYFAVCMA 312
Score = 75.9 bits (187), Expect = 5e-15
Identities = 31/112 (27%), Positives = 50/112 (44%), Gaps = 1/112 (0%)
Query: 184 YDKMRPPKKEGQPTIVYFHVTVMGLDSIDENSMTYAADIFFAQTWKDHRLRLPENMTSEY 243
YD P G P V F++ + + +DE +M Y +I+ Q W D RL+
Sbjct: 42 YDARVRPVFGGPPVTVSFNLFLRSIMDVDEKNMDYTTNIWLRQEWTDERLQWNPEEYPGV 101
Query: 244 RLLEVDWLKNMWRPDSFFKNAKAVTFQTMTIPNHYVWLYKDKTILYMVKFVF 295
L+ +W PD FF N K F +T+ N V ++ + ++LY +
Sbjct: 102 TLVRTPDDS-IWVPDIFFYNEKDARFHGITMTNVLVRIHPNGSVLYSPRITL 152
Score = 36.6 bits (85), Expect = 0.021
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 334 ARLLTGQPMIPPNHQQA-QRNLAQRARTRAINIDRFSRVFFPVLFAILNCTYWI 386
A +L + ++ + + + RA ID+ SR+ FP+ F + N YW+
Sbjct: 404 AGILEEVRIAHRFRKRDESEEVVRDWKFRAKVIDKLSRMAFPLAFLLFNIGYWM 457
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 86.6 bits (215), Expect = 1e-19
Identities = 24/66 (36%), Positives = 37/66 (56%)
Query: 101 TYIPTCLIVIMSWVSFWIKPEAAPARVTLGVTSLLTLSTQHAKSQASLPPVSYLKAVDAF 160
IP LI +SW+ FW+ +A P +VTLG+T+LLT++ + SLP SY+ +
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGK 60
Query: 161 MSACTV 166
T+
Sbjct: 61 YLVFTM 66
Score = 31.9 bits (73), Expect = 0.38
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 365 IDRFSRVFFPVLFAILNCTYW 385
IDR SR FP+ F + YW
Sbjct: 208 IDRLSRWIFPIAFVLGTLVYW 228
>gnl|CDD|217293 pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand
binding domain. This family is the extracellular ligand
binding domain of these ion channels. This domain forms
a pentameric arrangement in the known structure.
Length = 215
Score = 70.7 bits (174), Expect = 3e-14
Identities = 31/110 (28%), Positives = 48/110 (43%), Gaps = 7/110 (6%)
Query: 184 YDK-MRPPKKEGQPTIVYFHVTVMGLDSIDENSMTYAADIFFAQTWKDHRLRLPENMTSE 242
YDK +RP K P V + + + +DE + +++ Q W D RL +
Sbjct: 12 YDKRVRPVKNGSDPVTVSVGLYLTQIIDVDEKNQDLTTNVWLRQQWTDERLAWD---PED 68
Query: 243 YRLLEVDWL--KNMWRPDSFFKNAKAVTFQTMTIPNHYVWLYKDKTILYM 290
Y + L +W+PD N KA +T PN V +Y D T+L+
Sbjct: 69 YGGITSLRLPSDKIWKPDIVLYN-KADGIHDITTPNTNVRVYPDGTVLWS 117
Score = 69.6 bits (171), Expect = 1e-13
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 18/102 (17%)
Query: 5 YRLTLKLSCAMNFMIYPHDTQECSLQMESLSHTTDDLIFQWDPEMPLAVDEKIELPQLQL 64
K SC M+ +P D Q CSL+ S ++ +++ +W + P +DE+I+L
Sbjct: 118 PPAIYKSSCPMDLTYFPFDQQNCSLKFGSWTYNGEEVDLRWKDDTPPILDEEIDLSDFTE 177
Query: 65 -------------VKNKTADCSQVYSTGNFTCLEVIFVLKRR 93
+ S++Y F FVL+R+
Sbjct: 178 NGEWDIVDVPAKRNEYPYGCYSELYPDVTFY-----FVLRRK 214
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 32.6 bits (75), Expect = 0.41
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 348 QQAQRNLAQRARTRAINIDRFSRVFFPVLFAILNCTYWI 386
++AQ + +A + + DR + F PV+ I T+ +
Sbjct: 309 EEAQ---SSKAPIQRL-ADRVASYFVPVVLVIAALTFAL 343
>gnl|CDD|119131 pfam10611, DUF2469, Protein of unknown function (DUF2469). Member
proteins often found in Actinomycetes clustered with
signal peptidase and/or RNAse-HII.
Length = 101
Score = 30.5 bits (69), Expect = 0.42
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 250 WLKNMWRPDSFFKNAKAVTFQTMTI 274
W+ +M+RP F KN + VTF+ + I
Sbjct: 65 WVWDMYRPARFVKNVRVVTFKDVNI 89
>gnl|CDD|153352 cd07668, BAR_SNX9, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 9. 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. SNX9, also known as SH3PX1, is a
cytosolic protein that interacts with proteins
associated with clathrin-coated pits such as
Cdc-42-associated tyrosine kinase 2 (ACK2). It binds
class I polyproline sequences found in dynamin 1/2 and
the WASP/N-WASP actin regulators. SNX9 is localized to
plasma membrane endocytic sites and acts primarily in
clathrin-mediated endocytosis. Its array of interacting
partners suggests that SNX9 functions at the interface
between endocytosis and actin cytoskeletal organization.
BAR domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 210
Score = 30.8 bits (69), Expect = 0.87
Identities = 25/74 (33%), Positives = 32/74 (43%), Gaps = 10/74 (13%)
Query: 130 GVTSLLTLSTQHAKSQASLPPVSYLKAVDAFMSACTVSSTS-----LTFNDILPEDPKLY 184
GV LLT+ +H K P Y K A S TV STS ND + E K Y
Sbjct: 27 GVKELLTVGQEHWKRCTGPLPKEYQKIGKALQSLATVFSTSGYQGETDLNDAITEAGKTY 86
Query: 185 DKM-----RPPKKE 193
+++ PKK+
Sbjct: 87 EEIASLVAEQPKKD 100
>gnl|CDD|212506 cd11647, Diphthine_synthase, Diphthine synthase, also known as
DPH5. Diphthine synthase, also known as diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase, participates in the posttranslational
modification of a specific histidine residue in
elongation factor 2 (EF-2) of eukaryotes and archaea to
diphthamide. It catalyzes the trimethylation step in
diphthamide biosynthesis. Diphthamide is the target of
diphtheria toxin, which ADP-ribosylates diphthamide and
inhibits protein synthesis, leading to host cell death.
Length = 241
Score = 30.2 bits (69), Expect = 1.7
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 323 DKIFELAAKENARLLT-GQPMIPPNHQQAQRNLAQRARTRAIN 364
D+I E A +++ LL G P I H +L RA+ R I
Sbjct: 67 DEILEEAKEKDVALLVVGDPFIATTHS----DLRLRAKERGIE 105
>gnl|CDD|224711 COG1798, DPH5, Diphthamide biosynthesis methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 260
Score = 30.0 bits (68), Expect = 1.8
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 323 DKIFELAAKENARLLT-GQPMIPPNHQQAQRNLAQRARTRAI 363
I + A ++ LL G PM+ H L A+ R I
Sbjct: 67 RSILDRAKDKDVALLVAGDPMVATTHVD----LRIEAKRRGI 104
>gnl|CDD|233447 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase.
This model encompasses two equivalog models for the
copper and cadmium-type heavy metal transporting P-type
ATPases (TIGR01511 and TIGR01512) as well as those
species which score ambiguously between both models. For
more comments and references, see the files on TIGR01511
and 01512.
Length = 556
Score = 30.3 bits (69), Expect = 1.9
Identities = 10/42 (23%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 348 QQAQRNLAQRARTRAINIDRFSRVFFPVLFAILNCTYWIMFA 389
++AQ + +A + + DR + + P + AI T+ + A
Sbjct: 153 EEAQSS---KAPIQRL-ADRIASYYVPAVLAIALLTFVVWLA 190
>gnl|CDD|173868 cd08503, PBP2_NikA_DppA_OppA_like_17, 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 = 460
Score = 29.8 bits (68), Expect = 2.9
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 11/84 (13%)
Query: 190 PKKEGQPTIVYFHVTVMGLDSIDENSMTYAADIFFAQTWKDHRLRLPENMTSEYRLLEVD 249
PK+ G T+ D++D ++ +AD ++ + + + T L E
Sbjct: 1 PKRGG--TLRVAVPGGSTADTLDPHTADSSADYVRGFALYEYLVEIDPDGTLVPDLAE-S 57
Query: 250 WLKN----MWRPDSFFKNAKAVTF 269
W N W FK K VTF
Sbjct: 58 WEPNDDATTWT----FKLRKGVTF 77
>gnl|CDD|131100 TIGR02045, P_fruct_ADP, ADP-specific phosphofructokinase.
Phosphofructokinase is a key enzyme of glycolysis. The
phosphate group donor for different subtypes of
phosphofructokinase can be ATP, ADP, or pyrophosphate.
This family consists of ADP-dependent
phosphofructokinases. Members are more similar to
ADP-dependent glucokinases (excluded from this family)
than to other phosphofructokinases [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 446
Score = 29.0 bits (65), Expect = 4.6
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 4 EYRLTLKLSCAMNFMIYPHDTQE-CSLQMESLSHTTDDLIFQWDPEMPLAVDEKIELPQL 62
E+R + P + S + ESL T D + ++ PE+ VD I L
Sbjct: 160 EFRKGTNFKLGGETIKVPRSGRFIVSSRPESLRIETKDQLRKFLPEIGEPVDGAI-LSGY 218
Query: 63 QLVKNKTADCSQVYSTGNF---TCLEVIFVLKR 92
Q +K + +D T + E I +LK+
Sbjct: 219 QGIKEEYSDG----KTAKYYLERAKEDIELLKK 247
>gnl|CDD|131268 TIGR02213, lolE_release, lipoprotein releasing system,
transmembrane protein LolE. This protein is part of an
unusual ABC transporter complex that releases
lipoproteins from the periplasmic side of the bacterial
inner membrane, rather than transport any substrate
across the inner membrane. In some species, the
permease-like transmembrane protein is represented by
two paralogs, LolC and LolE, both in the LolCDE complex.
This family consists of LolE, as found in E. coli and
related species [Protein fate, Protein and peptide
secretion and trafficking].
Length = 411
Score = 28.7 bits (64), Expect = 5.3
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 113 WVSFWIKPE------AAPARVTLGVTSLLTLSTQHAKSQASLP 149
WV+ I + A P RV + VT +L L Q S A LP
Sbjct: 162 WVTLLIPQQNGDEKFAQPKRVRVQVTGILRLDGQLDHSYALLP 204
>gnl|CDD|220913 pfam10949, DUF2777, Protein of unknown function (DUF2777). This
family of proteins with unknown function appears to be
restricted to Bacillus cereus.
Length = 184
Score = 28.1 bits (63), Expect = 7.1
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 16 NFMIYPHDTQECSLQMESLSHTTDDLIFQW 45
NF+++ +D C+LQ + + F++
Sbjct: 142 NFLLFDNDEAICALQHHYDRGSKKNDRFEF 171
>gnl|CDD|222513 pfam14052, Caps_assemb_Wzi, Capsule assembly protein Wzi. Many
bacteria are covered in a layer of surface-associated
polysaccharide called the capsule. These capsules can be
divided into four groups depending upon the organisation
of genes responsible for capsule assembly, the assembly
pathway and regulation. This family plays a role in
group 1 capsule biosynthesis. It is likely to be
involved in the later stages of capsule assembly. It is
likely to consist of a beta-barrel structure.
Length = 441
Score = 28.1 bits (63), Expect = 8.8
Identities = 11/58 (18%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 201 FHVTVMGLDSIDENSMTYAADIFFAQTWKDHRLRLPENMTSEYRLLEVDW--LKNMWR 256
H+ + G N + Y + +++ D+ LLE+ + LK W
Sbjct: 360 LHLGLSG--QFS-NGLNYRLKLSYSRNNGDYNNPFAPPKKQFSLLLELSYRPLKGGWS 414
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 0.136 0.420
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,086,266
Number of extensions: 1915957
Number of successful extensions: 1987
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1983
Number of HSP's successfully gapped: 25
Length of query: 392
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 293
Effective length of database: 6,546,556
Effective search space: 1918140908
Effective search space used: 1918140908
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 (26.9 bits)