RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16206
(821 letters)
>gnl|CDD|107377 cd06382, PBP1_iGluR_Kainate, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the kainate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the kainate receptors, non-NMDA ionotropic
receptors which respond to the neurotransmitter
glutamate. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. Kainate receptors have five
subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are
structurally similar to AMPA and NMDA subunits of
ionotropic glutamate receptors. KA1 and KA2 subunits can
only form functional receptors with one of the GluR5-7
subunits. Moreover, GluR5-7 can also form functional
homomeric receptor channels activated by kainate and
glutamate when expressed in heterologous systems.
Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMAP receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 327
Score = 283 bits (726), Expect = 9e-89
Identities = 130/387 (33%), Positives = 211/387 (54%), Gaps = 61/387 (15%)
Query: 2 KIVGIFG-PNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNA 60
+I IF ++ AF A+ RIN++ K L + LE ++ V+ DS T K +C+
Sbjct: 1 RIGAIFDDDDDSGEELAFRYAIDRINRE-KELLANTTLEYDIKRVKPDDSFETTKKVCDL 59
Query: 61 TSEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLI 120
+G+AAIFGP S E +I++S+C +IPH++ WDP +N +N+YP + +
Sbjct: 60 LQQGVAAIFGPSSSEASSIVQSICDAKEIPHIQTRWDPEPK---SNRQFTINLYPSNADL 116
Query: 121 SKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTD 180
S+ + I+ +W +FTIIYE+ + L+ LQ++L+ ++T+RQL D
Sbjct: 117 SRAYADIVKSFNWKSFTIIYESAEGLLRLQELLQAFG-------ISGITITVRQLDDD-L 168
Query: 181 DYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTSYWINAHTVD 240
DYRPLLKEIKNS ++ I++DCS D + +LKQA++V +M +Y +YI +T+ ++ HT+D
Sbjct: 169 DYRPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMMSEYYHYI--ITN--LDLHTLD 224
Query: 241 FQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDAV 300
+D++ NIT R+++P +P ++ ++ +E R L V E+ALMYDAV
Sbjct: 225 LEDYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPST--GVTTESALMYDAV 282
Query: 301 YLFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGRINLDSQTGRRN 360
YLF G+TGRI DS +G+R+
Sbjct: 283 YLF-----------------------------------------GLTGRIEFDS-SGQRS 300
Query: 361 SFSLEFVEYVSDQWKVLGTWNTAFGLN 387
+F+L+ +E + +GTWN++ GLN
Sbjct: 301 NFTLDVIELTESGLRKVGTWNSSEGLN 327
>gnl|CDD|107363 cd06368, PBP1_iGluR_non_NMDA_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the non-NMDA (N-methyl-d-asparate) subtypes of
ionotropic glutamate receptors. While this N-terminal
domain belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. Glutamate
mediates the majority of excitatory synaptic
transmission in the central nervous system via two broad
classes of ionotropic receptors, characterized by their
response to glutamate agonists: N-methyl-d -aspartate
(NMDA) and non-NMDA receptors. NMDA receptors have
intrinsically slow kinetics, are highly permeable to
Ca2+, and are blocked by extracellular Mg2+ in a
voltage-dependent manner. Non-NMDA receptors have faster
kinetics, are most often only weakly permeable to Ca2+,
and are not blocked by extracellular Mg2+. While
non-NMDA receptors typically mediate excitatory synaptic
responses at resting membrane potentials, NMDA receptors
contribute several forms of synaptic plasticity and are
thought to play an important role in the development of
synaptic pathways. Non-NMDA receptors include
alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate
(AMPA) and kainate receptors.
Length = 324
Score = 259 bits (664), Expect = 9e-80
Identities = 121/386 (31%), Positives = 184/386 (47%), Gaps = 62/386 (16%)
Query: 2 KIVGIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNAT 61
+I IF + + AF A+ RIN + + + L P + + DS C+
Sbjct: 1 RIGAIFDEDARQEELAFRFAIDRINTN-EEILAKFTLVPDIDELNTNDSFELTNKACDLL 59
Query: 62 SEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLIS 121
S+G+AAIFGP S + N ++S+C +IPH+ W PN P +N+YP +S
Sbjct: 60 SQGVAAIFGPSSSSSANTVQSICDALEIPHITTSWSPN----PKPRQFTINLYPSMRDLS 115
Query: 122 KGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDD 181
+ +I W F IY++ + L+ LQ++L+ P VT+R+L DTD
Sbjct: 116 DALLDLIKYFGWRKFVYIYDSDEGLLRLQELLDALS-------PKGIQVTVRRLDDDTDM 168
Query: 182 YRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTSYWINAHTVDF 241
YRPLLKEIK E I+LDCS ++ L+QA EV +M +Y +YI LT+ + HT+D
Sbjct: 169 YRPLLKEIKREKERRIILDCSPERLKEFLEQAVEVGMMSEYYHYI--LTNL--DFHTLDL 224
Query: 242 QDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDAVY 301
+ F+ G NIT R+++P NP ++ + W E ++ + +K E+AL YDAV
Sbjct: 225 ELFRYGGVNITGFRLVDPDNPEVQKFIQRW--ERSDHRICPGSGLKPIKTESALTYDAVL 282
Query: 302 LFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGRINLDSQTGRRNS 361
LF TGRI D G+R++
Sbjct: 283 LF-------------------------------------------TGRIQFDE-NGQRSN 298
Query: 362 FSLEFVEYVSDQWKVLGTWNTAFGLN 387
F+L+ +E + +GTWN GLN
Sbjct: 299 FTLDILELKEGGLRKVGTWNPEDGLN 324
>gnl|CDD|107388 cd06393, PBP1_iGluR_Kainate_GluR5_7, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR5-7 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR5-7 subunits of Kainate
receptor. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. There are five types of
kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2,
which are structurally similar to AMPA and NMDA subunits
of ionotropic glutamate receptors. KA1 and KA2 subunits
can only form functional receptors with one of the
GluR5-7 subunits. Moreover, GluR5-7 can also form
functional homomeric receptor channels activated by
kainate and glutamate when expressed in heterologous
systems. Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMAP receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 384
Score = 206 bits (526), Expect = 2e-59
Identities = 118/400 (29%), Positives = 200/400 (50%), Gaps = 33/400 (8%)
Query: 1 MKIVGIF----GPNEEEVAT---AFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHT 53
++I GIF GPN + ++ AF + IN++ + L P+ L +Q + +DS
Sbjct: 3 IRIGGIFEYLDGPNNQVMSAEELAFRFSANIINRN-RTLLPNTTLTYDIQRIHFHDSFEA 61
Query: 54 AKLMCNATSEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNV 113
K C+ + G+ AIFGP N ++S+C ++PH++ W + + VN+
Sbjct: 62 TKKACDQLALGVVAIFGPSQGSCTNAVQSICNALEVPHIQLRW--KHHPLDNKDTFYVNL 119
Query: 114 YPESHLISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSV--T 171
YP+ +S I ++ + W + T++Y+ L+ LQ+++ + P R ++
Sbjct: 120 YPDYASLSHAILDLVQYLKWRSATVVYDDSTGLIRLQELI---------MAPSRYNIRLK 170
Query: 172 IRQLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTS 231
IRQLP D+DD RPLLKE+K E I+ DCS ILKQA + +M +Y ++I +
Sbjct: 171 IRQLPTDSDDARPLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTT-- 228
Query: 232 YWINAHTVDFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYE--ENERGRSLNVRAETV 289
++ + +D + ++ N+T R++N NPH+ SI+ W E + + +
Sbjct: 229 --LDLYALDLEPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVM 286
Query: 290 KIEAALMYDAVYLFAAALQSLGERKPLPT--PLSCENPSSWQHGLGIGNLMKSITIDGMT 347
+AAL+YDAV++ + Q R P T L C +W+ G N +K +G+T
Sbjct: 287 MTDAALLYDAVHMVSVCYQ----RAPQMTVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLT 342
Query: 348 GRINLDSQTGRRNSFSLEFVEYVSDQWKVLGTWNTAFGLN 387
GRI + +G R F L+ + D + +G WN GLN
Sbjct: 343 GRIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNPNTGLN 382
>gnl|CDD|107346 cd06351, PBP1_iGluR_N_LIVBP_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Glutamate mediates the majority of
excitatory synaptic transmission in the central nervous
system via two broad classes of ionotropic receptors
characterized by their response to glutamate agonists:
N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA
receptors have intrinsically slow kinetics, are highly
permeable to Ca2+, and are blocked by extracellular Mg2+
in a voltage-dependent manner. On the other hand,
non-NMDA receptors have faster kinetics, are weakly
permeable to Ca2+, and are not blocked by extracellular
Mg2+. While non-NMDA receptors typically mediate
excitatory synaptic responses at resting membrane
potentials, NMDA receptors contribute to several forms
of synaptic plasticity and are suggested to play an
important role in the development of synaptic pathways.
Length = 328
Score = 203 bits (518), Expect = 5e-59
Identities = 101/383 (26%), Positives = 168/383 (43%), Gaps = 65/383 (16%)
Query: 2 KIVGIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCN-A 60
I IF + + AF A+ +N + L V V D + +C+
Sbjct: 1 NIGAIFDRDARKEELAFRAAIDALNTE-NLNALPTKLSVEVVEVNTNDPFSLLRAVCDLL 59
Query: 61 TSEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLI 120
S+G+AAIFGP S E+ + ++S+C +IPH+ + +YP +
Sbjct: 60 VSQGVAAIFGPTSSESASAVQSICDALEIPHISISGGSEGLSDKEESSTTLQLYPSLEDL 119
Query: 121 SKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTD 180
+ + ++ +W F IIY++ + L LQ++L+ + VT+R+L D D
Sbjct: 120 ADALLDLLEYYNWTKFAIIYDSDEGLSRLQELLDESG-------IKGIQVTVRRLDLDDD 172
Query: 181 DYRPLLKEIKNSSESHILLDC-SMDKTVTILKQAKEVHLMGDYQNYILSLTSYWINAHTV 239
+YR LLKE+K S I+LDC S ++ IL+QA E+ +MG ++IL+ ++ +
Sbjct: 173 NYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMGYGYHWILTN----LDLSDI 228
Query: 240 DFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDA 299
D + FQ G ANIT R+++P +P + + W+ E +AAL+YDA
Sbjct: 229 DLEPFQYGPANITGFRLVDPDSPDVSQFLQRWLEESPGVNL------RAPIYDAALLYDA 282
Query: 300 VYLFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGRINLDSQTGRR 359
V L TG ++ D G R
Sbjct: 283 VLLL-------------------------------------------TGTVSFDED-GVR 298
Query: 360 NSFSLEFVEY-VSDQWKVLGTWN 381
++F+L+ +E S W+ +GTWN
Sbjct: 299 SNFTLDIIELNRSRGWRKVGTWN 321
>gnl|CDD|107375 cd06380, PBP1_iGluR_AMPA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the AMPA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor, a member of the glutamate-receptor ion
channels (iGluRs). AMPA receptors are the major
mediators of excitatory synaptic transmission in the
central nervous system. While this N-terminal domain
belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. AMPA
receptors consist of four types of subunits (GluR1,
GluR2, GluR3, and GluR4) which combine to form a
tetramer and play an important roles in mediating the
rapid excitatory synaptic current.
Length = 382
Score = 160 bits (408), Expect = 3e-43
Identities = 95/397 (23%), Positives = 172/397 (43%), Gaps = 40/397 (10%)
Query: 3 IVGIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNATS 62
I G+F +E++ +AF A+ + N + + P L P V +++ DS +C+ S
Sbjct: 2 IGGLFDVDEDQEYSAFRFAISQHNTNPNSTAP-FKLLPHVDNLDTSDSFALTNAICSQLS 60
Query: 63 EGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLISK 122
G+ AIFG + N + S +P + + + + P LI
Sbjct: 61 RGVFAIFGSYDKSSVNTLTSYSDALHVPFI--TPSFPTNDLDDGNQFVLQMRPS--LIQA 116
Query: 123 GISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDD- 181
+ +I + W +Y++ L+ LQQ+L+ + D + VT R++ TD+
Sbjct: 117 LVDLIEH-YGWRKVVYLYDSDRGLLRLQQLLDYLREKDNKW-----QVTARRVDNVTDEE 170
Query: 182 -YRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILS---LTSYWINAH 237
+ LL+++ E I+LDC ++ IL+Q +V +YIL+
Sbjct: 171 EFLRLLEDLDRRKEKRIVLDCESERLNKILEQIVDVGKNRKGYHYILANLGFDDI----- 225
Query: 238 TVDFQDFQPGYANITTVRMINPTNPHIRSIMNGWI-YEENERGRSLNVRAETVKIEAALM 296
D F G NIT ++++ TNP ++ + W + E + +K AAL
Sbjct: 226 --DLSKFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGT---SPIKYTAALA 280
Query: 297 YDAVYLFAAALQSLGERKP----------LPTPLSC--ENPSSWQHGLGIGNLMKSITID 344
+DAV + A A +SL ++ C W+HG+ I +K + +
Sbjct: 281 HDAVLVMAEAFRSLRRQRGSGRHRIDISRRGNGGDCLANPAVPWEHGIDIERALKKVQFE 340
Query: 345 GMTGRINLDSQTGRRNSFSLEFVEYVSDQWKVLGTWN 381
G+TG + D G+R +++L+ VE + + +G WN
Sbjct: 341 GLTGNVQFDEF-GQRTNYTLDVVELKTRGLRKVGYWN 376
>gnl|CDD|216296 pfam01094, ANF_receptor, Receptor family ligand binding region.
This family includes extracellular ligand binding
domains of a wide range of receptors. This family also
includes the bacterial amino acid binding proteins of
known structure.
Length = 343
Score = 159 bits (403), Expect = 5e-43
Identities = 84/358 (23%), Positives = 134/358 (37%), Gaps = 19/358 (5%)
Query: 13 EVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNATSEGIAAIFGPQ 72
+V A +A+ IN D L P I L DS A C S+G+ A+ GP
Sbjct: 1 QVLLAMRLAIEDINAD-GGLLPGITLGYED-DDTCDDSFAVAAAACLLKSKGVVAVIGPS 58
Query: 73 SIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLISKGISVIINDMD 132
+ + F IP + + T P ++ I+ I+
Sbjct: 59 CSSVAIAVARLAGAFGIPMISYGATSPELSDKTRYPTFARTVPSDSKQARAIADILKHFG 118
Query: 133 WDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDDYRPLLKEIKN- 191
W +IY+ D Y + LE D +E ++ DD+ LLKE+K+
Sbjct: 119 WKRVAVIYDDDD---YGEGGLEALEDALREAG-LNVVAVASEVIASDDDFTALLKELKDI 174
Query: 192 -SSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTSYWINAHTVDFQDFQPGYAN 250
S I++ S D IL+QA+E+ LM +IL+ W ++ +D +
Sbjct: 175 KSKARVIVVCGSSDDLRQILRQARELGLMSGGYVWILTDL--WSDSLDIDNDKAREAAKG 232
Query: 251 ITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDAVYLFAAALQSL 310
+ + P +P + + R A L YDAVYL A AL
Sbjct: 233 VLGFTLKPPDSPGFQEFVERLK---KLANRCTPALDTEPNGYALLAYDAVYLLAHALNEA 289
Query: 311 GERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGRINLDSQTGRRNSFSLEFVE 368
P T + S + ++++ +G+TG + D GRR +SLE +
Sbjct: 290 LRDDPNITRGLWVDGSQ------LLEYLRNVNFEGLTGPVQFDDNGGRRPDYSLEILN 341
>gnl|CDD|107385 cd06390, PBP1_iGluR_AMPA_GluR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR1 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR1 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 364
Score = 116 bits (291), Expect = 5e-28
Identities = 96/392 (24%), Positives = 174/392 (44%), Gaps = 46/392 (11%)
Query: 2 KIVGIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNAT 61
+I G+F + + AF A+ ++ + PP ++ P + V DS C+
Sbjct: 1 QIGGLFPNQQSQEHAAFRFALSQLTE-----PPKLL--PQIDIVNISDSFEMTYTFCSQF 53
Query: 62 SEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLIS 121
S+G+ AIFG + N++ S C HV F P+ + + T+ + + PE +
Sbjct: 54 SKGVYAIFGFYDRKTVNMLTSFCGAL---HV-CFITPS-FPVDTSNQFVLQLRPE---LQ 105
Query: 122 KGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDD 181
+ +I W F IY+ L LQ+VL+ A + + ++ + L +
Sbjct: 106 DALISVIEHYKWQKFVYIYDADRGLSVLQKVLDTAAEKNWQV------TAVNILTTTEEG 159
Query: 182 YRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTSYWINAHTVDF 241
YR L +++ E I++DC ++ IL Q ++ G +YIL+ + +D
Sbjct: 160 YRKLFQDLDKKKERLIVVDCESERLNAILNQIIKLEKNGIGYHYILANLGFM----DIDL 215
Query: 242 QDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSL-NVRAETVKIEAALMYDAV 300
F+ AN+T +++N T+ + IM W +N R L V + K +AL YD V
Sbjct: 216 TKFRESGANVTGFQLVNYTDTTVSRIMQQW---KNFDARDLPRVDWKRPKYTSALTYDGV 272
Query: 301 YLFAAALQSLGERKP-----------LPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGR 349
+ A A Q+L +++ L P W G+ I ++ + +G+TG
Sbjct: 273 RVMAEAFQNLRKQRIDISRRGNAGDCLANP-----AVPWGQGIDIQRALQQVRFEGLTGN 327
Query: 350 INLDSQTGRRNSFSLEFVEYVSDQWKVLGTWN 381
+ + + GRR +++L +E D + +G WN
Sbjct: 328 VQFNEK-GRRTNYTLHVIEMKHDGIRKIGYWN 358
>gnl|CDD|107384 cd06389, PBP1_iGluR_AMPA_GluR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR2 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR2 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 370
Score = 110 bits (275), Expect = 6e-26
Identities = 97/393 (24%), Positives = 183/393 (46%), Gaps = 43/393 (10%)
Query: 2 KIVGIFGPNEEEVATAFEIA-VRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNA 60
+I G+F ++ +AF + V+ +F+ L P + ++E +S C+
Sbjct: 1 QIGGLFPRGADQEYSAFRVGMVQFSTSEFR-------LTPHIDNLEVANSFAVTNAFCSQ 53
Query: 61 TSEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHG--VNVYPESH 118
S G+ AIFG ++ N I S C HV +F P+ PT+G H + + P+
Sbjct: 54 FSRGVYAIFGFYDKKSVNTITSFCGTL---HV-SFITPS---FPTDGTHPFVIQMRPD-- 104
Query: 119 LISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPD 178
+ + +I WD F +Y++ L LQ VL++A + ++ ++ + + D
Sbjct: 105 -LKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQV----TAINVGNINND 159
Query: 179 TDD--YRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEV--HLMGDYQNYILSLTSYWI 234
D YR L ++++N E ++LDC DK I+ Q + H+ G +YI++ +
Sbjct: 160 RKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVITIGKHVKG--YHYIIANLGFTD 217
Query: 235 NAHTVDFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAA 294
D Q G AN++ ++++ +P + + W E +T+K +A
Sbjct: 218 G----DLSKIQFGGANVSGFQIVDYDDPLVSKFIQRW--STLEEKEYPGAHTKTIKYTSA 271
Query: 295 LMYDAVYLFAAALQSLGERK----PLPTPLSC-ENPS-SWQHGLGIGNLMKSITIDGMTG 348
L YDAV + A ++L +++ C NP+ W G+ I +K + ++G+TG
Sbjct: 272 LTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLTG 331
Query: 349 RINLDSQTGRRNSFSLEFVEYVSDQWKVLGTWN 381
I D Q G+R ++++ +E S+ + +G W+
Sbjct: 332 NIKFD-QNGKRINYTINVMELKSNGPRKIGYWS 363
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 106 bits (267), Expect = 1e-25
Identities = 43/90 (47%), Positives = 60/90 (66%), Gaps = 8/90 (8%)
Query: 739 FFIYSILFFIY-TFVNE-------AVSTRLVAGMWWFFTLIMISSYTANLAAFLTNTRMN 790
F + + L+F + V + ++S R++ G+WWFF LI++SSYTANLAAFLT RM
Sbjct: 38 FTLSNSLWFSFGALVQQGHRELPRSLSGRILVGVWWFFALILLSSYTANLAAFLTVERMQ 97
Query: 791 PPIKNVEDLAKAGRIKYGCVEMGSTRNFFK 820
PI+++EDLAK +I YG + GST FFK
Sbjct: 98 SPIQSLEDLAKQNKIGYGTLRGGSTFEFFK 127
Score = 97.7 bits (244), Expect = 1e-22
Identities = 43/95 (45%), Positives = 54/95 (56%), Gaps = 2/95 (2%)
Query: 573 KNSNVSLYQRMHSAMESSRPSVFVKSNKEGVERVVKEKGKYAFFMESTGIEYEVEKN-CD 631
K S Y+RM M S + V V+S +EGV+RV K G YAF MES +EYEV ++ C
Sbjct: 127 KESKNPTYRRMWEYMISFKGEVNVESYEEGVQRVRKGNGLYAFLMESAYLEYEVARDPCK 186
Query: 632 LMQVGGLLDSKGYGIAMPT-SKFLAKFSFGFAKLR 665
L VG + +KGYGIA P S K S +LR
Sbjct: 187 LTTVGEVFGTKGYGIAFPKGSPLRDKLSRAILELR 221
Score = 37.3 bits (87), Expect = 0.020
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 540 DVWVYMATAYLGVSLLLFFLARIS 563
+VW+ + AYL V ++LF L R S
Sbjct: 1 EVWLCILAAYLLVGVVLFLLERFS 24
>gnl|CDD|153137 cd06269, PBP1_glutamate_receptors_like, Family C G-protein couples
receptors (GPCRs), membrane bound guanylyl cyclases such
as the family of natriuretic peptide receptors (NPRs),
and the N-terminal leucine/isoleucine/valine- binding
protein (LIVBP)-like domain of the ionotropic glutamate
receptors. This CD represents the ligand-binding domain
of the family C G-protein couples receptors (GPCRs),
membrane bound guanylyl cyclases such as the family of
natriuretic peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domain of the ionotropic glutamate receptors, all of
which are structurally similar and related to the
periplasmic-binding fold type I family. The family C
GPCRs consist of metabotropic glutamate receptor (mGluR)
receptors, a calcium-sensing receptor (CaSR),
gamma-aminobutyric receptors (GABAb), the promiscuous
L-alpha-amino acid receptor GPR6A, families of taste and
pheromone receptors, and orphan receptors. Truncated
splicing variants of the orphan receptors are not
included in this CD. The family C GPCRs are activated by
endogenous agonists such as amino acids, ions, and sugar
based molecules. Their amino terminal ligand-binding
region is homologous to the bacterial
leucine-isoleucine-valine binding protein (LIVBP) and a
leucine binding protein (LBP). The ionotropic glutamate
receptors (iGluRs) have an integral ion channel and are
subdivided into three major groups based on their
pharmacology and structural similarities: NMDA
receptors, AMPA receptors, and kainate receptors. The
family of membrane bound guanylyl cyclases is further
divided into three subfamilies: the ANP receptor
(GC-A)/C-type natriuretic peptide receptor (GC-B), the
heat-stable enterotoxin receptor (GC-C)/sensory organ
specific membrane GCs such as retinal receptors (GC-E,
GC-F), and olfactory receptors (GC-D and GC-G).
Length = 298
Score = 106 bits (265), Expect = 5e-25
Identities = 52/266 (19%), Positives = 101/266 (37%), Gaps = 25/266 (9%)
Query: 2 KIVGIF-----GPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENY--DSLHTA 54
+I G+F G EE A A+ + + LP L + D+ A
Sbjct: 1 RIGGLFPLHSGGRFGEEGAFRAAAALFAVEEINNDLPN-TTLGYEIYDSCCSPSDAFSAA 59
Query: 55 KLMCN--ATSEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVN 112
+C+ S G+ A+ GP S + + S+ IP + +
Sbjct: 60 LDLCSLLEKSRGVVAVIGPSSSSSAEAVASLLGALHIPQISYSATSPLLSDKEQFPSFLR 119
Query: 113 VYPESHLISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTI 172
P ++ I ++ W ++Y D L ++LE + + + +
Sbjct: 120 TVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLLELLEEELE--------KNGICV 171
Query: 173 RQL---PPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSL 229
+ P ++D R LLKE+K+S+ I++ S + + +L++A E+ +M Y +I +
Sbjct: 172 AFVESIPDGSEDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMMTGYH-WI--I 228
Query: 230 TSYWINAHTVDFQDFQPGYANITTVR 255
T W+ + + N+T
Sbjct: 229 TDLWLTSCLDLE-LLEYFPGNLTGFG 253
>gnl|CDD|107382 cd06387, PBP1_iGluR_AMPA_GluR3, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR3 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR3 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 372
Score = 103 bits (259), Expect = 7e-24
Identities = 92/393 (23%), Positives = 174/393 (44%), Gaps = 42/393 (10%)
Query: 3 IVGIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNATS 62
I G+F N + +AF AV+ N + L V H+++ +S C+ S
Sbjct: 2 IGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNAFCSQFS 61
Query: 63 EGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFW--DPNKYFIPTNGVHGVNVYPESHLI 120
G+ AIFG + N + S C + + D + F+ + + P +
Sbjct: 62 RGVYAIFGFYDQMSMNTLTSFCGALHTSFITPSFPTDADVQFV-------IQMRPA---L 111
Query: 121 SKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLP--PD 178
I ++ W+ F +Y+T LQ ++E A ++ + VT R + D
Sbjct: 112 KGAILSLLAHYKWEKFVYLYDTERGFSILQAIMEAAVQNNWQ-------VTARSVGNIKD 164
Query: 179 TDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQ---NYILSLTSYWIN 235
++R +++E+ E L+DC +++ TIL+Q V ++G + +Y+L+ +
Sbjct: 165 VQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQ---VVILGKHSRGYHYMLANLGF--- 218
Query: 236 AHTVDFQDFQPGYANITTVRMINPTNPHIRSIMNGWI-YEENERGRSLNVRAETVKIEAA 294
+ + G ANIT +++N NP ++ + W+ +E E + + +K +A
Sbjct: 219 -TDISLERVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEA---KNSPLKYTSA 274
Query: 295 LMYDAVYLFAAALQSLGERK----PLPTPLSC-ENPS-SWQHGLGIGNLMKSITIDGMTG 348
L +DA+ + A A + L ++ + C NP+ W G+ I +K + + GMTG
Sbjct: 275 LTHDAILVIAEAFRYLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTG 334
Query: 349 RINLDSQTGRRNSFSLEFVEYVSDQWKVLGTWN 381
I D+ GRR +++++ E + G WN
Sbjct: 335 NIQFDT-YGRRTNYTIDVYEMKPSGSRKAGYWN 366
>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
substrate binding proteins. Prokaryotic homologues are
represented by a separate alignment: PBPb.
Length = 133
Score = 95.0 bits (237), Expect = 4e-23
Identities = 46/106 (43%), Positives = 55/106 (51%), Gaps = 7/106 (6%)
Query: 573 KNSNVSLYQRMHSAMESSRPSVFVKSNKEGVERVVKEKGKYAFFMESTGIEYEVEKNCDL 632
K S Y RM M P VFVKS EGV+RV YAF MES ++YE+ +NCDL
Sbjct: 29 KRSGNPEYSRMWPYM--KSPEVFVKSYAEGVQRV--RVSNYAFIMESPYLDYELSRNCDL 84
Query: 633 MQVGGLLDSKGYGIAMP-TSKFLAKFSFGFAKLRVLFQGEPYMMKN 677
M VG KGYGIA P S S A L++ GE ++N
Sbjct: 85 MTVGEEFGRKGYGIAFPKGSPLRDDLS--RAILKLSESGELEKLRN 128
Score = 36.5 bits (85), Expect = 0.015
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 792 PIKNVEDLAKAGRIKYGCVEMGSTRNFFK 820
PI +VEDLAK +I+YG + ST FFK
Sbjct: 1 PITSVEDLAKQTKIEYGTQDGSSTLAFFK 29
>gnl|CDD|107383 cd06388, PBP1_iGluR_AMPA_GluR4, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR4 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR4 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 371
Score = 100 bits (250), Expect = 1e-22
Identities = 94/396 (23%), Positives = 176/396 (44%), Gaps = 48/396 (12%)
Query: 2 KIVGIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNAT 61
+I G+F N ++ TAF +A+ N A L P V ++E +S C+
Sbjct: 1 QIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVTNAFCSQY 60
Query: 62 SEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLIS 121
S G+ AIFG + + + S C I + + PT G + L
Sbjct: 61 SRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSF-------PTEGESQFVLQLRPSLRG 113
Query: 122 KGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDD 181
+S +++ +W+ F +Y+T LQ ++E A + ++ ++ + +
Sbjct: 114 ALLS-LLDHYEWNRFVFLYDTDRGYSILQAIMEKAGQNGWQVS----AICVENF--NDAS 166
Query: 182 YRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEV--HLMGDYQNYILSLTSYWINAHTV 239
YR LL+++ E ++DC +++ IL+Q V H+ G +YI++ + +
Sbjct: 167 YRRLLEDLDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKG--YHYIIANLGF----KDI 220
Query: 240 DFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVR----AET-VKIEAA 294
+ F G AN+T ++++ P + +M W + L+ R +E+ K +A
Sbjct: 221 SLERFMHGGANVTGFQLVDFNTPMVTKLMQRW--------KKLDQREYPGSESPPKYTSA 272
Query: 295 LMYDAVYLFAAALQSLGERKPLPTPLS--------CENPSS-WQHGLGIGNLMKSITIDG 345
L YD V + A A ++L +K +S NP++ W G+ + +K + I G
Sbjct: 273 LTYDGVLVMAEAFRNLRRQK---IDISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQG 329
Query: 346 MTGRINLDSQTGRRNSFSLEFVEYVSDQWKVLGTWN 381
+TG I D GRR +++++ E S+ + +G WN
Sbjct: 330 LTGNIQFD-HYGRRVNYTMDVFELKSNGPRKIGYWN 364
>gnl|CDD|107261 cd04509, PBP1_ABC_transporter_GCPR_C_like, Family C of G-protein
coupled receptors and their close homologs, the type I
periplasmic-binding proteins of ATP-binding cassette
transporter-like systems. This CD includes members of
the family C of G-protein coupled receptors and their
close homologs, the type I periplasmic-binding proteins
of ATP-binding cassette transporter-like systems. The
family C GPCR includes glutamate/glycine-gated ion
channels such as the NMDA receptor, G-protein-coupled
receptors, metabotropic glutamate, GABA-B, calcium
sensing, phermone receptors, and atrial natriuretic
peptide-guanylate cyclase receptors. The glutamate
receptors that form cation-selective ion channels,
iGluR, can be classified into three different subgroups
according to their binding-affinity for the agonists
NMDA (N-methyl-D-asparate), AMPA
(alpha-amino-3-dihydro-5-methyl-3-oxo-4-
isoxazolepropionic acid), and kainate. L-glutamate is a
major neurotransmitter in the brain of vertebrates and
acts through either mGluRs or iGluRs. mGluRs subunits
possess seven transmembrane segments and a large
N-terminal extracellular domain. ABC-type
leucine-isoleucine-valine-binding protein (LIVBP) is a
bacterial periplasmic binding protein that has homology
with the amino-terminal domain of the glutamate-receptor
ion channels (iGluRs). The extracellular regions of
iGluRs are made of two PBP-like domains in tandem, a
LIVBP-like domain that constitutes the N terminus -
which is included in this CD - followed by a domain
related to lysine-arginine-ornithine-binding protein
(LAOBP) that belongs to the type II periplasmic binding
fold protein superfamily. The uncharacterized
periplasmic components of various ABC-type transport
systems are included in this group.
Length = 299
Score = 91.4 bits (227), Expect = 4e-20
Identities = 61/301 (20%), Positives = 105/301 (34%), Gaps = 23/301 (7%)
Query: 5 GIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVEN--YDSLHTAKLMCNATS 62
G + ++AV IN K P LE ++ ++ +L A+ +C
Sbjct: 10 GPYAEYGAFRLAGAQLAVEEINA--KGGIPGRKLELVIYDDQSDPARALAAARRLCQQ-- 65
Query: 63 EGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLISK 122
EG+ A+ GP S + + + IP + + P ++
Sbjct: 66 EGVDALVGPVSSGVALAVAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQAE 125
Query: 123 GISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDDY 182
++ I + +W I+Y+ L + + A K V P T D+
Sbjct: 126 ALADYIKEYNWKKVAILYDDDSYGRGLLEAFK-AAFKKKGGTV----VGEEYYPLGTTDF 180
Query: 183 RPLLKEIKNSSESHILLDCSMDKT-VTILKQAKEVHLMGDYQNYILSLTSYWINAHTVDF 241
LL+++K ++ +++ C + TILKQA E L G Y IL +T +
Sbjct: 181 TSLLQKLKA-AKPDVIVLCGSGEDAATILKQAAEAGLTGGYP--ILGITLGLSDVLLEAG 237
Query: 242 QDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDAVY 301
+ G +T P E ++ + AAL YDAV
Sbjct: 238 GEAAEG--VLTGTPYFPGDPPPESFFFVRAAAREKKKYE------DQPDYFAALAYDAVL 289
Query: 302 L 302
L
Sbjct: 290 L 290
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 84.6 bits (210), Expect = 2e-18
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 14/97 (14%)
Query: 426 PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQE 485
P+ + E G+L G+ VDL K IA L +FV W+GLI L+
Sbjct: 11 PFSYVD-ENGKLVGFDVDLAKAIAKRLGVKVEFV-------------PVSWDGLIPALKS 56
Query: 486 QRADLAICDLTITSERRAAVDFTMPFMTLGISILYRK 522
+ D+ I +TIT ER+ VDF+ P+ G ++ RK
Sbjct: 57 GKVDIIIAGMTITPERKKQVDFSDPYYYSGQVLVVRK 93
Score = 43.8 bits (104), Expect = 1e-04
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 15/67 (22%)
Query: 672 PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQE 731
P+ + E G+L G+ VDL K IA L +FV W+GLI L+
Sbjct: 11 PFSYVD-ENGKLVGFDVDLAKAIAKRLGVKVEFV-------------PVSWDGLIPALKS 56
Query: 732 -QVDTFI 737
+VD I
Sbjct: 57 GKVDIII 63
>gnl|CDD|214911 smart00918, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called the
S1 domain, is the luminal domain just upstream of the
first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan.
Length = 62
Score = 72.3 bits (178), Expect = 6e-16
Identities = 26/63 (41%), Positives = 39/63 (61%), Gaps = 5/63 (7%)
Query: 426 PYMM--KNPETGEL--YGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIG 481
PY+M ++P+ G GY +DL+K +A +L FTY+ +L + YG P G WNG++G
Sbjct: 1 PYVMLKESPDGGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARLPN-GSWNGMVG 59
Query: 482 ELQ 484
EL
Sbjct: 60 ELV 62
Score = 72.3 bits (178), Expect = 6e-16
Identities = 26/63 (41%), Positives = 39/63 (61%), Gaps = 5/63 (7%)
Query: 672 PYMM--KNPETGEL--YGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIG 727
PY+M ++P+ G GY +DL+K +A +L FTY+ +L + YG P G WNG++G
Sbjct: 1 PYVMLKESPDGGNDRFEGYCIDLLKELAKKLGFTYEIILVPDGKYGARLPN-GSWNGMVG 59
Query: 728 ELQ 730
EL
Sbjct: 60 ELV 62
>gnl|CDD|204533 pfam10613, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called the
S1 domain, is the luminal domain just upstream of the
first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan,
pfam00060.
Length = 65
Score = 70.3 bits (173), Expect = 3e-15
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 426 PYMMKNPETGEL------YGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGL 479
PY+M L GY +DL+ +A L F Y+ L + YG+ + TG+WNG+
Sbjct: 1 PYVMLKENGENLTGNERFEGYCIDLLDELAKILGFNYEIYLVPDGKYGSEDK-TGEWNGM 59
Query: 480 IGELQE 485
IGEL
Sbjct: 60 IGELIR 65
Score = 70.3 bits (173), Expect = 3e-15
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 672 PYMMKNPETGEL------YGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGL 725
PY+M L GY +DL+ +A L F Y+ L + YG+ + TG+WNG+
Sbjct: 1 PYVMLKENGENLTGNERFEGYCIDLLDELAKILGFNYEIYLVPDGKYGSEDK-TGEWNGM 59
Query: 726 IGELQE 731
IGEL
Sbjct: 60 IGELIR 65
>gnl|CDD|107389 cd06394, PBP1_iGluR_Kainate_KA1_2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the KA1 and KA2 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the KA1 and KA2 subunits of
Kainate receptor. While this N-terminal domain belongs
to the periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. There are five types of
kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2,
which are structurally similar to AMPA and NMDA subunits
of ionotropic glutamate receptors. KA1 and KA2 subunits
can only form functional receptors with one of the
GluR5-7 subunits. Moreover, GluR5-7 can also form
functional homomeric receptor channels activated by
kainate and glutamate when expressed in heterologous
systems. Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMPA receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 333
Score = 76.1 bits (187), Expect = 1e-14
Identities = 77/345 (22%), Positives = 149/345 (43%), Gaps = 78/345 (22%)
Query: 53 TAKLMCNATSEGIAAIFGPQSI-ENRNIIESMCQMFDIPHVEAFWDPNKYF-IPTNGVHG 110
T MC +G+ ++ GP S + +I+ +C +IPH + P + +
Sbjct: 54 TTDTMCQILPKGVVSVLGPSSSPASSSIVSHICGEKEIPHFKV--GPEETPKLQYLRFAS 111
Query: 111 VNVYPESHLISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSV 170
VN++P + IS ++ I+N ++ T ++I + L+ L+++L ++ + ++
Sbjct: 112 VNLHPSNEDISVAVAGILNSFNYPTASLICAKAECLLRLEELL-------RQFLISKETL 164
Query: 171 TIRQLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLT 230
++R L D+ D PLLKEI++ + I++D + + TIL +A E+ + + YIL+
Sbjct: 165 SVRMLD-DSRDPTPLLKEIRDDKTATIIIDANASMSHTILLKASELGMTSAFYKYILT-- 221
Query: 231 SYWINAHTVDF-----QDFQPGYANITTVRMINPTNPH----IRSIMNGWIYEENERGRS 281
T+DF +NI M N ++ IRS+ W EN
Sbjct: 222 -------TMDFPLLRLDSIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSW--RENCDHSP 272
Query: 282 LNVRAETVKIEAALMYDAVYLFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSI 341
A + +AL++DAVY
Sbjct: 273 YTGPA----LSSALLFDAVY---------------------------------------- 288
Query: 342 TIDGMTGRINLDSQTGRRNSFSLEFVEYVSDQWKVLGTWNTAFGL 386
G+TGRI +S+ G+R++++L+ ++ ++ +G W++ L
Sbjct: 289 -AVGLTGRIEFNSK-GQRSNYTLKILQKTRSGFRQIGQWHSNETL 331
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins (PBPs)
to transport a wide variety of substrates, such as,
amino acids, peptides, sugars, vitamins and inorganic
ions. PBPs have two cell-membrane translocation
functions: bind substrate, and interact with the
membrane bound complex. A diverse group of periplasmic
transport receptors for lysine/arginine/ornithine (LAO),
glutamine, histidine, sulfate, phosphate, molybdate, and
methanol are included in the PBPb CD.
Length = 218
Score = 72.4 bits (178), Expect = 3e-14
Identities = 39/115 (33%), Positives = 52/115 (45%), Gaps = 16/115 (13%)
Query: 418 LRVLFQGE--PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGK 475
L V G P+ ++ GEL G+ VDL K IA EL KFV
Sbjct: 1 LTVGTAGTYPPFSFRD-ANGELTGFDVDLAKAIAKELGVKVKFV-------------EVD 46
Query: 476 WNGLIGELQEQRADLAICDLTITSERRAAVDFTMPFMTLGISILYRKPAKKQPDL 530
W+GLI L+ + DL +TIT ER VDF+ P+ G IL +K + +
Sbjct: 47 WDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSPIKSVK 101
Score = 36.6 bits (85), Expect = 0.028
Identities = 26/77 (33%), Positives = 33/77 (42%), Gaps = 17/77 (22%)
Query: 664 LRVLFQGE--PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGK 721
L V G P+ ++ GEL G+ VDL K IA EL KFV
Sbjct: 1 LTVGTAGTYPPFSFRD-ANGELTGFDVDLAKAIAKELGVKVKFV-------------EVD 46
Query: 722 WNGLIGELQE-QVDTFI 737
W+GLI L+ +VD
Sbjct: 47 WDGLITALKSGKVDLIA 63
>gnl|CDD|107347 cd06352, PBP1_NPR_GC_like, Ligand-binding domain of membrane
guanylyl-cyclase receptors. Ligand-binding domain of
membrane guanylyl-cyclase receptors. Membrane guanylyl
cyclases (GC) have a single membrane-spanning region and
are activated by endogenous and exogenous peptides. This
family can be divided into three major subfamilies: the
natriuretic peptide receptors (NPRs), sensory
organ-specific membrane GCs, and the
enterotoxin/guanylin receptors. The binding of peptide
ligands to the receptor results in the activation of the
cytosolic catalytic domain. Three types of NPRs have
been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/
GC-B, and NPR-C. In addition, two of the GCs, GC-D and
GC-G, appear to be pseudogenes in humans. Atrial
natriuretic peptide (ANP) and brain natriuretic peptide
(BNP) are produced in the heart, and both bind to the
NPR-A. NPR-C, also termed the clearance receptor, binds
each of the natriuretic peptides and can alter
circulating levels of these peptides. The ligand binding
domain of the NPRs exhibits strong structural similarity
to the type I periplasmic binding fold protein family.
Length = 389
Score = 72.3 bits (178), Expect = 2e-13
Identities = 73/369 (19%), Positives = 132/369 (35%), Gaps = 42/369 (11%)
Query: 14 VATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNATSEGIAAIFGPQS 73
V A ++AV R+N D L P + E +S+ + + A GP
Sbjct: 19 VGPAIQLAVERVNAD-PNLLPGYDFTFVYLDTECSESVALLAAVDLYWEHNVDAFIGPGC 77
Query: 74 IENRNIIESMCQMFDIPHV------EAFWDPNKYFIPTNGVHGVNVYPESHLISKGISVI 127
+ + ++IP + + D ++Y PT P + + + + +
Sbjct: 78 PYACAPVARLAAHWNIPMISWGCVALSLSDKSEY--PTL----TRTLPPARKLGEAVLAL 131
Query: 128 INDMDWDTFTIIYETHDNL-VYLQQVLENAHD-DDKEIRPGRPSVTIRQLPPDTDDYRPL 185
+ +W ++Y + + LE A + + V + +D +
Sbjct: 132 LRWFNWHVAVVVYSDDSENCFFTLEALEAALREFNLTVSH----VVFMEDNSGAEDLLEI 187
Query: 186 LKEIKNSSESHILLDCSMDKTVTILKQAKEVHLM-GDYQNYILSLTSYWINAHTVDFQDF 244
L++IK S I++ S + +L A ++ L GDY ++ L +Y + +
Sbjct: 188 LQDIKRRSRI-IIMCGSSEDVRELLLAAHDLGLTSGDYVFILIDLFNYSLPYQNSYPWER 246
Query: 245 QPG--------YANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALM 296
G Y + T+ + P NP + + E V A +
Sbjct: 247 GDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQVSPYAGYL 306
Query: 297 YDAVYLFAAAL-QSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGRINLDSQ 355
YDAV L+A AL ++L E GL I M + T G+TG + +D
Sbjct: 307 YDAVLLYAHALNETLAEGGDYNG------------GLIITRRMWNRTFSGITGPVTIDEN 354
Query: 356 TGRRNSFSL 364
R +SL
Sbjct: 355 GDREGDYSL 363
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 63.1 bits (154), Expect = 4e-11
Identities = 36/108 (33%), Positives = 52/108 (48%), Gaps = 16/108 (14%)
Query: 417 KLRVLFQGE--PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTG 474
LRV G+ P+ + + GEL G+ VDL K IA EL +FV +
Sbjct: 1 TLRVGTNGDYPPFSFADED-GELTGFDVDLAKAIAKELGLKVEFV-----------EVS- 47
Query: 475 KWNGLIGELQEQRADLAICDLTITSERRAAVDFTMPFMTLGISILYRK 522
++ L+ L+ + D+ +TIT ER VDF+ P+ G IL RK
Sbjct: 48 -FDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYRSGQVILVRK 94
Score = 32.7 bits (75), Expect = 0.56
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 663 KLRVLFQGE--PYMMKNPETGELYGYSVDLIKMIANELNFTYKFV 705
LRV G+ P+ + + GEL G+ VDL K IA EL +FV
Sbjct: 1 TLRVGTNGDYPPFSFADED-GELTGFDVDLAKAIAKELGLKVEFV 44
>gnl|CDD|223904 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 63.5 bits (154), Expect = 7e-11
Identities = 36/113 (31%), Positives = 52/113 (46%), Gaps = 14/113 (12%)
Query: 413 KTFAKLRVLFQGE---PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTL 469
K KLRV + P+ + + G+L G+ VDL K IA L K
Sbjct: 31 KARGKLRVGTEATYAPPFEFLDAKGGKLVGFDVDLAKAIAKRLGGDKKVEF--------- 81
Query: 470 NPQTGKWNGLIGELQEQRADLAICDLTITSERRAAVDFTMPFMTLGISILYRK 522
W+GLI L+ + D+ I +TIT ER+ VDF+ P+ G +L +K
Sbjct: 82 --VPVAWDGLIPALKAGKVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKK 132
Score = 33.4 bits (76), Expect = 0.38
Identities = 24/80 (30%), Positives = 33/80 (41%), Gaps = 15/80 (18%)
Query: 662 AKLRVLFQGE---PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQ 718
KLRV + P+ + + G+L G+ VDL K IA L K
Sbjct: 34 GKLRVGTEATYAPPFEFLDAKGGKLVGFDVDLAKAIAKRLGGDKKVEF-----------V 82
Query: 719 TGKWNGLIGELQ-EQVDTFI 737
W+GLI L+ +VD I
Sbjct: 83 PVAWDGLIPALKAGKVDIII 102
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 60.1 bits (146), Expect = 8e-10
Identities = 28/102 (27%), Positives = 45/102 (44%), Gaps = 17/102 (16%)
Query: 433 ETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQEQRADLAI 492
E G+L G+ V+ + +A L + KW+G++ L +R D+ I
Sbjct: 59 EDGKLTGFEVEFAEALAKHLGVKASL-------------KPTKWDGMLASLDSKRIDVVI 105
Query: 493 CDLTITSERRAAVDFTMPFMTLGISILYRK----PAKKQPDL 530
+TI+ ER+ DF+ P+ GI L +K K DL
Sbjct: 106 NQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGTIKTAADL 147
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 57.2 bits (138), Expect = 8e-09
Identities = 46/304 (15%), Positives = 85/304 (27%), Gaps = 61/304 (20%)
Query: 7 FGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVEN--YDSLHTAKLMCNATSEG 64
P ++ E+A I + LE I+ ++ +L + + +G
Sbjct: 11 SAPFGAQLLAGIELAAEEIGRG---------LEVILADSQSDPERALEALRDLIQ---QG 58
Query: 65 IAAIFGPQSIENRNIIESMCQMFDIPHV-----EAFWDPNKYFIPTNGVHGVNVYPESHL 119
+ I GP S + + + IP V Y V P++
Sbjct: 59 VDGIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDLTGYPYV--------FRVGPDNEQ 110
Query: 120 ISKGISVIINDMDWDTFTIIYET-HDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPD 178
+ + + + W +IY + + A
Sbjct: 111 AGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKK----AGIEVVAIEYGDLDT 166
Query: 179 TDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTSYWINAHT 238
++ LL+ +K + + + C+ + LK A+E L + I A
Sbjct: 167 EKGFQALLQLLKAAPKPDAIFACNDEMAAGALKAAREAGLTPGDISII---GFDGSPAAL 223
Query: 239 VDFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYD 298
+ + PG T + +P AAL YD
Sbjct: 224 LAAGEAGPG--LTTVAQPFPGDDPDQPDYP------------------------AALGYD 257
Query: 299 AVYL 302
AV L
Sbjct: 258 AVLL 261
>gnl|CDD|236540 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 53.2 bits (128), Expect = 1e-07
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 13/81 (16%)
Query: 439 GYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQEQRADLAICDLTIT 498
G+ +DL IA EL Y TL P ++G+I LQ + DLA+ +TIT
Sbjct: 48 GFDIDLWAAIAKELKLDY-----------TLKPM--DFSGIIPALQTKNVDLALAGITIT 94
Query: 499 SERRAAVDFTMPFMTLGISIL 519
ER+ A+DF+ + G+ ++
Sbjct: 95 DERKKAIDFSDGYYKSGLLVM 115
>gnl|CDD|233269 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 250
Score = 52.4 bits (126), Expect = 2e-07
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 14/103 (13%)
Query: 426 PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQE 485
P+ K+ G+L G+ VDL K + + KFV Q ++GLI L+
Sbjct: 36 PFESKDAN-GKLVGFDVDLAKALCKRMKAKCKFV-----------EQN--FDGLIPSLKA 81
Query: 486 QRADLAICDLTITSERRAAVDFTMPFMTLGISILYRKPAKKQP 528
++ D + ++IT +R+ +DF+ P+ G + +K +
Sbjct: 82 KKVDAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAK 124
Score = 31.2 bits (71), Expect = 1.8
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 14/59 (23%)
Query: 672 PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQ 730
P+ K+ G+L G+ VDL K + + KFV Q ++GLI L+
Sbjct: 36 PFESKDAN-GKLVGFDVDLAKALCKRMKAKCKFV-----------EQN--FDGLIPSLK 80
>gnl|CDD|107365 cd06370, PBP1_Speract_GC_like, Ligand-binding domain of membrane
bound guanylyl cyclases. Ligand-binding domain of
membrane bound guanylyl cyclases (GCs), which are known
to be activated by sperm-activating peptides (SAPs),
such as speract or resact. These ligand peptides are
released by a range of invertebrates to stimulate the
metabolism and motility of spermatozoa and are also
potent chemoattractants. These GCs contain a single
transmembrane segment, an extracellular ligand binding
domain, and intracellular protein kinase-like and
cyclase catalytic domains. GCs of insect and nematodes,
which exhibit high sequence similarity to the speract
receptor are also included in this model.
Length = 404
Score = 47.7 bits (114), Expect = 2e-05
Identities = 62/325 (19%), Positives = 116/325 (35%), Gaps = 45/325 (13%)
Query: 14 VATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNATSEGIAAIFGPQ- 72
++ A +AV +N D L P L+ + L + + + G+ A GP+
Sbjct: 21 ISGALTLAVEDVNAD-PNLLPGYKLQFEWVDTHGDEVLSI-RAVSDWWKRGVVAFIGPEC 78
Query: 73 --SIENRNIIESMCQMFDIPHVEAFWD----PNKYFIPTNGVHGVNVYPESHLISKGISV 126
+ E R + +++P + D +K PT P S + K +
Sbjct: 79 TCTTEAR-----LAAAWNLPMISYKCDEEPVSDKSKYPTF----ARTVPPSIQVVKSVIA 129
Query: 127 IINDMDWDTFTIIYETHDNLVYLQQVL-ENAHDDDKEIRPGRPSVTIRQLPPDTDDYRP- 184
++ +W+ F+++YE + + L E A + I P D+
Sbjct: 130 LLKHFNWNKFSVVYENDSKYSSVFETLKEEAELRNITISHVEYYADFYPPDPIMDNPFED 189
Query: 185 LLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLM--GDY-------QNYILSLTSYWIN 235
+++ K ++ ++ + ++ L + L+ GDY + Y Y+
Sbjct: 190 IIQRTKETTRIYVFIG-EANELRQFLMSMLDEGLLESGDYMVLGVDIEYYDRDSQDYYSL 248
Query: 236 AHTVDFQDFQPGYANIT-------TVRMINPTNPHIRSIMNGWIYEENERGRSLN---VR 285
FQ + ++ +V +I PT + N
Sbjct: 249 --HRGFQSREYNRSDDEKALEAMKSVLIIVPTPVSPDYDSFSIFVRKYNLEPPFNGDLGE 306
Query: 286 AETVK---IEAALMYDAVYLFAAAL 307
+E V IEAA +YDAV L+A AL
Sbjct: 307 SELVLEIDIEAAYLYDAVMLYAKAL 331
>gnl|CDD|107263 cd06268, PBP1_ABC_transporter_LIVBP_like, Periplasmic binding
domain of ATP-binding cassette transporter-like systems
that belong to the type I periplasmic binding fold
protein superfamily. Periplasmic binding domain of
ATP-binding cassette transporter-like systems that
belong to the type I periplasmic binding fold protein
superfamily. They are mostly present in archaea and
eubacteria, and are primarily involved in scavenging
solutes from the environment. ABC-type transporters
couple ATP hydrolysis with the uptake and efflux of a
wide range of substrates across bacterial membranes,
including amino acids, peptides, lipids and sterols, and
various drugs. These systems are comprised of
transmembrane domains, nucleotide binding domains, and
in most bacterial uptake systems, periplasmic binding
proteins (PBPs) which transfer the ligand to the
extracellular gate of the transmembrane domains. These
PBPs bind their substrates selectively and with high
affinity. Members of this group include ABC-type
Leucine-Isoleucine-Valine-Binding Proteins (LIVBP),
which are homologous to the aliphatic amidase
transcriptional repressor, AmiC, of Pseudomonas
aeruginosa. The uncharacterized periplasmic components
of various ABC-type transport systems are included in
this group.
Length = 298
Score = 47.0 bits (112), Expect = 2e-05
Identities = 54/314 (17%), Positives = 90/314 (28%), Gaps = 50/314 (15%)
Query: 5 GIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDS-------LHTAKLM 57
G E V E+AV IN L I E +V D+ A+ +
Sbjct: 10 GPLAALGEPVRNGAELAVEEINAAGGILGRKI--ELVV-----EDTQGDPEAAAAAAREL 62
Query: 58 CNATSEGIAAIFGPQSIENRNIIESMCQMFDIPHV-------EAFWDPNKYFIPTNGVHG 110
+G+ A+ GP S + + +P + N Y T
Sbjct: 63 ---VDDGVDAVIGPLSSGVALAAAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAP--- 116
Query: 111 VNVYPESHLISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSV 170
++ + + IIY+ + Y + + + K++ G V
Sbjct: 117 ----SDAQQAAALADYLAEKGKVKKVAIIYDDYA---YGRGLAAAFREALKKL--GGEVV 167
Query: 171 TIRQLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLT 230
PP D+ PL+ ++K + + L LKQA+E L
Sbjct: 168 AEETYPPGATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQARE-----------AGLK 216
Query: 231 SYWINAHTVDFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVK 290
+ A ++ T + ++ R
Sbjct: 217 VPIVGGDGAAAPALLE-LAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYGRPPDS- 274
Query: 291 IEAALMYDAVYLFA 304
AA YDAV L A
Sbjct: 275 -YAAAAYDAVRLLA 287
>gnl|CDD|107378 cd06383, PBP1_iGluR_AMPA_Like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of uncharacterized AMPA-like receptors.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of uncharacterized AMPA-like
receptors. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. AMPA receptors consist of
four types of subunits (GluR1, GluR2, GluR3, and GluR4)
which combine to form a tetramer and play an important
roles in mediating the rapid excitatory synaptic
current.
Length = 368
Score = 46.7 bits (111), Expect = 3e-05
Identities = 22/113 (19%), Positives = 46/113 (40%), Gaps = 12/113 (10%)
Query: 111 VNVYPESHLISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSV 170
+ + P + I + I I++ + I+Y+ D+ V + K + P+
Sbjct: 111 IQLMPPADDIVEAIRDIVSYYNITNAAILYD--DDFVMDHKY--------KSLLQNWPTR 160
Query: 171 T-IRQLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTV-TILKQAKEVHLMGD 221
I + D+ R +K ++N +I + S ++ + +L QA MG
Sbjct: 161 HVITIINSIIDEVREQIKRLRNLDIKNIFILGSTEEIIRYVLDQALAEGFMGR 213
>gnl|CDD|211985 TIGR04262, orph_peri_GRRM, extracellular substrate-binding orphan
protein, GRRM family. This subfamily belongs to
bacterial extracellular solute-binding protein family 3
(pfam00497). In that family, most members are ABC
transporter periplasmic substrate-binding proteins.
However, members of the present subfamily are orphans in
the sense of being adjacent to neither ABC transporter
ATP-binding proteins or permease subunits. Instead, most
members are encoded next to the two signature proteins
of the proposed Glycine-Rich Repeat Modification (GRRM)
system, a radical SAM/SPASM protein GrrM (TIGR04261) and
the Gly-rich repeat protein itself GrrA (TIGR04260).
Length = 257
Score = 45.8 bits (109), Expect = 3e-05
Identities = 28/116 (24%), Positives = 53/116 (45%), Gaps = 13/116 (11%)
Query: 417 KLRVLFQGE--PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQ-T 473
LR + +G+ P K+ G S D++++I ++L + + T+
Sbjct: 2 VLRAVVRGDVLPLYQKDDA--GYDGLSFDVLELIRDQLQ---AELGKPI----TIQFVVV 52
Query: 474 GKWNGLIGELQEQRADLAICDLTITSERRAAVDFTMPFMTLGISILYRKPAKKQPD 529
+ +L+ +AD+A C + T ER+ VD+++PF GI +L K P+
Sbjct: 53 NSVQEGLPKLRSGKADIA-CGVAFTWERQMFVDYSLPFAVSGIRLLAPKGNDGTPE 107
>gnl|CDD|107361 cd06366, PBP1_GABAb_receptor, Ligand-binding domain of GABAb
receptors, which are metabotropic transmembrane
receptors for gamma-aminobutyric acid (GABA).
Ligand-binding domain of GABAb receptors, which are
metabotropic transmembrane receptors for
gamma-aminobutyric acid (GABA). GABA is the major
inhibitory neurotransmitter in the mammalian CNS and,
like glutamate and other transmitters, acts via both
ligand gated ion channels (GABAa receptors) and
G-protein coupled receptors (GABAb). GABAa receptors are
members of the ionotropic receptor superfamily which
includes alpha-adrenergic and glycine receptors. The
GABAb receptor is a member of a receptor superfamily
which includes the mGlu receptors. The GABAb receptor is
coupled to G alpha_i proteins, and activation causes a
decrease in calcium, an increase in potassium membrane
conductance, and inhibition of cAMP formation. The
response is thus inhibitory and leads to
hyperpolarization and decreased neurotransmitter
release, for example.
Length = 350
Score = 44.9 bits (107), Expect = 1e-04
Identities = 78/418 (18%), Positives = 144/418 (34%), Gaps = 97/418 (23%)
Query: 2 KIVGIF----GPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQ--HVENYDSLHTA- 54
+I IF + A E+A+ +N D L P L V+ + + A
Sbjct: 1 RIGAIFDLSGSWIGKAALPAIEMALEDVNADNSIL-PGYRLVLHVRDSKCDPVQAASAAL 59
Query: 55 KLMCNATSEGIAAIFGPQSIENRNIIESMCQMFDIPHVE------AFWDPNK--YFIPTN 106
L+ N + + AI GPQ + + +++P + + + YF T
Sbjct: 60 DLLEN---KPVVAIIGPQCSSVAEFVAEVANEWNVPVLSFAATSPSLSSRLQYPYFFRT- 115
Query: 107 GVHGVNVYPESHLISKGISVIINDMDWDTFTIIYETHDN----LVYLQQVLENAHDDDKE 162
+S I+ ++ W IYE D L L L+ +
Sbjct: 116 ------TPSDSSQN-PAIAALLKKFGWRRVATIYEDDDYGSGGLPDLVDALQ-----EAG 163
Query: 163 IRPGRPSVTIRQ-LPPDTDDYRP--LLKEIKNSSESH-ILLDCSMDKTVTILKQAKEVHL 218
I ++ R PP +D LK++K +S I++ S D + +A ++ +
Sbjct: 164 IE-----ISYRAAFPPSANDDDITDALKKLK-EKDSRVIVVHFSPDLARRVFCEAYKLGM 217
Query: 219 MGD-YQNYIL--SLTSYW-INAHTVDFQDFQ--PGYANITTVRMINPTNPHIRSIMNGWI 272
MG Y +IL L+S W ++ D + + G I + ++ ++ + W
Sbjct: 218 MGKGYV-WILTDWLSSNWWSSSDCTDEEMLEAMQGV--IGVRSYVPNSSMTLQEFTSRW- 273
Query: 273 YEENERGRSLNVRAETVKIEAALMYDAVYLFAAALQSLGERKPLPTPLSCENPSSWQHGL 332
+R + N I A YDAV+
Sbjct: 274 ---RKRFGNENPELTEPSIYALYAYDAVWA------------------------------ 300
Query: 333 GIGNLMKSITIDGMTGRINLDSQTGRRNSFSLEFVEYVSDQWKVLGTWNTAFGLNHSR 390
S +G++G + D R S + E + + ++ +G W++ GL+
Sbjct: 301 -------STNFNGLSGPVQFDGG-RRLASPAFEIINIIGKGYRKIGFWSSESGLSVFL 350
>gnl|CDD|107374 cd06379, PBP1_iGluR_NMDA_NR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR1, an essential channel-forming subunit
of the NMDA receptor. The ionotropic N-methyl-d-asparate
(NMDA) subtype of glutamate receptor serves critical
functions in neuronal development, functioning, and
degeneration in the mammalian central nervous system.
The functional NMDA receptor is a heterotetramer
ccomposed of two NR1 and two NR2 (A, B, C, and D) or of
NR3 (A and B) subunits. The receptor controls a cation
channel that is highly permeable to monovalent ions and
calcium and exhibits voltage-dependent inhibition by
magnesium. Dual agonists, glutamate and glycine, are
required for efficient activation of the NMDA receptor.
When co-expressed with NR1, the NR3 subunits form
receptors that are activated by glycine alone and
therefore can be classified as excitatory glycine
receptors. NR1/NR3 receptors are calcium-impermeable and
unaffected by ligands acting at the NR2
glutamate-binding site.
Length = 377
Score = 43.6 bits (103), Expect = 3e-04
Identities = 40/189 (21%), Positives = 68/189 (35%), Gaps = 42/189 (22%)
Query: 174 QLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTSYW 233
+ P + LL+E K + ILL S D I + A +++ G+
Sbjct: 194 EFEPGEKNVTSLLQEAKELTSRVILLSASEDDAAVIYRNAGMLNMTGE------------ 241
Query: 234 INAHTVDFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEA 293
GY I + + N +G L ++ K E+
Sbjct: 242 -------------GYVWIVSEQAGAARN-----APDG----------VLGLQLINGKNES 273
Query: 294 ALMYDAVYLFAAALQSLGERKPLPT-PLSC-ENPSSWQHGLGIGNLMKSITIDGMTGRIN 351
+ + DAV + A+A+Q L E++ + P C N W+ G + S G TGR+
Sbjct: 274 SHIRDAVAVLASAIQELFEKENITEPPRECVGNTVIWETGPLFKRALMSSKYPGETGRVE 333
Query: 352 LDSQTGRRN 360
+ R+
Sbjct: 334 FNDDGDRKF 342
>gnl|CDD|107362 cd06367, PBP1_iGluR_NMDA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. While this N-terminal
domain belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. The function
of the NMDA subtype receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer comprising two NR1 and
two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The
receptor controls a cation channel that is highly
permeable to monovalent ions and calcium and exhibits
voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 362
Score = 41.9 bits (99), Expect = 9e-04
Identities = 53/265 (20%), Positives = 94/265 (35%), Gaps = 64/265 (24%)
Query: 132 DWDTFTIIYETH----DNLVYLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDDYRP-LL 186
DW F+++ D L ++ LE + + V L DD LL
Sbjct: 135 DWHQFSVVTSRDPGYRDFLDRVETTLEESF-----VGWEFQLVLT--LDLSDDDGDARLL 187
Query: 187 KEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSLTSYWINAHTVDFQDFQP 246
+++K ILL CS ++ I + A + L G Y+ WI
Sbjct: 188 RQLKKLESRVILLYCSKEEAERIFEAAASLGLTG--PGYV------WIVGELA------- 232
Query: 247 GYANITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDAVYLFAAA 306
+ + G L V +T A + DAV + A A
Sbjct: 233 -----------LGSGLAPEGLPVG----------LLGVGLDTWYSLEARVRDAVAIVARA 271
Query: 307 LQS-LGERKPLPTP-LSCENPSS--WQHGLGIGNLMKSITIDGMTGRINLDSQTGRRNSF 362
+S L ++ LP P ++C + ++ G + + ++T DG TG ++ + N
Sbjct: 272 AESLLRDKGALPEPPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSN-- 329
Query: 363 SLEFVEYV------SDQWKVLGTWN 381
+ V + +W+ +G+W
Sbjct: 330 ----PKLVIINLRRNRKWERVGSWE 350
>gnl|CDD|107376 cd06381, PBP1_iGluR_delta_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of an orphan family of delta receptors,
GluRdelta1 and GluRdelta2. This CD represents the
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of an orphan family of delta
receptors, GluRdelta1 and GluRdelta2. While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Although the delta receptors are a member
of the ionotropic glutamate receptor family, they cannot
be activated by AMPA, kainate, NMDA, glutamate, or any
other ligands. Phylogenetic analysis shows that both
GluRdelta1 and GluRalpha2 are more homologous to
non-NMDA receptors. GluRdelta2 was shown to function as
an AMPA-like receptor by mutation analysis. Moreover,
targeted disruption of GluRdelta2 gene caused motor
coordination impairment, Purkinje cell maturation, and
long-term depression of synaptic transmission. It has
been suggested that GluRdelta2 is the receptor for
cerebellin 1, a glycoprotein of the Clq, and the tumor
necrosis factor family which is secreted from cerebellar
granule cells. Furthermore, recent studies have shown
that the orphan GluRdelta1 plays an essential role in
high-frequency hearing and ionic homeostasis in the
basal cochlea and that the locus encoding GluRdelta1 may
be involved in congenial or acquired high-frequency
hearing loss in humans.
Length = 363
Score = 42.1 bits (99), Expect = 0.001
Identities = 56/341 (16%), Positives = 107/341 (31%), Gaps = 74/341 (21%)
Query: 2 KIVGIFGPN--EEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSL---HTAKL 56
I IF + E++ A + IN+ + E I + D +
Sbjct: 1 HIGAIFSESALEDDEVFAVAVIDLNINEQI------LQTEKITLSISFIDLNNHFDAVQE 54
Query: 57 MCNATSEGIAAIFGPQSIENRNIIESMCQMFDIPHVEAFWDPN----------KYFIPTN 106
C+ ++GI A+ + ++S+ IPH+ F P
Sbjct: 55 ACDLMNQGILALVTSTGCASAIALQSLTDAMHIPHL--FIQRGYGGSPRTACGLNPSPRG 112
Query: 107 GVHGVNVYPESHLISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAH--------- 157
+ + + P L + + ++ + W F Y+ ++ LQ+ L+
Sbjct: 113 QQYTLALRPPVRL-NDVMLRLVTEWRWQKFVYFYDNDYDIRGLQEFLDQLSRQGIDVLLQ 171
Query: 158 ----DDDKEIRPGRPSVTIRQLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQA 213
+ K ++ +L + YR L LL S + T + +
Sbjct: 172 KVDLNISKMATALFTTMRCEEL----NRYRDTL--------RRALLLLSPNGAYTFIDAS 219
Query: 214 KEVHLMGDYQNYIL-----------SLTSYWINAHTVDFQDFQPGYANITTVRMINPTNP 262
E +L ++ L L Y TV Q F N +R N
Sbjct: 220 VETNLAIKDSHWFLINEEISDTEIDELVRYAHGRMTVIRQTFSKEKTNQRCLR----NNH 275
Query: 263 HIRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDAVYLF 303
I S+ + + + + ++I +YD+V L
Sbjct: 276 RISSL----LCDPKDGYL------QMLEISNLYIYDSVLLL 306
>gnl|CDD|183381 PRK11917, PRK11917, bifunctional adhesin/ABC transporter
aspartate/glutamate-binding protein; Reviewed.
Length = 259
Score = 39.5 bits (92), Expect = 0.005
Identities = 26/96 (27%), Positives = 42/96 (43%), Gaps = 10/96 (10%)
Query: 427 YMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQEQ 486
Y + + TGE+ G+ +D+ K++A K +L + L K G + L
Sbjct: 51 YALLDQATGEIKGFEIDVAKLLA-------KSILGDDKKI-KLVAVNAKTRGPL--LDNG 100
Query: 487 RADLAICDLTITSERRAAVDFTMPFMTLGISILYRK 522
D I TIT ER+ +F+ P+ I +L K
Sbjct: 101 SVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLK 136
>gnl|CDD|107364 cd06369, PBP1_GC_C_enterotoxin_receptor, Ligand-binding domain of
the membrane guanylyl cyclase C. Ligand-binding domain
of the membrane guanylyl cyclase C (GC-C or StaR). StaR
is a key receptor for the STa (Escherichia coli Heat
Stable enterotoxin), a potent stimulant of intestinal
chloride and bicarbonate secretion that cause acute
secretory diarrhea. The catalytic domain of the
STa/guanylin receptor type membrane GC is highly similar
to those of the natriuretic peptide receptor (NPR) type
and sensory organ-specific type membrane GCs (GC-D, GC-E
and GC-F). The GC-C receptor is mainly expressed in the
intestine of most vertebrates, but is also found in the
kidney and other organs. Moreover, GC-C is activated by
guanylin and uroguanylin, endogenous peptide ligands
synthesized in the intestine and kidney. Consequently,
the receptor activation results in increased cGMP levels
and phosphorylation of the CFTR chloride channel and
secretion.
Length = 380
Score = 38.5 bits (90), Expect = 0.013
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 12/91 (13%)
Query: 293 AALMYDAVYLFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGRINL 352
A +D V LF L+ E + S N ++I+ +G G L
Sbjct: 287 VAAYHDGVLLFGHVLKKFLESQEGVQTFS------------FINEFRNISFEGAGGPYTL 334
Query: 353 DSQTGRRNSFSLEFVEYVSDQWKVLGTWNTA 383
D R +F+L + + ++KVL ++T+
Sbjct: 335 DEYGDRDVNFTLLYTSTDTSKYKVLFEFDTS 365
>gnl|CDD|107386 cd06391, PBP1_iGluR_delta_2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta2 receptor of an orphan glutamate
receptor family. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta2 receptor of an orphan glutamate
receptor family. While this N-terminal domain belongs to
the periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. Although the delta receptors
are a member of the ionotropic glutamate receptor
family, they cannot be activated by AMPA, kainate, NMDA,
glutamate, or any other ligands. Phylogenetic analysis
shows that both GluRdelta1 and GluRalpha2 are closer
related to non-NMDA receptors. GluRdelta2 was shown to
function as an AMPA-like receptor by mutation analysis.
Moreover, targeted disruption of GluRdelta2 gene caused
motor coordination impairment, Purkinje cell maturation,
and long-term depression of synaptic transmission. It
has been suggested that GluRdelta2 is the receptor for
cerebellin 1, a glycoprotein of the Clq and tumor
necrosis factor family that is secreted from cerebellar
granule cells.
Length = 400
Score = 38.5 bits (89), Expect = 0.014
Identities = 86/408 (21%), Positives = 163/408 (39%), Gaps = 33/408 (8%)
Query: 3 IVGIFGPNEEEVATAFEIAVRRINKDFKALPPDIILEPIVQHVENYDSLHTAKLMCNATS 62
I IF + ++ F +AV +N++ + L + I V V+ + + C +
Sbjct: 2 IGAIFDESAKKDDEVFRMAVADLNQNNEILQTEKITVS-VTFVDGNNPFQAVQEACELMN 60
Query: 63 EGIAAIFGPQSIENRNIIESMCQMFDIPHV----EAFWDPNKYFIPT----NGVHGVNVY 114
+GI A+ + ++S+ IPH+ P T N + ++V
Sbjct: 61 QGILALVSSIGCTSAGSLQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDYTLSVR 120
Query: 115 PESHLISKGISVIINDMDWDTFTIIYETHDNLVYLQQVLENAHDDDKEIRPGRPSVTIRQ 174
P +L + I ++ + W F I Y+T ++ +Q+ L DK + G V +++
Sbjct: 121 PPVYL-NDVILRVVTEYAWQKFIIFYDTDYDIRGIQEFL------DKVSQQGM-DVALQK 172
Query: 175 LPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDY-QNYILSLTSYW 233
+ + + L E + D ++ + + ++ A + + + +++ +W
Sbjct: 173 VENNINKMITGLFRTMRIEELNRYRD-TLRRAILVMNPATAKSFITEVVETNLVAFDCHW 231
Query: 234 I--NAHTVDFQDFQPGYANITTVRMINPTNPHIRSIMNGWIYEENERGRSL----NVRAE 287
I N D + +I + +I T P ++I + SL + A+
Sbjct: 232 IIINEEISDMDVQELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPFAQ 291
Query: 288 TVKIEAALMYDAVYLFAAAL-QSLGERK-PLPTPLSC--ENPSSWQHGLGIGNLMKSITI 343
++I +YD V L A A + L +RK LSC +N WQ G + +K +
Sbjct: 292 MMEISNLYIYDTVLLLANAFHKKLEDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGV 351
Query: 344 DGMTGRINLDSQTGRRN-SFSLEFVEYVSDQWK---VLGTWNTAFGLN 387
G+TG + + G N F + Y D + LG WN GLN
Sbjct: 352 SGLTGELEFNENGGNPNVHFEILGTNYGEDLGRGVRKLGCWNPITGLN 399
>gnl|CDD|185334 PRK15437, PRK15437, histidine ABC transporter substrate-binding
protein HisJ; Provisional.
Length = 259
Score = 37.3 bits (86), Expect = 0.020
Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 14/108 (12%)
Query: 426 PYMMKNPETGELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQE 485
P+ KN + GEL G+ +DL K + +N FV EN + LI L+
Sbjct: 38 PFESKNSQ-GELVGFDIDLAKELCKRINTQCTFV---ENPL----------DALIPSLKA 83
Query: 486 QRADLAICDLTITSERRAAVDFTMPFMTLGISILYRKPAKKQPDLFSF 533
++ D + L+IT +R+ + FT ++ K + QP + S
Sbjct: 84 KKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESL 131
>gnl|CDD|222144 pfam13458, Peripla_BP_6, Periplasmic binding protein. This family
includes a diverse range of periplasmic binding
proteins.
Length = 343
Score = 36.1 bits (84), Expect = 0.073
Identities = 35/192 (18%), Positives = 59/192 (30%), Gaps = 33/192 (17%)
Query: 170 VTIRQLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLMGDYQNYILSL 229
V P T D+ ++ +IK S +LL V +K A+E L + L
Sbjct: 167 VGEVYYPLGTTDFSSVVLQIKASGPDVVLLTLVGADAVAFIKAAREAGLDP--KGIPLVS 224
Query: 230 TSYWINAHTVDFQDFQPGYAN---ITTVRMINPTNPHIRSIMNGWIYEENERGRSLNVRA 286
S + D A + P R+ + + R
Sbjct: 225 LSGYEA----DLLALGGEAAEGVYTAAPYFPDLDTPANRAFVAAY----KARYGEDAPPT 276
Query: 287 ETVKIEAALMYDAVYLFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGM 346
+ AA Y A L AAAL++ G + + ++ + DG
Sbjct: 277 Q----FAAAAYAAADLLAAALEAAGS----LDREA------------VRAALRGLKFDGP 316
Query: 347 TGRINLDSQTGR 358
G + D++
Sbjct: 317 FGPVGFDAEDHH 328
>gnl|CDD|132040 TIGR02995, ectoine_ehuB, ectoine/hydroxyectoine ABC transporter
solute-binding protein. Members of this family are the
extracellular solute-binding proteins of ABC
transporters that closely resemble amino acid
transporters. The member from Sinorhizobium meliloti is
involved in ectoine uptake, both for osmoprotection and
for catabolism. All other members of the seed alignment
are found associated with ectoine catabolic genes
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 275
Score = 35.3 bits (81), Expect = 0.097
Identities = 27/104 (25%), Positives = 39/104 (37%), Gaps = 24/104 (23%)
Query: 448 IANELNFTY---------------KFVLER---ENTYGTLNPQTGKWNGLIGELQEQRAD 489
IANE FTY + + +R + ++ + LI LQ R D
Sbjct: 39 IANEPPFTYVGADGKVSGAAPDVARAIFKRLGIADVNASITE----YGALIPGLQAGRFD 94
Query: 490 LAICDLTITSERRAAVDFTMPFMTLGISILYRKPAKKQPDLFSF 533
L I ER V FT P + ++L +K K L S+
Sbjct: 95 AIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNPKG--LKSY 136
>gnl|CDD|236778 PRK10859, PRK10859, membrane-bound lytic transglycosylase F;
Provisional.
Length = 482
Score = 35.2 bits (82), Expect = 0.15
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 439 GYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQEQRADLAICDLTIT 498
G+ +L K A+ L + R+N + L L + +ADLA LT T
Sbjct: 65 GFEYELAKRFADYLGVKLEIK-VRDN-----------ISQLFDALDKGKADLAAAGLTYT 112
Query: 499 SERRAAVDFTMPFMTLGISILYRK 522
ER F P+ ++ ++YRK
Sbjct: 113 PERLKQFRFGPPYYSVSQQLVYRK 136
>gnl|CDD|107373 cd06378, PBP1_iGluR_NMDA_NR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NR2 subunit of NMDA receptor family.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the NR2 subunit of NMDA receptor
family. The ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer composed of two NR1
and two NR2 (A, B, C, and D) or of NR3 (A and B)
subunits. The receptor controls a cation channel that is
highly permeable to monovalent ions and calcium and
exhibits voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 362
Score = 35.0 bits (81), Expect = 0.16
Identities = 32/153 (20%), Positives = 61/153 (39%), Gaps = 33/153 (21%)
Query: 101 YFIPTNGVHGVNVYPESH------------LISKGISVIINDM---DWDTFTII---YET 142
F+P G+HG + + I + +V++ M DW F+++ +
Sbjct: 88 TFLPILGIHGGSSMIMAAKDSGSTFLQFGPSIEQQAAVMLKIMEEYDWHAFSVVTSRFPG 147
Query: 143 HDNLV-YLQQVLENAHDDDKEIRPGRPSVTIRQLPPDTDDYRPLLKEIKNSSESHILLDC 201
+D+ V ++ ++N+ + SV + D D R +++K ILL C
Sbjct: 148 YDDFVSAVRTTVDNSFVGWE-----LQSVLTLDMSDDDGDAR-TQRQLKKLESQVILLYC 201
Query: 202 SMDKTVTILKQAKEVHLMGDYQNYILSLTSYWI 234
S ++ I + A+ L G Y+ WI
Sbjct: 202 SKEEAEYIFRAARSAGLTG--PGYV------WI 226
>gnl|CDD|107342 cd06347, PBP1_ABC_ligand_binding_like_12, Type I periplasmic
ligand-binding domain of uncharacterized ABC (Atpase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (Atpase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT), such as
leucine/isoleucine/valine binding protein (LIVBP);
however its ligand specificity has not been determined
experimentally.
Length = 334
Score = 34.1 bits (79), Expect = 0.28
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 15/62 (24%)
Query: 293 AALMYDAVYLFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSITIDGMTGRINL 352
AAL YDA YL A A++ G P L K+ DG+TG+I +
Sbjct: 276 AALGYDAYYLLADAIERAGSTDP---------------EAIRDALAKTKDFDGVTGKITI 320
Query: 353 DS 354
D
Sbjct: 321 DE 322
>gnl|CDD|211833 TIGR03531, selenium_SpcS, O-phosphoseryl-tRNA(Sec) selenium
transferase. In the archaea and eukaryotes, the
conversion of the mischarged serine to selenocysteine
(Sec) on its tRNA is accomplished in two steps. This
enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase,
acts second, after a phosphophorylation step catalyzed
by a homolog of the bacterial SelA protein [Protein
synthesis, tRNA aminoacylation].
Length = 444
Score = 34.3 bits (79), Expect = 0.31
Identities = 35/140 (25%), Positives = 54/140 (38%), Gaps = 38/140 (27%)
Query: 69 FGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYPESHLISKGISV-- 126
F P+S ++ I +C +DIPH+ N +G+ LI+K I V
Sbjct: 216 FAPRSPDDIEEIAKICANYDIPHI------------VNNAYGLQSNKYMELINKAIKVGR 263
Query: 127 ---IINDMDWDTFT-----IIYETHDNLVYLQQVLENAHDDDKEIRPGRPS------VTI 172
+++ D + IIY +N +Q++ + PGR S V I
Sbjct: 264 VDAVVSSTDKNFMVPVGGAIIYSFDENF--IQEI--------SKSYPGRASASPSLDVLI 313
Query: 173 RQLPPDTDDYRPLLKEIKNS 192
L + Y LLKE K
Sbjct: 314 TLLSLGSKGYLELLKERKEM 333
>gnl|CDD|107367 cd06372, PBP1_GC_G_like, Ligand-binding domain of membrane guanylyl
cyclase G. This group includes the ligand-binding
domain of membrane guanylyl cyclase G (GC-G) which is a
sperm surface receptor and might function, similar to
its sea urchin counterpart, in the early signaling event
that regulates the Ca2+ influx/efflux and subsequent
motility response in sperm. GC-G appears to be a
pseudogene in human. Furthermore, in contrast to the
other orphan receptor GCs, GC-G has a broad tissue
distribution in rat, including lung, intestine, kidney,
and skeletal muscle.
Length = 391
Score = 31.4 bits (71), Expect = 2.1
Identities = 45/202 (22%), Positives = 88/202 (43%), Gaps = 37/202 (18%)
Query: 197 ILLDCSMDKTVTILKQAKEVHLM-GDYQNYIL--SLTSYWINAHTVDFQDFQPGYANITT 253
I+L CS + IL+ A+++ LM G + ++L ++W T D P +
Sbjct: 200 IILICSSEDAKAILQAAEKLGLMKGKFVFFLLQQFEDNFWKEVLTDDQVQHLP--KVYES 257
Query: 254 VRMINPTNPHIRSIMNGW---IYEENERG--RSLNVRAETVKIEAALMYDAVYLFAAALQ 308
V +I P++ S + +Y++ +R +S E V +A ++DAV L+A A++
Sbjct: 258 VFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSPYSAYLHDAVLLYALAVK 317
Query: 309 SLGERKPLPTPLSCENPSSWQHGLGIGNLMKS---ITIDGMTGRINLDSQTGRRNSFS-- 363
+ + +++G + + ++ + + G+TG + LD Q R+ +S
Sbjct: 318 EM-----------LKAGKDFRNGRQLVSTLRGANQVELQGITGLVLLDEQGKRQMDYSVY 366
Query: 364 -----------LEFVEYVSDQW 374
L F+ Y S Q
Sbjct: 367 ALQKSGNSSLFLPFLHYDSHQK 388
>gnl|CDD|218796 pfam05889, SLA_LP_auto_ag, Soluble liver antigen/liver pancreas
antigen (SLA/LP autoantigen). This family consists of
several eukaryotic and archaeal proteins which are
related to the human soluble liver antigen/liver
pancreas antigen (SLA/LP autoantigen). Autoantibodies
are a hallmark of autoimmune hepatitis, but most are not
disease specific. Autoantibodies to soluble liver
antigen (SLA) and to liver and pancreas antigen (LP)
have been described as disease specific, occurring in
about 30% of all patients with autoimmune hepatitis. The
function of SLA/LP is unknown, however, it has been
suggested that the protein may function as a serine
hydroxymethyltransferase and may be an important enzyme
in the thus far poorly understood selenocysteine
pathway. The archaeal sequences Methanopyrus kandleri
spcS and MK0229 are annotated as being pyridoxal
phosphate-dependent enzymes.
Length = 386
Score = 31.4 bits (71), Expect = 2.2
Identities = 42/189 (22%), Positives = 66/189 (34%), Gaps = 51/189 (26%)
Query: 62 SEGIAAI------FGPQSIENRNIIESMCQMFDIPHVEAFWDPNKYFIPTNGVHGVNVYP 115
E I A+ F P+S + I +C +D+PH+ NG +G+
Sbjct: 153 EEVILAVLSTTSCFAPRSPDRVKEIAKICAEYDVPHL------------VNGAYGIQSEK 200
Query: 116 ESHLISKG-----ISVIINDMDWDTFT-----IIYETHDNLVYLQQVLENAHDDDKEIRP 165
HLI + I ++ +D + II ++ ++Q++ E P
Sbjct: 201 YIHLIQQAAKVGRIDAVVQSLDKNFIVPVGGAIIAAFDES--FIQEI--------SEEYP 250
Query: 166 GRPS------VTIRQLPPDTDDYRPLLKEIKNSSESHILLDCSMDKTVTILKQAKEVHLM 219
GR S I L Y L+KE K E LL + L + L+
Sbjct: 251 GRASARPSKDKLITLLSLGCKAYLALMKEQK---EMFPLLRELIKD----LAEEVGEQLL 303
Query: 220 GDYQNYILS 228
N I S
Sbjct: 304 DVPHNPISS 312
>gnl|CDD|184969 PRK15007, PRK15007, putative ABC transporter arginine-biding
protein; Provisional.
Length = 243
Score = 30.8 bits (69), Expect = 2.4
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 13/76 (17%)
Query: 436 ELYGYSVDLIKMIANELNFTYKFVLERENTYGTLNPQTGKWNGLIGELQEQRADLAICDL 495
++ G+ VDL + + E++ T F + ++ LI L+ +R + + +
Sbjct: 42 QIVGFDVDLAQALCKEIDATCTFSNQ-------------AFDSLIPSLKFRRVEAVMAGM 88
Query: 496 TITSERRAAVDFTMPF 511
IT ER V FT P+
Sbjct: 89 DITPEREKQVLFTTPY 104
>gnl|CDD|176360 cd01764, Urm1, Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related
Modifier1) The Urm1 fold, like those of two closely
related proteins MoaD (molybdopterin synthase) and ThiS
(sulfur carrier protein), is similar to that of
ubiquitin although there is little or no sequence
similarity. The C-terminal glycines of Urm1 are
conjugated to an E1-like protein Uba4 as part of a novel
conjugation system in yeast. The Urm1 fold is found
only in eukaryotes.
Length = 94
Score = 28.8 bits (65), Expect = 3.3
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 123 GISVIINDMDWDT 135
GI V+IND DW+
Sbjct: 59 GIIVLINDTDWEL 71
>gnl|CDD|219163 pfam06757, Ins_allergen_rp, Insect allergen related repeat,
nitrile-specifier detoxification. This family
exemplifies a case of novel gene evolution. The case in
point is the arms-race between plants and their
infective insective herbivores in the area of the
glucosinolate-myrosinase system. Brassicas have
developed the glucosinolate-myrosinase system as
chemical defence mechanism against the insects, and
consequently the insects have adapted to produce a
detoxifying molecule, nitrile-specifier protein (NSP).
NSP is present in the small white butterfly Pieris
rapae. NSP is structurally different from and has no
amino acid homology to any known detoxifying enzymes,
and it appears to have arisen by a process of domain and
gene duplication of a sequence of unknown function that
is widespread in insect species and referred to as
insect-allergen-repeat protein. Thus this family is
found either as a single domain or as a multiple
repeat-domain.
Length = 181
Score = 29.9 bits (68), Expect = 3.8
Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 10/77 (12%)
Query: 412 SKTFAKLRVLFQGEPYMMKNPETGELYGY----SVDLIKMIANELNFTYKFVLERENTYG 467
S+ FA+L PE + Y +D++ + + + +
Sbjct: 43 SEEFAELWDQLF------SLPEVKDFLNYLEDAGLDVVDYLNQIADLLGLPPVNPTVSVE 96
Query: 468 TLNPQTGKWNGLIGELQ 484
+ + NG + ++
Sbjct: 97 LESMRGRGLNGFVDDVL 113
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 30.6 bits (70), Expect = 3.8
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 290 KIEAALMYDAVYLFAAALQSLGERKPLPTPLSCENPSSWQHGLGIGNLMKSI 341
KI+ + Y F SLG +P+P S +HG GIG+L+ ++
Sbjct: 121 KIDNLKAEELAYEFY----SLGFGEPVPI--------SAEHGRGIGDLLDAV 160
>gnl|CDD|220408 pfam09795, Atg31, Autophagy-related protein 31. Autophagy is an
intracellular degradation system that responds to
nutrient starvation. Cis1/Atg31 has been shown to be
required for autophagosome formation in Saccharomyces
cerevisiae. It interacts with Atg17.
Length = 159
Score = 29.5 bits (66), Expect = 4.5
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 360 NSFSLEFVEYVSDQWKVLGTWNTAFGLNHSRTVEQMDKEKKEKIENRTLTVTSKTFAKLR 419
S SLE VE +SDQ+++L + SR+ ++ IE LTV S+ FA L
Sbjct: 75 ESGSLENVELISDQYELLSFRPVSLASQRSRSWLTDGNDRDNDIE---LTVISE-FADLS 130
>gnl|CDD|223020 PHA03246, PHA03246, large tegument protein UL36; Provisional.
Length = 3095
Score = 29.9 bits (67), Expect = 7.3
Identities = 27/104 (25%), Positives = 47/104 (45%), Gaps = 3/104 (2%)
Query: 264 IRSIMNGWIYEENERGRSLNVRAETVKIEAALMYDAVYLFAAALQSLGERKPLPTPLSCE 323
+R + I + + +SL+ + T +A+++ A +AA Q G+ K T L E
Sbjct: 1285 VRDSLEAVI-DSITKIKSLDPKTYTYNTDASVIVSAKAEVSAATQQAGDCKDALTALENE 1343
Query: 324 NPSSWQH-GLGIGNLMKSI-TIDGMTGRINLDSQTGRRNSFSLE 365
+ H I L K I +++ G +++ QT RN S E
Sbjct: 1344 PLTYNPHIQRKIAELNKLIESVNQRVGELDIALQTYERNRISAE 1387
>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 = 29.5 bits (67), Expect = 8.2
Identities = 9/57 (15%), Positives = 17/57 (29%), Gaps = 3/57 (5%)
Query: 735 TFILFFIYSILFFIYTFVNEAVSTRLVAGMWWFFTLIMISSYTANLAAFLTNTRMNP 791
T + + F + +RL +W+ L ++ L L R
Sbjct: 72 TLTFLILALLAFLLKYGTE---FSRLWLLLWFLLALALLLLGRLILRLLLRRLRRKG 125
>gnl|CDD|227460 COG5131, URM1, Ubiquitin-like protein [Posttranslational
modification, protein turnover, chaperones].
Length = 96
Score = 27.5 bits (61), Expect = 8.3
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 97 DPNKYFIPTNGVHGVNVYPESHLISKGISVIINDMDWDTFTIIYETHDNLV 147
D +YFI +++ E + GI +INDMDW+ + E +
Sbjct: 37 DALRYFI--YAPTRDSIFIEHGELRPGIICLINDMDWE----LLEKERYPL 81
>gnl|CDD|107379 cd06384, PBP1_NPR_B, Ligand-binding domain of type B natriuretic
peptide receptor. Ligand-binding domain of type B
natriuretic peptide receptor (NPR-B). NPR-B is one of
three known single membrane-spanning natriuretic peptide
receptors that have been identified. Natriuretic
peptides are family of structurally related but
genetically distinct hormones/paracrine factors that
regulate blood volume, blood pressure, ventricular
hypertrophy, pulmonary hypertension, fat metabolism, and
long bone growth. In mammals there are three natriuretic
peptides: ANP, BNP, and CNP. Like NPR-A (or GC-A), NPR-B
(or GC-B) is a transmembrane guanylyl cyclase, an enzyme
that catalyzes the synthesis of cGMP. NPR-B is the
predominant natriuretic peptide receptor in the brain.
The rank of order activation of NPR-B by natriuretic
peptides is CNP>>ANP>BNP. Homozygous inactivating
mutations in human NPR-B cause a form of short-limbed
dwarfism known as acromesomelic dysplasia type
Maroteaux.
Length = 399
Score = 29.4 bits (66), Expect = 9.7
Identities = 52/211 (24%), Positives = 83/211 (39%), Gaps = 48/211 (22%)
Query: 177 PDTDDYRPLLKEIKNSSESHILLDCS-MDKTVTILKQA-KEVHLMGDYQNYIL-----SL 229
D +++ IK + I+ C ++ + I+ QA +E GDY + L SL
Sbjct: 187 EKNSDIIEIIQFIKQNGR--IVYICGPLETFLEIMLQAQREGLTPGDYVFFYLDVFGESL 244
Query: 230 T--SYWINAHTVDFQDFQPGYANITTVRMIN---PTNPHIRSIMNGWIYEENERGRSLNV 284
S + ++ + +V +I P NP E E R L+
Sbjct: 245 RVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENP-----------EYKEFQRELHA 293
Query: 285 RAE---TVKIEAALM-------YDAVYLFAAAL-QSLGERKPLPTPLSCENPSSWQHGLG 333
RA+ V++E +LM YD V L+A AL ++L E S + GL
Sbjct: 294 RAKEDFGVELEPSLMNFIAGCFYDGVMLYAMALNETLAE------------GGSQKDGLN 341
Query: 334 IGNLMKSITIDGMTGRINLDSQTGRRNSFSL 364
I M+ G+TG +++D R F L
Sbjct: 342 ITRKMQDRRFWGVTGLVSIDKNNDRDIDFDL 372
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
0.320 0.136 0.404
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 42,628,708
Number of extensions: 4271534
Number of successful extensions: 4651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4548
Number of HSP's successfully gapped: 95
Length of query: 821
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 716
Effective length of database: 6,280,432
Effective search space: 4496789312
Effective search space used: 4496789312
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (28.0 bits)