RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2797
(225 letters)
>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane,
glycoprotein, transport, membrane, postsynaptic cell
membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus
norvegicus}
Length = 823
Score = 215 bits (548), Expect = 2e-65
Identities = 129/204 (63%), Positives = 152/204 (74%), Gaps = 11/204 (5%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLDPLSEEIWVAIIFSY 60
+AIAPL+IT RE V+DFSKPFM+LGISIMIKKP K KP V SFLDPL+ EIW+ I+F+Y
Sbjct: 465 IAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAY 524
Query: 61 IMVSVVLFLVSRFSPHEWRLLNYSDPGHPHHSPSPHHGPSPPSVIANDFSLSNSFWFSLG 120
I VSVVLFLVSRFSP+EW + D S N+F + NS WFSLG
Sbjct: 525 IGVSVVLFLVSRFSPYEWHTEEFEDGRETQ-----------SSESTNEFGIFNSLWFSLG 573
Query: 121 AFMQQGSDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVERMVNPINSVEDLADQ 180
AFMQQG+DISPRS+SGRIVG VWWFFTLI+ISSYTANLAAFLTVERMV+PI S EDL+ Q
Sbjct: 574 AFMQQGADISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQ 633
Query: 181 SDVLYGTVKDASTYHFFEVSAVNL 204
+++ YGT+ ST FF S + +
Sbjct: 634 TEIAYGTLDSGSTKEFFRRSKIAV 657
>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell
junction, cell membrane, glycoprotein, ION transport,
ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus
norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A* 3g3g_A*
3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A* 2xxr_A*
2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A* 3qxm_A*
2i0c_A* ...
Length = 259
Score = 75.4 bits (185), Expect = 1e-16
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLDPLSEEIWVAIIFSY 60
+A+APL+IT RE V+DFSKPFMTLGISI+ +K + D L+++ +
Sbjct: 85 LAVAPLAITYVREEVIDFSKPFMTLGISILYRKGTPIDS-----ADDLAKQTKIEYGAVE 139
Query: 61 IMVSVVLFLVSRFSPHEWR 79
++ F S+ S ++
Sbjct: 140 DGATMTFFKRSKISTYDKM 158
>1yae_A Glutamate receptor, ionotropic kainate 2; kainate receptor,
membrane protein; HET: NAG FUC DOQ; 3.11A {Rattus
norvegicus} SCOP: c.94.1.1
Length = 312
Score = 67.5 bits (164), Expect = 2e-13
Identities = 31/64 (48%), Positives = 42/64 (65%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLDPLSEEIWVAIIFSY 60
+A+APL+IT RE+V+DFSKPFMTLGISI+ +KP+ P V SFL+ S +
Sbjct: 94 LAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNGGSLVPRGSERMES 153
Query: 61 IMVS 64
+ S
Sbjct: 154 PIDS 157
Score = 49.4 bits (117), Expect = 2e-07
Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 9/100 (9%)
Query: 122 FMQQGSDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVERMVNPINSVEDLADQS 181
FM G I R +G F+ + S ERM +PI+S +DLA Q+
Sbjct: 115 FMTLGISILYRKPNGTN----PGVFSFLNGGSLV-----PRGSERMESPIDSADDLAKQT 165
Query: 182 DVLYGTVKDASTYHFFEVSAVNLVADVVRALGEQKNGLNP 221
+ YG V+D +T FF+ S ++ + + ++ +
Sbjct: 166 KIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLV 205
>2v3u_A Glutamate receptor delta-2 subunit; postsynaptic membrane,
ionotropic glutamate receptors, transmembrane, membrane
protein; 1.74A {Rattus norvegicus} PDB: 2v3t_A
Length = 265
Score = 67.0 bits (163), Expect = 2e-13
Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 3/89 (3%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVL---SFLDPLSEEIWVAII 57
+ I+ L+IT +RE VVDF+ +M + +++++ + + P + A+
Sbjct: 81 IGISALTITPDRENVVDFTTRYMDYSVGVLLRRGTSIQSLQDLSKQTDIPYGTVLDSAVY 140
Query: 58 FSYIMVSVVLFLVSRFSPHEWRLLNYSDP 86
M + F WR++N S+
Sbjct: 141 QHVRMKGLNPFERDSMYSQMWRMINRSNG 169
Score = 26.6 bits (58), Expect = 7.3
Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 6/87 (6%)
Query: 119 LGAFMQQGSDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVERMVNPINSVEDLA 178
+G + + +DI +++ FT + + R I S++DL+
Sbjct: 71 VGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVG------VLLRRGTSIQSLQDLS 124
Query: 179 DQSDVLYGTVKDASTYHFFEVSAVNLV 205
Q+D+ YGTV D++ Y + +N
Sbjct: 125 KQTDIPYGTVLDSAVYQHVRMKGLNPF 151
>1pb7_A N-methyl-D-aspartate receptor subunit 1; ligand binding receptor,
NR1, ligand binding protein; 1.35A {Rattus norvegicus}
SCOP: c.94.1.1 PDB: 1pbq_A* 1y1m_A 1y1z_A 1y20_A 2a5t_A*
1pb8_A 1pb9_A
Length = 292
Score = 66.2 bits (161), Expect = 3e-13
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQK-PRVLSFLDPLSEEIWVAIIFS 59
M +APL+I +ER + ++FSKPF G++I++KK ++ +P + I+ + S
Sbjct: 120 MIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQS 179
Query: 60 YIMVSVVLFLVSRFSPHEWRLLNYSD 85
+ + + NY
Sbjct: 180 SVDIYFRRQVELSTMYRHMEKHNYES 205
>1mqi_A Glutamate receptor 2; GLUR2, ligand binding core, S1S2, partial
agonist, WILLARDIINES, fluoro-WILLARDIINE, membrane
protein; HET: FWD; 1.35A {Rattus norvegicus} SCOP:
c.94.1.1 PDB: 1ftj_A* 1ftl_A* 1fto_A 1fw0_A* 1m5b_A*
1ftm_A* 1m5c_A* 1mm6_A* 1mm7_A* 1mqg_A* 1m5e_A* 1mqj_A*
1ms7_A* 1mxu_A* 1mxv_A 1mxw_A 1mxx_A 1mxy_A 1mxz_A
1my0_A ...
Length = 263
Score = 56.6 bits (136), Expect = 6e-10
Identities = 26/44 (59%), Positives = 32/44 (72%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSF 44
+AIAPL+IT RE V+DFSKPFM+LGISIMIKK + +
Sbjct: 85 IAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLS 128
Score = 49.2 bits (117), Expect = 2e-07
Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 6/105 (5%)
Query: 112 SNSFWFSLGAFMQQGSDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVERMVNPI 171
+ + +G + +DI+ I+ + V +I S +L + + + PI
Sbjct: 68 TKIWNGMVGELVYGKADIA---IAPLTITLVRE--EVIDFSKPFMSLGISIMI-KKGTPI 121
Query: 172 NSVEDLADQSDVLYGTVKDASTYHFFEVSAVNLVADVVRALGEQK 216
S EDL+ Q+++ YGT+ ST FF S + + + + +
Sbjct: 122 ESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAE 166
>2rc8_A Glutamate [NMDA] receptor subunit 3A; membrane protein, cell
junction, glycoprotein, ION transport channel,
magnesium; 1.45A {Rattus norvegicus} PDB: 2rc7_A 2rc9_A
2rca_A 2rcb_A
Length = 294
Score = 54.3 bits (130), Expect = 4e-09
Identities = 11/47 (23%), Positives = 23/47 (48%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLDP 47
MA+ SI + R +V+DF+ PF + + I+++ + +
Sbjct: 119 MAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRGTELSGIHDPKLH 165
>2a5s_A N-methyl-D-aspartate receptor nmdar2A subunit, NMDA receptor
nmdar2A; protein-ligand complex, metal
transport,membrane protein; HET: GLU; 1.70A {Rattus
norvegicus} SCOP: c.94.1.1 PDB: 2a5t_B* 3oen_A* 3oel_A*
3oem_A* 3oek_A*
Length = 284
Score = 52.3 bits (125), Expect = 2e-08
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQK 38
MA+ L+I ER VVDFS PF+ GIS+M+ + ++
Sbjct: 108 MAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVT 145
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 46.1 bits (110), Expect = 2e-06
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLD 46
+ IA +SIT+ERE+ DFS P G+ IM++ + S D
Sbjct: 64 LGIAAISITAEREQNFDFSLPIFASGLQIMVRNLESGTGDIRSIDD 109
>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system, THER
bacterium, transport protein; HET: LYS; 1.79A
{Geobacillus stearothermophilus} PDB: 2q2a_A* 2q2c_A*
Length = 272
Score = 46.2 bits (110), Expect = 2e-06
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
M I+ ++IT ER++ DFS P+ I++K+ S
Sbjct: 103 MGISGITITDERKQSYDFSDPYFEATQVILVKQGSP 138
>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginos structural
genomics, PSI-2, protein structure initiative; HET: EPE;
1.66A {Pseudomonas aeruginosa}
Length = 239
Score = 45.8 bits (109), Expect = 3e-06
Identities = 12/46 (26%), Positives = 25/46 (54%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLD 46
+A++ +SI ER+R FS P++ G + + + + + L +D
Sbjct: 77 IAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEARFQTLEQID 122
>1wdn_A GLNBP, glutamine binding protein; closed form, complex, peptide,
complex (binding protein/peptide); 1.94A {Escherichia
coli} SCOP: c.94.1.1 PDB: 1ggg_A
Length = 226
Score = 45.7 bits (109), Expect = 3e-06
Identities = 12/33 (36%), Positives = 23/33 (69%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKK 33
+A+A ++IT ER++ +DFS + G+ +M+K
Sbjct: 64 LALAGITITDERKKAIDFSDGYYKSGLLVMVKA 96
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 45.8 bits (109), Expect = 3e-06
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
+ +A + T ER VDF+ P+M + + ++ K
Sbjct: 120 LILANFTQTPERAEAVDFADPYMKVALGVVSPKNKP 155
>4dz1_A DALS D-alanine transporter; D-alanine binding, periplasmic,
transport protein; 1.90A {Salmonella enterica} PDB:
3r39_A 4f3s_A
Length = 259
Score = 45.4 bits (108), Expect = 4e-06
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKP 39
+A + +SIT +R++V+DFS+P+ ++ K
Sbjct: 91 VAFSGISITDKRKKVIDFSEPYYINSFYLVSMANHKITL 129
>1xt8_A Putative amino-acid transporter periplasmic solut protein; ABC
transport, cysteine uptake; 2.00A {Campylobacter jejuni}
SCOP: c.94.1.1
Length = 292
Score = 45.5 bits (108), Expect = 5e-06
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
+ +A + T +R VDF P+M + + + + K S
Sbjct: 109 IILANFTQTPQRAEQVDFCSPYMKVALGVAVPKDSN 144
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 44.9 bits (107), Expect = 5e-06
Identities = 9/38 (23%), Positives = 20/38 (52%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQK 38
IA + +T +RE+ V FS+P+ ++++ +
Sbjct: 68 AVIAGMDMTPKREQQVSFSQPYYEGLSAVVVTRKGAYH 105
>3k4u_A Binding component of ABC transporter; structural genomics, protein
structure INI NEW YORK structural genomix research
consortium, nysgxrc; HET: LYS; 2.62A {Wolinella
succinogenes}
Length = 245
Score = 45.0 bits (107), Expect = 6e-06
Identities = 11/38 (28%), Positives = 26/38 (68%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQK 38
+ I+ ++I+ ER V+F +P++ +G S+++KK ++
Sbjct: 67 IIISGMTISQERNLRVNFVEPYIVVGQSLLVKKGLEKG 104
>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics,
GLUT seattle structural genomics center for infectious
disease; 2.40A {Burkholderia pseudomallei}
Length = 249
Score = 45.0 bits (107), Expect = 6e-06
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKK 33
+A++ ++I ER + +DFS P+ G++ M++
Sbjct: 85 VALSGMTIKEERRKAIDFSDPYYDSGLAAMVQA 117
>1lst_A Lysine, arginine, ornithine-binding protein; amino-acid binding
protein; HET: LYS; 1.80A {Salmonella typhimurium} SCOP:
c.94.1.1 PDB: 2lao_A 1lag_E* 1lah_E 1laf_E 1hsl_A*
1hpb_P*
Length = 239
Score = 44.5 bits (106), Expect = 7e-06
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKP 39
I+ LSIT +R++ + FS ++ K S +P
Sbjct: 66 AIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQP 104
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 44.5 bits (106), Expect = 8e-06
Identities = 10/39 (25%), Positives = 20/39 (51%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKP 39
++IT+ R++ VDF+ P+ T +S + K +
Sbjct: 64 ALFGGMNITTARQKEVDFTDPYYTNSVSFIADKNTPLTL 102
>3qax_A Probable ABC transporter arginine-binding protein; periplasmic,
transport PR; HET: ARG; 2.00A {Chlamydophila pneumoniae}
PDB: 3g41_A* 3n26_A*
Length = 268
Score = 44.6 bits (106), Expect = 8e-06
Identities = 6/38 (15%), Positives = 15/38 (39%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQK 38
+A +SIT R++ + + +M+ +
Sbjct: 93 AILAGMSITPSRQKEIALLPYYGDEVQELMVVSKRSLE 130
>2q88_A EHUB, putative ABC transporter amino acid-binding prote;
substrate-binding protein, compatible solues,
ABC-transporte osmoprotection; HET: 4CS; 1.90A
{Sinorhizobium meliloti} PDB: 2q89_A*
Length = 257
Score = 44.2 bits (105), Expect = 9e-06
Identities = 9/49 (18%), Positives = 18/49 (36%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLDPLS 49
A L + ER V +S+P + + +KK + + +
Sbjct: 75 AITAGLFMKPERCAAVAYSQPILCDAEAFALKKGNPLGLKSYKDIADNP 123
>3kzg_A Arginine 3RD transport system periplasmic binding protein; arginine
transport system, protein structure initiative II(PSI
II); 2.06A {Legionella pneumophila subsp}
Length = 237
Score = 44.2 bits (105), Expect = 1e-05
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
+ IA + IT ER++ FS P+M + SK
Sbjct: 66 LVIASMIITDERKKHFIFSLPYMESNSQYITTVDSK 101
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 43.4 bits (103), Expect = 2e-05
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 2 AIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
+ +S + +R R +DF+ P + +I ++ S
Sbjct: 73 VLQGISWSEKRARQIDFTPPHTIVYHAIFARRDSP 107
>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic
protein, arginine protein binding, transport protein;
1.92A {Chlamydia trachomatis}
Length = 242
Score = 43.0 bits (102), Expect = 3e-05
Identities = 6/39 (15%), Positives = 14/39 (35%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKP 39
I +SIT R + + + +++ + K
Sbjct: 73 AVITGMSITPSRLKEILMIPYYGEEIKHLVLVFKGENKH 111
>3hv1_A Polar amino acid ABC uptake transporter substrate binding protein;
protein structure initiative II(PSI II), nysgxrc; 1.90A
{Streptococcus thermophilus lmg 18311}
Length = 268
Score = 43.1 bits (102), Expect = 3e-05
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
+ S+T ER++ DF++P+M ++ KK S
Sbjct: 83 LIWNGYSVTDERKQSADFTEPYMVNEQVLVTKKSSG 118
>3i6v_A Periplasmic His/Glu/Gln/Arg/opine family-binding; structural
genomics, transporter, PSI-2, protein structure
initiative; HET: LYS; 2.00A {Silicibacter pomeroyi}
Length = 232
Score = 43.0 bits (102), Expect = 3e-05
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
IA +SIT ER+ V+DF++ ++ S +
Sbjct: 67 TIIAGMSITDERDEVIDFTQNYIPPTASSYVATSDG 102
>2iee_A ORF2, probable ABC transporter extracellular-binding protein YCKB;
SR574, NESG, X-RAY, structural genomics, PSI-2; 2.20A
{Bacillus subtilis}
Length = 271
Score = 42.7 bits (101), Expect = 3e-05
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKK 33
A + +T +RE FS P+ + +++K
Sbjct: 86 AAANDIDVTKDREEKFAFSTPYKYSYGTAIVRK 118
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
transport, ABC transport, virulence factor, receptor;
1.49A {Campylobacter jejuni}
Length = 259
Score = 42.3 bits (100), Expect = 5e-05
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
IA +IT ER+R+ +FS+P+ I +++ K K
Sbjct: 104 AVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEKK 139
>2vha_A Periplasmic binding transport protein; periplasmic binding protein,
ligand binding, ultrahigh resolution; HET: GLU; 1.00A
{Shigella flexneri} PDB: 2ia4_A*
Length = 287
Score = 42.0 bits (99), Expect = 6e-05
Identities = 7/36 (19%), Positives = 13/36 (36%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
+ ER++ FS +G ++ KK
Sbjct: 86 FECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGD 121
>4eq9_A ABC transporter substrate-binding protein-amino A transport;
structural genomics, niaid; HET: GSH; 1.40A
{Streptococcus pneumoniae}
Length = 246
Score = 41.1 bits (97), Expect = 1e-04
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKK 33
MA+ LS T ER ++ P +++KK
Sbjct: 70 MAVNNLSYTKERAEKYLYAAPIAQNPNVLVVKK 102
>1ii5_A SLR1257 protein; membrane protein; HET: GLU; 1.60A {Synechocystis
SP} SCOP: c.94.1.1 PDB: 1iit_A 1iiw_A
Length = 233
Score = 40.0 bits (94), Expect = 2e-04
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 1 MAIAPLSITSERERV--VDFSKPFMTLGISIMIKKPSKQK 38
+ I P+S+T ER + + F++P+ + GI ++I +
Sbjct: 68 ILIGPISVTPERAAIEGITFTQPYFSSGIGLLIPGTATPL 107
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
signaling protein; 2.04A {Bordetella pertussis} PDB:
3mpl_A
Length = 267
Score = 40.0 bits (94), Expect = 3e-04
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 3 IAPLSITSERERVVDFSKPFMTLGISIMIKK 33
L + S RE + FS+P++ G+ I+ ++
Sbjct: 96 AGALFVNSARESFLSFSRPYVRNGMVIVTRQ 126
>2yln_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-BIND protein; HET: CYS GOL;
1.12A {Neisseria gonorrhoeae} PDB: 3zsf_A
Length = 283
Score = 37.7 bits (88), Expect = 0.002
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 1 MAIAPLSITS-ERERVVDFSKPFMTLGISIMIKKPSK 36
+ + +TS ER+ D S+P+ G ++ S
Sbjct: 119 VVANQVGLTSPERQATFDKSEPYSWSGAVLVAHNDSN 155
>2o1m_A Probable amino-acid ABC transporter extracellular-binding protein
YTMK; NESG X-RAY O34852 YTMK_bacsu, structural genomics,
PSI-2; 2.00A {Bacillus subtilis}
Length = 258
Score = 36.9 bits (86), Expect = 0.003
Identities = 5/38 (13%), Positives = 12/38 (31%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQK 38
+ + + ERE+ F+K + +
Sbjct: 79 IVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQNNDT 116
>3ouf_A Potassium channel protein; ION channel, membrane, membrane protein;
1.55A {Bacillus cereus} PDB: 3t4z_A 3tcu_A 3t1c_A 3tet_A
3t4d_A 3t2m_A 3e86_A 3e83_A 3e89_A 3e8b_A 3e8f_A 3e8g_A
3e8h_A 3k0d_A 3k0g_A 3k06_A 3k08_A 3k04_A 3k03_A
Length = 97
Score = 32.1 bits (73), Expect = 0.033
Identities = 12/63 (19%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 108 DFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVER 166
++ +FS+ G D SP++ G+I ++ F + L+ + LA + +
Sbjct: 30 GLRPIDALYFSVVTLTTVGYGDFSPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPS 89
Query: 167 MVN 169
+++
Sbjct: 90 ILS 92
>2q67_A Potassium channel protein; inverted teepee, helix bundle, tetramer,
central cavity, ION metal transport, membrane protein;
2.30A {Bacillus cereus} PDB: 2q68_A 2q6a_A 2q69_A 2ahy_A
2ahz_A
Length = 114
Score = 31.0 bits (70), Expect = 0.12
Identities = 11/65 (16%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 108 DFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVER 166
++ +FS+ G + SP++ G+I ++ F + L+ + LA + +
Sbjct: 47 GLRPIDALYFSVVTLTTVGAGNFSPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPS 106
Query: 167 MVNPI 171
+++ +
Sbjct: 107 ILSNL 111
>3vou_A ION transport 2 domain protein, voltage-gated SOD channel;
4-helical bundle, ION channel, membrane, transport
protein; 3.20A {Bacillus weihenstephanensis}
Length = 148
Score = 30.7 bits (69), Expect = 0.20
Identities = 10/63 (15%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 108 DFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVER 166
++ +FS+ G + SP++ G++ ++ F + L+ + LA + +
Sbjct: 50 GLRPLDALYFSVVTLTTVGDGNFSPQTDFGKVFTILYIFIGIGLVFGFIHKLAVNVQLPS 109
Query: 167 MVN 169
+++
Sbjct: 110 ILS 112
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 31.7 bits (71), Expect = 0.21
Identities = 45/314 (14%), Positives = 78/314 (24%), Gaps = 123/314 (39%)
Query: 15 VVDFSKPFMTLG-ISIMIKKP--------------SKQKPRVLSFLDPLSEE----IWVA 55
V D K ++ I +I SKQ+ V F++ + +
Sbjct: 38 VQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSP 97
Query: 56 IIFSYIMVSVVLFLVSRFSPHEWRLLNYSDPGHPHHSPSPH------------------- 96
I S++ + RL N + ++
Sbjct: 98 IKTEQRQPSMM---TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL 154
Query: 97 -HGP--SPPSVIANDFSLSNS---------FWFSLG---------AFMQ----------- 124
G S + +A D LS FW +L +Q
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 125 QGSDISPR------SISGR---------------IVGAVW----W-FFTL---ILISSYT 155
SD S SI ++ V W F L IL+++
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRF 274
Query: 156 ANLAAFLTVERMVNPINSVEDLADQSDVLYGTVKDASTYHFFEVSAVNLVADVVR----A 211
+ FL+ + S++ + +L+ +
Sbjct: 275 KQVTDFLSAATTTHI--SLDHHSMT---------------LTPDEVKSLLLKYLDCRPQD 317
Query: 212 LGEQKNGLNPLILS 225
L + NP LS
Sbjct: 318 LPREVLTTNPRRLS 331
Score = 31.0 bits (69), Expect = 0.38
Identities = 36/239 (15%), Positives = 69/239 (28%), Gaps = 72/239 (30%)
Query: 13 ERVVDFSKPFMTLGISIMIKKPSKQKPRVLSFLDPLSEEIWVAIIFSYIMVSVVLFL--- 69
E V+ + F+ I ++PS + D L +F
Sbjct: 84 EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN-------------DNQVFAKYN 130
Query: 70 VSRFSPHEWRLLN--YSDPGHPHHSPSPH---HGP--SPPSVIANDFSLSNS-------- 114
VSR P+ +L P+ + G S + +A D LS
Sbjct: 131 VSRLQPY-LKLRQALLEL------RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK 183
Query: 115 -FWFSLGAFMQQGSDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVERMVNPINS 173
FW +L + SP ++ + + ++T+ + N
Sbjct: 184 IFWLNL------KNCNSPETVLEML-----QKLLYQIDPNWTSRS------DHSSNIKLR 226
Query: 174 VEDLADQSDVLYGT------------VKDASTYHFFEVSAVNLV----ADVVRALGEQK 216
+ + + L + V++A ++ F +S L+ V L
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285
>1lnq_A MTHK channels, potassium channel related protein; rossman fold,
helix bundle, membrane protein; 3.30A
{Methanothermobacter thermautotrophicusorganism_taxid}
SCOP: c.2.1.9 d.286.1.1 f.14.1.1 PDB: 3rbz_A
Length = 336
Score = 29.7 bits (67), Expect = 0.64
Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 1/57 (1%)
Query: 108 DFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLT 163
S + S +++ G D SP + G + + L FL
Sbjct: 43 GESWTVSLYWTFVTIATVGYGDYSPSTPLGMYFTVTLIVLGIGTFAVAVERLLEFLI 99
>3ldc_A Calcium-gated potassium channel MTHK; transmembrane, ION channel,
open conformation, IO transport; 1.45A
{Methanothermobacter thermautotrophicusorganism_taxid}
PDB: 3lde_A 3r65_A 3ous_A 3ldd_A
Length = 82
Score = 28.1 bits (63), Expect = 0.69
Identities = 10/56 (17%), Positives = 17/56 (30%), Gaps = 1/56 (1%)
Query: 108 DFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTANLAAFL 162
S + S +++ G D SP + G + + L FL
Sbjct: 26 GESWTVSLYWTFVTIATVGYGDYSPHTPLGMYFTCTLIVLGIGTFAVAVERLLEFL 81
>3sjr_A Uncharacterized protein; PSI-biology, MCSG, midwest center for
structural genomics, U function, structural genomics;
2.94A {Chromobacterium violaceum}
Length = 175
Score = 27.5 bits (60), Expect = 3.3
Identities = 4/31 (12%), Positives = 11/31 (35%)
Query: 118 SLGAFMQQGSDISPRSISGRIVGAVWWFFTL 148
+ S+++ S S ++ + L
Sbjct: 77 DIEPVRLPESELTGDSHSQHLLLGMEILMEL 107
>3svk_A Acetyl-COA acetyltransferase; ssgcid, NIH, niaid, SBRI, UW, emerald
biostructures, structu genomics; 2.20A {Mycobacterium
avium}
Length = 407
Score = 27.5 bits (62), Expect = 3.4
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 198 EVSAVNLVADVVRALGEQKNGLNP 221
EV +NLV +V L + L+
Sbjct: 29 EVKPLNLVVGLVDELRRRYPDLDE 52
>3eff_K Voltage-gated potassium channel; FULL length KCSA, bulge helix,
cell membrane, ION transport, ionic channel, membrane,
transmembrane; 3.80A {Streptomyces lividans}
Length = 139
Score = 26.8 bits (59), Expect = 4.1
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 4/67 (5%)
Query: 98 GPSPPSVIANDFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTA 156
+P + + + + W+S+ G D+ P ++ GR+V V + TA
Sbjct: 31 RGAPGAQLI---TYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTA 87
Query: 157 NLAAFLT 163
LA +
Sbjct: 88 ALATWFV 94
>3pjs_K KCSA, voltage-gated potassium channel; ION channel, conducts K+
IONS, cell membrane, transport PROT; 3.80A {Streptomyces
lividans} PDB: 1f6g_A
Length = 166
Score = 26.4 bits (58), Expect = 5.7
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 4/69 (5%)
Query: 98 GPSPPSVIANDFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTA 156
+P + + + + W+S+ G D+ P ++ GR+V V + TA
Sbjct: 58 RGAPGAQLI---TYPRALWWSVETATTVGYGDLYPVTLWGRLVAVVVMVAGITSFGLVTA 114
Query: 157 NLAAFLTVE 165
LA + +
Sbjct: 115 ALATWFVGQ 123
>4ege_A Dipeptidase PEPE; structural genomics, seattle structural genomics
center for infectious disease, ssgcid, hydrolase; 2.20A
{Mycobacterium ulcerans}
Length = 378
Score = 26.9 bits (60), Expect = 6.5
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 7/42 (16%)
Query: 91 HSPSPHHGPSPPSVIANDFSLSNSFWFSLGAFMQQG--SDIS 130
H PHHG S + D + +G + G SD +
Sbjct: 212 HGADPHHGYSDRKLQVGDIVV-----VDIGGTYEPGYYSDST 248
>3afv_A DYP; DYE-decolorizing peroxidase, beta barrel, oxidoreductas
aspartic acid; HET: HEM NAG; 1.40A {Bjerkandera adusta}
PDB: 2d3q_A* 3mm2_A* 3mm3_A* 3mm1_A*
Length = 442
Score = 26.7 bits (58), Expect = 7.6
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 176 DLAD-QSDVLYGTVKDASTYHFFEV 199
L + Q D+L G K + FF+V
Sbjct: 7 PLNNIQGDILVGMKKQKERFVFFQV 31
>3lwj_A Putative TETR-family transcriptional regulator; structural G joint
center for structural genomics, JCSG, protein structu
initiative; 2.07A {Syntrophomonas wolfei subsp}
Length = 202
Score = 26.2 bits (58), Expect = 7.7
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 5/26 (19%)
Query: 173 SVEDLADQSDVLYGTVKDASTYHFFE 198
S+ D+ S+V GT Y++F
Sbjct: 34 SIRDIIALSEVGTGTF-----YNYFV 54
>2r9r_B Paddle chimera voltage gated potassium channel KV; voltage sensor,
voltage dependent, ION CH shaker, membrane protein,
eukaryotic; HET: NAP PGW; 2.40A {Rattus norvegicus} PDB:
3lnm_B* 3lut_B* 2a79_B*
Length = 514
Score = 26.6 bits (58), Expect = 8.2
Identities = 13/48 (27%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 107 NDF-SLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILIS 152
+ F S+ ++FW+++ + G D+ P +I G+IVG++ ++ I+
Sbjct: 371 SQFPSIPDAFWWAVVSMTTVGYGDMVPTTIGGKIVGSLCAIAGVLTIA 418
>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted
DNA-binding transcriptional regulator TETR/ACRR family;
2.10A {Clostridium acetobutylicum atcc 824}
Length = 203
Score = 25.9 bits (57), Expect = 9.8
Identities = 4/26 (15%), Positives = 12/26 (46%), Gaps = 5/26 (19%)
Query: 173 SVEDLADQSDVLYGTVKDASTYHFFE 198
++ + ++ + G + YH+F
Sbjct: 33 TLAFIINKLGISKGAL-----YHYFS 53
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.135 0.409
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,561,843
Number of extensions: 208286
Number of successful extensions: 465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 69
Length of query: 225
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 135
Effective length of database: 4,188,903
Effective search space: 565501905
Effective search space used: 565501905
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 (21.9 bits)
S2: 55 (24.9 bits)