RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13439
(261 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 = 126 bits (318), Expect = 3e-33
Identities = 51/229 (22%), Positives = 88/229 (38%), Gaps = 48/229 (20%)
Query: 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGI-ISPT 90
+ WNG++ +LV K D+A+ L I RE V+DF+ P M GI+I++ K
Sbjct: 447 DTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVF 506
Query: 91 AFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTAS 150
+FL+P WM + I + +F SP
Sbjct: 507 SFLDPLAYEIWMCIVFAYI-GVSVVLFLVSRFSP-------------------------- 539
Query: 151 WMLVGVVAIQASAFTIFFFEWLSPSGFDMKTT-ALQPSHRFSLFRTYWLVWAVLFQAAVH 209
+EW + D + T + + ++ F +F + W Q
Sbjct: 540 ------------------YEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGAD 581
Query: 210 IDTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMITREEFHEFTGVDD 258
I +P+ + + + +W F ++ ++ YTANLAAF+ +D
Sbjct: 582 I-SPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAED 629
>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 = 73.5 bits (180), Expect = 2e-15
Identities = 27/96 (28%), Positives = 46/96 (47%)
Query: 18 LTVYLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIA 77
+Y+ + + +NG W GL+ DL++ +MA+TS IN+ R V+DFT P T +
Sbjct: 87 FDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLG 146
Query: 78 IVVAKRTGIISPTAFLEPFDTASWMLVGVVAIQASA 113
I+V R +S + + G V ++
Sbjct: 147 ILVRTRGTELSGIHDPKLHHPSQGFRFGTVRESSAE 182
>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 = 72.0 bits (176), Expect = 5e-15
Identities = 28/113 (24%), Positives = 48/113 (42%)
Query: 19 TVYLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAI 78
+YL + + N WNG+I ++V ++ MA+ SL IN R VVDF+VP +ETGI++
Sbjct: 77 DLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISV 136
Query: 79 VVAKRTGIISPTAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKI 131
+V++ T + + + + M
Sbjct: 137 MVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTR 189
>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 = 71.2 bits (174), Expect = 9e-15
Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 2/90 (2%)
Query: 24 SKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKR 83
++ V + +WNG++ +L++ + DM + L IN+ R ++F+ P G+ I+V K
Sbjct: 94 TQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKG 153
Query: 84 TGIISPT--AFLEPFDTASWMLVGVVAIQA 111
T I P D + V ++
Sbjct: 154 TRITGINDPRLRNPSDKFIYATVKQSSVDI 183
>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 = 70.0 bits (171), Expect = 2e-14
Identities = 33/117 (28%), Positives = 50/117 (42%), Gaps = 5/117 (4%)
Query: 25 KNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84
K NG+WNG++ +L++ K D+A+ L I RE V+DF+ P M GI+I+ K T
Sbjct: 60 KYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREEVIDFSKPFMTLGISILYRKGT 119
Query: 85 GIISPTAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFL 141
I S + + G V + T F +S S R +
Sbjct: 120 PIDSADDLAKQT----KIEYGAVED-GATMTFFKRSKISTYDKMWAFMSSRRQSVLV 171
>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 = 69.4 bits (169), Expect = 6e-14
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 25 KNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84
K NG+WNG++ +L++ K D+A+ L I RE V+DF+ P M GI+I+ K
Sbjct: 69 KYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPN 128
Query: 85 G-IISPTAFLEPFDTASWM 102
G +FL
Sbjct: 129 GTNPGVFSFLNGGSLVPRG 147
>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 = 67.8 bits (165), Expect = 1e-13
Identities = 31/129 (24%), Positives = 52/129 (40%), Gaps = 1/129 (0%)
Query: 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTA 91
E+G WNGL+ +LV ++ D+ +++L I RE+VVDFT M+ + +++ + T I S
Sbjct: 63 EDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRGTSIQSLQD 122
Query: 92 FLEPFDTASWM-LVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTAS 150
+ D L V + FE S ++ E
Sbjct: 123 LSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQ 182
Query: 151 WMLVGVVAI 159
+ G A
Sbjct: 183 KVKYGNYAF 191
>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 = 58.9 bits (142), Expect = 2e-10
Identities = 24/63 (38%), Positives = 35/63 (55%)
Query: 25 KNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRT 84
K + WNG++ +LV K D+A+ L I RE V+DF+ P M GI+I++ K T
Sbjct: 60 KYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGT 119
Query: 85 GII 87
I
Sbjct: 120 PIE 122
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 55.3 bits (134), Expect = 2e-09
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
N ++ LI L +K D + + + +RE V F+ P E A+VV ++ +
Sbjct: 51 NQSFDSLIPSLRFKKFDAVIAGMDMTPKREQQVSFSQPYYEGLSAVVVTRKGAYHTF 107
>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 = 54.6 bits (132), Expect = 4e-09
Identities = 14/59 (23%), Positives = 28/59 (47%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
E ++ L L NR+ D+ + S++I R+ F++P ME+ + + I +
Sbjct: 47 FEAYIFDDLFPALKNREVDLVIASMIITDERKKHFIFSLPYMESNSQYITTVDSKISTF 105
>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 = 54.6 bits (132), Expect = 4e-09
Identities = 14/62 (22%), Positives = 28/62 (45%)
Query: 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAF 92
++ LI L +K D ++SL I +R+ + F+ + ++ AK + I
Sbjct: 49 ASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLES 108
Query: 93 LE 94
L+
Sbjct: 109 LK 110
>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 = 53.1 bits (128), Expect = 2e-08
Identities = 15/59 (25%), Positives = 23/59 (38%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
+ W+ +L N D+ + R+ DFT P M +V K +GI S
Sbjct: 64 WQAIDWDMKETELKNGTIDLIWNGYSVTDERKQSADFTEPYMVNEQVLVTKKSSGIDSV 122
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 52.6 bits (127), Expect = 2e-08
Identities = 16/59 (27%), Positives = 25/59 (42%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAFLE 94
W+ LI L K D + I + R+ VDFT P ++ + K T + L+
Sbjct: 50 WDSLIPSLKLGKFDALFGGMNITTARQKEVDFTDPYYTNSVSFIADKNTPLTLSKQGLK 108
>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 = 51.9 bits (125), Expect = 4e-08
Identities = 10/52 (19%), Positives = 20/52 (38%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
++ +I L + D L + R + V ++ PI+ A + K
Sbjct: 56 ASISEYGAMIPGLQAGRHDAITAGLFMKPERCAAVAYSQPILCDAEAFALKK 107
>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 = 51.6 bits (124), Expect = 6e-08
Identities = 11/63 (17%), Positives = 24/63 (38%)
Query: 29 LSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88
L V ++ LI +L + D L + I R+ + + ++V + + +
Sbjct: 72 LEVREFAFDALILNLKKHRIDAILAGMSITPSRQKEIALLPYYGDEVQELMVVSKRSLET 131
Query: 89 PTA 91
P
Sbjct: 132 PVL 134
>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 = 51.2 bits (123), Expect = 6e-08
Identities = 15/59 (25%), Positives = 31/59 (52%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
++N W+ L A L +++ DM ++ + I R+ DF+ P E I+V + + + +
Sbjct: 84 LKNIGWDPLFASLQSKEVDMGISGITITDERKQSYDFSDPYFEATQVILVKQGSPVKNA 142
>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 = 51.1 bits (123), Expect = 6e-08
Identities = 12/58 (20%), Positives = 29/58 (50%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88
++ ++G+I L + D+AL + I R+ +DF+ ++G+ ++V +
Sbjct: 45 LKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVK 102
>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 = 50.3 bits (121), Expect = 1e-07
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
W+ +I +LV+ D + + I R+ V+DFT + + VA
Sbjct: 50 KNDWDSIIPNLVSGNYDTIIAGMSITDERDEVIDFTQNYIPPTASSYVAT 99
>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 = 50.4 bits (121), Expect = 1e-07
Identities = 12/66 (18%), Positives = 23/66 (34%)
Query: 29 LSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88
L V ++ LI +L + D +T + I R + E +V+ +
Sbjct: 52 LDVREFSFDALILNLKQHRIDAVITGMSITPSRLKEILMIPYYGEEIKHLVLVFKGENKH 111
Query: 89 PTAFLE 94
P +
Sbjct: 112 PLPLTQ 117
>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 = 50.0 bits (120), Expect = 2e-07
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
+ W+GLI LV K D+ ++ + I+ R V+F P + G +++V K
Sbjct: 48 LVPTSWDGLIPGLVTEKFDIIISGMTISQERNLRVNFVEPYIVVGQSLLVKK 99
>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 = 49.7 bits (119), Expect = 2e-07
Identities = 12/59 (20%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 32 ENGKWNGLIADLVNRKTDMALTSLVINSR-RESVVDFTVPIMETGIAIVVAKRTGIISP 89
+ +W+ ++A L + D+ + + S R++ D + P +G +V + I S
Sbjct: 101 KETQWDSMMAGLKAGRFDVVANQVGLTSPERQATFDKSEPYSWSGAVLVAHNDSNIKSI 159
>4dz1_A DALS D-alanine transporter; D-alanine binding, periplasmic,
transport protein; 1.90A {Salmonella enterica} PDB:
3r39_A 4f3s_A
Length = 259
Score = 49.7 bits (119), Expect = 2e-07
Identities = 12/61 (19%), Positives = 27/61 (44%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPT 90
+ W+G++ + + + D+A + + I +R+ V+DF+ P +V I
Sbjct: 72 ITEYAWDGMLGAVASGQADVAFSGISITDKRKKVIDFSEPYYINSFYLVSMANHKITLNN 131
Query: 91 A 91
Sbjct: 132 L 132
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 48.8 bits (117), Expect = 3e-07
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
+E LI+ + + K ++ + ++ I + RE DF++PI +G+ I+V
Sbjct: 45 IEYSSVPELISAIKDNKVNLGIAAISITAEREQNFDFSLPIFASGLQIMVRN 96
>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics,
GLUT seattle structural genomics center for infectious
disease; 2.40A {Burkholderia pseudomallei}
Length = 249
Score = 48.4 bits (116), Expect = 5e-07
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
++ + GLI L + D+AL+ + I R +DF+ P ++G+A +V
Sbjct: 66 IQPMDFAGLIPALQTQNIDVALSGMTIKEERRKAIDFSDPYYDSGLAAMVQA 117
>4eq9_A ABC transporter substrate-binding protein-amino A transport;
structural genomics, niaid; HET: GSH; 1.40A
{Streptococcus pneumoniae}
Length = 246
Score = 48.5 bits (116), Expect = 5e-07
Identities = 14/51 (27%), Positives = 24/51 (47%)
Query: 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
E +W+G+ A L + +MA+ +L R + PI + +VV K
Sbjct: 52 EKTEWSGVFAGLDADRYNMAVNNLSYTKERAEKYLYAAPIAQNPNVLVVKK 102
>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginos structural
genomics, PSI-2, protein structure initiative; HET: EPE;
1.66A {Pseudomonas aeruginosa}
Length = 239
Score = 48.1 bits (115), Expect = 6e-07
Identities = 11/50 (22%), Positives = 23/50 (46%)
Query: 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
W L+ D + + D+A++ + IN R+ F++P + G +
Sbjct: 60 PTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLC 109
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
signaling protein; 2.04A {Bordetella pertussis} PDB:
3mpl_A
Length = 267
Score = 48.1 bits (115), Expect = 7e-07
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88
+ LIA L + + DM +L +NS RES + F+ P + G+ IV +
Sbjct: 76 IGVDTVEELIAKLRSGEADM-AGALFVNSARESFLSFSRPYVRNGMVIVTRQDPDAPV 132
>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 = 48.1 bits (115), Expect = 7e-07
Identities = 9/51 (17%), Positives = 21/51 (41%)
Query: 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
+ +G++ + + + D A + + RE F+ P + +V K
Sbjct: 68 KEMGIDGMLTAVNSGQVDAAANDIDVTKDREEKFAFSTPYKYSYGTAIVRK 118
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 47.2 bits (113), Expect = 1e-06
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88
G W+ + + L + + D+ L + + +R +DFT P AI + + +
Sbjct: 54 FRLGAWSEMFSALKSGRVDV-LQGISWSEKRARQIDFTPPHTIVYHAIFARRDSPPAA 110
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 47.4 bits (113), Expect = 1e-06
Identities = 12/54 (22%), Positives = 20/54 (37%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
+ + + K D+ L + R VDF P M+ + +V K I
Sbjct: 106 AANRVEYVRSGKVDLILANFTQTPERAEAVDFADPYMKVALGVVSPKNKPITDM 159
>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 = 45.7 bits (109), Expect = 4e-06
Identities = 9/54 (16%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 31 VENGKWNGLIADLVNRKTDMALTSLVINSRRESV--VDFTVPIMETGIAIVVAK 82
V + I + + D+ + + + R ++ + FT P +GI +++
Sbjct: 49 VRQNSISAGITAVAEGELDILIGPISVTPERAAIEGITFTQPYFSSGIGLLIPG 102
>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 = 44.7 bits (106), Expect = 1e-05
Identities = 12/54 (22%), Positives = 16/54 (29%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
I L N D S N R+ F+ I G ++ K I
Sbjct: 72 SQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDF 125
>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 = 44.7 bits (106), Expect = 1e-05
Identities = 14/54 (25%), Positives = 23/54 (42%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
+ L + K D+ L + +R VDF P M+ + + V K + I S
Sbjct: 95 AANRVEFLKSNKVDIILANFTQTPQRAEQVDFCSPYMKVALGVAVPKDSNITSV 148
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 45.0 bits (106), Expect = 1e-05
Identities = 40/259 (15%), Positives = 74/259 (28%), Gaps = 74/259 (28%)
Query: 38 GLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETG-I-AIV----------VAKRTG 85
G ++ LV ++ + +F +E I A+ + K
Sbjct: 66 GYVSSLVEPSKVGQFDQVL----NLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKE 121
Query: 86 IISPTAFLE-------PFDTA--SWMLVGVVAIQASAFTIF--------FFEWLSPSGFD 128
+I ++ PFD S + V A IF +FE L
Sbjct: 122 LI--KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELR----- 174
Query: 129 MKISFSYRPL--PFLPPEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFD----MKTT 182
+ +Y L ++ L ++ A +F G + ++
Sbjct: 175 -DLYQTYHVLVGDL-----IKFSAETLSELIRTTLDAEKVF------TQGLNILEWLENP 222
Query: 183 ALQPSHRFSLFRTYWLVWA-------VLFQAAVHIDTPK--GFTAKFMTNMWAMFAVVFL 233
+ P +L+ + Q A ++ T K GFT + +
Sbjct: 223 SNTPD-------KDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ 275
Query: 234 AIYTANLAAFMITREEFHE 252
+ TA A + E F
Sbjct: 276 GLVTAVAIAETDSWESFFV 294
Score = 39.3 bits (91), Expect = 0.001
Identities = 37/214 (17%), Positives = 60/214 (28%), Gaps = 83/214 (38%)
Query: 29 LSVENGKWNGLIA--DLVN------RKTDMALTSLVINSRRESVVDFTVPIMETGIAIVV 80
LS+ N + + N ++ +++L +N + VV +G
Sbjct: 339 LSISNLTQEQVQDYVNKTNSHLPAGKQVEISL----VNGAKNLVV--------SG----- 381
Query: 81 AKRTGIISPTAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFD-MKISFSYRPLP 139
P L + L A PSG D +I FS R L
Sbjct: 382 --------PPQSLYGLNLT---LRKAKA---------------PSGLDQSRIPFSERKLK 415
Query: 140 ----FLP-PEPF----------DTASWMLVGVVAIQAS--AFTIFFFEWLSPSGFDMKTT 182
FLP PF ++ V+ A ++ G D++
Sbjct: 416 FSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTF----DGSDLRV- 470
Query: 183 ALQPSHRFSLFRTYWLV-----W-AVLFQAAVHI 210
L S + ++ W A HI
Sbjct: 471 -LSGSISERIVD--CIIRLPVKWETTTQFKATHI 501
Score = 36.2 bits (83), Expect = 0.010
Identities = 31/170 (18%), Positives = 49/170 (28%), Gaps = 62/170 (36%)
Query: 37 NGLIADLVNRKTDMALTSLVINSRRESVV--------------------DF--TVPIMET 74
+ L+ DL+ + L+ L+ + V D+ ++PI
Sbjct: 181 HVLVGDLIKFSAET-LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCP 239
Query: 75 GIA-------IVVAKRTGIISPTAFLEPFDTASWMLVGVVA--IQASAFTIFFFEWLSPS 125
I +V AK G +P A+ G+V A + W S
Sbjct: 240 LIGVIQLAHYVVTAKLLGF-TPGELRSYLKGATGHSQGLVTAVAIAETDS-----WES-- 291
Query: 126 GFD------MKISFS--YR-----PLPFLPPEPFD--------TASWMLV 154
F + + F R P LPP + S ML
Sbjct: 292 -FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340
Score = 29.2 bits (65), Expect = 1.6
Identities = 22/128 (17%), Positives = 36/128 (28%), Gaps = 52/128 (40%)
Query: 6 NQHESLKKKRKLL--TVYL------HSK---------NEVLSVENGKWNG---------- 38
+Q +RKL +L HS N+ L N +N
Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT 462
Query: 39 --------LIADLVNRKTDMALTSLV-----INSRRESVVDF-----------TVPIME- 73
L + R D + V + ++DF T +
Sbjct: 463 FDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDG 522
Query: 74 TGIAIVVA 81
TG+ ++VA
Sbjct: 523 TGVRVIVA 530
Score = 26.9 bits (59), Expect = 8.2
Identities = 8/51 (15%), Positives = 13/51 (25%), Gaps = 23/51 (45%)
Query: 234 AIYTANLAAFMITREEF----------H---EFT------GV----DDVRI 261
A+ AAF + + H E+ V V +
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEV 1785
>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 = 42.3 bits (100), Expect = 6e-05
Identities = 9/57 (15%), Positives = 18/57 (31%), Gaps = 2/57 (3%)
Query: 32 ENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIA--IVVAKRTGI 86
+ +++ L+ L K D+ + + RE F V+ I
Sbjct: 61 KTMEFSNLLVSLGQHKVDIVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQNNDTI 117
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
transport, ABC transport, virulence factor, receptor;
1.49A {Campylobacter jejuni}
Length = 259
Score = 41.6 bits (98), Expect = 9e-05
Identities = 11/54 (20%), Positives = 20/54 (37%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
L N D + + I R+ + +F+ P + I ++V K S
Sbjct: 90 AKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEKKYKSL 143
>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 = 39.1 bits (90), Expect = 0.001
Identities = 40/235 (17%), Positives = 67/235 (28%), Gaps = 65/235 (27%)
Query: 2 DHEDN----QHESLKKKRKLLTVYLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVI 57
DH N H + R+LL L V N + N + LT+
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLK--SKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT--- 272
Query: 58 NSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAFLEPFDTASWMLVGVVAIQASAFTIF 117
R + V DF T I++ T L P + S
Sbjct: 273 --RFKQVTDFLSAATTTHISLDHHSMT--------LTPDEVKS----------------L 306
Query: 118 FFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGF 177
++L D LP E T + + ++A + W +
Sbjct: 307 LLKYLDCRPQD------------LPREVLTT-NPRRLSIIAESIRDGLATWDNWKHVNCD 353
Query: 178 DMKTT------ALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKFMTNMWA 226
+ T L+P + +R + +V F + HI ++ +W
Sbjct: 354 KLTTIIESSLNVLEP----AEYRKMFDRLSV-FPPSAHI------PTILLSLIWF 397
>3ixz_A Potassium-transporting ATPase alpha; ION pump, H+, K+-ATPase,
P-type ATPase, membrane protein, hydrolase, aluminium
fluoride, ATP-binding; 6.50A {Sus scrofa} PDB: 2xzb_A
1iwc_A 1iwf_A
Length = 1034
Score = 30.7 bits (70), Expect = 0.58
Identities = 20/120 (16%), Positives = 41/120 (34%), Gaps = 12/120 (10%)
Query: 100 SWMLVGVVAIQASAFTIFFFEWLSPSGFDMK----ISFSYRPLPFLPPEPFDTASWMLVG 155
++ + AIQ+ A +F ++ G+ + + + W
Sbjct: 861 AYSYFQIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQ 920
Query: 156 VVAIQASAFTIFF-----FEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHI 210
+ Q + +T+FF + KT + + FR LV A++FQ +
Sbjct: 921 RLYQQYTCYTVFFISIEMCQIA--DVLIRKTR-RLSAFQQGFFRNRILVIAIVFQVCIGC 977
>3ar4_A Sarcoplasmic/endoplasmic reticulum calcium ATPase; P-type ATPase,
hydrolase, calcium transport, calcium binding binding;
HET: ATP TG1 PTY; 2.15A {Oryctolagus cuniculus} PDB:
2ear_A* 2eas_A* 2eat_A* 2eau_A* 2dqs_A* 2zbe_A 2zbf_A*
2zbg_A* 3ar2_A* 2zbd_A* 3ar3_A* 3ar5_A* 3ar6_A* 3ar7_A*
3ar8_A* 3ar9_A* 3n5k_A* 1kju_A 1iwo_A 1t5s_A* ...
Length = 995
Score = 29.1 bits (66), Expect = 1.5
Identities = 11/112 (9%), Positives = 30/112 (26%), Gaps = 7/112 (6%)
Query: 102 MLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQA 161
M +G + A+ + ++ + A +
Sbjct: 839 MAIGGY-VGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEP 897
Query: 162 S--AFTIF-FFEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHI 210
A ++ E + + + Q R + WL+ ++ ++H
Sbjct: 898 MTMALSVLVTIEMCN--ALNSLSE-NQSLMRMPPWVNIWLLGSICLSMSLHF 946
>2zxe_A Na, K-ATPase alpha subunit; membrane protein, ION pump, ATPase, K+
binding, haloacid dehydrogenease superfamily, phosphate
analogue; HET: CLR NAG NDG; 2.40A {Squalus acanthias}
PDB: 3a3y_A* 3b8e_A* 3kdp_A* 3n2f_A* 3n23_A* 1mo7_A
1mo8_A* 1q3i_A
Length = 1028
Score = 29.1 bits (66), Expect = 1.9
Identities = 23/134 (17%), Positives = 39/134 (29%), Gaps = 21/134 (15%)
Query: 90 TAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTA 149
T L S + IQA +F L+ +GF R
Sbjct: 846 TDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPMDLIGKRVRWDDRWISDVED 905
Query: 150 S----WMLVGVVAIQASAFTIFF-----FEWLSPSGFDMKTTALQPSHRFSLFRT----Y 196
S W ++ + T FF +W K + R S+F+
Sbjct: 906 SFGQQWTYEQRKIVEFTCHTSFFISIVVVQWAD--LIICK------TRRNSIFQQGMKNK 957
Query: 197 WLVWAVLFQAAVHI 210
L++ + + A+
Sbjct: 958 ILIFGLFEETALAA 971
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.0 bits (61), Expect = 2.2
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 26/56 (46%)
Query: 7 QHESLKKKRKLLTVYLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRE 62
+ ++LKK + L +Y AD D A +L I + E
Sbjct: 18 EKQALKKLQASLKLY-------------------AD------DSA-PALAIKATME 47
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 28.6 bits (65), Expect = 2.4
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 83 RTGIISPTAFLEP 95
RTG I+P A LEP
Sbjct: 333 RTGAITPVARLEP 345
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 28.2 bits (64), Expect = 3.0
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 83 RTGIISPTAFLEP 95
RTG ++P LEP
Sbjct: 331 RTGRVTPVGVLEP 343
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 28.3 bits (64), Expect = 3.3
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 83 RTGIISPTAFLEP 95
RTG I+P AF+ P
Sbjct: 343 RTGRITPFAFMTP 355
>3b46_A Aminotransferase BNA3; kynurenine aminotransferase, LLP, PLP,
cytoplasm, mitochondrion, pyridoxal phosphate; HET: LLP;
2.00A {Saccharomyces cerevisiae}
Length = 447
Score = 27.3 bits (61), Expect = 5.4
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 118 FFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWML--VGVVAIQASAF 164
+F + S + + Y + F + W++ +GVVAI + F
Sbjct: 361 YFVLVDFSKVKIPEDYPYPEEILNKGKDFRISHWLINELGVVAIPPTEF 409
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
0.326 0.136 0.423
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: 4,135,209
Number of extensions: 247252
Number of successful extensions: 725
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 61
Length of query: 261
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 169
Effective length of database: 4,133,061
Effective search space: 698487309
Effective search space used: 698487309
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.3 bits)