RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254780170|ref|YP_003064583.1| cationic amino acid ABC
transporter, periplasmic binding protein [Candidatus Liberibacter
asiaticus str. psy62]
         (342 letters)



>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 =  108 bits (270), Expect = 2e-24
 Identities = 36/228 (15%), Positives = 76/228 (33%), Gaps = 8/228 (3%)

Query: 17  FTSFSTNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPS 76
            + F+T         K   +K G +   V     + +G + GFD+D   A+         
Sbjct: 4   RSHFATQKDQWQTYTKEKKIKIGFDATFVPMGYEEKDGSYIGFDIDLANAVFKLY---GI 60

Query: 77  KIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKG 136
            +++  ++   +   L++  ID++      T  R+ S    F      + Q  +  K  G
Sbjct: 61  DVEWQAIDWDMKETELKNGTIDLIWNGYSVTDERKQS--ADFTEPYMVNEQVLVTKKSSG 118

Query: 137 ISSVSQLSGASICVQAGTTTELTLA---DYFKAHNMKYHPIVFERVEEIDAAYRAHRCDA 193
           I SV+ ++G ++  QAG++            K        + +    +      + R D 
Sbjct: 119 IDSVAGMAGKTLGAQAGSSGYDAFNASPKILKDVVANQKVVQYSTFTQALIDLNSGRIDG 178

Query: 194 YTGDISALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
              D          +    ++ ++P        A    + D      +
Sbjct: 179 LLIDRVYANYYLEKSGVLDQYNVMPAGYEGESFAVGARKVDKTLIKKI 226


>2vha_A Periplasmic binding transport protein; periplasmic binding protein,
           ligand binding, ultrahigh resolution; HET: GLU; 1.0A
           {Shigella flexneri} PDB: 2ia4_A*
          Length = 287

 Score = 95.1 bits (235), Expect = 2e-20
 Identities = 45/235 (19%), Positives = 88/235 (37%), Gaps = 6/235 (2%)

Query: 24  ASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPS----KIQ 79
            S L  I K G +  G     V F+         G+  D+  A+  A+    +    +++
Sbjct: 7   GSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVK 66

Query: 80  YLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISS 139
            +P+ ++ R   LQ+   D    +T   +  E     AF    +  G   +  K   I  
Sbjct: 67  LIPITSQNRIPLLQNGTFDFECGSTTNNV--ERQKQAAFSDTIFVVGTRLLTKKGGDIKD 124

Query: 140 VSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDIS 199
            + L G ++ V +GTT+E+ L    +   M    I  +   +      + R  A+  D +
Sbjct: 125 FADLKGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDA 184

Query: 200 ALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEEL 254
            L   +    +P    I+    S+      + + D ++  ++  T   + T+ E 
Sbjct: 185 LLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEA 239


>1xt8_A Putative amino-acid transporter periplasmic solute-binding protein;
           ABC transport, cysteine uptake, spine, structural
           genomics; 2.00A {Campylobacter jejuni} SCOP: c.94.1.1
          Length = 292

 Score = 88.6 bits (218), Expect = 2e-18
 Identities = 58/256 (22%), Positives = 110/256 (42%), Gaps = 11/256 (4%)

Query: 18  TSFSTNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSK 77
            S S   + L  IK+ G ++ G+      F  V   G+ +G+D+   + ++  +F D +K
Sbjct: 28  NSDSKTLNSLDKIKQNGVVRIGVFGDKPPFGYVDEKGNNQGYDIALAKRIAKELFGDENK 87

Query: 78  IQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGI 137
           +Q++ + A  R   L+S ++DI+  N   T  R     + F         G  + K   I
Sbjct: 88  VQFVLVEAANRVEFLKSNKVDIILANFTQTPQRAEQ--VDFCSPYMKVALGVAVPKDSNI 145

Query: 138 SSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD 197
           +SV  L   ++ +  GTT +     YF  +      + +++  E  AA    R DA + D
Sbjct: 146 TSVEDLKDKTLLLNKGTTAD----AYFTQNYPNIKTLKYDQNTETFAALMDKRGDALSHD 201

Query: 198 ISALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEELGIT 257
            + L+A    +  P   + + ++ +K  +APA+ +GD E    +      ++   +    
Sbjct: 202 NTLLFAWVKDH--PDFKMGIKELGNKDVIAPAVKKGDKELKEFIDN---LIIKLGQEQFF 256

Query: 258 QKNINQVSKDTTNPDV 273
            K  ++  K     DV
Sbjct: 257 HKAYDETLKAHFGDDV 272


>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 = 79.6 bits (195), Expect = 1e-15
 Identities = 36/211 (17%), Positives = 72/211 (34%), Gaps = 11/211 (5%)

Query: 36  LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
           ++ G +T    F+   A G++ GFD+D    +   +     K  ++  +      +L++K
Sbjct: 6   VRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQV---KCTWVASDFDALIPSLKAK 62

Query: 96  QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTT 155
           +ID +  +   T  R+  +      +   D +           ++  L G  + V  G+T
Sbjct: 63  KIDAIISSLSITDKRQQEI-AFSDKLYAADSRLIAAKGSPIQPTLESLKGKHVGVLQGST 121

Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHV 215
            E    D ++   +      +   + I +   A R DA   D  A     L      E+ 
Sbjct: 122 QEAYANDNWRTKGVDVVA--YANQDLIYSDLTAGRLDAALQDEVAASEGFLKQPAGKEYA 179

Query: 216 ILPDIISKSP-----LAPAIIQGDTEWYNIV 241
                +             + + DTE     
Sbjct: 180 FAGPSVKDKKYFGDGTGVGLRKDDTELKAAF 210


>3g41_A Amino acid ABC transporter, periplasmic amino acid-binding protein;
           aminoacid transporter, structural genomics, bacabs EU
           FP6 programme; HET: ARG; 2.10A {Chlamydophila
           pneumoniae}
          Length = 246

 Score = 79.2 bits (194), Expect = 1e-15
 Identities = 34/213 (15%), Positives = 63/213 (29%), Gaps = 9/213 (4%)

Query: 30  IKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERF 89
           I +      G N     F  V A G+  GFD+D  +A+S  +     +++          
Sbjct: 6   IDRNRIWIVGTNATYPPFEYVDAQGEVVGFDIDLAKAISEKL---GKQLEVREFAFDALI 62

Query: 90  LALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASIC 149
           L L+  +ID +      T  R+  + L             +  +      +     +S+ 
Sbjct: 63  LNLKKHRIDAILAGMSITPSRQKEIALLPYYGDEVQELMVVSKRSLETPVLPLTQYSSVA 122

Query: 150 VQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD-ISALYALKLTN 208
           VQ GT  E  L          +         E+    R  +      +       LK   
Sbjct: 123 VQTGTYQEHYLLSQPGICVRSFDST-----LEVIMEVRYGKSPVAVLEPSVGRVVLKDFP 177

Query: 209 DRPSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
           +  +  + LP           + +   E    +
Sbjct: 178 NLVATRLELPPECWVLGCGLGVAKDRPEEIQTI 210


>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
           signaling protein; 2.04A {Bordetella pertussis} PDB:
           3mpl_A
          Length = 267

 Score = 76.6 bits (188), Expect = 8e-15
 Identities = 26/212 (12%), Positives = 55/212 (25%), Gaps = 8/212 (3%)

Query: 30  IKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERF 89
           +     +K  +      F   + +  + G      + L      D   I       +E  
Sbjct: 28  MADHPVVKVAVLNLFAPFTLFRTDEQFGGISAAVLQLLQLRTGLDFEIIGVDT--VEELI 85

Query: 90  LALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASIC 149
             L+S + D+          RE  L  + RP                      L G ++ 
Sbjct: 86  AKLRSGEADMAGALF-VNSARESFLSFS-RPYVRNGMVIVTRQDPDAPVDADHLDGRTVA 143

Query: 150 VQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTND 209
           +   +          +    +   +  +   E        + DA      +         
Sbjct: 144 LVRNSAAI----PLLQRRYPQAKVVTADNPSEAMLMVANGQADAVVQTQISASYYVNRYF 199

Query: 210 RPSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
                +     +  + +A A  +G TE  +I+
Sbjct: 200 AGKLRIASALDLPPAEIALATTRGQTELMSIL 231


>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
           transport, ABC transport, virulence factor, receptor;
           1.49A {Campylobacter jejuni}
          Length = 259

 Score = 75.6 bits (184), Expect = 2e-14
 Identities = 59/245 (24%), Positives = 103/245 (42%), Gaps = 11/245 (4%)

Query: 1   MYKDFFVSILCLII---LFFTSFSTNASILGDIKKRGFLKCGINTGLVGFAEV-KANGDW 56
           +++   + +    +   + F++ +     L  IK +G L  G+   +  +A + +A G+ 
Sbjct: 2   VFRKSLLKLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEI 61

Query: 57  KGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGL 116
           KGF+VD  + L+ +I  D  KI+ + +NAK R   L +  +D +      T  R+     
Sbjct: 62  KGFEVDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRI--Y 119

Query: 117 AFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVF 176
            F    Y D  G ++ K+K   S++ + GA+I V    TT+  + +  K   +      F
Sbjct: 120 NFSEPYYQDAIGLLVLKEKKYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEF 179

Query: 177 ERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTE 236
                I AA  A R DA++ D S L           +  ILPD            + D  
Sbjct: 180 PDYPSIKAALDAKRVDAFSVDKSILLGY-----VDDKSEILPDSFEPQSYGIVTKKDDPA 234

Query: 237 WYNIV 241
           +   V
Sbjct: 235 FAKYV 239


>1ii5_A Hypothetical protein SLR1257; membrane protein; HET: GLU; 1.60A
           {Synechocystis SP} SCOP: c.94.1.1 PDB: 1iit_A 1iiw_A
          Length = 233

 Score = 74.3 bits (181), Expect = 4e-14
 Identities = 34/209 (16%), Positives = 65/209 (31%), Gaps = 13/209 (6%)

Query: 36  LKCGINTGL-VGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQS 94
           LK G+       F     N  + G  +D  RA++ +   +   ++   ++      A+  
Sbjct: 6   LKVGVVGNPPFVFYGEGKNAAFTGISLDVWRAVAESQKWNSEYVRQNSIS--AGITAVAE 63

Query: 95  KQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFI--MHKKKGISSVSQLSGASICVQA 152
            ++DIL      T  R    G+ F    +  G G +          SV  L    + V  
Sbjct: 64  GELDILIGPISVTPERAAIEGITFTQPYFSSGIGLLIPGTATPLFRSVGDLKNKEVAVVR 123

Query: 153 GTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPS 212
            TT          A+  +        +       +  + +A   D  AL      N   +
Sbjct: 124 DTTAVD------WANFYQADVRETNNLTAAITLLQKKQVEAVMFDRPALIYYTRQNPNLN 177

Query: 213 EHVILPDIISKSPLAPAIIQGDTEWYNIV 241
             V     +S  P     ++ ++     +
Sbjct: 178 LEVT-EIRVSLEPYGFV-LKENSPLQKTI 204


>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 = 73.8 bits (180), Expect = 5e-14
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 16/213 (7%)

Query: 36  LKCGINTGLVGFAEVKA-NGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQS 94
           L  G +     F      N    GFD+D  + +   +        +      + F AL++
Sbjct: 5   LTIGTSKFNPPFEVWSGNNSSLYGFDIDLMQEICRRLHA---TCTFEAYIFDDLFPALKN 61

Query: 95  KQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGT 154
           +++D++  +   T  R+      F          +I      IS+   L G  I V+ GT
Sbjct: 62  REVDLVIASMIITDERKKH--FIFSLPYMESNSQYITTVDSKISTFDDLHGKKIGVRKGT 119

Query: 155 TTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEH 214
                      + N     I +E ++++      ++ DA   D  A      +     + 
Sbjct: 120 PYA----RQVLSENRNNQVIFYELIQDMLLGLSNNQVDASLMDYEAAKYWMASEPYAYKL 175

Query: 215 V------ILPDIISKSPLAPAIIQGDTEWYNIV 241
           +      I   I      +             +
Sbjct: 176 IGKKYKLIGKKISIGEGYSIMANPDQFVLIKKI 208


>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
           phosphoprotein, transferase; 2.40A {Geobacter
           sulfurreducens}
          Length = 234

 Score = 73.1 bits (178), Expect = 1e-13
 Identities = 32/211 (15%), Positives = 68/211 (32%), Gaps = 10/211 (4%)

Query: 31  KKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFL 90
            +   +  G +     +  +  NG   G++V+  RA++  +      +++      E F 
Sbjct: 8   DRHRTIVVGGDRDYPPYEFIDQNGKPAGYNVELTRAIAEVM---GMTVEFRLGAWSEMFS 64

Query: 91  ALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICV 150
           AL+S ++D+  +   W+  R   +     P T      F        + +  L G  + +
Sbjct: 65  ALKSGRVDV-LQGISWSEKRARQIDFT-PPHTIVYHAIFARRDSPPAAGLEDLRGRKVAL 122

Query: 151 QAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDR 210
                      +Y          ++     +      A  CD     +       +  +R
Sbjct: 123 HRDGIMH----EYLAERGYGKDLVLTPTPADALRLLAAGGCDYAVVAMVPGMY-IIRENR 177

Query: 211 PSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
            +  V +   I+      A+ QGD E     
Sbjct: 178 LTNLVPVARSIAAQRYGYAVRQGDAELLARF 208


>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 = 71.9 bits (175), Expect = 2e-13
 Identities = 45/220 (20%), Positives = 78/220 (35%), Gaps = 12/220 (5%)

Query: 36  LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
           L    +T  V F E K    + GFDVD   A++  +       +  P++      ALQ+K
Sbjct: 5   LVVATDTAFVPF-EFKQGDLYVGFDVDLWAAIAKEL---KLDYELKPMDFSGIIPALQTK 60

Query: 96  QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKK-KGISSVSQLSGASICVQAGT 154
            +D+       T  R+ +  + F    Y  G   ++      + SV  L G  + V++GT
Sbjct: 61  NVDLALAGITITDERKKA--IDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGT 118

Query: 155 TTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEH 214
            +     DY KA+        F  ++        +R DA   D   +     T     + 
Sbjct: 119 GSV----DYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNG-QF 173

Query: 215 VILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEEL 254
             + D +       A  +G  E  + V+     +      
Sbjct: 174 KAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTY 213


>3i6v_A Periplasmic His/Glu/Gln/Arg/opine family-binding protein;
           structural genomics, transporter, PSI-2, protein
           structure initiative; HET: LYS; 2.00A {Silicibacter
           pomeroyi}
          Length = 232

 Score = 71.4 bits (174), Expect = 3e-13
 Identities = 30/206 (14%), Positives = 55/206 (26%), Gaps = 17/206 (8%)

Query: 36  LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
           ++ G       +  +   G+  GF+ +    L           +++  +       L S 
Sbjct: 7   VRMGTEGAYPPYNFINDAGEVDGFERELGDELCKRAG---LTCEWVKNDWDSIIPNLVSG 63

Query: 96  QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTT 155
             D +      T  R+    + F            +    G    + LSG  +  Q  T 
Sbjct: 64  NYDTIIAGMSITDERDEV--IDFTQNYIPPTASSYVATSDG----ADLSG-IVAAQTATI 116

Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHV 215
                             + F   EE  AA R    DA   D   L  +   +       
Sbjct: 117 Q------AGYIAESGATLVEFATPEETIAAVRNGEADAVFADRDYLVPIVAESG-GELMF 169

Query: 216 ILPDIISKSPLAPAIIQGDTEWYNIV 241
           +  D+     +   + + D E     
Sbjct: 170 VGDDVPLGGGVGMGLRESDGELRGKF 195


>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 = 68.6 bits (166), Expect = 2e-12
 Identities = 29/222 (13%), Positives = 74/222 (33%), Gaps = 5/222 (2%)

Query: 21  STNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQY 80
           + + +     KK   +  G  T       +   GD  G+DV+  + L   +     K  +
Sbjct: 3   AGSQTTGAGQKKVQTITVGTGTQFPNICFIDEKGDLTGYDVELIKELDKRLPHY--KFTF 60

Query: 81  LPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSV 140
             +      ++L   ++DI++   + +  RE           +F  +  ++     I  +
Sbjct: 61  KTMEFSNLLVSLGQHKVDIVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQNNDTIRGI 120

Query: 141 SQLSGASICVQAGTTTELTLADYFKAHNMKYHPI-VFERVEEIDAAYRAHRCDAYTGDIS 199
             L G  +   A +   L L  + + +   +      +   E     ++ R DA      
Sbjct: 121 EDLKGKRVITSATSNGALVLKKWNEDNGRPFEIAYEGQGANETANQLKSGRADATISTPF 180

Query: 200 ALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
           A+           +   + +++S + +     + +    + +
Sbjct: 181 AVDFQN--KTSTIKEKTVGNVLSNAKVYFMFNKNEQTLSDDI 220


>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 = 68.4 bits (166), Expect = 2e-12
 Identities = 29/236 (12%), Positives = 59/236 (25%), Gaps = 21/236 (8%)

Query: 18  TSFSTNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAI------ 71
                    +     +  +  G N    G           GF +D    L+  +      
Sbjct: 25  DGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEV 84

Query: 72  --------FDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITY 123
                                       L S Q D++         R     + F     
Sbjct: 85  HLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQY--IEFSKPFK 142

Query: 124 FDGQGFIMHKKKGISSVSQL--SGASICVQAGTTTELTLADYFKAHNMK---YHPIVFER 178
           + G   ++ K   I+ ++       S      T  + ++  YF+        Y  +    
Sbjct: 143 YQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHN 202

Query: 179 VEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGD 234
            E    A +A R +     I     L+    +  + V   ++  +S     + +  
Sbjct: 203 YESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDS 258


>3k4u_A Binding component of ABC transporter; structural genomics, protein
           structure initiative, NEW YORK structural genomix
           research consortium; HET: LYS; 2.62A {Wolinella
           succinogenes}
          Length = 245

 Score = 66.3 bits (160), Expect = 1e-11
 Identities = 39/212 (18%), Positives = 77/212 (36%), Gaps = 6/212 (2%)

Query: 30  IKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERF 89
           +  RG L+ G+  G + F      G+  GFDVD  R ++ A+     K++ +P +     
Sbjct: 1   MSLRGELRVGLEPGYLPFEMKDKKGNVIGFDVDLAREMAKAM---GVKLKLVPTSWDGLI 57

Query: 90  LALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASIC 149
             L +++ DI+      +  +E +L + F       GQ  ++ K       S        
Sbjct: 58  PGLVTEKFDIIISGMTIS--QERNLRVNFVEPYIVVGQSLLVKKGLEKGVKSYKDLDKPE 115

Query: 150 VQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTND 209
           +   T   ++     K          ++   E        + D +  D+    A      
Sbjct: 116 LTLVTKFGVSAEYAAKRLFKNAKLKTYDTEAEAVQEVLNGKADMFIFDLPFNVAFMAQKG 175

Query: 210 RPSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
           +     +    ++  PL  AI +GD ++ N +
Sbjct: 176 QGYLVHL-DTSLTYEPLGWAIKKGDPDFLNWL 206


>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic
           protein, protein binding, transport protein; 1.92A
           {Chlamydia trachomatis}
          Length = 242

 Score = 62.7 bits (151), Expect = 1e-10
 Identities = 33/207 (15%), Positives = 58/207 (28%), Gaps = 10/207 (4%)

Query: 36  LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
              G N     F  V   G+  GFD+D  R +S+ +      +     +     L L+  
Sbjct: 13  FIVGTNATYPPFEFVDKRGEVVGFDIDLAREISNKLGK---TLDVREFSFDALILNLKQH 69

Query: 96  QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTT 155
           +ID +      T  R     L             ++ K +    +      S+ VQ GT 
Sbjct: 70  RIDAVITGMSITPSRLKE-ILMIPYYGEEIKHLVLVFKGENKHPLPLTQYRSVAVQTGTY 128

Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD-ISALYALKLTNDRPSEH 214
            E  L    + H   +         E+       +      +   A   LK      +  
Sbjct: 129 QEAYLQSLSEVHIRSFDST-----LEVLMEVMHGKSPVAVLEPSIAQVVLKDFPALSTAT 183

Query: 215 VILPDIISKSPLAPAIIQGDTEWYNIV 241
           + LP+          +          +
Sbjct: 184 IDLPEDQWVLGYGIGVASDRPALALKI 210


>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginosa PA01,structural
           genomics, PSI-2, protein structure initiative; HET: EPE;
           1.66A {Pseudomonas aeruginosa}
          Length = 239

 Score = 56.4 bits (134), Expect = 9e-09
 Identities = 27/221 (12%), Positives = 59/221 (26%), Gaps = 7/221 (3%)

Query: 21  STNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQY 80
           +   S L  I + G L+         F+     G + GFDVD  + L+ ++      +  
Sbjct: 2   NAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESLGAKLVVV-- 59

Query: 81  LPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSV 140
            P +           + DI        L R+     +   +        +  ++    ++
Sbjct: 60  -PTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEARFQTL 118

Query: 141 SQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISA 200
            Q+    +                 A        +    + +    +     A      A
Sbjct: 119 EQIDQPGVTAIVNPGGTN----EKFARANLKKARILVHPDNVTIFQQIVDGKADLMMTDA 174

Query: 201 LYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
           + A   +   P    + P           ++  D  +   V
Sbjct: 175 IEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDEAFKRYV 215


>2q88_A EHUB, putative ABC transporter amino acid-binding protein;
           substrate-binding protein, compatible solues,
           osmoprotection; HET: 4CS; 1.90A {Sinorhizobium meliloti}
           PDB: 2q89_A*
          Length = 257

 Score = 53.6 bits (127), Expect = 6e-08
 Identities = 31/227 (13%), Positives = 67/227 (29%), Gaps = 4/227 (1%)

Query: 23  NASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLP 82
           + + L ++K++GF +  I      F  V A+G   G   D  R +   +    + +    
Sbjct: 2   DENKLEELKEQGFARIAIANE-PPFTAVGADGKVSGAAPDVAREIFKRL--GVADVVASI 58

Query: 83  LNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQ 142
                    LQ+ + D ++        R  ++  +   +   +          G+ S   
Sbjct: 59  SEYGAMIPGLQAGRHDAITAGLFMKPERCAAVAYSQPILCDAEAFALKKGNPLGLKSYKD 118

Query: 143 LSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD-ISAL 201
           ++                    +A   +   IV    +      +  R D Y+   +S  
Sbjct: 119 IADNPDAKIGAPGGGTEEKLALEAGVPRDRVIVVPDGQSGLKMLQDGRIDVYSLPVLSIN 178

Query: 202 YALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAM 248
             +   ND   E +   +         A  +GD    +        +
Sbjct: 179 DLVSKANDPNVEVLAPVEGAPVYCDGAAFRKGDEALRDAFDVELAKL 225


>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 = 53.2 bits (126), Expect = 8e-08
 Identities = 36/260 (13%), Positives = 75/260 (28%), Gaps = 14/260 (5%)

Query: 21  STNASILGDIKKRGFLKCGINTGLVGFA---EVKANGDWKGFDVDFCRALSSAIFDDPSK 77
            +  +    IK +G +    +  L   +       +    G++V+  R  +  +      
Sbjct: 8   DSKDTGWEQIKDKGKIVVATSGTLYPTSYHDTDSGSDKLTGYEVEVVREAAKRLGLKVEF 67

Query: 78  IQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGI 137
                +       A+ S Q+D  + + D T  RE     +      +           GI
Sbjct: 68  K---EMGIDGMLTAVNSGQVDAAANDIDVTKDREEKFAFSTPYKYSYGTAIVRKDDLSGI 124

Query: 138 SSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD 197
            ++  L G      A T       +  + +  K         E+        R D    D
Sbjct: 125 KTLKDLKGKKAAGAATTVYM----EVARKYGAKEVIYDNATNEQYLKDVANGRTDVILND 180

Query: 198 ISALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEELG-I 256
                         +  +        +  A  + + +      ++     M     L  +
Sbjct: 181 YYLQTLALAAFPDLNITIHPDIKYMPNKQALVMKKSNAALQKKMNEALKEMSKDGSLTKL 240

Query: 257 TQKNINQ--VSKDTTNPDVQ 274
           +++  N+  VSK   + DVQ
Sbjct: 241 SKQFFNKADVSK-KIDADVQ 259


>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system,
           thermophilic bacterium, transport protein; HET: LYS;
           1.79A {Geobacillus stearothermophilus} PDB: 2q2a_A*
           2q2c_A*
          Length = 272

 Score = 50.8 bits (120), Expect = 5e-07
 Identities = 43/221 (19%), Positives = 68/221 (30%), Gaps = 9/221 (4%)

Query: 21  STNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQY 80
           ++++S       +  +  G +     F E    G   GFDVD   A+  A        + 
Sbjct: 29  TSSSSGGDGGATKKKVVVGTDAAFAPF-EYMQKGKIVGFDVDLLDAVMKAAGL---DYEL 84

Query: 81  LPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSV 140
             +     F +LQSK++D+       T   E      F    +   Q  ++ +   + + 
Sbjct: 85  KNIGWDPLFASLQSKEVDMGISGITIT--DERKQSYDFSDPYFEATQVILVKQGSPVKNA 142

Query: 141 SQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISA 200
             L G +I VQ  TT +       K      H   FE              DA   D + 
Sbjct: 143 LDLKGKTIGVQNATTGQ---EAAEKLFGKGPHIKKFETTVVAIMELLNGGVDAVITDNAV 199

Query: 201 LYALKLTNDRPSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
                  N      VI       S     I   ++E    V
Sbjct: 200 ANEYVKNNPNKKLQVIEDPKNFASEYYGMIFPKNSELKAKV 240


>2rc8_A Glutamate [NMDA] receptor subunit 3A; membrane protein, alternative
           splicing, calcium, cell junction, coiled coil,
           glycoprotein, ION transport; 1.45A {Rattus norvegicus}
           PDB: 2rc7_A 2rc9_A 2rca_A 2rcb_A
          Length = 294

 Score = 50.1 bits (118), Expect = 7e-07
 Identities = 32/259 (12%), Positives = 72/259 (27%), Gaps = 27/259 (10%)

Query: 1   MYKDFFVSILCLIILFFTSFSTNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFD 60
             ++     LC          TN S    +  R F     +   V     K      G+ 
Sbjct: 19  FTREVDDEGLCPAGQLCLDPMTNDS---SMLDRLFSSLHSSNDTVPI---KFKKCCYGYC 72

Query: 61  VDFCRALSSAI--------FDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREI 112
           +D    L+  +          D     +   +       L S   ++   +      R  
Sbjct: 73  IDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQ 132

Query: 113 SLGLAFRPITYFDGQGFIMHKKKG---ISSVSQLSGASICVQAGTTTELTLADYFKAHNM 169
              + F    +    G ++  +          +L   S   + GT  E +  DY +    
Sbjct: 133 V--IDFTSPFFSTSLGILVRTRGTELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFP 190

Query: 170 K-YHPIVFERVEEIDAAYRA-----HRCDAYTGDISALYALKLTNDRPSEHVILPDIISK 223
           + +  +    V       +       + DA+  D + L    ++ D   + + +    + 
Sbjct: 191 EMHEYMRRYNVPATPDGVQYLKNDPEKLDAFIMDKALLDYE-VSIDADCKLLTVGKPFAI 249

Query: 224 SPLAPAIIQGDTEWYNIVS 242
                  +  ++   + +S
Sbjct: 250 EGYGIG-LPPNSPLTSNIS 267


>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 = 47.3 bits (111), Expect = 5e-06
 Identities = 28/206 (13%), Positives = 58/206 (28%), Gaps = 28/206 (13%)

Query: 52  ANGDWKGFDVDFCRALSSAI----------FDDPSKIQYLPLNAKERFLALQSKQIDILS 101
            N  ++G+ VD    ++                                 L   + DI  
Sbjct: 28  GNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAI 87

Query: 102 RNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLA 161
                TL+RE    + F       G   ++ K   I S   LS  +  +  GT    +  
Sbjct: 88  APLTITLVREEV--IDFSKPFMSLGISIMIKKGTPIESAEDLSKQTE-IAYGTLDSGSTK 144

Query: 162 DYFKAHNMKYHP-------------IVFERVEEIDAAYRAHRCDAYTGDISALYALKLTN 208
           ++F+   +                  V    E +    ++    AY  + +    ++   
Sbjct: 145 EFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIE--Q 202

Query: 209 DRPSEHVILPDIISKSPLAPAIIQGD 234
            +P + + +   +       A  +G 
Sbjct: 203 RKPCDTMKVGGNLDSKGYGIATPKGS 228


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 46.5 bits (110), Expect = 9e-06
 Identities = 79/408 (19%), Positives = 120/408 (29%), Gaps = 178/408 (43%)

Query: 4   DFFVSI---LCLI-ILFFTSFSTNASIL----GDIKKRGFLKCGINTG----LVGFAEVK 51
           D+ +SI     LI ++    +   A +L    G++  R +LK G  TG    LV    + 
Sbjct: 229 DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGEL--RSYLK-GA-TGHSQGLVTAVAIA 284

Query: 52  ANGDWKGFD--------VDF---CR--------ALSSAIFDD--------PS---KIQYL 81
               W+ F         V F    R        +L  +I +D        PS    I  L
Sbjct: 285 ETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL 344

Query: 82  PLNAKERFLA-----L-QSKQIDILSRNTDWTLLREI-------SL-GLA--FRPITYFD 125
                + ++      L   KQ++I   N      + +       SL GL    R      
Sbjct: 345 TQEQVQDYVNKTNSHLPAGKQVEISLVNGA----KNLVVSGPPQSLYGLNLTLRKAKAPS 400

Query: 126 G--QGFIMHKKKG---------ISSV--SQ-LSGASICVQAGTTTELTLADY------FK 165
           G  Q  I   ++          ++S   S  L  A         ++L   D       F 
Sbjct: 401 GLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPA---------SDLINKDLVKNNVSFN 451

Query: 166 AHNMKYHPIVFERVEEIDAAYRAHRCDAYTG-DISALYALKLTNDRPSEHVILPDIISKS 224
           A +++  P V+               D + G D+  L          S   I   I+   
Sbjct: 452 AKDIQI-P-VY---------------DTFDGSDLRVL----------SGS-ISERIVD-- 481

Query: 225 PLAPAIIQGDTEWYNIVSWTHYAMVTAEELGITQKNINQVSKDTTNPDVQRFL--GIDKS 282
                II         V W                        TT       L  G   +
Sbjct: 482 ----CII---RL---PVKWE----------------------TTTQFKATHILDFGPGGA 509

Query: 283 SNIGEALGLT---KDWT-YRIIRHMGNYGEMFDRNLGNQSELKIPRGY 326
           S +G    LT   KD T  R+I  +   G + D N     +     G+
Sbjct: 510 SGLG---VLTHRNKDGTGVRVI--VA--GTL-DINP--DDDY----GF 543



 Score = 41.5 bits (97), Expect = 3e-04
 Identities = 43/258 (16%), Positives = 78/258 (30%), Gaps = 96/258 (37%)

Query: 62  DFCRAL-----SSAIFDDP-SKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLG 115
            F + L       A  D+P +  + +      +FL   S  ++         +L    L 
Sbjct: 36  QFNKILPEPTEGFAADDEPTTPAELV-----GKFLGYVSSLVEPSKVGQFDQVLNLC-LT 89

Query: 116 LAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELT----LADYFKAHNMKY 171
             F    Y +G    +H     +  ++L   +       TT +     + +Y  A  M  
Sbjct: 90  -EFE-NCYLEGND--IH-----ALAAKLLQEN------DTTLVKTKELIKNYITARIMAK 134

Query: 172 HPIVFERVEEIDAAYRAHRCDAYTGDISALYAL----KLTND------------RPSEHV 215
            P   ++     A +RA       G+   L A+      T+D                  
Sbjct: 135 RPF--DKKSN-SALFRA----VGEGNAQ-LVAIFGGQGNTDDYFEELRDLYQTYHV---- 182

Query: 216 ILPDIISK-SPLAPAIIQGDTEW---Y----NIVSW------------------------ 243
           ++ D+I   +     +I+   +    +    NI+ W                        
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242

Query: 244 ----THYAMVTAEELGIT 257
                HY +VTA+ LG T
Sbjct: 243 VIQLAHY-VVTAKLLGFT 259


>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*
          Length = 284

 Score = 44.2 bits (103), Expect = 4e-05
 Identities = 22/200 (11%), Positives = 55/200 (27%), Gaps = 20/200 (10%)

Query: 53  NGDWKGFDVDFCRALSSAI--------FDDPSKIQYLPLNAKERFLALQSKQIDILSRNT 104
               KGF +D  + LS  +          +    + +          +  ++  +   + 
Sbjct: 54  KKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSL 113

Query: 105 DWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGAS---------ICVQAGTT 155
                 E S  + F       G   ++ +   ++ +S                      +
Sbjct: 114 TIN--EERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFGTVPNGS 171

Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD-ISALYALKLTNDRPSEH 214
           TE  + + +   +          VE+   + +  + DA+  D     Y            
Sbjct: 172 TERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVT 231

Query: 215 VILPDIISKSPLAPAIIQGD 234
           +    I + +    A+ +G 
Sbjct: 232 IGSGYIFATTGYGIALQKGS 251


>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
           binding domain, transport protein; HET: GLU; 2.10A
           {Nostoc punctiforme pcc 73102}
          Length = 228

 Score = 42.4 bits (98), Expect = 2e-04
 Identities = 29/210 (13%), Positives = 67/210 (31%), Gaps = 16/210 (7%)

Query: 49  EVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTL 108
            +   G+  GF +D  R++++ I  +   I+Y  +      L    K   +       ++
Sbjct: 16  VLSNKGELSGFSIDLWRSIATQIGIESKLIEYSSVPE----LISAIKDNKVNLGIAAISI 71

Query: 109 LREISLGLAFRPITYFDGQGFIMHKKKGIS----SVSQLSGASICVQAGTTTELTLADYF 164
             E      F    +  G   ++   +  +    S+  L G  +   AG+T         
Sbjct: 72  TAEREQNFDFSLPIFASGLQIMVRNLESGTGDIRSIDDLPGKVVATTAGST------AAT 125

Query: 165 KAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPDIISKS 224
                    +   ++EE   A +  + DA   D   L        +  +  I+  I+ + 
Sbjct: 126 YLREHHISVLEVPKIEEAYKALQTKKADAVVFDAPVLLFYAANEGKG-KVEIVGSILREE 184

Query: 225 PLAPAIIQGDTEWYNIVSWTHYAMVTAEEL 254
                I+  ++ +   ++     +      
Sbjct: 185 SYG-IILPNNSPYRKPINQALLNLKENGTY 213


>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 = 40.0 bits (92), Expect = 7e-04
 Identities = 26/208 (12%), Positives = 56/208 (26%), Gaps = 17/208 (8%)

Query: 53  NGDWKGFDVDFCRALSSAI---------FDDPSKIQYLPLNAKERFLALQSKQIDILSRN 103
              ++GF +D   ALS+ +          D                  L  K+ DI    
Sbjct: 26  PKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISA 85

Query: 104 TDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLADY 163
              T   +    + F         G ++ +   I S+  LS     +  GT  +  +  +
Sbjct: 86  LTIT--PDRENVVDFTTRYMDYSVGVLLRRGTSIQSLQDLSK-QTDIPYGTVLDSAVYQH 142

Query: 164 FKAHNMKYHPIVFERVEEIDAAYRAH-RCDAYTGDISALYALKLTNDRPSEHVILPDIIS 222
            +   +          +      R++   +      + +  +K  N       +    + 
Sbjct: 143 VRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNY----AFVWDAAVL 198

Query: 223 KSPLAPAIIQGDTEWYNIVSWTHYAMVT 250
           +               N V+   Y +  
Sbjct: 199 EYVAINDPDCSFYTVGNTVADRGYGIAL 226


>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* 2i0c_A*
           3c31_A* 1txf_A* 3c32_A* 3c33_A* 3c34_A* 3c35_A* 3c36_A*
           2wky_A* ...
          Length = 259

 Score = 37.4 bits (85), Expect = 0.005
 Identities = 20/200 (10%), Positives = 48/200 (24%), Gaps = 21/200 (10%)

Query: 53  NGDWKGFDVDFCRALSSAI----------FDDPSKIQYLPLNAKERFLALQSKQIDILSR 102
           N  ++G+ +D  R LS+ +                   +          L   + D+   
Sbjct: 29  NDRFEGYCIDLLRELSTHLGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAV- 87

Query: 103 NTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLAD 162
                +       + F       G   +  K   I S   L+  +     G   +     
Sbjct: 88  -APLAITYVREEVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEY-GAVEDGATMT 145

Query: 163 YFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD--------ISALYALKLTNDRPSEH 214
           +FK   +  +  ++  +     +      +             +     ++    R    
Sbjct: 146 FFKRSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNL 205

Query: 215 VILPDIISKSPLAPAIIQGD 234
             +  +I           G 
Sbjct: 206 TQIGGLIDSKGYGVGTPMGS 225


>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 = 33.4 bits (75), Expect = 0.079
 Identities = 21/225 (9%), Positives = 50/225 (22%), Gaps = 46/225 (20%)

Query: 53  NGDWKGFDVDFCRALSSAI----------FDDPSKIQYLPLNAKERFLALQSKQIDILSR 102
           N  ++G+ +D  R LS+ +                   +          L   + D+   
Sbjct: 38  NDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLA-- 95

Query: 103 NTDWTLLREISLGLAFRPITYFDGQGFIMHKKKG-------------------------I 137
                +       + F       G   +  K  G                         I
Sbjct: 96  VAPLAITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNGGSLVPRGSERMESPI 155

Query: 138 SSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGD 197
            S   L+     ++ G   +     +FK   +  +  ++  +     +      +     
Sbjct: 156 DSADDLAK-QTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQR 214

Query: 198 --------ISALYALKLTNDRPSEHVILPDIISKSPLAPAIIQGD 234
                   +     ++    R      +  +I           G 
Sbjct: 215 VLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGS 259


>2i9f_A Nucleocapsid; structure, crystallography, assembly, viral protein;
           2.00A {Equine arteritis virus} SCOP: d.254.1.1
          Length = 69

 Score = 28.6 bits (63), Expect = 2.0
 Identities = 15/40 (37%), Positives = 22/40 (55%)

Query: 253 ELGITQKNINQVSKDTTNPDVQRFLGIDKSSNIGEALGLT 292
           E G  + ++NQ  + T + +VQRF  I   S   +A GLT
Sbjct: 9   EPGDLRHDLNQQERATLSSNVQRFFMIGHGSLTADAGGLT 48


>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein
           fold, OPPF, structural genomics, oxford protein
           production facility; 2.80A {Neisseria gonorrhoeae}
          Length = 141

 Score = 28.4 bits (63), Expect = 2.3
 Identities = 6/45 (13%), Positives = 16/45 (35%), Gaps = 6/45 (13%)

Query: 251 AEELGITQKNINQVSKDTTNPDVQRFLGIDKSSNIGEALGLTKDW 295
           A   G+ Q  ++++     +   +          +  ALG++   
Sbjct: 88  ATAAGLPQPYLSRIENSKQSLQDKTVQ------KLANALGVSPLE 126


>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid,
           structural genomics, PSI-2, protein structure
           initiative; NMR {Bacteroides thetaiotaomicron}
          Length = 77

 Score = 27.0 bits (59), Expect = 6.1
 Identities = 10/39 (25%), Positives = 22/39 (56%)

Query: 247 AMVTAEELGITQKNINQVSKDTTNPDVQRFLGIDKSSNI 285
           A   AEE+GI+++ +  + +  T P V +++   +S  +
Sbjct: 18  AKSVAEEMGISRQQLCNIEQSETAPVVVKYIAFLRSKGV 56


>1r8j_A KAIA; circadian clock protein; 2.03A {Synechococcus elongatus pcc
           7942} SCOP: a.186.1.1 c.23.1.5 PDB: 1m2e_A 1m2f_A
          Length = 289

 Score = 27.0 bits (60), Expect = 6.3
 Identities = 20/107 (18%), Positives = 38/107 (35%), Gaps = 9/107 (8%)

Query: 171 YHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPDIISKSPLAPAI 230
           Y   V E  E +    + HR          +  L L    PS   ++  +  +  + PAI
Sbjct: 34  YQLQVCESGEMLLEYAQTHR--------DQIDCLILVAANPSFRAVVQQLCFEGVVVPAI 85

Query: 231 IQGDTEWYNIVSWTHYAMVTAEELGITQKNINQVSKDTTNPDVQRFL 277
           + GD +  +        +  + EL +    + Q+     +  +  FL
Sbjct: 86  VVGDRDSEDPDEPAKEQLYHSAELHLGIHQLEQLP-YQVDAALAEFL 131


>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
           system, phosphoryltransferase, helix-turn-helix motif,
           transcription regulator; 3.20A {Streptococcus pneumoniae
           TIGR4}
          Length = 158

 Score = 27.0 bits (59), Expect = 7.2
 Identities = 5/45 (11%), Positives = 18/45 (40%), Gaps = 6/45 (13%)

Query: 251 AEELGITQKNINQVSKDTTNPDVQRFLGIDKSSNIGEALGLTKDW 295
           A  +GI++ ++++    T++   +          I +   ++   
Sbjct: 21  ARIVGISRNSLSRYENGTSSVSTELID------IICQKFNVSYVD 59


>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix,
           DNA-binding, transcription, transcription regulation;
           1.53A {Enterobacteria phage P22} SCOP: a.35.1.2
          Length = 68

 Score = 26.3 bits (58), Expect = 9.1
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 6/45 (13%)

Query: 251 AEELGITQKNINQVSKDTTNPDVQRFLGIDKSSNIGEALGLTKDW 295
            + +G++   I+Q  +  T P+ +  L       + +AL  + D+
Sbjct: 25  GKMVGVSNVAISQWERSETEPNGENLL------ALSKALQCSPDY 63


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.322    0.138    0.418 

Gapped
Lambda     K      H
   0.267   0.0539    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,030,231
Number of extensions: 135498
Number of successful extensions: 408
Number of sequences better than 10.0: 1
Number of HSP's gapped: 391
Number of HSP's successfully gapped: 41
Length of query: 342
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 249
Effective length of database: 3,438,538
Effective search space: 856195962
Effective search space used: 856195962
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: 57 (26.2 bits)