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)