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)