RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781112|ref|YP_003065525.1| putative amino acid-binding
periplasmic ABC transporter protein [Candidatus Liberibacter asiaticus
str. psy62]
(274 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 = 146 bits (368), Expect = 6e-36
Identities = 52/233 (22%), Positives = 99/233 (42%), Gaps = 14/233 (6%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+++G D + P + + G GFDIDL V + VE+ T L
Sbjct: 23 IKIGFDATFVPMGYE--EKDGSYIGFDIDLANAVFKLYGIDVEWQAIDWDMKETELKNGT 80
Query: 103 YDVLVNV-AITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D++ N ++T ER++ DF+ PY+ + +LV + I S + KT+ G+
Sbjct: 81 IDLIWNGYSVTDERKQSADFTEPYMVNEQVLVTKKS-SGIDSVAGMAGKTLGAQAGSSGY 139
Query: 162 RFAKE---------LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNL 212
+V F Q+L L S R D +I D + N+ + +
Sbjct: 140 DAFNASPKILKDVVANQKVVQYSTFTQALIDLNSGRIDGLLI-DRVYANYYLEKSGVLDQ 198
Query: 213 FKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+ + + + A RK + L + IN+ ++ +G ++KI +++F +++
Sbjct: 199 YNVMPAGYEGESFAVGARKVDKTLIKKINQGFETLYKNGEFQKISNKWFGEDV 251
>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 = 143 bits (361), Expect = 4e-35
Identities = 57/232 (24%), Positives = 99/232 (42%), Gaps = 11/232 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+R+GTD Y P S +D +GE GFDIDL E+ R+ +K + + LI L +
Sbjct: 6 VRIGTDTTYAPFSS--KDAKGEFIGFDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAKK 63
Query: 103 YDVLVNV-AITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D +++ +IT +RQ++ FS A L+ + + L K V + G+
Sbjct: 64 IDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLESLKGKHVGVLQGSTQE 123
Query: 162 RFAKELKSHLVFSH----NFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIAD 217
+A + N + L + R DA + ++ ++P
Sbjct: 124 AYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDEVAASEGFLKQPAGKEYAFAGP 183
Query: 218 RMKDN----SAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+KD +RK + +L + ++ L + DGTY K+ +YFD N+
Sbjct: 184 SVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGTYDKMAKKYFDFNV 235
>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 = 143 bits (361), Expect = 4e-35
Identities = 51/224 (22%), Positives = 97/224 (43%), Gaps = 11/224 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+R+GT+G YPP++F + GE+ GF+ +L E+ R L E+ + +I L +
Sbjct: 7 VRMGTEGAYPPYNF--INDAGEVDGFERELGDELCKRAGLTCEWVKNDWDSIIPNLVSGN 64
Query: 103 YDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
YD ++ ++IT ER + DF+ YI V + DL+ AQ T +
Sbjct: 65 YDTIIAGMSITDERDEVIDFTQNYIPPTASSYVATS-----DGADLSGIVAAQT-ATIQA 118
Query: 162 RFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKD 221
+ E + LV E+++ + + DA + G L + D +
Sbjct: 119 GYIAESGATLVEFATPEETIAAVRNGEADAVFADRDYLVPIVAESG--GELMFVGDDVPL 176
Query: 222 NSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
V +R+ + +L + + ++ DGT + ++F ++
Sbjct: 177 GGGVGMGLRESDGELRGKFDAAITSMKEDGTLNTMIKKWFGEDA 220
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
signaling protein; 2.04A {Bordetella pertussis} PDB:
3mpl_A
Length = 267
Score = 138 bits (349), Expect = 1e-33
Identities = 39/226 (17%), Positives = 88/226 (38%), Gaps = 7/226 (3%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGLDTN 101
++V ++ P + D + G +++ + R L E V LI L +
Sbjct: 34 VKVAVLNLFAPFTLFRTDE--QFGGISAAVLQLLQLRTGLDFEIIGVDTVEELIAKLRSG 91
Query: 102 RYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D+ + + R+ FS PY+ + +++V R D L +TVA + +
Sbjct: 92 EADMAGALFVNSARESFLSFSRPYVRNGMVIVTRQDPDAPVDADHLDGRTVALVRNSAAI 151
Query: 162 RFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRM 219
+ ++ +V + N +++ ++ + + DA + ++ R G L +
Sbjct: 152 PLLQRRYPQAKVVTADNPSEAMLMVANGQADAVVQ-TQISASYYVNRYFAGKLRIASALD 210
Query: 220 KDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+ +A +G +L +N+ L +I + I R+ +
Sbjct: 211 LPPAEIALATTRGQTELMSILNKALYSIS-NDELASIISRWRGSDG 255
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 135 bits (341), Expect = 8e-33
Identities = 49/221 (22%), Positives = 95/221 (42%), Gaps = 6/221 (2%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+ VG D YPP+ F D G+ G++++L + +A + + VEF A S + + L + R
Sbjct: 13 IVVGGDRDYPPYEF--IDQNGKPAGYNVELTRAIAEVMGMTVEFRLGAWSEMFSALKSGR 70
Query: 103 YDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSR 162
DVL ++ + +R ++ DF+ P+ + R D +DL + VA +
Sbjct: 71 VDVLQGISWSEKRARQIDFTPPHTIVYHAIFARRDSPPAAGLEDLRGRKVALHRDGIMHE 130
Query: 163 FAKE--LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMK 220
+ E LV + +L+LL + D ++ +P + + R
Sbjct: 131 YLAERGYGKDLVLTPTPADALRLLAAGGCDYAVVAMVPGMYIIRE--NRLTNLVPVARSI 188
Query: 221 DNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
+ +R+G+ +L +E L + G Y+ I ++
Sbjct: 189 AAQRYGYAVRQGDAELLARFSEGLAILRKTGQYEAIRAKWL 229
>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 = 134 bits (338), Expect = 2e-32
Identities = 57/228 (25%), Positives = 99/228 (43%), Gaps = 10/228 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
L +GT PP + + L GFDIDL++E+ RL+ F L L
Sbjct: 5 LTIGTSKFNPPFEVWSGNN-SSLYGFDIDLMQEICRRLHATCTFEAYIFDDLFPALKNRE 63
Query: 103 YD-VLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D V+ ++ IT ER+K + FS+PY+ + D I +F DL K + GT +
Sbjct: 64 VDLVIASMIITDERKKHFIFSLPYMESNSQYITTVD-SKISTFDDLHGKKIGVRKGTPYA 122
Query: 162 RF--AKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPH-----DGNLFK 214
R ++ + ++F + L L + + DA+++ ++ P+
Sbjct: 123 RQVLSENRNNQVIFYELIQDMLLGLSNNQVDASLMDYEAAKYWMASEPYAYKLIGKKYKL 182
Query: 215 IADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFD 262
I ++ + M L + IN+IL + DGTY +++ YF+
Sbjct: 183 IGKKISIGEGYSIMANPDQFVLIKKINKILLEMEADGTYLRLYSEYFE 230
>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 = 129 bits (324), Expect = 8e-31
Identities = 43/226 (19%), Positives = 87/226 (38%), Gaps = 5/226 (2%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
VGT+ YPP + D +GE+ GFDIDL K ++ +L ++E E A LI L +R
Sbjct: 12 WIVGTNATYPPFEY--VDAQGEVVGFDIDLAKAISEKLGKQLEVREFAFDALILNLKKHR 69
Query: 103 YDVLV-NVAITPERQKKYDFS-IPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDL 160
D ++ ++ITP RQK+ + L+VV + +VA GT
Sbjct: 70 IDAILAGMSITPSRQKEIALLPYYGDEVQELMVVSKRSLETPVLPLTQYSSVAVQTGTYQ 129
Query: 161 SRFAKEL-KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRM 219
+ + + + + + ++ ++ L+ P+
Sbjct: 130 EHYLLSQPGICVRSFDSTLEVIMEVRYGKSPVAVLEPSVGRVVLKDFPNLVATRLELPPE 189
Query: 220 KDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+ K + ++I + + + +G + + ++ +
Sbjct: 190 CWVLGCGLGVAKDRPEEIQTIQQAITDLKSEGVIQSLTKKWQLSEV 235
>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 = 125 bits (315), Expect = 8e-30
Identities = 62/223 (27%), Positives = 97/223 (43%), Gaps = 10/223 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITG-LDTN 101
L V TD + P F GFD+DL +A L L E SG+I N
Sbjct: 5 LVVATDTAFVPFEFKQG---DLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKN 61
Query: 102 RYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGT--- 158
L + IT ER+K DFS Y +L++V+++ D++S KDL K VA GT
Sbjct: 62 VDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSV 121
Query: 159 DLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADR 218
D ++ + K F N + + L + R DA + F++ + FK
Sbjct: 122 DYAKANIKTKDLRQFP-NIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQ--FKAVGD 178
Query: 219 MKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
+ KG+++L +N L + +GTY +I+ ++F
Sbjct: 179 SLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWF 221
>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 = 124 bits (312), Expect = 2e-29
Identities = 51/229 (22%), Positives = 99/229 (43%), Gaps = 9/229 (3%)
Query: 42 ALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFE-TAVSGLITGLDT 100
AL+VG G PP F+ + TG +D+ + VA E+ ++S IT +
Sbjct: 5 ALKVGVVG-NPPFVFYGEGKNAAFTGISLDVWRAVAESQKWNSEYVRQNSISAGITAVAE 63
Query: 101 NRYDVLV-NVAITPERQK--KYDFSIPYIAHR-VLLVVRSDQQDIRSFKDLTDKTVAQIL 156
D+L+ +++TPER F+ PY + LL+ + RS DL +K VA +
Sbjct: 64 GELDILIGPISVTPERAAIEGITFTQPYFSSGIGLLIPGTATPLFRSVGDLKNKEVAVVR 123
Query: 157 GTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA 216
T +A ++ + ++N ++ LL K+ +A M + + P ++
Sbjct: 124 DTTAVDWANFYQADVRETNNLTAAITLLQKKQVEAVMFDRPALIYYTRQNP--NLNLEVT 181
Query: 217 DRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+ F++++ N+ L ++IN + + + +R+ I
Sbjct: 182 EIRVSLEPYGFVLKE-NSPLQKTINVEMLNLLYSRVIAEFTERWLGPGI 229
>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic
protein, protein binding, transport protein; 1.92A
{Chlamydia trachomatis}
Length = 242
Score = 124 bits (312), Expect = 2e-29
Identities = 47/225 (20%), Positives = 89/225 (39%), Gaps = 4/225 (1%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
VGT+ YPP F D RGE+ GFDIDL +E++++L ++ E + LI L +R
Sbjct: 13 FIVGTNATYPPFEF--VDKRGEVVGFDIDLAREISNKLGKTLDVREFSFDALILNLKQHR 70
Query: 103 YDVL-VNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D + ++ITP R K+ Y LV+ ++ ++VA GT
Sbjct: 71 IDAVITGMSITPSRLKEILMIPYYGEEIKHLVLVFKGENKHPLPLTQYRSVAVQTGTYQE 130
Query: 162 RFAKEL-KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMK 220
+ + L + H+ + + L ++ ++ ++ L+ P +
Sbjct: 131 AYLQSLSEVHIRSFDSTLEVLMEVMHGKSPVAVLEPSIAQVVLKDFPALSTATIDLPEDQ 190
Query: 221 DNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
+ L I + I +G ++ ++ N+
Sbjct: 191 WVLGYGIGVASDRPALALKIEAAVQEIRKEGVLAELEQKWGLNNL 235
>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 = 115 bits (287), Expect = 2e-26
Identities = 34/253 (13%), Positives = 79/253 (31%), Gaps = 38/253 (15%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAV----------- 91
+ G + P H GF IDL+ ++A +N E A
Sbjct: 43 ICTGPNDTSPGSPRH--TVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNN 100
Query: 92 ------SGLITGLDTNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQ-DIRS 143
+G++ L + + D++V + I ER + +FS P+ + ++V+ + +
Sbjct: 101 SNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGIN 160
Query: 144 FKDLTDKTVAQILGTDLSRFAKELKSH------------LVFSHNFEQSLQLLLSKRTDA 191
L + + I T + +++Q + + A
Sbjct: 161 DPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHA 220
Query: 192 TMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDG 251
+ ++ + S MRK + ++++ + H +G
Sbjct: 221 FIWDSAVLEFEASQKCD----LVTTGELFFRSGFGIGMRKD-SPWKQNVSLSILKSHENG 275
Query: 252 TYKKIFDRYFDKN 264
+ + +
Sbjct: 276 FMEDLDKTWVRYQ 288
>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 = 109 bits (272), Expect = 8e-25
Identities = 55/223 (24%), Positives = 100/223 (44%), Gaps = 6/223 (2%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
LRVG + Y P +D +G + GFD+DL +E+A + +K++ T+ GLI GL T +
Sbjct: 7 LRVGLEPGYLPFEM--KDKKGNVIGFDVDLAREMAKAMGVKLKLVPTSWDGLIPGLVTEK 64
Query: 103 YDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQD-IRSFKDLTDKTVAQILG--T 158
+D+++ + I+ ER + +F PYI L+V+ + ++S+KDL + +
Sbjct: 65 FDIIISGMTISQERNLRVNFVEPYIVVGQSLLVKKGLEKGVKSYKDLDKPELTLVTKFGV 124
Query: 159 DLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADR 218
AK L + ++ + A M FN D
Sbjct: 125 SAEYAAKRLFKNAKLKTYDTEAEAVQEVLNGKADMFIFDLPFNVAFMAQKGQGYLVHLDT 184
Query: 219 MKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
+ + ++KG+ +N L I DG+Y ++++R+F
Sbjct: 185 SLTYEPLGWAIKKGDPDFLNWLNHFLAQIKHDGSYDELYERWF 227
>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 = 104 bits (260), Expect = 2e-23
Identities = 54/223 (24%), Positives = 96/223 (43%), Gaps = 9/223 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
+ VGTD + P + + G++ GFD+DL+ V L E L L +
Sbjct: 44 VVVGTDAAFAPFEYMQK---GKIVGFDVDLLDAVMKAAGLDYELKNIGWDPLFASLQSKE 100
Query: 103 YDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS 161
D+ ++ + IT ER++ YDFS PY +++V+ DL KT+ T
Sbjct: 101 VDMGISGITITDERKQSYDFSDPYFEATQVILVKQGSPVKN-ALDLKGKTIGVQNATTGQ 159
Query: 162 RFAKELKSHLVFSHNFEQSLQLL---LSKRTDATMIPDIPFFNFLERRPHDGNLFKIADR 218
A++L FE ++ + L+ DA + + +++ P+ L I D
Sbjct: 160 EAAEKLFGKGPHIKKFETTVVAIMELLNGGVDAVITDNAVANEYVKNNPNK-KLQVIEDP 218
Query: 219 MKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
S M+ N++L ++E L + G Y +I+ ++F
Sbjct: 219 KNFASEYYGMIFPKNSELKAKVDEALKNVINSGKYTEIYKKWF 261
>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 = 102 bits (254), Expect = 1e-22
Identities = 37/258 (14%), Positives = 87/258 (33%), Gaps = 41/258 (15%)
Query: 43 LRVGTDGIYPPHSFHAQ-----DGRGELTGFDIDLIKEVAHRLNLKVEFFE--------- 88
+ V T + P+ + +G G+ +DL E+A K +
Sbjct: 6 VVVTTI-LESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGAR 64
Query: 89 ----TAVSGLITGLDTNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRS 143
+G++ L + D+ + + IT R++ DFS P+++ + ++ I S
Sbjct: 65 DADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGI-SIMIKKGTPIES 123
Query: 144 FKDLTDKTVAQILGTDLSRFAKELKSH-----------------LVFSHNFEQSLQLLLS 186
+DL+ +T D + + VF + + +
Sbjct: 124 AEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRK 183
Query: 187 KRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCA 246
+ + + ++E+R D+ KG + L ++N +
Sbjct: 184 SKGKYAYLLESTMNEYIEQRKPCD--TMKVGGNLDSKGYGIATPKG-SSLGNAVNLAVLK 240
Query: 247 IHLDGTYKKIFDRYFDKN 264
++ G K+ ++++
Sbjct: 241 LNEQGLLDKLKNKWWYDK 258
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme pcc 73102}
Length = 228
Score = 102 bits (253), Expect = 1e-22
Identities = 59/231 (25%), Positives = 110/231 (47%), Gaps = 13/231 (5%)
Query: 40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFE-TAVSGLITG- 97
Q L V T + PP + GEL+GF IDL + +A ++ ++ + E ++V LI+
Sbjct: 2 QQPLLVATR-VIPPFVLSNK---GELSGFSIDLWRSIATQIGIESKLIEYSSVPELISAI 57
Query: 98 LDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLVV---RSDQQDIRSFKDLTDKTVAQ 154
D + ++IT ER++ +DFS+P A + ++V S DIRS DL K VA
Sbjct: 58 KDNKVNLGIAAISITAEREQNFDFSLPIFASGLQIMVRNLESGTGDIRSIDDLPGKVVAT 117
Query: 155 ILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFK 214
G+ + + +E ++ E++ + L +K+ DA + +
Sbjct: 118 TAGSTAATYLREHHISVLEVPKIEEAYKALQTKKADAVVFDAPVLLFYAANEGKGKVEIV 177
Query: 215 IADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFD-KN 264
+ +++ + N+ + IN+ L + +GTY+ ++D++FD KN
Sbjct: 178 GSILREESYGII---LPNNSPYRKPINQALLNLKENGTYQSLYDKWFDPKN 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 = 99.3 bits (246), Expect = 8e-22
Identities = 40/280 (14%), Positives = 87/280 (31%), Gaps = 63/280 (22%)
Query: 43 LRVGTDGIYPPHSFHAQD-----GRGELTGFDIDLIKEVAHRLNLKVEFFE--------- 88
L V T + P+ + G G+ IDL++E++ L E
Sbjct: 15 LIVTTI-LEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQ 73
Query: 89 ----TAVSGLITGLDTNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSD------ 137
+G++ L ++ D+ V +AIT R+K DFS P++ + ++ R
Sbjct: 74 DDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGTNPG 133
Query: 138 ------------------QQDIRSFKDLTDKTVAQILGTDLSRFAKELKSHLVFSHN--- 176
+ I S DL +T + + K + +++
Sbjct: 134 VFSFLNGGSLVPRGSERMESPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMW 193
Query: 177 ------------FEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSA 224
+ +D + + F+ +R + + D+
Sbjct: 194 AFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCN---LTQIGGLIDSKG 250
Query: 225 VAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKN 264
G + I + + +G + ++++ N
Sbjct: 251 YGVGTPMG-SPYRDKITIAILQLQEEGKLHMMKEKWWRGN 289
>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 = 98.6 bits (244), Expect = 1e-21
Identities = 60/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)
Query: 43 LRVGTDGIYPPHSFHAQDG-RGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTN 101
+ V T G P S+H D +LTG+++++++E A RL LKVEF E + G++T +++
Sbjct: 23 IVVATSGTLYPTSYHDTDSGSDKLTGYEVEVVREAAKRLGLKVEFKEMGIDGMLTAVNSG 82
Query: 102 RYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVR---SDQQDIRSFKDLTDKTVAQILG 157
+ D N + +T +R++K+ FS PY +VR A
Sbjct: 83 QVDAAANDIDVTKDREEKFAFSTPYKYSYGTAIVRKDDLSGIKTLKDLKGKKAAGAATTV 142
Query: 158 TDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIAD 217
K + + EQ L+ + + RTD + L P D N+ D
Sbjct: 143 YMEVARKYGAKEVIYDNATNEQYLKDVANGRTDVILNDYYLQTLALAAFP-DLNITIHPD 201
Query: 218 RMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNIIS 267
+ A +M+K N L + +NE L + DG+ K+ ++F+K +S
Sbjct: 202 IKYMPNKQALVMKKSNAALQKKMNEALKEMSKDGSLTKLSKQFFNKADVS 251
>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 = 95.9 bits (237), Expect = 8e-21
Identities = 41/236 (17%), Positives = 78/236 (33%), Gaps = 16/236 (6%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-------NLKVEFFETAVSGLI 95
+ VG P S++ D + ++ G+ D + + +L+V+ I
Sbjct: 19 IVVGHRESSVPFSYY--DNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRI 76
Query: 96 TGLDTNRYDV-LVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQ 154
L +D + ERQK+ FS L+ + V
Sbjct: 77 PLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFADLKGKAVVVT 136
Query: 155 ILGTDLSRFAKELKSHLVFSHNF-----EQSLQLLLSKRTDATMIPDIPFFNFLERRPHD 209
T K + + S + L S R A M+ D +
Sbjct: 137 SGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKP 196
Query: 210 GNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
N + I + + A M+RK + + + +++ + + G +K FD++F I
Sbjct: 197 DN-WDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPI 251
>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 = 96.0 bits (237), Expect = 8e-21
Identities = 56/233 (24%), Positives = 97/233 (41%), Gaps = 15/233 (6%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTN 101
+ VGT +P F D +G+LTG+D++LIKE+ RL + K F S L+ L +
Sbjct: 18 ITVGTGTQFPNICFI--DEKGDLTGYDVELIKELDKRLPHYKFTFKTMEFSNLLVSLGQH 75
Query: 102 RYDVLVNVA-ITPERQKKYD-FSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTD 159
+ D++ + + ER+KK+ + Y + + V + IR +DL K V ++
Sbjct: 76 KVDIVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQNNDTIRGIEDLKGKRVITSATSN 135
Query: 160 LSRFAKELKSHLVFSH-------NFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNL 212
+ K+ ++ L S R DAT+ +
Sbjct: 136 GALVLKKWNEDNGRPFEIAYEGQGANETANQLKSGRADATISTPFAVDFQNKTSTIK--- 192
Query: 213 FKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNI 265
K + N+ V FM K L+ I++ L I DGT K++ ++ +
Sbjct: 193 EKTVGNVLSNAKVYFMFNKNEQTLSDDIDKALQEIIDDGTLKRLSLKWLGDDY 245
>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 = 91.7 bits (226), Expect = 2e-19
Identities = 35/251 (13%), Positives = 85/251 (33%), Gaps = 29/251 (11%)
Query: 37 TEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAV----- 91
T D S L ++ + + G+ IDL++++A +N + +
Sbjct: 40 TNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGA 99
Query: 92 ------SGLITGLDTNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSF 144
+GL+ L + ++ V +I R + DF+ P+ + + ++VR+ ++
Sbjct: 100 WKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRGTELSGI 159
Query: 145 KDLTDK--TVAQILGTDLSRFAKELK-------SHLVFSHNFEQSLQ-----LLLSKRTD 190
D + GT A++ + +N + ++ D
Sbjct: 160 HDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDPEKLD 219
Query: 191 ATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLD 250
A ++ + + + N+ LT +I+E++
Sbjct: 220 AFIMDKALLDYEVSIDADCK--LLTVGKPFAIEGYGIGLPP-NSPLTSNISELISQYKSH 276
Query: 251 GTYKKIFDRYF 261
G + D+++
Sbjct: 277 GFMDVLHDKWY 287
>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 = 90.1 bits (222), Expect = 5e-19
Identities = 46/226 (20%), Positives = 89/226 (39%), Gaps = 10/226 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLN---LKVEFFETAVSGLITGLD 99
+R+G G PP + D +G G+DI L K +A L KV+F + + L
Sbjct: 46 VRIGVFGDKPPFGYV--DEKGNNQGYDIALAKRIAKELFGDENKVQFVLVEAANRVEFLK 103
Query: 100 TNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGT 158
+N+ D+++ TP+R ++ DF PY+ + + V D I S +DL DKT+ GT
Sbjct: 104 SNKVDIILANFTQTPQRAEQVDFCSPYMKVALGVAVPKDSN-ITSVEDLKDKTLLLNKGT 162
Query: 159 DLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATM-IPDIPFFNFLERRPHDGNLFKIAD 217
+ + ++ + + D +
Sbjct: 163 TADAYFTQNYPNIKTLKYDQNTETFAALMDKRGDALSHDNTLLFAW--VKDHPDFKMGIK 220
Query: 218 RMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDK 263
+ + +A ++KG+ +L I+ ++ + + + K +D
Sbjct: 221 ELGNKDVIAPAVKKGDKELKEFIDNLIIKLGQEQFFHKAYDETLKA 266
>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 = 88.6 bits (218), Expect = 1e-18
Identities = 37/260 (14%), Positives = 93/260 (35%), Gaps = 42/260 (16%)
Query: 43 LRVGTDGIYPPHSFHAQD---GRGELTGFDIDLIKEVAHRLNLKVEFFETA--------- 90
LRV T + P +++ + GF ID++ +++ L E +
Sbjct: 5 LRVVTV-LEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQE 63
Query: 91 ---VSGLITGLDTNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKD 146
+GL+ L R D+ ++ + ITP+R+ DF+ Y+ + + V+ I+S +D
Sbjct: 64 DGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYS-VGVLLRRGTSIQSLQD 122
Query: 147 LTDKTVAQILGTDLSRFAKELK----SHLVFSHNFEQSLQLLLSKRTDATM--------- 193
L+ +T S + ++ + + Q +++
Sbjct: 123 LSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQ 182
Query: 194 ---------IPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEIL 244
+ D ++ D + + + + + + ++ G + ++ +
Sbjct: 183 KVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTV-ADRGYGIALQHG-SPYRDVFSQRI 240
Query: 245 CAIHLDGTYKKIFDRYFDKN 264
+ G + +++ KN
Sbjct: 241 LELQQSGDMDILKHKWWPKN 260
>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 = 84.0 bits (206), Expect = 3e-17
Identities = 38/257 (14%), Positives = 85/257 (33%), Gaps = 40/257 (15%)
Query: 43 LRVGTDGIYPPHSFHAQD-----GRGELTGFDIDLIKEVAHRLNLKVEFFE--------- 88
L V T + P+ + G G+ IDL++E++ L E
Sbjct: 6 LIVTTI-LEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTHLGFTYEIRLVEDGKYGAQ 64
Query: 89 ----TAVSGLITGLDTNRYDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRS 143
+G++ L ++ D+ V +AIT R++ DFS P++ + ++ I S
Sbjct: 65 DDVNGQWNGMVRELIDHKADLAVAPLAITYVREEVIDFSKPFMTLG-ISILYRKGTPIDS 123
Query: 144 FKDLTDKTVAQILGTDLSRFAKELKSHLVFSHNFEQSLQ---------------LLLSKR 188
DL +T + + K + +++ + +
Sbjct: 124 ADDLAKQTKIEYGAVEDGATMTFFKRSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLT 183
Query: 189 TDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIH 248
+D + + F+ +R + + D+ G + I + +
Sbjct: 184 SDYAFLMESTTIEFVTQRNCN---LTQIGGLIDSKGYGVGTPMG-SPYRDKITLAILKLQ 239
Query: 249 LDGTYKKIFDRYFDKNI 265
G + ++++ N
Sbjct: 240 EQGKLHMMKEKWWRGNG 256
>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 = 82.0 bits (201), Expect = 1e-16
Identities = 39/235 (16%), Positives = 79/235 (33%), Gaps = 29/235 (12%)
Query: 54 HSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEF-----------FETAVSGLITGLDTNR 102
+ + + GF ID++K+++ + + +G+I + R
Sbjct: 46 STNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQR 105
Query: 103 YDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQ----DIRSFKDLTDKTVAQILG 157
+ V + I ER + DFS+P++ + ++V Q + F+ D + G
Sbjct: 106 AVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRPHDYSPPFRFG 165
Query: 158 TDLSRFAKE----------LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRP 207
T + + E +L L + + D I D N+ R
Sbjct: 166 TVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLD-AFIYDAAVLNYKAGRD 224
Query: 208 HDGNLFKIADRMK-DNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261
L I + ++KG+ R I+ L DG +++ +
Sbjct: 225 EGCKLVTIGSGYIFATTGYGIALQKGS-PWKRQIDLALLQFVGDGEMEELETLWL 278
>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginosa PA01,structural
genomics, PSI-2, protein structure initiative; HET: EPE;
1.66A {Pseudomonas aeruginosa}
Length = 239
Score = 81.0 bits (198), Expect = 2e-16
Identities = 43/225 (19%), Positives = 84/225 (37%), Gaps = 9/225 (4%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
LRV T G Y P S+ G GFD+D+ + +A L K+ T+ L+ +R
Sbjct: 17 LRVATTGDYKPFSYR--TEEGGYAGFDVDMAQRLAESLGAKLVVVPTSWPNLMRDFADDR 74
Query: 103 YDVLVN-VAITPERQKKYDFSIPYIAHRVLLVVR----SDQQDIRSFKDLTDKTVAQILG 157
+D+ ++ ++I ERQ++ FSIPY+ + + Q + + G
Sbjct: 75 FDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEARFQTLEQIDQPGVTAIVNPGG 134
Query: 158 TDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIAD 217
T+ LK + H ++ + M+ D R L +
Sbjct: 135 TNEKFARANLKKARILVHPDNVTIFQQIVDGKADLMMTDAIEARLQSRL--HPELCAVHP 192
Query: 218 RMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFD 262
+ + A + + R +++ L G ++ + + +
Sbjct: 193 QQPFDFAEKAYLLPRDEAFKRYVDQWLHIAEQSGLLRQRMEHWLE 237
>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 = 80.2 bits (196), Expect = 4e-16
Identities = 31/237 (13%), Positives = 68/237 (28%), Gaps = 13/237 (5%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR 102
R+ PP + G+++G D+ +E+ RL + + G +
Sbjct: 15 ARIAIAN-EPPFTA--VGADGKVSGAAPDVAREIFKRLGVADVVASISEYGAMIPGLQAG 71
Query: 103 YDVLVNVAITPERQKKYDFSIPYIAHRVLLVVR---------SDQQDIRSFKDLTDKTVA 153
+ + + ++ + +DI D
Sbjct: 72 RHDAITAGLFMKPERCAAVAYSQPILCDAEAFALKKGNPLGLKSYKDIADNPDAKIGAPG 131
Query: 154 QILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLF 213
L+ A + ++ + + L++L R D +P + + + +
Sbjct: 132 GGTEEKLALEAGVPRDRVIVVPDGQSGLKMLQDGRIDVYSLPVLSINDLVSKANDPNVEV 191
Query: 214 KIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRY-FDKNIISSV 269
RKG+ L + + L + G + KI + Y F S
Sbjct: 192 LAPVEGAPVYCDGAAFRKGDEALRDAFDVELAKLKESGEFAKIIEPYGFSAKAAMST 248
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
transport, ABC transport, virulence factor, receptor;
1.49A {Campylobacter jejuni}
Length = 259
Score = 61.0 bits (146), Expect = 3e-10
Identities = 36/227 (15%), Positives = 82/227 (36%), Gaps = 18/227 (7%)
Query: 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHR---LNLKVEFFETAVSGLITGLD 99
L VG P ++ Q GE+ GF++D+ K +A + K++ LD
Sbjct: 40 LIVGVKNDVPHYALLDQAT-GEIKGFEVDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLD 98
Query: 100 TNRYDVLVNV-AITPERQKKYDFSIPYIAHRVLLVVRSDQ-----QDIRSFKDLTDKTVA 153
D ++ ITPER++ Y+FS PY + L+V ++ D++ +
Sbjct: 99 NGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEKKYKSLADMKGANIGVAQAAT 158
Query: 154 QILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLF 213
+ + ++ L +KR DA + +++ +
Sbjct: 159 TKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDKS------ 212
Query: 214 KIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRY 260
+I + + + +K + + +++ + + ++
Sbjct: 213 EILPDSFEPQSYGIVTKKDDPAFAKYVDDFVKEH--KNEIDALAKKW 257
>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 = 44.9 bits (106), Expect = 2e-05
Identities = 76/425 (17%), Positives = 118/425 (27%), Gaps = 210/425 (49%)
Query: 24 ILFSYY---FVIY-PFRTEDQSAL-RVGTDGIYPPHSFHAQ-----DGRG-------EL- 65
++ +Y + PF + SAL R +G +AQ G+G EL
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFRAVGEG-------NAQLVAIFGGQGNTDDYFEELR 174
Query: 66 ------TGFDIDLIKEVAHRLN-LKVEFFETAVSGLIT-GLDTNRYDVLVNVAITPERQK 117
DLIK A L+ L + T GL+ + L N + TP++
Sbjct: 175 DLYQTYHVLVGDLIKFSAETLSELIRT--TLDAEKVFTQGLNILEW--LENPSNTPDK-- 228
Query: 118 KYDF------SIPYI-----AH-----RVL--------------------LVV-----RS 136
D+ S P I AH ++L LV +
Sbjct: 229 --DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET 286
Query: 137 DQQDIRSFKDLTDKTVAQIL-----------------------------GT--------D 159
D + SF K + +L G +
Sbjct: 287 DSWE--SFFVSVRKAI-TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN 343
Query: 160 LSRFAKELKSHL--VFSH----------------NF-----EQSLQ---LLLSKRTDATM 193
L++ ++++ ++ SH N QSL L L K A
Sbjct: 344 LTQ--EQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK-APS 400
Query: 194 IPD---IPFFNFLERRPHDGNLF-----------------KIADRMKDNSAVAFM----- 228
D IP F ER+ N F I + N+ V+F
Sbjct: 401 GLDQSRIP---FSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNN-VSFNAKDIQ 456
Query: 229 -----------MRK-GNNKLTRSINEILC-------AIHLDGTYKKIFDRYFDKNIISSV 269
+R + R ++ I+ T+ I D F
Sbjct: 457 IPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATH--ILD--FG------- 505
Query: 270 PGCSS 274
PG +S
Sbjct: 506 PGGAS 510
Score = 36.8 bits (85), Expect = 0.006
Identities = 42/230 (18%), Positives = 73/230 (31%), Gaps = 71/230 (30%)
Query: 22 FFILFSYYFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRG----EL----TGFDIDLI 73
+ + +F+ + + L T+G A D EL G+ L+
Sbjct: 20 LLVPTASFFIASQLQEQFNKILPEPTEGF-------AADDEPTTPAELVGKFLGYVSSLV 72
Query: 74 --KEVAHR---LNLKVEFFETAVSGLITGLDTNRYDV------LVNVAITPERQKKYDFS 122
+V LNL + FE L+ N D+ L+ T + K
Sbjct: 73 EPSKVGQFDQVLNLCLTEFENCY------LEGN--DIHALAAKLLQENDTTLVKTKELIK 124
Query: 123 IPYIAHRVL-----------LVVRSDQQDIRS-------------FKDLTD--KTVAQIL 156
A + L + + + F++L D +T ++
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184
Query: 157 GTDLSRFAKELKSHLV-----FSHNFEQSLQLL--LSKRTDATMIPDIPF 199
G DL +F+ E S L+ F Q L +L L + + PD +
Sbjct: 185 G-DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE---NPSNTPDKDY 230
Score = 26.8 bits (59), Expect = 5.0
Identities = 35/165 (21%), Positives = 47/165 (28%), Gaps = 72/165 (43%)
Query: 1 MRRLLRDLRK-----------IFFSK------YLF---FAPF----------FI---LFS 27
+ L LRK I FS+ F +PF I L
Sbjct: 386 LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVK 445
Query: 28 YYFVI------YP-FRTEDQSALRVGTDGIYP---------P---------HSFHAQD-G 61
P + T D S LRV + I P + H D G
Sbjct: 446 NNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFG 505
Query: 62 RGELTGFDIDLIKEVAHRLNLKVEFFE-TAVSGLITG-LDTNRYD 104
G +G + + HR + T V ++ G LD N D
Sbjct: 506 PGGASG-----LGVLTHRN------KDGTGVRVIVAGTLDINPDD 539
>3ksx_A Nitrate transport protein; SSUA, alkanesulfonate-binding protein,
periplasmic-binding P transport protein; HET: MPO; 1.70A
{Xanthomonas axonopodis PV} PDB: 3e4r_A* 3ksj_A*
Length = 324
Score = 38.9 bits (90), Expect = 0.001
Identities = 29/196 (14%), Positives = 60/196 (30%), Gaps = 36/196 (18%)
Query: 39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSG--LIT 96
+ + LR+G Q L+++ K+ + E +G L+
Sbjct: 27 EPAQLRIGYQKAVSSLVLAKQHR----------LLEQ--RFPRTKITWVEFP-AGPQLLE 73
Query: 97 GLDTNRYDVLVNVAITP---ERQKKYDFSIPYIAHR----VLLVVRSDQQDIRSFKDLTD 149
L+ D+ P + D ++V S +R+ DL
Sbjct: 74 ALNVGSIDL-GGAGDIPPLFAQAAGADLLYVGWVPPTPKAETILVPSKS-ALRTVADLKG 131
Query: 150 KTVAQILGTDLSRFAKEL--------KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFN 201
K +A G+ + + + + + + DA I D P+++
Sbjct: 132 KRIAFQKGSSAHNLLLRVLAKSGLSMRDITPLYLSPANARAAFAAGQVDAWAIWD-PWYS 190
Query: 202 FLERRPHDGNLFKIAD 217
L G+ +A+
Sbjct: 191 ALTLD---GSARLLAN 203
>3kg2_A Glutamate receptor 2; ION channel, membrane protein, alternative
splicing, cell membrane, glycoprotein, ION transport,
membrane; HET: ZK1 NAG BMA; 3.60A {Rattus norvegicus}
Length = 823
Score = 34.2 bits (77), Expect = 0.030
Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 14/98 (14%)
Query: 61 GRGELTGFDIDLIKEVAHRLNLKVEFFETA-------------VSGLITGLDTNRYDVLV 107
G G+ +DL E+A K + +G++ L + D+ +
Sbjct: 408 GNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAI 467
Query: 108 N-VAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSF 144
+ IT R++ DFS P+++ + ++++ Q+
Sbjct: 468 APLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGV 505
Score = 32.6 bits (73), Expect = 0.10
Identities = 19/150 (12%), Positives = 45/150 (30%), Gaps = 20/150 (13%)
Query: 131 LLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKELKSHL-----------------VF 173
L V I S +DL+ +T D + + VF
Sbjct: 614 FLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVF 673
Query: 174 SHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGN 233
+ + + + + + ++E+R + K+ + KG+
Sbjct: 674 VRTTAEGVARVRKSKGKYAYLLESTMNEYIEQR-KPCDTMKVGGNLDSKG-YGIATPKGS 731
Query: 234 NKLTRSINEILCAIHLDGTYKKIFDRYFDK 263
L +N + + G K+ ++++
Sbjct: 732 -SLGTPVNLAVLKLSEQGLLDKLKNKWWYD 760
>2g29_A Nitrate transport protein NRTA; solute-binding protein, alpha-beta
protein; 1.50A {Synechocystis SP}
Length = 417
Score = 31.0 bits (69), Expect = 0.29
Identities = 17/136 (12%), Positives = 34/136 (25%), Gaps = 14/136 (10%)
Query: 106 LVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTD-----L 160
+ +A + Y +V +F +TD VA +
Sbjct: 115 MYILARLNVNGQGIQLGNNYKDLKVGTDAAPL---KEAFAKVTDPKVAMTFPGGTHDMWI 171
Query: 161 SRFAKE-----LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKI 215
+ K Q + + ++ + + P+ +
Sbjct: 172 RYWLAAGGMEPGKDFSTIVVPPAQMVANVKVNAMESFCVGE-PWPLQTVNQGVGYQALTT 230
Query: 216 ADRMKDNSAVAFMMRK 231
KD+ AF MR
Sbjct: 231 GQLWKDHPEKAFGMRA 246
>1zel_A Hypothetical protein RV2827C; winged-helix, helix-turn- helix,
auto-rickshaw, structural genomics, PSI; 1.93A
{Mycobacterium tuberculosis H37RV} SCOP: a.4.5.83
d.377.1.1
Length = 298
Score = 28.2 bits (62), Expect = 2.0
Identities = 14/49 (28%), Positives = 23/49 (46%)
Query: 120 DFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKELK 168
D IP A RV+ + D+ + + +DLT + G D +EL+
Sbjct: 11 DRRIPTWASRVVSGLARDRPVVVTKEDLTQRLTEAGCGRDPDSAIRELR 59
>1jvn_A Glutamine, bifunctional histidine biosynthesis protein hishf;
substrate channeling, amidotransferase, TIM-barrel AS A
substrate tunnel; HET: 143; 2.10A {Saccharomyces
cerevisiae} SCOP: c.1.2.1 c.23.16.1 PDB: 1ox4_B* 1ox5_A*
1ox6_A 1ox4_A
Length = 555
Score = 28.0 bits (62), Expect = 2.4
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 63 GELTGFDIDLIKEVAHRLNLKV 84
G +G+D++LI+ V + + V
Sbjct: 478 GSNSGYDLELIEHVKDAVKIPV 499
>2x26_A Periplasmic aliphatic sulphonates-binding protein; transport
protein; 1.75A {Escherichia coli}
Length = 308
Score = 27.8 bits (61), Expect = 2.5
Identities = 20/146 (13%), Positives = 46/146 (31%), Gaps = 17/146 (11%)
Query: 77 AHRLNLKVEFFETAVSG--LITGLDTNRYDVLVNVAITPERQKKYDFSIPYIA-----HR 129
K+ + E +G ++ L+ D+ I P + + Y+ +
Sbjct: 27 KRYPESKISWVEFP-AGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVGVEPPKPK 85
Query: 130 VLLVVRSDQQDIRSFKDLTDKTVAQILGTD--------LSRFAKELKSHLVFSHNFEQSL 181
+++ ++ I++ DL VA G+ L + + +
Sbjct: 86 AEVILVAENSPIKTVADLKGHKVAFQKGSSSHNLLLRALRQAGLKFTDIQPTYLTPADAR 145
Query: 182 QLLLSKRTDATMIPDIPFFNFLERRP 207
DA I D P+++ +
Sbjct: 146 AAFQQGNVDAWAIWD-PYYSAALLQG 170
>1fob_A Beta-1,4-galactanase; B/A barrel, glycosyl hydrolase, family 53,
CLAN GH-A; 1.80A {Aspergillus aculeatus} SCOP: c.1.8.3
PDB: 1fhl_A
Length = 334
Score = 27.8 bits (61), Expect = 3.1
Identities = 6/65 (9%), Positives = 17/65 (26%)
Query: 55 SFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPE 114
S++ + + + V ET L ++ +
Sbjct: 213 SYYPFYSASATLASLKTSLANLQSTYDKPVVVVETNWPVSCPNPAYAFPSDLSSIPFSVA 272
Query: 115 RQKKY 119
Q+++
Sbjct: 273 GQQEF 277
>3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding,
nucleotide-binding, membrane, transmembrane, transport
protein; 3.00A {Methanosarcina acetivorans} SCOP:
f.58.1.1
Length = 295
Score = 27.7 bits (61), Expect = 3.2
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 2/35 (5%)
Query: 1 MRRLLRDLRKIFFSKYLFFAPFFILFSYYFVIYPF 35
M+ R RK F F F +L + F+
Sbjct: 24 MKAKNRKTRK--FEPLTFVFSFLLLVLFLFIFLTL 56
>2wjn_H Reaction center protein H chain; bacteriochlorophyll,
lipidic-sponge phase, photosynthesis, electron
transport, cell membrane; HET: HEM FME BCB BPB MPG MQ7
NS5; 1.86A {Rhodopseudomonas viridis} PDB: 1prc_H*
1r2c_H* 1vrn_H* 1dxr_H* 2jbl_H* 2prc_H* 2i5n_H* 2wjm_H*
3d38_H* 3prc_H* 5prc_H* 6prc_H* 7prc_H* 3g7f_H*
Length = 258
Score = 27.4 bits (61), Expect = 3.3
Identities = 9/58 (15%), Positives = 13/58 (22%), Gaps = 10/58 (17%)
Query: 16 YLFFAPFFILFSYYFVI------YPFRTEDQSALRVGTDGIYP----PHSFHAQDGRG 63
Y + + + Y YP DG P +F G
Sbjct: 18 YAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGT 75
>3foa_A Tail sheath protein GP18; alpha-beta, viral structural protein,
bacteriophage T4, viral protein; 3.50A {Enterobacteria
phage T4} PDB: 3foh_A 3foi_A
Length = 510
Score = 27.2 bits (59), Expect = 3.9
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 249 LDGTYKKIFDRYFDKNI 265
+DG YK +D+Y D N
Sbjct: 450 IDGNYKYQYDKYNDVNR 466
>1vzv_A Assemblin, varicella-zoster virus protease; hydrolase, serine
protease, viral protease, coat protein; 3.00A {Human
herpesvirus 3} SCOP: b.57.1.1
Length = 221
Score = 27.0 bits (60), Expect = 4.6
Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 141 IRSFKDLTDKTVAQILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPD 196
I F+ L+ ++ A++L S + V+ + ++ ++LLS + ++ D
Sbjct: 153 IEPFRVLSMESKARLL----SLVKDYAGLNKVWKVSEDKLAKVLLSTAVNNMLLRD 204
>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1;
transferase, ATP sulfurylase, APS kinase, PAPS; HET:
ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5
c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*
Length = 630
Score = 26.4 bits (58), Expect = 7.5
Identities = 10/47 (21%), Positives = 19/47 (40%)
Query: 32 IYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAH 78
+ R E++ A + GT P+ + L G D+ ++ V
Sbjct: 343 FFEHRKEERCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRVYW 389
>3hn0_A Nitrate transport protein; YP_001302749.1, structural genomics,
joint center for structural genomics, JCSG; 1.75A
{Parabacteroides distasonis}
Length = 283
Score = 26.3 bits (57), Expect = 7.6
Identities = 17/164 (10%), Positives = 43/164 (26%), Gaps = 15/164 (9%)
Query: 74 KEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLV 133
+ ++V+ ++ L D+ V I I
Sbjct: 27 PPIIDNKKVQVKVVDSP-DLAQALLIKQETDIAVLPMINAANLYNKGIKIKLAG-----C 80
Query: 134 VRSDQQDIRSFKDLTDKTVA--------QILGTDLSRFAKELKSHLVFSHNFEQSLQLLL 185
+ L + + IL + + + Q +L
Sbjct: 81 PIWGTLYLVEKTPLKEPALYVFGNGTTPDILTRYYLGRQRLDYPLNYAFNTAGEITQGIL 140
Query: 186 SKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMM 229
+ + + ++ + PF + R+ + + + DN + F
Sbjct: 141 AGKVNRAVLGE-PFLSIALRKDSSLRITADLNHLTDNDTLGFAQ 183
>2ws9_1 P1; 3.00A {Equine rhinitis a virus} PDB: 2wff_1
Length = 246
Score = 26.2 bits (57), Expect = 8.8
Identities = 7/18 (38%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 115 RQKKYDFSIPYIA-HRVL 131
R + FS+PY + RV+
Sbjct: 150 RSQACGFSVPYTSMWRVV 167
>1rwh_A Chondroitin AC lyase; chondroitinase, chondroitin lyase; HET: ASG
GCT GAD; 1.25A {Arthrobacter aurescens} SCOP: a.102.3.2
b.24.1.1 b.30.5.2 PDB: 1rwc_A* 1rwf_A* 1rwg_A* 1rwa_A*
1rw9_A
Length = 757
Score = 26.1 bits (57), Expect = 9.0
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 2/75 (2%)
Query: 144 FKDLTDKTVAQILGTDLSRFAKELKSHLV--FSHNFEQSLQLLLSKRTDATMIPDIPFFN 201
F L ++ V QI G ++ + + + ++ SL L + ++ D+
Sbjct: 9 FAALRNRWVDQITGRNVIQAGDPDFAKAITALNNKAADSLAKLDAAAGRTSVFTDLSLAK 68
Query: 202 FLERRPHDGNLFKIA 216
E L ++A
Sbjct: 69 DAEMVTTYTRLSQLA 83
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
0.327 0.142 0.417
Gapped
Lambda K H
0.267 0.0529 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,403,513
Number of extensions: 110170
Number of successful extensions: 503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 443
Number of HSP's successfully gapped: 52
Length of query: 274
Length of database: 5,693,230
Length adjustment: 91
Effective length of query: 183
Effective length of database: 3,487,026
Effective search space: 638125758
Effective search space used: 638125758
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.8 bits)