RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12229
(444 letters)
>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane,
glycoprotein, transport, membrane, postsynaptic cell
membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus
norvegicus}
Length = 823
Score = 248 bits (633), Expect = 2e-74
Identities = 119/377 (31%), Positives = 178/377 (47%), Gaps = 57/377 (15%)
Query: 14 QEPFVMREESEG--GGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMD-ENGQWN 70
+ P+VM + + G +Y+GYC+DL EI K GF+Y++ + D +G D + WN
Sbjct: 393 ESPYVMMKANHAALAGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWN 452
Query: 71 GMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKP-KTPTSLFKFLTV 129
GM+ EL+ +ADIA+ L++ RE V+DF+ P+ L GI+I++KKP K+ +F FL
Sbjct: 453 GMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSL-GISIMIKKPQKSKPGVFSFLDP 511
Query: 130 LETGVWLCILAAYCNLDGEQMKYLIQVNPPGDILPEVIRAIILMQNITDAGILFDDSF-- 187
L +W+CI+ AY + + + +P E + + +S
Sbjct: 512 LAYEIWMCIVFAYI-GVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWF 570
Query: 188 --------SGGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDL 239
+P++LSGR+V WW F III+SYTANLAAFLTV R+ +PIES +DL
Sbjct: 571 SLGAFMQQGADISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDL 630
Query: 240 SKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSD 299
SKQ +I Y L+ + +F+R
Sbjct: 631 SKQTEIAYGTLDSGSTKEFFRRSKI----------------------------------A 656
Query: 300 KYTKMWQAMKEAK---LPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVM-TNCDLQM 355
+ KMW M+ A+ + E V RVR SK + YL ++T Y+ CD
Sbjct: 657 VFDKMWTYMRSAEPSVFVRTTAEGVARVRKSK---GKYAYLLESTMNEYIEQRKPCDTMK 713
Query: 356 VGDEFSRKPYAIAVQQD 372
VG K Y IA +
Sbjct: 714 VGGNLDSKGYGIATPKG 730
>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 = 129 bits (324), Expect = 4e-34
Identities = 51/149 (34%), Positives = 86/149 (57%), Gaps = 5/149 (3%)
Query: 12 LKQEPFVMREESEGG--GGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDE-NGQ 68
+ +EP+V+ ++S+ G +++GYCIDL+ E+ ++GF YEI + D +G D+ NGQ
Sbjct: 20 ILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQ 79
Query: 69 WNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKP-KTPTSLFKFL 127
WNGM++ELI+ +AD+A+ L++ RE V+DF+ P+ L GI+IL +KP T +F FL
Sbjct: 80 WNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTL-GISILYRKPNGTNPGVFSFL 138
Query: 128 TVLETGVWLCILAAYCNLDGEQMKYLIQV 156
+ + ++
Sbjct: 139 NGGSLVPRGSERMESPIDSADDLAKQTKI 167
Score = 78.7 bits (193), Expect = 2e-16
Identities = 39/177 (22%), Positives = 66/177 (37%), Gaps = 41/177 (23%)
Query: 203 ATWWLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRM 262
+F F+ S R+++PI+S DDL+KQ KI+Y + A MT+F++
Sbjct: 130 TNPGVFSFLNGGSLV-----PRGSERMESPIDSADDLAKQTKIEYGAVEDGATMTFFKKS 184
Query: 263 ADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQ 322
DK + +++ L S EE +Q
Sbjct: 185 -------------------------------KISTYDKMWAFMSSRRQSVLVKSNEEGIQ 213
Query: 323 RVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDRDARELF 379
RV S + +L ++T I ++ NC+L +G K Y + R+
Sbjct: 214 RVLTSD-----YAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKI 265
>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 = 125 bits (315), Expect = 3e-33
Identities = 48/122 (39%), Positives = 77/122 (63%), Gaps = 1/122 (0%)
Query: 14 QEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMI 73
+EPFVM E+ G KY+G+ ID+++ + +GF YEI+VAPD+ +G+ E+G WNG++
Sbjct: 12 EEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLV 71
Query: 74 KELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETG 133
EL+ KRADI + +L++ +RENVVDFT Y D + +L+++ + SL +
Sbjct: 72 GELVFKRADIGISALTITPDRENVVDFTTRYMDY-SVGVLLRRGTSIQSLQDLSKQTDIP 130
Query: 134 VW 135
Sbjct: 131 YG 132
Score = 56.6 bits (136), Expect = 3e-09
Identities = 31/161 (19%), Positives = 60/161 (37%), Gaps = 39/161 (24%)
Query: 225 TVSRLDTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSD 284
+ R T I+SL DLSKQ I Y + SA + +
Sbjct: 109 VLLRRGTSIQSLQDLSKQTDIPYGTVLDSAVYQHVR------------------------ 144
Query: 285 VERAKLAVWDYPVSDKYTKMWQAMKEAK----LPNSLEEAVQRVRDSKSSSEGFGYLGDA 340
+ + Y++MW+ + + + +Q+V+ + ++ DA
Sbjct: 145 ----MKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGN-----YAFVWDA 195
Query: 341 TDIRYLVMTN--CDLQMVGDEFSRKPYAIAVQQDRDARELF 379
+ Y+ + + C VG+ + + Y IA+Q R++F
Sbjct: 196 AVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVF 236
>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell
junction, cell membrane, glycoprotein, ION transport,
ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus
norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A* 3g3g_A*
3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A* 2xxr_A*
2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A* 3qxm_A*
2i0c_A* ...
Length = 259
Score = 121 bits (305), Expect = 5e-32
Identities = 53/199 (26%), Positives = 94/199 (47%), Gaps = 10/199 (5%)
Query: 12 LKQEPFVMREESEG--GGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMD-ENGQ 68
+ +EP+V+ ++S+ G +++GYCIDL+ E+ +GF YEI + D +G D NGQ
Sbjct: 11 ILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTHLGFTYEIRLVEDGKYGAQDDVNGQ 70
Query: 69 WNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFL- 127
WNGM++ELI+ +AD+A+ L++ RE V+DF+ P+ L GI+IL +K S
Sbjct: 71 WNGMVRELIDHKADLAVAPLAITYVREEVIDFSKPFMTL-GISILYRKGTPIDSADDLAK 129
Query: 128 --TVLETGVWLCILAAYC---NLDGEQMKYLIQVNPPGDILPEVIRAIILMQNITDAGIL 182
+ V + + + + +L + I +D L
Sbjct: 130 QTKIEYGAVEDGATMTFFKRSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFL 189
Query: 183 FDDSFSGGEAPKNLSGRLV 201
+ + +N + +
Sbjct: 190 MESTTIEFVTQRNCNLTQI 208
Score = 55.0 bits (132), Expect = 1e-08
Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 8/84 (9%)
Query: 299 DKYTKMWQAMKEAK---LPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQM 355
Y KMW M + L S EE +QRV S + +L ++T I ++ NC+L
Sbjct: 153 STYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSD-----YAFLMESTTIEFVTQRNCNLTQ 207
Query: 356 VGDEFSRKPYAIAVQQDRDARELF 379
+G K Y + R+
Sbjct: 208 IGGLIDSKGYGVGTPMGSPYRDKI 231
>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 = 106 bits (266), Expect = 1e-26
Identities = 43/116 (37%), Positives = 69/116 (59%), Gaps = 4/116 (3%)
Query: 14 QEPFVMREESEG--GGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMD-ENGQWN 70
+ P+VM +++ G +Y+GYC+DL EI K GF+Y++ + D +G D + WN
Sbjct: 13 ESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWN 72
Query: 71 GMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKF 126
GM+ EL+ +ADIA+ L++ RE V+DF+ P+ L GI+I++KK S
Sbjct: 73 GMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSL-GISIMIKKGTPIESAEDL 127
Score = 60.4 bits (146), Expect = 2e-10
Identities = 36/170 (21%), Positives = 58/170 (34%), Gaps = 36/170 (21%)
Query: 211 IIIASYTANLAAFLTVSRLDTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFY 270
I + +L + + + TPIES +DLSKQ +I Y L+ + +F+R
Sbjct: 100 IDFSKPFMSLGISIMIKK-GTPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKI------ 152
Query: 271 EIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVRDSKSS 330
+ KMW M+ A+ + + V + S
Sbjct: 153 ----------------------------AVFDKMWTYMRSAEPSVFVRTTAEGVARVRKS 184
Query: 331 SEGFGYLGDATDIRYLVMTN-CDLQMVGDEFSRKPYAIAVQQDRDARELF 379
+ YL ++T Y+ CD VG K Y IA +
Sbjct: 185 KGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAV 234
>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 = 93.9 bits (233), Expect = 8e-22
Identities = 31/134 (23%), Positives = 62/134 (46%), Gaps = 13/134 (9%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMD-----ENGQWN 70
+ G+CIDL+ ++ + + F YE+ + D FG + +WN
Sbjct: 53 GSPRHTVPQ-----CCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWN 107
Query: 71 GMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL--FKFLT 128
GM+ EL+ +AD+ + L++ ER ++F+ P+ G+TIL+KK T + +
Sbjct: 108 GMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKY-QGLTILVKKGTRITGINDPRLRN 166
Query: 129 VLETGVWLCILAAY 142
+ ++ + +
Sbjct: 167 PSDKFIYATVKQSS 180
Score = 43.1 bits (101), Expect = 9e-05
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 298 SDKYTKMWQAMKEAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVG 357
+ + M++ M++ ++ EA+Q VRD+K ++ D+ + + CDL G
Sbjct: 188 QVELSTMYRHMEKHNYESA-AEAIQAVRDNK----LHAFIWDSAVLEFEASQKCDLVTTG 242
Query: 358 DEFSRKPYAIAVQQDRDARELF 379
+ F R + I +++D ++
Sbjct: 243 ELFFRSGFGIGMRKDSPWKQNV 264
>2a5s_A N-methyl-D-aspartate receptor nmdar2A subunit, NMDA receptor
nmdar2A; protein-ligand complex, metal
transport,membrane protein; HET: GLU; 1.70A {Rattus
norvegicus} SCOP: c.94.1.1 PDB: 2a5t_B* 3oen_A* 3oel_A*
3oem_A* 3oek_A*
Length = 284
Score = 89.7 bits (222), Expect = 2e-20
Identities = 39/138 (28%), Positives = 71/138 (51%), Gaps = 28/138 (20%)
Query: 12 LKQEPFVMREESEGGGGV--------------------------KYKGYCIDLIEEIRKL 45
L++ PFV+ E+ + KG+CID+++++ +
Sbjct: 12 LEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRT 71
Query: 46 VGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYY 105
V F Y++++ + G N WNGMI E++ +RA +A+GSL++ ER VVDF+VP+
Sbjct: 72 VKFTYDLYLVTNGKHGKK-VNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFV 130
Query: 106 DLVGITILMKKPKTPTSL 123
+ GI++++ + T L
Sbjct: 131 E-TGISVMVSRGTQVTGL 147
>2rc8_A Glutamate [NMDA] receptor subunit 3A; membrane protein, cell
junction, glycoprotein, ION transport channel,
magnesium; 1.45A {Rattus norvegicus} PDB: 2rc7_A 2rc9_A
2rca_A 2rcb_A
Length = 294
Score = 89.7 bits (222), Expect = 3e-20
Identities = 29/107 (27%), Positives = 57/107 (53%), Gaps = 2/107 (1%)
Query: 30 KYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSLS 89
GYCIDL+E++ + + F++++++ D +G +NG W G++ +L+ A++A+ S S
Sbjct: 67 CCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAW-KNGHWTGLVGDLLSGTANMAVTSFS 125
Query: 90 VMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFLTVLETGVWL 136
+ R V+DFT P++ + IL++ T S +
Sbjct: 126 INTARSQVIDFTSPFFS-TSLGILVRTRGTELSGIHDPKLHHPSQGF 171
Score = 37.3 bits (86), Expect = 0.007
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 5/85 (5%)
Query: 297 VSDKYTKMWQAMKEAKLPNSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTN--CDLQ 354
V + +M + M+ +P + + VQ +++ + F + D + Y V + C L
Sbjct: 185 VRQSFPEMHEYMRRYNVPAT-PDGVQYLKNDPEKLDAF--IMDKALLDYEVSIDADCKLL 241
Query: 355 MVGDEFSRKPYAIAVQQDRDARELF 379
VG F+ + Y I + +
Sbjct: 242 TVGKPFAIEGYGIGLPPNSPLTSNI 266
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 65.7 bits (161), Expect = 1e-12
Identities = 23/110 (20%), Positives = 50/110 (45%), Gaps = 18/110 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PFV+ + + G+ IDL I +G E ++ E +I
Sbjct: 14 PFVLSNKG------ELSGFSIDLWRSIATQIGIESKLI-----------EYSSVPELISA 56
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFK 125
+ + + ++ + ++S+ AERE DF++P + G+ I+++ ++ T +
Sbjct: 57 IKDNKVNLGIAAISITAEREQNFDFSLPIFA-SGLQIMVRNLESGTGDIR 105
>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics,
GLUT seattle structural genomics center for infectious
disease; 2.40A {Burkholderia pseudomallei}
Length = 249
Score = 65.8 bits (161), Expect = 2e-12
Identities = 28/101 (27%), Positives = 48/101 (47%), Gaps = 19/101 (18%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF ++ KY G+ +DL EI K G+ Y+I + + G+I
Sbjct: 36 PFEFKQGD------KYVGFDLDLWAEIAKGAGWTYKI------------QPMDFAGLIPA 77
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L + D+AL +++ ER +DF+ PYYD G+ +++
Sbjct: 78 LQTQNIDVALSGMTIKEERRKAIDFSDPYYD-SGLAAMVQA 117
>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system, THER
bacterium, transport protein; HET: LYS; 1.79A
{Geobacillus stearothermophilus} PDB: 2q2a_A* 2q2c_A*
Length = 272
Score = 65.8 bits (161), Expect = 3e-12
Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 19/108 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF ++ K G+ +DL++ + K G +YE+ +N W+ +
Sbjct: 54 PFEYMQKG------KIVGFDVDLLDAVMKAAGLDYEL------------KNIGWDPLFAS 95
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
L K D+ + +++ ER+ DF+ PY++ IL+K+ +
Sbjct: 96 LQSKEVDMGISGITITDERKQSYDFSDPYFE-ATQVILVKQGSPVKNA 142
>3k4u_A Binding component of ABC transporter; structural genomics, protein
structure INI NEW YORK structural genomix research
consortium, nysgxrc; HET: LYS; 2.62A {Wolinella
succinogenes}
Length = 245
Score = 65.0 bits (159), Expect = 4e-12
Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 18/101 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF M+++ G+ +DL E+ K +G + ++ W+G+I
Sbjct: 17 PFEMKDKKG-----NVIGFDVDLAREMAKAMGVKLKL------------VPTSWDGLIPG 59
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L+ ++ DI + +++ ER V+F PY VG ++L+KK
Sbjct: 60 LVTEKFDIIISGMTISQERNLRVNFVEPYIV-VGQSLLVKK 99
>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 = 64.5 bits (158), Expect = 4e-12
Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 19/101 (18%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF ++ Y G+ +DL I K + +YE+ + ++G+I
Sbjct: 15 PFEFKQGD------LYVGFDVDLWAAIAKELKLDYEL------------KPMDFSGIIPA 56
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L K D+AL +++ ER+ +DF+ YY G+ +++K
Sbjct: 57 LQTKNVDLALAGITITDERKKAIDFSDGYYK-SGLLVMVKA 96
>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic
protein, arginine protein binding, transport protein;
1.92A {Chlamydia trachomatis}
Length = 242
Score = 64.6 bits (158), Expect = 4e-12
Identities = 19/108 (17%), Positives = 38/108 (35%), Gaps = 17/108 (15%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF ++ + G+ IDL EI +G + ++ +I
Sbjct: 23 PFEFVDKRG-----EVVGFDIDLAREISNKLGKTLD--------VREFS----FDALILN 65
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
L + R D + +S+ R + Y + + +L+ K + L
Sbjct: 66 LKQHRIDAVITGMSITPSRLKEILMIPYYGEEIKHLVLVFKGENKHPL 113
>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 = 64.7 bits (158), Expect = 6e-12
Identities = 21/101 (20%), Positives = 39/101 (38%), Gaps = 15/101 (14%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P + G K GY ++++ E K +G + E + +GM+
Sbjct: 33 PTSYHDTDSGSD--KLTGYEVEVVREAAKRLGLKVEF------------KEMGIDGMLTA 78
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
+ + D A + V +RE F+ PY T +++K
Sbjct: 79 VNSGQVDAAANDIDVTKDREEKFAFSTPYKY-SYGTAIVRK 118
>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 = 63.4 bits (155), Expect = 1e-11
Identities = 17/101 (16%), Positives = 37/101 (36%), Gaps = 17/101 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF + + G+ IDL++EI + + E ++ +
Sbjct: 15 PFEVWSGNNS----SLYGFDIDLMQEICRRLHATCTF------------EAYIFDDLFPA 58
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L + D+ + S+ + ER+ F++PY + +
Sbjct: 59 LKNREVDLVIASMIITDERKKHFIFSLPYME-SNSQYITTV 98
>4dz1_A DALS D-alanine transporter; D-alanine binding, periplasmic,
transport protein; 1.90A {Salmonella enterica} PDB:
3r39_A 4f3s_A
Length = 259
Score = 63.9 bits (156), Expect = 1e-11
Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 18/101 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P + + K +G ++L + + W+GM+
Sbjct: 41 PMLFKSADG-----KLQGIDLELFSSYCQSRHCKLN--------ITEYA----WDGMLGA 83
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
+ +AD+A +S+ +R+ V+DF+ PYY ++
Sbjct: 84 VASGQADVAFSGISITDKRKKVIDFSEPYYI-NSFYLVSMA 123
>1ii5_A SLR1257 protein; membrane protein; HET: GLU; 1.60A {Synechocystis
SP} SCOP: c.94.1.1 PDB: 1iit_A 1iiw_A
Length = 233
Score = 63.1 bits (154), Expect = 1e-11
Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 17/103 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PFV E + + G +D+ + + + E +V + I
Sbjct: 15 PFVFYGEGKNA---AFTGISLDVWRAVAESQKWNSE-YV----------RQNSISAGITA 60
Query: 76 LIEKRADIALGSLSVMAERENV--VDFTVPYYDLVGITILMKK 116
+ E DI +G +SV ER + + FT PY+ GI +L+
Sbjct: 61 VAEGELDILIGPISVTPERAAIEGITFTQPYFS-SGIGLLIPG 102
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 62.6 bits (153), Expect = 2e-11
Identities = 19/108 (17%), Positives = 40/108 (37%), Gaps = 18/108 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P+ + K G+ ID+ + K + E N ++ +I
Sbjct: 18 PYEFVDADN-----KIVGFDIDVANAVCKEMQAECSF------------TNQSFDSLIPS 60
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
L K+ D + + + +RE V F+ PYY+ +++ + +
Sbjct: 61 LRFKKFDAVIAGMDMTPKREQQVSFSQPYYE-GLSAVVVTRKGAYHTF 107
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 65.5 bits (159), Expect = 2e-11
Identities = 73/430 (16%), Positives = 138/430 (32%), Gaps = 136/430 (31%)
Query: 4 ITNISDSRLKQEPFVMREESEGG-------GGVKYKGYCIDLIEEIRKLVGFEYEIFVAP 56
S+S L R EG GG +G D EE+R L Y+ +
Sbjct: 137 FDKKSNSAL------FRAVGEGNAQLVAIFGG---QGNTDDYFEELRDL----YQTY--- 180
Query: 57 DNSFGNMDENGQWNGMIKELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITIL--M 114
+ ++ +LI+ + L L +D + G+ IL +
Sbjct: 181 -------------HVLVGDLIK-FSAETLSELI-----RTTLDAEKVFTQ--GLNILEWL 219
Query: 115 KKP-KTPTSLFKFLTVLETGVWLCI--LAAY---CNLDGEQMKYLIQVNPPGDILPEVIR 168
+ P TP + L++ + + + LA Y L G PG++ +
Sbjct: 220 ENPSNTPDKDY-LLSIPISCPLIGVIQLAHYVVTAKLLGF---------TPGELRSYLKG 269
Query: 169 AIILMQNITDAGILFDDSFSGGEAPKNLSGRLVAA--TWWLFGFIIIASYTANLAAFLTV 226
A Q + ++ +A +W S+ ++ +TV
Sbjct: 270 ATGHSQGL-------------------VTAVAIAETDSW--------ESFFVSVRKAITV 302
Query: 227 -------SRLDTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEG-RFYEIWKDMS- 277
P SL ++ + N + M I ++ ++
Sbjct: 303 LFFIGVRCYEAYPNTSLPPSI----LEDSLENNEGVPSP---MLSISNLTQEQVQDYVNK 355
Query: 278 LNDSLSDVERAKLAVWDYP----VS----DKYTKMWQAMKEAKLPNSLEEAVQRVRDSK- 328
N L ++ ++++ + VS Y + +++AK P+ L+++ R+ S+
Sbjct: 356 TNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYG-LNLTLRKAKAPSGLDQS--RIPFSER 412
Query: 329 --SSSEGFG---------YLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDRDARE 377
S F L A+D L+ DL F+ K I V D +
Sbjct: 413 KLKFSNRFLPVASPFHSHLLVPASD---LINK--DLVKNNVSFNAKDIQIPVYDTFDGSD 467
Query: 378 LFCNVHANIL 387
L + +I
Sbjct: 468 L-RVLSGSIS 476
Score = 43.5 bits (102), Expect = 1e-04
Identities = 58/388 (14%), Positives = 113/388 (29%), Gaps = 131/388 (33%)
Query: 120 PTSLFKFLTVLETGVWLCILAAYCNL--DGEQ----------MKYLIQVNPPGDI--LPE 165
PT+ F + L+ + D E + Y+ + P + +
Sbjct: 23 PTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQ 82
Query: 166 VIRAIILMQNITDAGILFDDSFSGG--------EAPKNLSGRLVAATWWLFGFIIIASYT 217
V+ + F++ + G + + LV +I +Y
Sbjct: 83 VLNLCLTE---------FENCYLEGNDIHALAAKLLQENDTTLVKT------KELIKNYI 127
Query: 218 ANLAAFLTVSRLDTPIESLDDL-----SKQYKIQYAPLNG-SAAMTYFQRMADIEGRFYE 271
A + D S L ++ A G YF+ + D+ Y+
Sbjct: 128 T--ARIMAKRPFDKKSNSA--LFRAVGEGNAQL-VAIFGGQGNTDDYFEELRDL----YQ 178
Query: 272 IWKDM----------SLNDSLSDVERAK--------LAVW----------DY----PVSD 299
+ + +L++ + A+ + W DY P+S
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS- 237
Query: 300 KYTKMWQAMKEAKLP-NSLEEAVQRVRDSKSSSEGFGYLGDATDIRYLV--MTNCDLQMV 356
P + + V +K G+ ++R + T +V
Sbjct: 238 -------------CPLIGVIQLAHYVVTAKLL----GF--TPGELRSYLKGATGHSQGLV 278
Query: 357 GDEFSRKPYAIAVQQDRDARELFCNVHANILSIPFPFIGVDG------TSVCSSIFD--T 408
A+A+ + F +V +++ F FIGV TS+ SI +
Sbjct: 279 T--------AVAIAETDSWESFFVSV-RKAITVLF-FIGVRCYEAYPNTSLPPSILEDSL 328
Query: 409 DGKTKVSCP------LKKDHVYRYINTF 430
+ V P L ++ V Y+N
Sbjct: 329 ENNEGVPSPMLSISNLTQEQVQDYVNKT 356
Score = 42.0 bits (98), Expect = 4e-04
Identities = 36/206 (17%), Positives = 62/206 (30%), Gaps = 78/206 (37%)
Query: 71 GMIKELIEKRAD-------------IALGSLSVMAERENVVDFTVPYYDLVGITILMKKP 117
+ +E ++ + I+L V + VV + P L G+ + ++K
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEISL----VNGAKNLVV--SGPPQSLYGLNLTLRKA 396
Query: 118 KTPTSL------F---------KFLTV--------LE----------TGVWLCILAA--- 141
K P+ L F +FL V L + A
Sbjct: 397 KAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQ 456
Query: 142 ---YCNLDGEQMKYLIQVNPPGDILPEVIRAIILM----QNITDAG----ILFDDSFSGG 190
Y DG ++ L G I ++ II + + T + F + G
Sbjct: 457 IPVYDTFDGSDLRVL-----SGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASG 511
Query: 191 EAPKNLSGRLVAATWWLFGF-IIIAS 215
L+ R T G +I+A
Sbjct: 512 LGV--LTHRNKDGT----GVRVIVAG 531
Score = 41.2 bits (96), Expect = 8e-04
Identities = 51/336 (15%), Positives = 91/336 (27%), Gaps = 146/336 (43%)
Query: 68 QWNGMIKELIEK---------RADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPK 118
Q GM +L + RAD + Y + I++ P
Sbjct: 1627 QEQGMGMDLYKTSKAAQDVWNRAD----------------NHFKDTYGFSILDIVINNPV 1670
Query: 119 TPTSLFKFLTVLETGVWLC-ILAAYCNLDGEQM--------KYLIQVNP---------PG 160
LT+ G I Y + E + K ++N
Sbjct: 1671 N-------LTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK 1723
Query: 161 DIL-------PEVIRAIILM-----QNITDAGILFDDS-FSG---GEAPKNLSGRLVAAT 204
+L P A+ LM +++ G++ D+ F+G GE
Sbjct: 1724 GLLSATQFTQP----ALTLMEKAAFEDLKSKGLIPADATFAGHSLGE------------- 1766
Query: 205 WWLFGFIIIASYTANLAAF---LTVSRLDTPIESLDDLSKQ--YKIQYAPLNGSAAMTYF 259
Y A LA+ + IESL ++ +Q A + +
Sbjct: 1767 -----------YAA-LASLADVM-------SIESLVEVVFYRGMTMQVAVPRDELGRSNY 1807
Query: 260 QRMADIEGRFYEIWKDMSL------------------ND-----------SLSDVERAKL 290
+A GR + +L N L ++
Sbjct: 1808 GMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTN 1867
Query: 291 AVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVRD 326
+ + K+ Q + +L SL +++ V
Sbjct: 1868 VL-------NFIKL-QKIDIIELQKSL--SLEEVEG 1893
Score = 37.0 bits (85), Expect = 0.016
Identities = 43/275 (15%), Positives = 69/275 (25%), Gaps = 109/275 (39%)
Query: 220 LAAFLT-VSRL--DTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADIEGRFYEIWKDM 276
+ FL VS L + + D + +T F+ + +
Sbjct: 61 VGKFLGYVSSLVEPSKVGQFDQVLN------------LCLTEFEN------CY------L 96
Query: 277 SLND------SLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEAVQRVRDS--- 327
ND L L + + A AK P + +S
Sbjct: 97 EGNDIHALAAKLLQENDTTLVKTKELIKNYI----TARIMAKRPFD------KKSNSALF 146
Query: 328 KSSSEG-------FGYLGDATDIRYLVMTNCDLQMVGDEFSR--KPYAIAVQQDRDAREL 378
++ EG FG G Y +E + Y + V
Sbjct: 147 RAVGEGNAQLVAIFG--GQGNTDDYF-----------EELRDLYQTYHVLVGD------- 186
Query: 379 FCNVHANILSIPFPFIGVDGTSVCSSIFD-----TDGKTK----------VSCPL----K 419
A LS +D V + + + +SCPL +
Sbjct: 187 LIKFSAETLS-ELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQ 245
Query: 420 KDHVYRYINTFKILDRYPK-----------CSKDL 443
H Y+ T K+L P S+ L
Sbjct: 246 LAH---YVVTAKLLGFTPGELRSYLKGATGHSQGL 277
Score = 28.9 bits (64), Expect = 5.0
Identities = 27/213 (12%), Positives = 58/213 (27%), Gaps = 87/213 (40%)
Query: 235 SLDDLSKQYKIQYAPLNGSA----------AMTYFQRMADIEGRFYEIWKDMSLNDSLSD 284
S+ D+ + G AM + + + D + + +I+K+ +N+ +
Sbjct: 1660 SILDIVINNPVNLTIHFGGEKGKRIRENYSAMIF-ETIVDGKLKTEKIFKE--INEHSTS 1716
Query: 285 VERAKLAVWDYPVSD----KYTK---------MWQAMKEAKL-PN--------------- 315
+ ++T+ ++ +K L P
Sbjct: 1717 Y------TFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAAL 1770
Query: 316 -------SLEEAVQRVRDSKSSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAI- 367
S+E V+ V R + M + DE R Y +
Sbjct: 1771 ASLADVMSIESLVEVVF-----------------YRGMTMQVA---VPRDELGRSNYGMI 1810
Query: 368 AVQQDR-------DARELFCNVHAN----ILSI 389
A+ R +A + ++ I
Sbjct: 1811 AINPGRVAASFSQEALQYVVERVGKRTGWLVEI 1843
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 62.6 bits (153), Expect = 2e-11
Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 19/101 (18%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P+ +++ K GY ++L I +++G E G W+ M
Sbjct: 23 PYEFIDQNG-----KPAGYNVELTRAIAEVMGMTVEF------------RLGAWSEMFSA 65
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L R D+ L +S +R +DFT P+ V I ++
Sbjct: 66 LKSGRVDV-LQGISWSEKRARQIDFTPPHTI-VYHAIFARR 104
>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 = 62.3 bits (152), Expect = 4e-11
Identities = 27/108 (25%), Positives = 38/108 (35%), Gaps = 18/108 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P E+ Y G+ IDL + KL G + E + W+ E
Sbjct: 33 PMGYEEKDG-----SYIGFDIDLANAVFKLYGIDVEW------------QAIDWDMKETE 75
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
L D+ SV ER+ DFT PY ++ KK S+
Sbjct: 76 LKNGTIDLIWNGYSVTDERKQSADFTEPYMV-NEQVLVTKKSSGIDSV 122
>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 = 61.9 bits (151), Expect = 4e-11
Identities = 16/102 (15%), Positives = 39/102 (38%), Gaps = 18/102 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEI-RKLVGFEYEIFVAPDNSFGNMDENGQWNGMIK 74
+E GY ++LI+E+ ++L +++ + +++ ++
Sbjct: 28 NICFIDEKG-----DLTGYDVELIKELDKRLPHYKFTF------------KTMEFSNLLV 70
Query: 75 ELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L + + DI + ERE F Y+ + I + +
Sbjct: 71 SLGQHKVDIVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQ 112
Score = 31.9 bits (73), Expect = 0.35
Identities = 14/92 (15%), Positives = 31/92 (33%), Gaps = 8/92 (8%)
Query: 216 YTANLAAFLTVSRLDTPIESLDDLS-KQYKIQYAPLNGSAAMTYFQRM-ADIEGRFYEIW 273
+ +TV + + I ++DL K+ S ++ D F +
Sbjct: 100 AYNHFPLKITVLQNNDTIRGIEDLKGKRVITS----ATSNGALVLKKWNEDNGRPFEIAY 155
Query: 274 KDMSLNDSLSDVE--RAKLAVWDYPVSDKYTK 303
+ N++ + ++ RA + D K
Sbjct: 156 EGQGANETANQLKSGRADATISTPFAVDFQNK 187
>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginos structural
genomics, PSI-2, protein structure initiative; HET: EPE;
1.66A {Pseudomonas aeruginosa}
Length = 239
Score = 61.6 bits (150), Expect = 4e-11
Identities = 21/106 (19%), Positives = 43/106 (40%), Gaps = 18/106 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF R E Y G+ +D+ + + + +G + + W ++++
Sbjct: 27 PFSYRTEEG-----GYAGFDVDMAQRLAESLGAKLVV------------VPTSWPNLMRD 69
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPT 121
+ R DIA+ +S+ ER+ F++PY G T + +
Sbjct: 70 FADDRFDIAMSGISINLERQRQAYFSIPYLR-DGKTPITLCSEEAR 114
>3qax_A Probable ABC transporter arginine-binding protein; periplasmic,
transport PR; HET: ARG; 2.00A {Chlamydophila pneumoniae}
PDB: 3g41_A* 3n26_A*
Length = 268
Score = 61.6 bits (150), Expect = 7e-11
Identities = 21/112 (18%), Positives = 41/112 (36%), Gaps = 17/112 (15%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF + + G+ IDL + I + +G + E+ ++ +I
Sbjct: 43 PFEYVDAQG-----EVVGFDIDLAKAISEKLGKQLEV------------REFAFDALILN 85
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSLFKFL 127
L + R D L +S+ R+ + Y D V +++ K T +
Sbjct: 86 LKKHRIDAILAGMSITPSRQKEIALLPYYGDEVQELMVVSKRSLETPVLPLT 137
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 59.6 bits (145), Expect = 2e-10
Identities = 22/101 (21%), Positives = 41/101 (40%), Gaps = 18/101 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P+V S + +G+ D+++ + K + I N W+ +I
Sbjct: 14 PYVYMGPSG-----QVEGFGADIVKAVCKQMQAVCTI------------SNQPWDSLIPS 56
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L + D G +++ R+ VDFT PYY ++ + K
Sbjct: 57 LKLGKFDALFGGMNITTARQKEVDFTDPYYT-NSVSFIADK 96
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
signaling protein; 2.04A {Bordetella pertussis} PDB:
3mpl_A
Length = 267
Score = 59.3 bits (144), Expect = 4e-10
Identities = 21/108 (19%), Positives = 43/108 (39%), Gaps = 17/108 (15%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF + E ++ G +++ ++ G ++E + D +I +
Sbjct: 44 PFTLFRTDE-----QFGGISAAVLQLLQLRTGLDFE-IIGVDT----------VEELIAK 87
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
L AD+ G+L V + RE+ + F+ PY + + + P P
Sbjct: 88 LRSGEADM-AGALFVNSARESFLSFSRPYVRNGMVIVTRQDPDAPVDA 134
>2q88_A EHUB, putative ABC transporter amino acid-binding prote;
substrate-binding protein, compatible solues,
ABC-transporte osmoprotection; HET: 4CS; 1.90A
{Sinorhizobium meliloti} PDB: 2q89_A*
Length = 257
Score = 58.9 bits (143), Expect = 5e-10
Identities = 23/110 (20%), Positives = 32/110 (29%), Gaps = 19/110 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF K G D+ EI K +G + ++ MI
Sbjct: 24 PFTAVGADG-----KVSGAAPDVAREIFKRLGVADVVAS-----------ISEYGAMIPG 67
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK--PKTPTSL 123
L R D L + ER V ++ P +KK P S
Sbjct: 68 LQAGRHDAITAGLFMKPERCAAVAYSQPILC-DAEAFALKKGNPLGLKSY 116
>2yln_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-BIND protein; HET: CYS GOL;
1.12A {Neisseria gonorrhoeae} PDB: 3zsf_A
Length = 283
Score = 58.9 bits (143), Expect = 5e-10
Identities = 20/109 (18%), Positives = 40/109 (36%), Gaps = 19/109 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF ++ K GY +++ + + +G + E + QW+ M+
Sbjct: 69 PFTYHDKDG-----KLTGYDVEVTRAVAEKLGVKVEF------------KETQWDSMMAG 111
Query: 76 LIEKRADIALGSLSV-MAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
L R D+ + + ER+ D + PY G ++ S+
Sbjct: 112 LKAGRFDVVANQVGLTSPERQATFDKSEPYSW-SGAVLVAHNDSNIKSI 159
>3i6v_A Periplasmic His/Glu/Gln/Arg/opine family-binding; structural
genomics, transporter, PSI-2, protein structure
initiative; HET: LYS; 2.00A {Silicibacter pomeroyi}
Length = 232
Score = 58.4 bits (142), Expect = 6e-10
Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 17/104 (16%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
P+ ++ + G+ +L +E+ K G E W+ +I
Sbjct: 17 PYNFINDAG-----EVDGFERELGDELCKRAGLTCEW------------VKNDWDSIIPN 59
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKKPKT 119
L+ D + +S+ ER+ V+DFT Y + +
Sbjct: 60 LVSGNYDTIIAGMSITDERDEVIDFTQNYIPPTASSYVATSDGA 103
>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 = 57.6 bits (140), Expect = 9e-10
Identities = 22/112 (19%), Positives = 42/112 (37%), Gaps = 22/112 (19%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKE 75
PF ++ ++ G+ IDL E+ K + + ++ +I
Sbjct: 16 PFSSKDAKG-----EFIGFDIDLGNEMCKRMQVKCTW------------VASDFDALIPS 58
Query: 76 LIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK----PKTPTSL 123
L K+ D + SLS+ +R+ + F+ Y ++ K T SL
Sbjct: 59 LKAKKIDAIISSLSITDKRQQEIAFSDKLYA-ADSRLIAAKGSPIQPTLESL 109
>1xwv_A DER F II; beta sheets, allergen; HET: PE3 XPE; 1.83A
{Dermatophagoides farinae} SCOP: b.1.18.7 PDB: 1ahk_A
1ahm_A 1wrf_A 2f08_A* 1a9v_A 1ktj_A
Length = 129
Score = 53.0 bits (127), Expect = 8e-09
Identities = 17/101 (16%), Positives = 37/101 (36%), Gaps = 12/101 (11%)
Query: 340 ATDIRYLVMTNCDLQMVGDEFSRKPYAIAV--QQDRDARELFCNVHANILSIPFPFIGVD 397
+I+ +++ C KP+ + +++ + + A++ + G+D
Sbjct: 10 NNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGID 69
Query: 398 GTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFKILDRYPK 438
T+ C + CPL K Y T+ + PK
Sbjct: 70 -TNACHFM---------KCPLVKGQQYDAKYTWNVPKIAPK 100
>4eq9_A ABC transporter substrate-binding protein-amino A transport;
structural genomics, niaid; HET: GSH; 1.40A
{Streptococcus pneumoniae}
Length = 246
Score = 54.2 bits (131), Expect = 2e-08
Identities = 18/95 (18%), Positives = 38/95 (40%), Gaps = 13/95 (13%)
Query: 30 KYKGYCIDLIEEI-RKLVGFEYEIFVAPDNSFGNMDENGQWNGMIKELIEKRADIALGSL 88
+ GY I+++ I + ++ + E +W+G+ L R ++A+ +L
Sbjct: 28 ELTGYEIEVVRAIFKDSDKYDVKF------------EKTEWSGVFAGLDADRYNMAVNNL 75
Query: 89 SVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
S ER + P + ++ K + SL
Sbjct: 76 SYTKERAEKYLYAAPIAQNPNVLVVKKDDSSIKSL 110
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 52.4 bits (126), Expect = 8e-08
Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 14/96 (14%)
Query: 30 KYKGYCIDLIEEI-RKLVGFEYEI-FVAPDNSFGNMDENGQWNGMIKELIEKRADIALGS 87
K +G+ +++ +++ + L+G ++ FV + ++ + + D+ L +
Sbjct: 76 KNQGFDVEIAKDLAKDLLGSPDKVEFVLTE-----------AANRVEYVRSGKVDLILAN 124
Query: 88 LSVMAERENVVDFTVPYYDLVGITILMKKPKTPTSL 123
+ ER VDF PY V + ++ K K T +
Sbjct: 125 FTQTPERAEAVDFADPYMK-VALGVVSPKNKPITDM 159
>1nep_A EPV20, BNPC2, epididymal secretory protein E1; niemann-PICK C2,
LDL, cholesterol, lipid bindin; HET: NAG; 1.70A {Bos
taurus} SCOP: b.1.18.7 PDB: 2hka_A*
Length = 130
Score = 46.9 bits (111), Expect = 9e-07
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 372 DRDARELFCNVHANILSIPFPFIGVDGTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTFK 431
+ ++ VH ++ IP PF + + C K+ + CP++KD Y Y+N
Sbjct: 45 NTQSQSSKAVVHGIVMGIPVPFPIPE-SDGC--------KSGIRCPIEKDKTYNYVNKLP 95
Query: 432 ILDRYPK 438
+ + YP
Sbjct: 96 VKNEYPS 102
>1xt8_A Putative amino-acid transporter periplasmic solut protein; ABC
transport, cysteine uptake; 2.00A {Campylobacter jejuni}
SCOP: c.94.1.1
Length = 292
Score = 46.6 bits (111), Expect = 7e-06
Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 14/89 (15%)
Query: 30 KYKGYCIDLIEEI-RKLVGFEYEI-FVAPDNSFGNMDENGQWNGMIKELIEKRADIALGS 87
+GY I L + I ++L G E ++ FV + ++ L + DI L +
Sbjct: 65 NNQGYDIALAKRIAKELFGDENKVQFVLVE-----------AANRVEFLKSNKVDIILAN 113
Query: 88 LSVMAERENVVDFTVPYYDLVGITILMKK 116
+ +R VDF PY V + + + K
Sbjct: 114 FTQTPQRAEQVDFCSPYMK-VALGVAVPK 141
>2vha_A Periplasmic binding transport protein; periplasmic binding protein,
ligand binding, ultrahigh resolution; HET: GLU; 1.00A
{Shigella flexneri} PDB: 2ia4_A*
Length = 287
Score = 46.2 bits (110), Expect = 1e-05
Identities = 19/93 (20%), Positives = 28/93 (30%), Gaps = 18/93 (19%)
Query: 30 KYKGYCIDLIEEIRKLVGFEYEI------FVAPDNSFGNMDENGQWNGMIKELIEKRADI 83
K GY D I + V + + I L D
Sbjct: 38 KVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPIT-----------SQNRIPLLQNGTFDF 86
Query: 84 ALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
GS + ER+ F+ + +VG +L KK
Sbjct: 87 ECGSTTNNVERQKQAAFSDTIF-VVGTRLLTKK 118
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
transport, ABC transport, virulence factor, receptor;
1.49A {Campylobacter jejuni}
Length = 259
Score = 42.3 bits (100), Expect = 2e-04
Identities = 19/103 (18%), Positives = 46/103 (44%), Gaps = 18/103 (17%)
Query: 16 PFVMREESEGGGGVKYKGYCIDLIEEI-RKLVGFEYEI-FVAPDNSFGNMDENGQWNGMI 73
+ + +++ G + KG+ +D+ + + + ++G + +I VA +
Sbjct: 50 HYALLDQATG----EIKGFEVDVAKLLAKSILGDDKKIKLVAVN-----------AKTRG 94
Query: 74 KELIEKRADIALGSLSVMAERENVVDFTVPYYDLVGITILMKK 116
L D + + ++ ER+ + +F+ PYY I +L+ K
Sbjct: 95 PLLDNGSVDAVIATFTITPERKRIYNFSEPYYQ-DAIGLLVLK 136
Score = 27.7 bits (62), Expect = 6.4
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 352 DLQMVGDEFSRKPYAIAVQQDRDA 375
+++ D F + Y I ++D A
Sbjct: 211 KSEILPDSFEPQSYGIVTKKDDPA 234
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 38.3 bits (88), Expect = 0.006
Identities = 49/314 (15%), Positives = 92/314 (29%), Gaps = 81/314 (25%)
Query: 144 NLDGE--QMKYLIQVNPPGDILPEVIRAIIL---MQNITDA--GIL----FDDSFSGGEA 192
++D E + +Y + DIL A + +++ D IL D +
Sbjct: 6 HMDFETGEHQYQYK-----DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHII---MS 57
Query: 193 PKNLSGRLVAATWWLFGFIIIASYTANLAA-FLTVSRLDTPIESLDDLSKQYKIQYAPLN 251
+SG T LF + S + F+ + L YK +P+
Sbjct: 58 KDAVSG-----TLRLFW--TLLSKQEEMVQKFVE-----------EVLRINYKFLMSPIK 99
Query: 252 GSAAMTYFQRMADIEGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEA 311
QR + R Y +D ND+ V KY +
Sbjct: 100 ------TEQRQPSMMTRMYIEQRDRLYNDN--------------QVFAKYN-----VSRL 134
Query: 312 KLPNSLEEAVQRVRDSKSSS-EGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQ 370
+ L +A+ +R +K+ +G G + + C V + K + + ++
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTW----VALDVCLSYKVQCKMDFKIFWLNLK 190
Query: 371 QDRDARELFCNVHANILSIPFPFIGVDGTSVCSSIFDTDGKTKVSCPLKKDHVYRYINTF 430
+ + +L I + TS + L+ + +
Sbjct: 191 NCNSPETVLEML-QKLLYQ----IDPNWTSRSDHSSNI--------KLRIHSIQAELRRL 237
Query: 431 KILDRYPKCSKDLD 444
Y C L
Sbjct: 238 LKSKPYENCLLVLL 251
>3ldc_A Calcium-gated potassium channel MTHK; transmembrane, ION channel,
open conformation, IO transport; 1.45A
{Methanothermobacter thermautotrophicusorganism_taxid}
PDB: 3lde_A 3r65_A 3ous_A 3ldd_A
Length = 82
Score = 27.7 bits (62), Expect = 2.1
Identities = 8/33 (24%), Positives = 10/33 (30%)
Query: 192 APKNLSGRLVAATWWLFGFIIIASYTANLAAFL 224
+P G T + G A L FL
Sbjct: 49 SPHTPLGMYFTCTLIVLGIGTFAVAVERLLEFL 81
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest
center for structural genomics; 2.99A {Leptotrichia
buccalis c-1013-b}
Length = 266
Score = 29.4 bits (66), Expect = 2.2
Identities = 8/54 (14%), Positives = 19/54 (35%)
Query: 14 QEPFVMREESEGGGGVKYKGYCIDLIEEIRKLVGFEYEIFVAPDNSFGNMDENG 67
QE + ++ + Y L+E ++K +Y + + + G
Sbjct: 41 QEVNQLMNNKIIFDDIREENYAWVLLETLQKYTDTDYYLHWSNSHIGFGKYNEG 94
>3ouf_A Potassium channel protein; ION channel, membrane, membrane protein;
1.55A {Bacillus cereus} PDB: 3t4z_A 3tcu_A 3t1c_A 3tet_A
3t4d_A 3t2m_A 3e86_A 3e83_A 3e89_A 3e8b_A 3e8f_A 3e8g_A
3e8h_A 3k0d_A 3k0g_A 3k06_A 3k08_A 3k04_A 3k03_A
Length = 97
Score = 27.5 bits (61), Expect = 2.7
Identities = 6/41 (14%), Positives = 17/41 (41%)
Query: 189 GGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRL 229
G +P+ G++ + G ++ + LA + + +
Sbjct: 50 GDFSPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPSI 90
>3tbd_A Netrin-G2, laminet-2; laminin N-terminal domain, domain VI,
LE-domain, N neuronal cell adhesion molecule, netrin G
ligand 2, nervous system; HET: NAG; 1.80A {Homo sapiens}
PDB: 3zyg_A* 3zyi_B*
Length = 338
Score = 29.1 bits (64), Expect = 2.9
Identities = 12/57 (21%), Positives = 20/57 (35%)
Query: 329 SSSEGFGYLGDATDIRYLVMTNCDLQMVGDEFSRKPYAIAVQQDRDARELFCNVHAN 385
S++G TD+R ++ + Y A+ CN+HAN
Sbjct: 221 ESAKGLKEFFTLTDLRMRLLRPALGGTYVQRENLYKYFYAISNIEVIGRCKCNLHAN 277
>1rcw_A CT610, CADD; iron, DI-iron, redox enzyme, metallo enzyme,
oxidoreductase,; 2.50A {Chlamydia trachomatis} SCOP:
a.132.1.4
Length = 231
Score = 28.7 bits (63), Expect = 3.9
Identities = 14/115 (12%), Positives = 31/115 (26%), Gaps = 5/115 (4%)
Query: 206 WLFGFIIIASYTANLAAFLTVSRLDTPIESLDDLSKQYKIQYAPLNGSAAMTYFQRMADI 265
+ S A +AA + I + +Y + YF +
Sbjct: 121 TFMRWCTGDSLAAGVAALYSYESQIPRI---AREKIRGLTEYFGFSNPEDYAYFTEHEEA 177
Query: 266 EGRFYEIWKDMSLNDSLSDVERAKLAVWDYPVSDKYTKMWQAMKEAKLPNSLEEA 320
+ R K + D ++ A + V+ + + S ++
Sbjct: 178 DVRHAREEKALIEMLLKDDADKVLEASQE--VTQSLYGFLDSFLDPGTCCSCHQS 230
>2q67_A Potassium channel protein; inverted teepee, helix bundle, tetramer,
central cavity, ION metal transport, membrane protein;
2.30A {Bacillus cereus} PDB: 2q68_A 2q6a_A 2q69_A 2ahy_A
2ahz_A
Length = 114
Score = 26.8 bits (59), Expect = 6.4
Identities = 6/41 (14%), Positives = 17/41 (41%)
Query: 189 GGEAPKNLSGRLVAATWWLFGFIIIASYTANLAAFLTVSRL 229
G +P+ G++ + G ++ + LA + + +
Sbjct: 67 GNFSPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPSI 107
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.137 0.410
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,050,394
Number of extensions: 437118
Number of successful extensions: 944
Number of sequences better than 10.0: 1
Number of HSP's gapped: 896
Number of HSP's successfully gapped: 75
Length of query: 444
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 347
Effective length of database: 3,993,456
Effective search space: 1385729232
Effective search space used: 1385729232
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 (21.8 bits)
S2: 59 (26.5 bits)