RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1412
(504 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 = 382 bits (981), Expect = e-124
Identities = 185/545 (33%), Positives = 277/545 (50%), Gaps = 61/545 (11%)
Query: 11 GLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTAEPALMYDSVHVLAAGLALL---- 66
G ++D + + + + ++ + AL YD+V V+ L
Sbjct: 235 GFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQR 294
Query: 67 -DKSSVIKTSNLSCDLEVPWRDGLSLYNYIN----------------------TLDLLKL 103
+ S + + VPW G+ + + T+++++L
Sbjct: 295 IEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMEL 354
Query: 104 KREELRKVGHWTPAEGINITDRSAFYETSTNNVTLIVMTREEKPYVMVK-NDANLTGNAM 162
K RK+G+W+ + + +T+ T++V T E PYVM+K N A L GN
Sbjct: 355 KTNGPRKIGYWSEVDKMVLTEDDTSG---LEQKTVVVTTILESPYVMMKANHAALAGNER 411
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
+EG+C+DL IA GF + L +V D YG D +TK WNG+V EL+ KAD+A+A +T
Sbjct: 412 YEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLT 471
Query: 223 INYARESVIDFTKPFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTL 282
I RE VIDF+KPFM+LGI I+ K P +FSF++PLA EIW+ ++ AY+ VS L
Sbjct: 472 ITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVL 531
Query: 283 FVMARFSPYEWSNPH---PCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGS 339
F+++RFSPYEW +S N+F + NS WF G F++QG+ + S
Sbjct: 532 FLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGA---DISPRSLS 588
Query: 340 SRTLD--------------TALDSKIEIYQKMWRYMESKKCILFLGGQGDETFVTIDLSQ 385
R + TA + ++M +ES + L Q + + T+D
Sbjct: 589 GRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAED---LSKQTEIAYGTLDSGS 645
Query: 386 RAD----SKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVL--EGDYAFLMESTMLDYEVQ 439
+ SKI ++ KMW YM S PSVFV EGV RV +G YA+L+ESTM +Y Q
Sbjct: 646 TKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQ 705
Query: 440 R-NCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNTGDVC 498
R C+ ++GG LDSKGYGIATPKGS ++LA+L+L E+G + L +KWW + G+
Sbjct: 706 RKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGLLDKLKNKWWYDKGECG 765
Query: 499 NRDED 503
+D
Sbjct: 766 AKDSG 770
>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 = 271 bits (694), Expect = 6e-88
Identities = 143/388 (36%), Positives = 192/388 (49%), Gaps = 93/388 (23%)
Query: 117 AEGINITDRSAFYETSTNNVTLIVMTREEKPYVMVK-NDANLTGNAMFEGFCIDLLKSIA 175
+ NITD S +N +LIV T E+PYV+ K +D L GN FEG+CIDLL+ ++
Sbjct: 1 GKPANITD-------SLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELS 53
Query: 176 AQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTK 235
+GF + +RLV D YG D +WNG+V+EL+D KADLAVA + I Y RE VIDF+K
Sbjct: 54 TILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSK 113
Query: 236 PFMNLGIGILFKVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSN 295
PFM LGI IL++ P +FSF+N ++ R S
Sbjct: 114 PFMTLGISILYRKPNGTNPGVFSFLNGGSLVPR---------------GSERMESPIDS- 157
Query: 296 PHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQ 355
++ G T+ SKI Y
Sbjct: 158 -------------ADDLAKQTKIEYGA--------------VEDGATMTFFKKSKISTYD 190
Query: 356 KMWRYMESKKCILFLGGQGDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEE 415
KMW +M S++ SV V EE
Sbjct: 191 KMWAFMSSRR----------------------------------------QSVLVKSNEE 210
Query: 416 GVKRVLEGDYAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAIL 475
G++RVL DYAFLMEST +++ QRNCNLTQIGGL+DSKGYG+ TP GSP+RD+I++AIL
Sbjct: 211 GIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAIL 270
Query: 476 ELQEKGTIQMLYDKWWKNTGDVCNRDED 503
+LQE+G + M+ +KWW+ G C +E
Sbjct: 271 QLQEEGKLHMMKEKWWRGNG--CPEEES 296
>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 = 163 bits (414), Expect = 4e-47
Identities = 70/166 (42%), Positives = 98/166 (59%), Gaps = 6/166 (3%)
Query: 134 NNVTLIVMTREEKPYVMVK-NDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTY 192
+N +LIV T E+PYV+ K +D L GN FEG+CIDLL+ ++ +GF + +RLV D Y
Sbjct: 2 SNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTHLGFTYEIRLVEDGKY 61
Query: 193 GVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQ 252
G D +WNG+V+EL+D KADLAVA + I Y RE VIDF+KPFM LGI IL++ T
Sbjct: 62 GAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREEVIDFSKPFMTLGISILYRKGTPI 121
Query: 253 PTRLFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSNPHP 298
+ + LA + + A + T F ++ S Y+
Sbjct: 122 DS-----ADDLAKQTKIEYGAVEDGATMTFFKRSKISTYDKMWAFM 162
Score = 148 bits (376), Expect = 1e-41
Identities = 69/146 (47%), Positives = 92/146 (63%), Gaps = 5/146 (3%)
Query: 350 KIEIYQKMWRYMESKKCILFLGGQGDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVF 409
+ + + I + + T SKI Y KMW +M S+R SV
Sbjct: 116 RKGTPIDSADDLAKQTKIEYGAVEDGATMTFF-----KRSKISTYDKMWAFMSSRRQSVL 170
Query: 410 VSDYEEGVKRVLEGDYAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSPWRDR 469
V EEG++RVL DYAFLMEST +++ QRNCNLTQIGGL+DSKGYG+ TP GSP+RD+
Sbjct: 171 VKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDK 230
Query: 470 ISLAILELQEKGTIQMLYDKWWKNTG 495
I+LAIL+LQE+G + M+ +KWW+ G
Sbjct: 231 ITLAILKLQEQGKLHMMKEKWWRGNG 256
>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 = 145 bits (368), Expect = 1e-40
Identities = 50/177 (28%), Positives = 84/177 (47%), Gaps = 5/177 (2%)
Query: 135 NVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGV 194
V L V+T E+P+VMV + L ++GF ID+L +++ +GF++ + + PDH YG
Sbjct: 2 GVVLRVVTVLEEPFVMVSENV-LGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGS 60
Query: 195 YDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPT 254
E WNG+V EL+ K+AD+ ++++TI RE+V+DFT +M+ +G+L + TS +
Sbjct: 61 PQ-EDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRGTSIQS 119
Query: 255 R---LFSFMNPLAVEIWLYVLAAYLLVSFTLFVMARFSPYEWSNPHPCLAESPIVEN 308
P + V + F W + V
Sbjct: 120 LQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLE 176
Score = 131 bits (331), Expect = 3e-35
Identities = 39/113 (34%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 390 KIEIYQKMWRYMESKRPSVF-VSDYEEGVKRVLEGDYAFLMESTMLDYEVQRN--CNLTQ 446
+ +Y +MWR + S V + + G+++V G+YAF+ ++ +L+Y + C+
Sbjct: 153 RDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYT 212
Query: 447 IGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNTGDVCN 499
+G + +GYGIA GSP+RD S ILELQ+ G + +L KWW G C+
Sbjct: 213 VGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNGQ-CD 264
>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 = 140 bits (354), Expect = 2e-38
Identities = 59/120 (49%), Positives = 77/120 (64%), Gaps = 1/120 (0%)
Query: 135 NVTLIVMTREEKPYVMVKNDAN-LTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYG 193
N T++V T E PYVM+K + L GN +EG+C+DL IA GF + L +V D YG
Sbjct: 3 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYG 62
Query: 194 VYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQP 253
D +TK WNG+V EL+ KAD+A+A +TI RE VIDF+KPFM+LGI I+ K T
Sbjct: 63 ARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIE 122
Score = 134 bits (339), Expect = 2e-36
Identities = 59/115 (51%), Positives = 78/115 (67%), Gaps = 4/115 (3%)
Query: 388 DSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLE--GDYAFLMESTMLDYEVQRN-CNL 444
SKI ++ KMW YM S PSVFV EGV RV + G YA+L+ESTM +Y QR C+
Sbjct: 149 RSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDT 208
Query: 445 TQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNTGDVCN 499
++GG LDSKGYGIATPKGS + ++LA+L+L E+G + L +KWW + G+ C
Sbjct: 209 MKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGE-CG 262
>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 = 108 bits (270), Expect = 1e-26
Identities = 49/179 (27%), Positives = 72/179 (40%), Gaps = 37/179 (20%)
Query: 134 NNVTLIVMTREEKPYVMVKNDA--------------------------------NLTGNA 161
+ L ++T ++P+V VK T
Sbjct: 2 MSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQ 61
Query: 162 MFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDH----ETKEWNGIVKELMDKKADLA 217
GFCIDLL +A + F + + LV D +G + KEWNG++ EL+ +AD+
Sbjct: 62 CCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMI 121
Query: 218 VASMTINYARESVIDFTKPFMNLGIGILFKVPTS-QPTRLFSFMNPLAVEIWLYVLAAY 275
VA +TIN R I+F+KPF G+ IL K T NP I+ V +
Sbjct: 122 VAPLTINNERAQYIEFSKPFKYQGLTILVKKGTRITGINDPRLRNPSDKFIYATVKQSS 180
Score = 95.1 bits (236), Expect = 5e-22
Identities = 32/141 (22%), Positives = 58/141 (41%), Gaps = 10/141 (7%)
Query: 355 QKMWRYMESKKCILFLGGQGDETFVTIDLSQRADSKIEIYQKMWRYMESKRPSVFVSDYE 414
+ F+ ++ V + M+R+ME
Sbjct: 157 TGINDPRLRNPSDKFIYATVKQSSV-----DIYFRRQVELSTMYRHMEKHN----YESAA 207
Query: 415 EGVKRVLEGD-YAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSPWRDRISLA 473
E ++ V + +AF+ +S +L++E + C+L G L G+GI K SPW+ +SL+
Sbjct: 208 EAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLS 267
Query: 474 ILELQEKGTIQMLYDKWWKNT 494
IL+ E G ++ L W +
Sbjct: 268 ILKSHENGFMEDLDKTWVRYQ 288
>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 = 99.3 bits (247), Expect = 2e-23
Identities = 41/140 (29%), Positives = 70/140 (50%), Gaps = 27/140 (19%)
Query: 133 TNNVTLIVMTREEKPYVMVKNDANLTGNAM-------------------------FEGFC 167
++ L ++T EE P+V+V++ LT + +GFC
Sbjct: 2 PDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFC 61
Query: 168 IDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYAR 227
ID+LK ++ V F + L LV + +G WNG++ E++ ++A +AV S+TIN R
Sbjct: 62 IDILKKLSRTVKFTYDLYLVTNGKHGKK--VNNVWNGMIGEVVYQRAVMAVGSLTINEER 119
Query: 228 ESVIDFTKPFMNLGIGILFK 247
V+DF+ PF+ GI ++
Sbjct: 120 SEVVDFSVPFVETGISVMVS 139
Score = 72.0 bits (176), Expect = 3e-14
Identities = 30/108 (27%), Positives = 50/108 (46%), Gaps = 5/108 (4%)
Query: 392 EIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGDY-AFLMESTMLDYEVQRN--CNLTQIG 448
+ + YM E+ + + G AF+ ++ +L+Y+ R+ C L IG
Sbjct: 174 RNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIG 233
Query: 449 G--LLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWKNT 494
+ + GYGIA KGSPW+ +I LA+L+ G ++ L W
Sbjct: 234 SGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGI 281
>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 = 92.4 bits (229), Expect = 5e-21
Identities = 45/151 (29%), Positives = 70/151 (46%), Gaps = 38/151 (25%)
Query: 133 TNNVTLIVMTREEKPYVMVK-------------------NDANLTGN-----------AM 162
+N + L V+T E P+V + ND+++
Sbjct: 2 SNKLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVP 61
Query: 163 FE------GFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADL 216
+ G+CIDLL+ +A + F F L +V D YG + + W G+V +L+ A++
Sbjct: 62 IKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAW--KNGHWTGLVGDLLSGTANM 119
Query: 217 AVASMTINYARESVIDFTKPFMNLGIGILFK 247
AV S +IN AR VIDFT PF + +GIL +
Sbjct: 120 AVTSFSINTARSQVIDFTSPFFSTSLGILVR 150
Score = 70.9 bits (173), Expect = 1e-13
Identities = 33/106 (31%), Positives = 51/106 (48%), Gaps = 9/106 (8%)
Query: 392 EIYQKMWRYMESKRPSVFVSDYEEGVKRVLEG---DYAFLMESTMLDYEVQRN--CNLTQ 446
+ + +M YM V +GV+ + AF+M+ +LDYEV + C L
Sbjct: 187 QSFPEMHEYMRRYN----VPATPDGVQYLKNDPEKLDAFIMDKALLDYEVSIDADCKLLT 242
Query: 447 IGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKWWK 492
+G +GYGI P SP IS I + + G + +L+DKW+K
Sbjct: 243 VGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYK 288
>3om0_A Glutamate receptor, ionotropic kainate 5; membrane protein, ION
channel; HET: NAG BMA GOL; 1.40A {Rattus norvegicus}
PDB: 3om1_A* 3qlu_A* 3qlv_A
Length = 393
Score = 67.1 bits (163), Expect = 3e-12
Identities = 31/137 (22%), Positives = 53/137 (38%), Gaps = 24/137 (17%)
Query: 11 GLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYIN-TAEPALMYDSVHVLAAGLALLDKS 69
G ++ + S + L + WR+ Y ALM+D+VHV+ + + L++S
Sbjct: 247 GFSMFNTSHPFYPEFVRS-LNMSWRENCEASTYPGPALSAALMFDAVHVVVSAVRELNRS 305
Query: 70 SVIKTSNLSCDLEVPWRDGLSLYNYIN----------------------TLDLLKLKREE 107
I L+C W G SL NY+ TL +L+ R+
Sbjct: 306 QEIGVKPLACTSANIWPHGTSLMNYLRMVEYDGLTGRVEFNSKGQRTNYTLRILEKSRQG 365
Query: 108 LRKVGHWTPAEGINITD 124
R++G W + +
Sbjct: 366 HREIGVWYSNRTLAMNA 382
>3h6g_A Glutamate receptor, ionotropic kainate 2; membrane protein
glycoprotein, cell junction, cell membrane,
glycoprotein, ION transport; HET: NAG TLA; 2.70A {Rattus
norvegicus} PDB: 3h6h_A* 3qlv_C 3qlu_C* 3qlt_A* 3olz_A*
Length = 395
Score = 64.7 bits (157), Expect = 2e-11
Identities = 32/109 (29%), Positives = 49/109 (44%), Gaps = 26/109 (23%)
Query: 39 SLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYIN-- 96
L + T + ALMYD+VHV++ + + + S+L C+ PWR G + I
Sbjct: 279 GLLDGFMTTDAALMYDAVHVVSVAV---QQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEA 335
Query: 97 ---------------------TLDLLKLKREELRKVGHWTPAEGINITD 124
LD++ LK E L K+G W PA G+N+T+
Sbjct: 336 HWEGLTGRITFNKTNGLRTDFDLDVISLKEEGLEKIGTWDPASGLNMTE 384
>3hsy_A Glutamate receptor 2; ligand-gated ION channel, synapse, cell CELL
membrane, endoplasmic reticulum, glycoprotein, ION TRA
ionic channel; HET: NAG BMA; 1.75A {Rattus norvegicus}
PDB: 3h5v_A* 3h5w_A 3o2j_A* 2wjw_A* 2wjx_A 3n6v_A
Length = 376
Score = 64.0 bits (155), Expect = 3e-11
Identities = 20/117 (17%), Positives = 42/117 (35%), Gaps = 27/117 (23%)
Query: 34 WRDGLSLYNYINTAEPALMYDSVHVLAAGLALL-----DKSSVIKTSNLSCDLEVPWRDG 88
++ + AL YD+V V+ L + S + + VPW G
Sbjct: 258 EKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQG 317
Query: 89 LSLYNYIN----------------------TLDLLKLKREELRKVGHWTPAEGINIT 123
+ + + T+++++LK RK+G+W+ + + +T
Sbjct: 318 VEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVT 374
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 61.5 bits (150), Expect = 5e-11
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 19/111 (17%)
Query: 137 TLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYD 196
L+V TR P+V+ GF IDL +SIA Q+G L
Sbjct: 4 PLLVATRVIPPFVLSNKGE-------LSGFSIDLWRSIATQIGIESKL------------ 44
Query: 197 HETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFK 247
E ++ + D K +L +A+++I RE DF+ P G+ I+ +
Sbjct: 45 IEYSSVPELISAIKDNKVNLGIAAISITAEREQNFDFSLPIFASGLQIMVR 95
Score = 48.0 bits (115), Expect = 2e-06
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 430 ESTMLDYEVQR-NCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYD 488
+L Y + +G +L + YGI P SP+R I+ A+L L+E GT Q LYD
Sbjct: 159 APVLLFYAANEGKGKVEIVGSILREESYGIILPNNSPYRKPINQALLNLKENGTYQSLYD 218
Query: 489 KW 490
KW
Sbjct: 219 KW 220
>4dz1_A DALS D-alanine transporter; D-alanine binding, periplasmic,
transport protein; 1.90A {Salmonella enterica} PDB:
3r39_A 4f3s_A
Length = 259
Score = 60.8 bits (148), Expect = 2e-10
Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 13/85 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
+G ++L S + W+G++ + +AD+A + ++
Sbjct: 51 LQGIDLELFSSYCQSRHCK-------------LNITEYAWDGMLGAVASGQADVAFSGIS 97
Query: 223 INYARESVIDFTKPFMNLGIGILFK 247
I R+ VIDF++P+ ++
Sbjct: 98 ITDKRKKVIDFSEPYYINSFYLVSM 122
Score = 47.0 bits (112), Expect = 6e-06
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 424 DYAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTI 483
D AF+ E ++ ++ + + GIA KGSP RD +L L+ Q I
Sbjct: 186 DLAFIEEPVYFTFKNKKKMPIESRYVFKNVDQLGIAFKKGSPVRDDFNLW-LKEQGPQKI 244
Query: 484 QMLYDKWWKNT 494
+ D W K+
Sbjct: 245 SGIVDSWMKHH 255
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
signaling protein; 2.04A {Bordetella pertussis} PDB:
3mpl_A
Length = 267
Score = 60.1 bits (146), Expect = 2e-10
Identities = 18/99 (18%), Positives = 41/99 (41%), Gaps = 19/99 (19%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
P+ + + D G +L+ + + G F + ++
Sbjct: 44 PFTLFRTDEQFGG------ISAAVLQLLQLRTGLDFEII------------GVDTVEELI 85
Query: 207 KELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245
+L +AD+ ++ +N ARES + F++P++ G+ I+
Sbjct: 86 AKLRSGEADM-AGALFVNSARESFLSFSRPYVRNGMVIV 123
Score = 38.5 bits (90), Expect = 0.003
Identities = 16/88 (18%), Positives = 28/88 (31%), Gaps = 6/88 (6%)
Query: 408 VFVSDYEEGVKRVLEGD-YAFLMESTMLDYEVQRN--CNLTQIGGL-LDSKGYGIATPKG 463
V + E + V G A + Y V R L L L +AT +G
Sbjct: 164 VTADNPSEAMLMVANGQADAVVQTQISASYYVNRYFAGKLRIASALDLPPAEIALATTRG 223
Query: 464 SP-WRDRISLAILELQEKGTIQMLYDKW 490
++ A+ + + + +W
Sbjct: 224 QTELMSILNKALYSI-SNDELASIISRW 250
>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 = 59.7 bits (145), Expect = 3e-10
Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 13/85 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
GF +DLL ++ G Y+ + W+ + L K+ D+ ++ +T
Sbjct: 63 IVGFDVDLLDAVMKAAGLD-------------YELKNIGWDPLFASLQSKEVDMGISGIT 109
Query: 223 INYARESVIDFTKPFMNLGIGILFK 247
I R+ DF+ P+ IL K
Sbjct: 110 ITDERKQSYDFSDPYFEATQVILVK 134
Score = 41.9 bits (99), Expect = 2e-04
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 451 LDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYDKW 490
S+ YG+ PK S + ++ A+ + G +Y KW
Sbjct: 221 FASEYYGMIFPKNSELKAKVDEALKNVINSGKYTEIYKKW 260
>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 = 59.1 bits (144), Expect = 4e-10
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 13/85 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
+ GF +DL +IA ++ + L + +++GI+ L K DLA+A +T
Sbjct: 24 YVGFDVDLWAAIAKELKLDYEL-------------KPMDFSGIIPALQTKNVDLALAGIT 70
Query: 223 INYARESVIDFTKPFMNLGIGILFK 247
I R+ IDF+ + G+ ++ K
Sbjct: 71 ITDERKKAIDFSDGYYKSGLLVMVK 95
Score = 42.6 bits (101), Expect = 1e-04
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 441 NCNLTQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
N +G L+++ YGIA PKGS RD+++ A+ L+E GT +Y KW
Sbjct: 170 NGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKW 220
>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 = 59.3 bits (144), Expect = 4e-10
Identities = 18/123 (14%), Positives = 40/123 (32%), Gaps = 20/123 (16%)
Query: 137 TLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYD 196
+ E P+ V D ++G D+ + I ++G V
Sbjct: 14 FARIAIANEPPFTAVGADGKVSG------AAPDVAREIFKRLGVADV------------V 55
Query: 197 HETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVPTSQPTRL 256
E+ ++ L + D A + + R + + +++P + + P L
Sbjct: 56 ASISEYGAMIPGLQAGRHDAITAGLFMKPERCAAVAYSQPILCDAEAFA--LKKGNPLGL 113
Query: 257 FSF 259
S+
Sbjct: 114 KSY 116
Score = 36.1 bits (84), Expect = 0.016
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 6/89 (6%)
Query: 408 VFVSDYEEGVKRVLEG--DYAFLMESTMLDYEVQRNCNLTQIGGLLDSK---GYGIATPK 462
+ V D + G+K + +G D L ++ D + N ++ ++ G A K
Sbjct: 150 IVVPDGQSGLKMLQDGRIDVYSLPVLSINDLVSKANDPNVEVLAPVEGAPVYCDGAAFRK 209
Query: 463 GSP-WRDRISLAILELQEKGTIQMLYDKW 490
G RD + + +L+E G + + +
Sbjct: 210 GDEALRDAFDVELAKLKESGEFAKIIEPY 238
>4f3p_A Glutamine-binding periplasmic protein; ssgcid, structural genomics,
GLUT seattle structural genomics center for infectious
disease; 2.40A {Burkholderia pseudomallei}
Length = 249
Score = 58.8 bits (143), Expect = 6e-10
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 13/83 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
+ GF +DL IA G+ + + + ++ G++ L + D+A++ MT
Sbjct: 45 YVGFDLDLWAEIAKGAGWTYKI-------------QPMDFAGLIPALQTQNIDVALSGMT 91
Query: 223 INYARESVIDFTKPFMNLGIGIL 245
I R IDF+ P+ + G+ +
Sbjct: 92 IKEERRKAIDFSDPYYDSGLAAM 114
Score = 46.9 bits (112), Expect = 5e-06
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 426 AFLMESTMLDYEVQRNCN--LTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTI 483
A + ++ + + V + G + YGI PKGSP +++ + ++ G
Sbjct: 174 AAMHDTPNVLFFVNNEGKGRVKVAGAPVSGDKYGIGFPKGSPLVAKVNAELARMKADGRY 233
Query: 484 QMLYDKW 490
+Y KW
Sbjct: 234 AKIYKKW 240
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 58.6 bits (142), Expect = 1e-09
Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 12/84 (14%)
Query: 163 FEGFCIDLLKSIAAQVGFHFV-LRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASM 221
+GF +++ K +A + + V E V+ + K DL +A+
Sbjct: 77 NQGFDVEIAKDLAKDLLGSPDKVEFVL-----------TEAANRVEYVRSGKVDLILANF 125
Query: 222 TINYARESVIDFTKPFMNLGIGIL 245
T R +DF P+M + +G++
Sbjct: 126 TQTPERAEAVDFADPYMKVALGVV 149
Score = 42.8 bits (101), Expect = 2e-04
Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 426 AFLMESTMLDYEVQRNCNLTQIGGLLDSK-GYGIATPKGSP-WRDRISLAILELQEKGTI 483
A ++ +L + N N G L A KG+ + ++ I +++ G +
Sbjct: 208 ALAHDNALLWAWAKENPNFEVAIGNLGPAEFIAPAVQKGNADLLNWVNGEIAAMKKDGRL 267
Query: 484 QMLYDKW 490
+ Y+K
Sbjct: 268 KAAYEKT 274
>3saj_A Glutamate receptor 1; rossman fold, ION channel, membrane,
transport protein; HET: NAG BMA MAN; 2.50A {Rattus
norvegicus}
Length = 384
Score = 58.6 bits (141), Expect = 2e-09
Identities = 21/124 (16%), Positives = 41/124 (33%), Gaps = 27/124 (21%)
Query: 34 WRDGLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSV-----IKTSNLSCDLEVPWRDG 88
RD + AL YD V V+A L + + + + VPW G
Sbjct: 261 SRDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQG 320
Query: 89 LSLYNYIN----------------------TLDLLKLKREELRKVGHWTPAEGINITDRS 126
+ + + TL ++++K + +RK+G+W +
Sbjct: 321 IDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDDKFVPAALE 380
Query: 127 AFYE 130
++
Sbjct: 381 VLFQ 384
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 56.9 bits (138), Expect = 2e-09
Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 13/85 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
GF ID+ ++ ++ + ++ ++ L KK D +A M
Sbjct: 28 IVGFDIDVANAVCKEMQAECSF-------------TNQSFDSLIPSLRFKKFDAVIAGMD 74
Query: 223 INYARESVIDFTKPFMNLGIGILFK 247
+ RE + F++P+ ++
Sbjct: 75 MTPKREQQVSFSQPYYEGLSAVVVT 99
Score = 40.3 bits (95), Expect = 7e-04
Identities = 10/71 (14%), Positives = 24/71 (33%), Gaps = 6/71 (8%)
Query: 426 AFLMESTMLDYEVQRNCNLTQIGGLLDSK-----GYGIATPKGSP-WRDRISLAILELQE 479
+ + ++ N + + G GIA K + I+ A+ +++
Sbjct: 156 GVFGDVAAIGKWLKNNPDYAIMDERASDPDYYGKGLGIAVRKDNDALLQEINAALDKVKA 215
Query: 480 KGTIQMLYDKW 490
+ +KW
Sbjct: 216 SPEYAQMQEKW 226
>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 = 57.3 bits (139), Expect = 2e-09
Identities = 20/101 (19%), Positives = 35/101 (34%), Gaps = 19/101 (18%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
P + D + G F IDL ++ G + +W+
Sbjct: 33 PMGYEEKDGSYIG------FDIDLANAVFKLYGIDVEW-------------QAIDWDMKE 73
Query: 207 KELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFK 247
EL + DL ++ R+ DFT+P+M ++ K
Sbjct: 74 TELKNGTIDLIWNGYSVTDERKQSADFTEPYMVNEQVLVTK 114
Score = 43.5 bits (103), Expect = 9e-05
Identities = 15/115 (13%), Positives = 42/115 (36%), Gaps = 10/115 (8%)
Query: 385 QRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLE---G--DYAFLMESTMLDYEVQ 439
Q S + + + ++ + V Y + +++ G D L++ +Y ++
Sbjct: 133 QAGSSGYDAFNASPKILKDVVANQKVVQYSTFTQALIDLNSGRID-GLLIDRVYANYYLE 191
Query: 440 RN---CNLTQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
++ + + + + + K +I+ L + G Q + +KW
Sbjct: 192 KSGVLDQYNVMPAGYEGESFAVGARKVDKTLIKKINQGFETLYKNGEFQKISNKW 246
>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 = 57.3 bits (139), Expect = 2e-09
Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 13/83 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
GF +DL + +A +G L W+G++ L+ +K D+ ++ MT
Sbjct: 27 VIGFDVDLAREMAKAMGVKLKL-------------VPTSWDGLIPGLVTEKFDIIISGMT 73
Query: 223 INYARESVIDFTKPFMNLGIGIL 245
I+ R ++F +P++ +G +L
Sbjct: 74 ISQERNLRVNFVEPYIVVGQSLL 96
Score = 44.2 bits (105), Expect = 3e-05
Identities = 13/72 (18%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 426 AFLMESTMLDYEVQRNCN--LTQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGT 482
F+ + + + L + L + G A KG P + + ++ + +++ G+
Sbjct: 159 MFIFDLPFNVAFMAQKGQGYLVHLDTSLTYEPLGWAIKKGDPDFLNWLNHFLAQIKHDGS 218
Query: 483 IQMLYDKWWKNT 494
LY++W+ +T
Sbjct: 219 YDELYERWFVDT 230
>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 = 56.9 bits (138), Expect = 2e-09
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 13/84 (15%)
Query: 164 EGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTI 223
GF IDL++ I ++ E ++ + L +++ DL +ASM I
Sbjct: 27 YGFDIDLMQEICRRLHATCTF-------------EAYIFDDLFPALKNREVDLVIASMII 73
Query: 224 NYARESVIDFTKPFMNLGIGILFK 247
R+ F+ P+M +
Sbjct: 74 TDERKKHFIFSLPYMESNSQYITT 97
Score = 39.9 bits (94), Expect = 8e-04
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 455 GYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
GY I +I+ +LE++ GT LY ++
Sbjct: 192 GYSIMANPDQFVLIKKINKILLEMEADGTYLRLYSEY 228
>3kbr_A Cyclohexadienyl dehydratase; pseudomonas aeruginos structural
genomics, PSI-2, protein structure initiative; HET: EPE;
1.66A {Pseudomonas aeruginosa}
Length = 239
Score = 56.6 bits (137), Expect = 3e-09
Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 19/100 (19%)
Query: 146 KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGI 205
KP+ + G F +D+ + +A +G L +VP W +
Sbjct: 26 KPFSYRTEEGGYAG------FDVDMAQRLAESLGAK--LVVVP-----------TSWPNL 66
Query: 206 VKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245
+++ D + D+A++ ++IN R+ F+ P++ G +
Sbjct: 67 MRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPI 106
Score = 49.2 bits (118), Expect = 8e-07
Identities = 8/90 (8%), Positives = 32/90 (35%), Gaps = 5/90 (5%)
Query: 408 VFVSDYEEGVKRVLEG--DYAFLMESTMLDYEVQRNCNLTQI--GGLLDSKGYGIATPKG 463
+ D +++++G D + ++ + + + L + D P+
Sbjct: 150 LVHPDNVTIFQQIVDGKAD-LMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRD 208
Query: 464 SPWRDRISLAILELQEKGTIQMLYDKWWKN 493
++ + + ++ G ++ + W +
Sbjct: 209 EAFKRYVDQWLHIAEQSGLLRQRMEHWLEY 238
>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 = 56.1 bits (136), Expect = 5e-09
Identities = 13/85 (15%), Positives = 29/85 (34%), Gaps = 13/85 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
GF IDL + I+ ++G + ++ ++ L + D + M+
Sbjct: 33 VVGFDIDLAREISNKLGKTLDV-------------REFSFDALILNLKQHRIDAVITGMS 79
Query: 223 INYARESVIDFTKPFMNLGIGILFK 247
I +R I + ++
Sbjct: 80 ITPSRLKEILMIPYYGEEIKHLVLV 104
Score = 43.4 bits (103), Expect = 8e-05
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 5/70 (7%)
Query: 426 AFLMESTMLDYEVQRNCNLTQIGGLLDSK----GYGIATPKGSPW-RDRISLAILELQEK 480
++E ++ ++ L+ L GYGI P +I A+ E++++
Sbjct: 161 VAVLEPSIAQVVLKDFPALSTATIDLPEDQWVLGYGIGVASDRPALALKIEAAVQEIRKE 220
Query: 481 GTIQMLYDKW 490
G + L KW
Sbjct: 221 GVLAELEQKW 230
>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 = 55.8 bits (135), Expect = 5e-09
Identities = 20/113 (17%), Positives = 44/113 (38%), Gaps = 22/113 (19%)
Query: 137 TLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGF--HFVLRLVPDHTYGV 194
L V P+V N F G +D+ +++A + +V
Sbjct: 5 ALKVGVVGNPPFVFYGEGKN--AA--FTGISLDVWRAVAESQKWNSEYV----------- 49
Query: 195 YDHETKEWNGIVKELMDKKADLAVASMTINYARESV--IDFTKPFMNLGIGIL 245
+ + + + + D+ + +++ R ++ I FT+P+ + GIG+L
Sbjct: 50 ---RQNSISAGITAVAEGELDILIGPISVTPERAAIEGITFTQPYFSSGIGLL 99
Score = 47.3 bits (113), Expect = 3e-06
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 430 ESTMLDYEVQR-NCNLTQIGGLLDSKGYGIATPKGSPWRDRISLAILELQEKGTIQMLYD 488
++ Y Q N NL + + YG + SP + I++ +L L I +
Sbjct: 163 RPALIYYTRQNPNLNLEVTEIRVSLEPYGFVLKENSPLQKTINVEMLNLLYSRVIAEFTE 222
Query: 489 KW 490
+W
Sbjct: 223 RW 224
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 55.7 bits (135), Expect = 5e-09
Identities = 20/99 (20%), Positives = 37/99 (37%), Gaps = 19/99 (19%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
PYV + + G F D++K++ Q+ + + W+ ++
Sbjct: 14 PYVYMGPSGQVEG---FG---ADIVKAVCKQMQAVCTI-------------SNQPWDSLI 54
Query: 207 KELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245
L K D M I AR+ +DFT P+ + +
Sbjct: 55 PSLKLGKFDALFGGMNITTARQKEVDFTDPYYTNSVSFI 93
Score = 41.1 bits (97), Expect = 4e-04
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 455 GYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
G GIA KG+ +++ A+ ++ G + K+
Sbjct: 190 GVGIAVKKGNQALLLKLNKALAAIKANGVYAAIVQKY 226
>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 = 56.2 bits (136), Expect = 7e-09
Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 12/84 (14%)
Query: 163 FEGFCIDLLKSIAAQVGFHFV-LRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASM 221
+G+ I L K IA ++ ++ V E V+ L K D+ +A+
Sbjct: 66 NQGYDIALAKRIAKELFGDENKVQFVL-----------VEAANRVEFLKSNKVDIILANF 114
Query: 222 TINYARESVIDFTKPFMNLGIGIL 245
T R +DF P+M + +G+
Sbjct: 115 TQTPQRAEQVDFCSPYMKVALGVA 138
Score = 42.4 bits (100), Expect = 2e-04
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 426 AFLMESTMLDYEVQRNCNLTQIGGLLDSK-GYGIATPKGSP-WRDRISLAILELQEKGTI 483
A ++T+L V+ + + L +K A KG ++ I I++L ++
Sbjct: 197 ALSHDNTLLFAWVKDHPDFKMGIKELGNKDVIAPAVKKGDKELKEFIDNLIIKLGQEQFF 256
Query: 484 QMLYDKWWK 492
YD+ K
Sbjct: 257 HKAYDETLK 265
>3o21_A Glutamate receptor 3; periplasmatic binding protein,
oligomerization, membrane, TR protein; HET: NAG; 2.20A
{Rattus norvegicus} PDB: 3p3w_A
Length = 389
Score = 56.7 bits (136), Expect = 8e-09
Identities = 23/146 (15%), Positives = 50/146 (34%), Gaps = 29/146 (19%)
Query: 1 MYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTAEPALMYDSVHVLA 60
M+ ++ G +++ + + + + + R+ N AL +D++ V+A
Sbjct: 233 MHGGANIT--GFQIVNNENPMVQQFIQRWVRLDEREFPEAKNAPLKYTSALTHDAILVIA 290
Query: 61 AGLALLDKSSV-----IKTSNLSCDLEVPWRDGLSLYNYIN------------------- 96
L + V + + VPW G+ + +
Sbjct: 291 EAFRYLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRR 350
Query: 97 ---TLDLLKLKREELRKVGHWTPAEG 119
T+D+ ++K RK G+W E
Sbjct: 351 TNYTIDVYEMKVSGSRKAGYWNEYER 376
>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 = 55.8 bits (135), Expect = 8e-09
Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 13/83 (15%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
GF IDL K+I+ ++G + ++ ++ L + D +A M+
Sbjct: 53 VVGFDIDLAKAISEKLGKQLEV-------------REFAFDALILNLKKHRIDAILAGMS 99
Query: 223 INYARESVIDFTKPFMNLGIGIL 245
I +R+ I + + ++
Sbjct: 100 ITPSRQKEIALLPYYGDEVQELM 122
Score = 44.2 bits (105), Expect = 5e-05
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 5/70 (7%)
Query: 426 AFLMESTMLDYEVQRNCNLTQIGGLLDSK----GYGIATPKGSP-WRDRISLAILELQEK 480
++E ++ ++ NL L + G G+ K P I AI +L+ +
Sbjct: 182 VAVLEPSVGRVVLKDFPNLVATRLELPPECWVLGCGLGVAKDRPEEIQTIQQAITDLKSE 241
Query: 481 GTIQMLYDKW 490
G IQ L KW
Sbjct: 242 GVIQSLTKKW 251
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 54.6 bits (132), Expect = 1e-08
Identities = 17/99 (17%), Positives = 34/99 (34%), Gaps = 20/99 (20%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
PY + + G + ++L ++IA +G + W+ +
Sbjct: 23 PYEFIDQNGKPAG------YNVELTRAIAEVMGMT-------------VEFRLGAWSEMF 63
Query: 207 KELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245
L + D + ++ + R IDFT P + I
Sbjct: 64 SALKSGRVD-VLQGISWSEKRARQIDFTPPHTIVYHAIF 101
Score = 44.2 bits (105), Expect = 4e-05
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 408 VFVSDYEEGVKRVLEG--DYAFLMESTMLDYEVQR-NCNLTQIGGLLDSKGYGIATPKGS 464
V + ++ + G DYA + + + NL + + ++ YG A +G
Sbjct: 142 VLTPTPADALRLLAAGGCDYAVVAMVPGMYIIRENRLTNLVPVARSIAAQRYGYAVRQGD 201
Query: 465 P-WRDRISLAILELQEKGTIQMLYDKW 490
R S + L++ G + + KW
Sbjct: 202 AELLARFSEGLAILRKTGQYEAIRAKW 228
>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 = 53.4 bits (129), Expect = 3e-08
Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 17/83 (20%)
Query: 165 GFCIDLLKSIAAQVGF--HFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
GF IDL + ++ +V +++ ++ L KK D ++S++
Sbjct: 28 GFDIDLGNEMCKRMQVKCTWV---------------ASDFDALIPSLKAKKIDAIISSLS 72
Query: 223 INYARESVIDFTKPFMNLGIGIL 245
I R+ I F+ ++
Sbjct: 73 ITDKRQQEIAFSDKLYAADSRLI 95
Score = 38.0 bits (89), Expect = 0.004
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)
Query: 448 GGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
G G+ K + A+ EL++ GT + K+
Sbjct: 187 DKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGTYDKMAKKY 230
>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 = 52.6 bits (127), Expect = 6e-08
Identities = 21/101 (20%), Positives = 38/101 (37%), Gaps = 23/101 (22%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGF--HFVLRLVPDHTYGVYDHETKEWNG 204
PY + + + G FE +L + + G +V +W+
Sbjct: 17 PYNFINDAGEVDG---FE---RELGDELCKRAGLTCEWV---------------KNDWDS 55
Query: 205 IVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGIL 245
I+ L+ D +A M+I R+ VIDFT+ ++
Sbjct: 56 IIPNLVSGNYDTIIAGMSITDERDEVIDFTQNYIPPTASSY 96
Score = 43.0 bits (102), Expect = 1e-04
Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 2/69 (2%)
Query: 424 DYAFLMESTMLDYEVQRNCNLTQIGG-LLDSKGYGIATPKGSP-WRDRISLAILELQEKG 481
D F ++ + L +G + G G+ + R + AI ++E G
Sbjct: 147 DAVFADRDYLVPIVAESGGELMFVGDDVPLGGGVGMGLRESDGELRGKFDAAITSMKEDG 206
Query: 482 TIQMLYDKW 490
T+ + KW
Sbjct: 207 TLNTMIKKW 215
>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 = 52.4 bits (126), Expect = 1e-07
Identities = 14/85 (16%), Positives = 23/85 (27%), Gaps = 6/85 (7%)
Query: 163 FEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMT 222
G+ D +I V + + L + D S T
Sbjct: 39 VVGYSQDYSNAIVEAVKKKLNKPDLQ------VKLIPITSQNRIPLLQNGTFDFECGSTT 92
Query: 223 INYARESVIDFTKPFMNLGIGILFK 247
N R+ F+ +G +L K
Sbjct: 93 NNVERQKQAAFSDTIFVVGTRLLTK 117
Score = 45.1 bits (107), Expect = 2e-05
Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 7/89 (7%)
Query: 408 VFVSDYEEGVKRVLEG--DYAFLMESTMLDYEV---QRNCNLTQIGGLLDSKGYGIATPK 462
+ D+ + + + G AF+M+ +L E ++ N +G + YG K
Sbjct: 159 ISAKDHGDSFRTLESGRAV-AFMMDDALLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRK 217
Query: 463 GSP-WRDRISLAILELQEKGTIQMLYDKW 490
P ++ + I ++Q G + +DKW
Sbjct: 218 DDPQFKKLMDDTIAQVQTSGEAEKWFDKW 246
>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 = 50.4 bits (121), Expect = 4e-07
Identities = 10/81 (12%), Positives = 29/81 (35%), Gaps = 13/81 (16%)
Query: 165 GFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTIN 224
G+ +++++ A ++G + +G++ + + D A + +
Sbjct: 48 GYEVEVVREAAKRLGLKVEF-------------KEMGIDGMLTAVNSGQVDAAANDIDVT 94
Query: 225 YARESVIDFTKPFMNLGIGIL 245
RE F+ P+ +
Sbjct: 95 KDREEKFAFSTPYKYSYGTAI 115
Score = 40.4 bits (95), Expect = 8e-04
Identities = 7/69 (10%), Positives = 24/69 (34%), Gaps = 4/69 (5%)
Query: 426 AFLMESTMLDYEVQRNCNL---TQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKG 481
L + + + +L + K + + +++ A+ E+ + G
Sbjct: 176 VILNDYYLQTLALAAFPDLNITIHPDIKYMPNKQALVMKKSNAALQKKMNEALKEMSKDG 235
Query: 482 TIQMLYDKW 490
++ L ++
Sbjct: 236 SLTKLSKQF 244
>4eq9_A ABC transporter substrate-binding protein-amino A transport;
structural genomics, niaid; HET: GSH; 1.40A
{Streptococcus pneumoniae}
Length = 246
Score = 49.2 bits (118), Expect = 8e-07
Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 16/85 (18%)
Query: 165 GFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKE--WNGIVKELMDKKADLAVASMT 222
G+ I+++++I YD + ++ W+G+ L + ++AV +++
Sbjct: 31 GYEIEVVRAIFKD--------------SDKYDVKFEKTEWSGVFAGLDADRYNMAVNNLS 76
Query: 223 INYARESVIDFTKPFMNLGIGILFK 247
R + P ++ K
Sbjct: 77 YTKERAEKYLYAAPIAQNPNVLVVK 101
Score = 35.4 bits (82), Expect = 0.028
Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 426 AFLMESTMLDYEVQRN--CNLTQIGGLLDSKGYGIA-TPKGSP-WRDRISLAILELQEKG 481
+ + ++ ++ NL I D + Y +G + + I EL + G
Sbjct: 165 YKIFDKIGVETVIKNQGLDNLKVIELPSDQQPYVYPLLAQGQDELKSFVDKRIKELYKDG 224
Query: 482 TIQMLYDKW 490
T++ L ++
Sbjct: 225 TLEKLSKQF 233
>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 = 49.7 bits (119), Expect = 9e-07
Identities = 14/102 (13%), Positives = 40/102 (39%), Gaps = 20/102 (19%)
Query: 147 PYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEWNGIV 206
P+ D LTG + +++ +++A ++G + +W+ ++
Sbjct: 69 PFTYHDKDGKLTG------YDVEVTRAVAEKLGVKVEF-------------KETQWDSMM 109
Query: 207 KELMDKKADLAVASMTINYA-RESVIDFTKPFMNLGIGILFK 247
L + D+ + + R++ D ++P+ G ++
Sbjct: 110 AGLKAGRFDVVANQVGLTSPERQATFDKSEPYSWSGAVLVAH 151
Score = 37.3 bits (87), Expect = 0.008
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 452 DSKGYGIATPKGSP-WRDRISLAILELQEKGTIQMLYDKW 490
+ G G+ KG+ + S AI EL+ GT++ L +++
Sbjct: 236 EKVGSGLIVNKGNDEAVAKFSTAINELKADGTLKKLGEQF 275
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
transport, ABC transport, virulence factor, receptor;
1.49A {Campylobacter jejuni}
Length = 259
Score = 48.1 bits (115), Expect = 2e-06
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 12/86 (13%)
Query: 163 FEGFCIDLLKSIAAQVGFHFV-LRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASM 221
+GF +D+ K +A + ++LV L + D +A+
Sbjct: 61 IKGFEVDVAKLLAKSILGDDKKIKLVA-----------VNAKTRGPLLDNGSVDAVIATF 109
Query: 222 TINYARESVIDFTKPFMNLGIGILFK 247
TI R+ + +F++P+ IG+L
Sbjct: 110 TITPERKRIYNFSEPYYQDAIGLLVL 135
Score = 40.4 bits (95), Expect = 7e-04
Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 8/86 (9%)
Query: 408 VFVSDYEEGVKRVLEG--DYAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIATPKGSP 465
DY + D AF ++ ++L V + + + + YGI T K P
Sbjct: 177 SEFPDYPSIKAALDAKRVD-AFSVDKSILLGYVDDKSEI--LPDSFEPQSYGIVTKKDDP 233
Query: 466 -WRDRISLAILELQEKGTIQMLYDKW 490
+ + + E K I L KW
Sbjct: 234 AFAKYVDDFVKEH--KNEIDALAKKW 257
>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 = 47.7 bits (114), Expect = 3e-06
Identities = 17/105 (16%), Positives = 36/105 (34%), Gaps = 20/105 (19%)
Query: 146 KPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQ-VGFHFVLRLVPDHTYGVYDHETKEWNG 204
+ +LTG ++ ++L+K + + + F +T E++
Sbjct: 27 PNICFIDEKGDLTG---YD---VELIKELDKRLPHYKFTF-------------KTMEFSN 67
Query: 205 IVKELMDKKADLAVASMTINYARESVIDFTKPFMNLGIGILFKVP 249
++ L K D+ M + RE F K N + +
Sbjct: 68 LLVSLGQHKVDIVAHQMEKSKEREKKFLFNKVAYNHFPLKITVLQ 112
Score = 45.4 bits (108), Expect = 2e-05
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 426 AFLMESTMLDYEVQ-RNCNLTQIGGLLDSKGYGIATPKGSP-WRDRISLAILELQEKGTI 483
A + +D++ + +G +L + K D I A+ E+ + GT+
Sbjct: 174 ATISTPFAVDFQNKTSTIKEKTVGNVLSNAKVYFMFNKNEQTLSDDIDKALQEIIDDGTL 233
Query: 484 QMLYDKW 490
+ L KW
Sbjct: 234 KRLSLKW 240
>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 = 45.0 bits (106), Expect = 5e-05
Identities = 36/253 (14%), Positives = 66/253 (26%), Gaps = 101/253 (39%)
Query: 234 TKPFMNLGIGIL---FKVPTS-----------------QPTRLFSFMNPLA--VEIWLYV 271
T+P L G L VPT+ +PT F+ + E
Sbjct: 6 TRPL-TLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAE----- 59
Query: 272 LAAYLLVSFTLFVMARFSPYEWS---------------------NPHPCLAESPIVENQF 310
L+ F +V + P + + H LA + EN
Sbjct: 60 ----LVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH-ALAAKLLQENDT 114
Query: 311 SVSNSFWFITGTFLRQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFL 370
++ + I ++ ++ +S + ++ +F
Sbjct: 115 TLVKTKELIK-NYITARIMAKRPFDKKSNSALFRAVGEGNAQLV------------AIF- 160
Query: 371 GGQG------DE---------TFVT----------IDLSQRADSKIEIYQK-----MWRY 400
GGQG +E V +L + +++ + W
Sbjct: 161 GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE 220
Query: 401 MESKRPSVFVSDY 413
S P DY
Sbjct: 221 NPSNTPDK---DY 230
Score = 43.9 bits (103), Expect = 1e-04
Identities = 73/494 (14%), Positives = 132/494 (26%), Gaps = 203/494 (41%)
Query: 3 DSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTAEPALMYDS-VHVLAA 61
++ L + SS+++ S + +V L + E + + +H LAA
Sbjct: 56 TPAELVGKFLGYV--SSLVEPSKVGQFDQV-------LNLCLTEFENCYLEGNDIHALAA 106
Query: 62 GLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTLDLLKLKREELRKVGHWTPAEGIN 121
L + ++++KT L + NYI + K R +
Sbjct: 107 KLLQENDTTLVKTKEL-------------IKNYITARIMAK------RPFDKKSN----- 142
Query: 122 ITDRSAFYETSTNNVTLIVMTREEKPYVMVKNDANLTGNAMFEGFCIDLLKSIAAQVGFH 181
SA + + +A L A+F G Q G
Sbjct: 143 ----SALFRAVG------------------EGNAQLV--AIFGG-----------Q-G-- 164
Query: 182 FVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVIDFTKPFMNLG 241
Y +EL DL Y +
Sbjct: 165 ------NTDDY-------------FEEL----RDL--------YQTYH--VLVGDLIKFS 191
Query: 242 IGILFKVPTSQPTRLFSFMNPLAVEIWL----------YVLAAYLLVSFTLFVMARFSPY 291
L ++ + F L + WL Y+L+ +S L + + + Y
Sbjct: 192 AETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSI--PISCPLIGVIQLAHY 249
Query: 292 EWSNPHPCLAESPIVENQFSVSNSFWFITGTFLRQGSGLNPKVLQQ------GSSRTLDT 345
+ G P L+ G S+ L T
Sbjct: 250 V-----------------------------VTAKL-LGFTPGELRSYLKGATGHSQGLVT 279
Query: 346 AL-----DSKIEIYQKMWRYMESKKCILF-LGGQGDETFVTIDLSQRADSKIEIYQKMWR 399
A+ DS + + + + +LF +G + E + L
Sbjct: 280 AVAIAETDSWESFFVSVRKAIT----VLFFIGVRCYEAYPNTSLP--------------- 320
Query: 400 YMESKRPSVFVSDYEEGVKRVLEGDYAFLMESTMLDYEVQRNCNLTQIGGLLDSKGYGIA 459
PS+ + D E EG + S ML + N Q+ ++
Sbjct: 321 ------PSI-LEDSLENN----EG-----VPSPML--SI-SNLTQEQVQDYVN------K 355
Query: 460 TPKGSPWRDRISLA 473
T P ++ ++
Sbjct: 356 TNSHLPAGKQVEIS 369
Score = 35.4 bits (81), Expect = 0.046
Identities = 63/432 (14%), Positives = 116/432 (26%), Gaps = 204/432 (47%)
Query: 5 VHVLAAGL------ALLDKSSVIKT-----------------SNL--SCD---------- 29
+H LAA L L+ +IK S L +
Sbjct: 101 IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
Query: 30 -----LEVPWRDGLSLYN-YINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLS--CDL 81
+ + + LY Y L+ D + A L+ L ++++ + ++
Sbjct: 161 GGQGNTDDYFEELRDLYQTY-----HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215
Query: 82 E--------VPWRD------------GL-SLYNYINTLDLLKLKREELRK-----VGHWT 115
P +D G+ L +Y+ T LL ELR GH
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGH-- 273
Query: 116 PAEGINIT--------DRSAFYETSTNNVTL--------------------IV------- 140
++G+ +T +F+ + +T+ I+
Sbjct: 274 -SQGL-VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENN 331
Query: 141 ------M-----------------TREEKP-----YVMVKNDAN---LTGNAM-FEGFCI 168
M T P + + N A ++G G +
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 169 DLLKSIA------AQVGF-----HFVLR-L---VPDHT-Y-------------------- 192
L K+ A +++ F F R L P H+
Sbjct: 392 TLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFN 451
Query: 193 ------GVYDHET-----KEWNGIVKELMDKKADLAVASMTINYARES------VIDFTK 235
VYD I + ++D + + + + + ++DF
Sbjct: 452 AKDIQIPVYDTFDGSDLRVLSGSISERIVD-----CIIRLPVKWETTTQFKATHILDF-G 505
Query: 236 PFMNLGIGILFK 247
P G+G+L
Sbjct: 506 PGGASGLGVLTH 517
Score = 35.4 bits (81), Expect = 0.050
Identities = 31/215 (14%), Positives = 62/215 (28%), Gaps = 88/215 (40%)
Query: 45 NTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRD---GLSL--Y------- 92
T +PAL A +K+ L +P G SL Y
Sbjct: 1731 FT-QPALT-------LMEKAAF---EDLKSKGL-----IPADATFAGHSLGEYAALASLA 1774
Query: 93 NYINTLDLLKLKREELRKVGHWTPAEGINITDRSAFYETSTNNVTLIVMTREE---KPYV 149
+ ++ L+++ + R + + R+E Y
Sbjct: 1775 DVMSIESLVEV----VFY--------------RGMTMQV--------AVPRDELGRSNYG 1808
Query: 150 MVKNDANLTGNAMFEGFCIDLLKSIAAQVGFH--FVLRLV----PDHTY---GVYDHETK 200
M + + F + L+ + +VG +++ +V + Y G
Sbjct: 1809 M----IAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAG------- 1857
Query: 201 EWNGIVKELMDKKADLAVASMTINYARESVIDFTK 235
D +A L + +N+ + ID +
Sbjct: 1858 ----------DLRA-LDTVTNVLNFIKLQKIDIIE 1881
Score = 32.7 bits (74), Expect = 0.37
Identities = 26/158 (16%), Positives = 47/158 (29%), Gaps = 46/158 (29%)
Query: 62 GLALLDKSSVIKTSNLSCDLEVPWR--DGLSLYNYINTLDLLKLKREE-LRKVGHWTPAE 118
G+ L S + +V W D Y +L + + H+ +
Sbjct: 1632 GMDLYKTSKAAQ--------DV-WNRADNHFKDTY--GFSILDIVINNPVNLTIHFGGEK 1680
Query: 119 GINITDR--SAFYETSTNNVT----LIVMTREEKPYVMVKNDA---NLTGN---AMFEGF 166
G I + + +ET + + E +++ + T A+
Sbjct: 1681 GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALT--- 1737
Query: 167 CIDLLKSIAAQVGFHFVLR---LVPD------HTYGVY 195
L AA F L+ L+P H+ G Y
Sbjct: 1738 ----LMEKAA---FE-DLKSKGLIPADATFAGHSLGEY 1767
Score = 32.3 bits (73), Expect = 0.45
Identities = 20/118 (16%), Positives = 35/118 (29%), Gaps = 32/118 (27%)
Query: 326 QGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGGQGDETFVTIDLSQ 385
P L GS L+ + + + F+ Q E F I L +
Sbjct: 2 DAYSTRPLTLSHGS-------LEHVLLVPTASF----------FIASQLQEQFNKI-LPE 43
Query: 386 RAD---------SKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGDYAFLMESTML 434
+ + E+ K Y+ S V +++ + L F E+ L
Sbjct: 44 PTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLT---EF--ENCYL 96
Score = 28.9 bits (64), Expect = 5.0
Identities = 25/143 (17%), Positives = 51/143 (35%), Gaps = 43/143 (30%)
Query: 10 AGL------ALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTAEPALMYDSVHVLAAGL 63
AG AL + V+ +L ++ V +R G+ + A P D + G+
Sbjct: 1760 AGHSLGEYAALASLADVMSIESL-VEV-VFYR-GM----TMQVAVPR---DELGRSNYGM 1809
Query: 64 ALLDKSSVIKTSNLS-----CDLEVPWRDGLSL----YN-----YI------------NT 97
++ V + + + V R G + YN Y+ N
Sbjct: 1810 IAINPGRVAASFSQEALQYVVE-RVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNV 1868
Query: 98 LDLLKLKREELRKVGHWTPAEGI 120
L+ +KL++ ++ ++ E +
Sbjct: 1869 LNFIKLQKIDIIELQKSLSLEEV 1891
>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 = 43.3 bits (101), Expect = 2e-04
Identities = 27/144 (18%), Positives = 48/144 (33%), Gaps = 41/144 (28%)
Query: 382 DLSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGDYAFLMES---------- 431
+ D+ + W + SK+ + ++ V+ VL +Y FLM
Sbjct: 53 HIIMSKDAVSGTLRLFW-TLLSKQEEM----VQKFVEEVLRINYKFLMSPIKTEQRQPSM 107
Query: 432 TMLDYEVQRN--CNLTQIGGLLDSKGYGIATPKGSPWR----DRISLAILELQEKGTIQM 485
Y QR+ N Q+ K + R ++ A+LEL+ + +
Sbjct: 108 MTRMYIEQRDRLYNDNQV------------FAKYNVSRLQPYLKLRQALLELRPAKNV-L 154
Query: 486 LY-----DKWWKNTGDVCNRDEDL 504
+ K W DVC +
Sbjct: 155 IDGVLGSGKTWV-ALDVC-LSYKV 176
Score = 42.9 bits (100), Expect = 2e-04
Identities = 75/494 (15%), Positives = 148/494 (29%), Gaps = 123/494 (24%)
Query: 7 VLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTAEPAL--MYDSVHVLAAGL- 63
+A L K ++ W L+L N N+ E L + ++ +
Sbjct: 165 WVAL-DVCLSYKVQCKMDF-----KIFW---LNLKNC-NSPETVLEMLQKLLYQIDPNWT 214
Query: 64 ALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTLDLLKLKREELRKVGHWTPAEGINIT 123
+ D SS IK S E+ R L Y N L +L V
Sbjct: 215 SRSDHSSNIKLRIHSIQAEL--RRLLKSKPYENCLLVL-------LNV--QNA----KAW 259
Query: 124 DRSAF-------YETSTNNVTLIVMTREEKPYVMVKNDANLTGNAMFEGF--CIDL-LKS 173
+ AF T VT + + + LT + + +D +
Sbjct: 260 N--AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317
Query: 174 IAAQV--GFHFVLRLVPDHTYGVYDHETKEWNGIVKELMDKKADLAVASMTINYARESVI 231
+ +V L ++ + W+ DK + ++N +
Sbjct: 318 LPREVLTTNPRRLSIIAE----SIRDGLATWDNWKHVNCDKLTT--IIESSLNVLEPA-- 369
Query: 232 DFTKPFMNLGIGILF----KVPTSQPTRLFSFMNPLAVEIWLYVLAAYLLV-----SFTL 282
++ K F L + F +PT + ++ + V + + L Y LV T+
Sbjct: 370 EYRKMFDRLSV---FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI 426
Query: 283 FVMARF------------------SPYEWSNPHPCLAESPIVENQFSVSNSFWFITGTFL 324
+ + + Y P +Q+ + I G L
Sbjct: 427 SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY----FYSHI-GHHL 481
Query: 325 RQGSGLNPKVLQQGSSRTLDTALDSKIEIYQKMWRYMESKKCILFLGGQGDETFVTIDLS 384
+ ++ TL ++ R++E K I + + ++
Sbjct: 482 KN--------IEHPERMTLFR------MVFLDF-RFLEQK--IRHDSTAWNASGSILNTL 524
Query: 385 QRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLEGDYAFLM--ESTMLDYEVQRNC 442
Q+ ++ Y+ Y+ P YE V +L+ FL E ++ +
Sbjct: 525 QQ----LKFYKP---YICDNDP-----KYERLVNAILD----FLPKIEENLICSK---YT 565
Query: 443 NLTQIGGLLDSKGY 456
+L +I + + +
Sbjct: 566 DLLRIALMAEDEAI 579
>3qek_A NMDA glutamate receptor subunit; amino terminal domain, ION
channel, NMDA receptor, allosteri modulation,
phenylethanolamine, polyamine; HET: NAG BMA; 2.00A
{Xenopus laevis} PDB: 3qel_A* 3qem_A* 3q41_A*
Length = 384
Score = 38.9 bits (90), Expect = 0.003
Identities = 18/118 (15%), Positives = 34/118 (28%), Gaps = 24/118 (20%)
Query: 27 SCDLEVPWRDGLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSC-DLEVPW 85
L + L E A + D+V V+A + L + I C W
Sbjct: 256 GSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIW 315
Query: 86 RDGLSLYNYINT-----------------------LDLLKLKREELRKVGHWTPAEGI 120
+ G + + ++ L+ +L +VG + + I
Sbjct: 316 KTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYII 373
>3c1d_A Protein ORAA, regulatory protein RECX; tandem repeats,
helix-turn-helix, cytoplasm, DNA damage, DNA repair, SOS
response, DNA binding protein; 1.80A {Escherichia coli}
Length = 159
Score = 28.5 bits (64), Expect = 3.5
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 383 LSQRADSKIEIYQKMWRYMESKRPSVFVSDYEEGVKRVLE 422
L+ R S+ E+ +K+ + K + E +RV+
Sbjct: 15 LAVRDHSEQELRRKLAAPIMGKNGPEEIDATAEDYERVIA 54
>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative
initiation, ATP-binding, DNA- binding, hydrolase,
nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB:
3ezk_A*
Length = 592
Score = 28.8 bits (63), Expect = 4.6
Identities = 15/171 (8%), Positives = 39/171 (22%), Gaps = 3/171 (1%)
Query: 32 VPWRDGLSLYNYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSL 91
+ L +++ + + H + +LD++
Sbjct: 191 KTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQPGIVEWNKGS 250
Query: 92 YNYINTLDLLKLKREELRKVGHWTPAEGINITDRSAFYETSTNNVTLIVMTREEKPYVMV 151
N + G+ + + + AF ++ I +
Sbjct: 251 IELDNGSSIGAYASSPDAVRGN---SFAMIYIEDCAFIPNFHDSWLAIQPVISSGRRSKI 307
Query: 152 KNDANLTGNAMFEGFCIDLLKSIAAQVGFHFVLRLVPDHTYGVYDHETKEW 202
G F ++ + + + V + Y D W
Sbjct: 308 IITTTPNGLNHFYDIWTAAVEGKSGFEPYTAIWNSVKERLYNDEDIFDDGW 358
>4ain_A Glycine betaine transporter BETP; membrane protein, chemosensor and
osmosensor, secondary TRAN sodium coupled transport;
HET: FLC CM5; 3.10A {Corynebacterium glutamicum} PDB:
4doj_A* 2w8a_A 2wit_A 3p03_A
Length = 539
Score = 28.8 bits (65), Expect = 4.7
Identities = 5/24 (20%), Positives = 11/24 (45%), Gaps = 2/24 (8%)
Query: 268 WLYVLAAYLLVSFTLFVMARFSPY 291
W ++L + V F + + S +
Sbjct: 61 WAFILFGTVFVFFIVVIA--ASKF 82
>3n9r_A Fructose-bisphosphate aldolase; FBP aldolase, class II, inhibitor,
lyase; HET: TD3; 1.80A {Helicobacter pylori} PDB:
3c52_A* 3c56_A* 3c4u_A* 3n9s_A*
Length = 307
Score = 28.4 bits (64), Expect = 5.2
Identities = 11/74 (14%), Positives = 23/74 (31%), Gaps = 8/74 (10%)
Query: 168 IDLLKSIAAQVGFHFVL---RLVPDHTYGV---YDHETKEWNGIVKELMDKKADLAVASM 221
+ L+ + VL +PD+ + K G+ E + + +
Sbjct: 193 FERLQEVKRLTNIPLVLHGASAIPDNVRKSYLDAGGDLKGSKGVPFEFLQESVKGGINK- 251
Query: 222 TINYARESVIDFTK 235
+N + I F
Sbjct: 252 -VNTDTDLRIAFIA 264
>3qfk_A Uncharacterized protein; structural genomics, center for structural
genomics of infec diseases, csgid, phosphoesterase,
hydrolase; HET: MSE AKG; 2.05A {Staphylococcus aureus
subsp}
Length = 527
Score = 28.5 bits (64), Expect = 5.8
Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 11/70 (15%)
Query: 42 NYINTAEPALMYDSVHVLAAGLALLDKSSVIKTSNLSCDLEVPWRDGLSLYNYINTLDLL 101
N++N A + + A AL D +S K V RD ++ Y + NT +L
Sbjct: 345 NFMNYA----LLEKSDADVACTALFDSASGFKQ-------VVTMRDVINNYPFPNTFKVL 393
Query: 102 KLKREELRKV 111
+ +L++
Sbjct: 394 AVSGAKLKEA 403
>3k9v_A 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial;
mitochondrial cytochrome P450, monotopic membrane
protein, monooxygenase; HET: HEM CPS; 2.50A {Rattus
norvegicus} PDB: 3k9y_A*
Length = 482
Score = 28.4 bits (64), Expect = 6.1
Identities = 12/82 (14%), Positives = 27/82 (32%), Gaps = 18/82 (21%)
Query: 392 EIYQKMWRYMESKRPSVFVSDYEEGVKRVL--EGDYA--FLMESTMLDYEVQRNCNLTQI 447
+ Y +++R SV + ++ + E + ++ Y RN
Sbjct: 59 KKYGQIFRMKLGSFDSVHLGSPSL-LEALYRTESAHPQRLEIKP-WKAYRDHRN------ 110
Query: 448 GGLLDSKGYGIATPKGSPWRDR 469
+ YG+ +G W+
Sbjct: 111 ------EAYGLMILEGQEWQRV 126
>2iru_A Putative DNA ligase-like protein RV0938/MT0965; polymerase,
primase, NHEJ, transferase; 1.65A {Mycobacterium
tuberculosis} PDB: 2irx_A* 2iry_A* 2r9l_A* 3pky_A*
Length = 303
Score = 28.2 bits (63), Expect = 6.7
Identities = 9/58 (15%), Positives = 18/58 (31%), Gaps = 6/58 (10%)
Query: 179 GFHFVLRLVPDHTYGVYDHETKEW-NGIVKELMDKKADLAVASMTINYARESV-IDFT 234
G H L + + + L L ++MT + V +D++
Sbjct: 179 GLHLYTPLDEPVSSR----GATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWS 232
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 0.136 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: 7,682,680
Number of extensions: 453630
Number of successful extensions: 916
Number of sequences better than 10.0: 1
Number of HSP's gapped: 826
Number of HSP's successfully gapped: 106
Length of query: 504
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 406
Effective length of database: 3,965,535
Effective search space: 1610007210
Effective search space used: 1610007210
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)