RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780140|ref|YP_003064553.1| putative ABC transporter,
substrate-binding protein [Candidatus Liberibacter asiaticus str.
psy62]
(452 letters)
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 51.5 bits (123), Expect = 4e-07
Identities = 72/512 (14%), Positives = 127/512 (24%), Gaps = 241/512 (47%)
Query: 4 KNYYTSVGL-------FVVSILF-------FSFFSIYWLSRSNQ-------------YD- 35
KNY T+ + S LF +I+ Q Y
Sbjct: 124 KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF----GGQGNTDDYFEELRDLYQT 179
Query: 36 -GPMAEVIIRIPGSV-DGLSTDSSVRFNGIPVGRIVGLFLD----QEYPNHSLAKALIRP 89
+ +I+ L + ++ L+ E P++ P
Sbjct: 180 YHVLVGDLIKFSAETLSELIRTTLDAE------KVFTQGLNILEWLENPSN-------TP 226
Query: 90 DT----------PL--------Y----------PS------TTATIRTQGL---AGI--- 109
D PL Y P AT +QGL I
Sbjct: 227 DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET 286
Query: 110 ----TYIELSTLRKEKKTIFQIATERNQRAMITA-TPSGINYFISNAENT-----SKKIS 159
++ RK +F I + T+ PS + + N E S IS
Sbjct: 287 DSWESFFVSV--RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS--IS 342
Query: 160 DSSR-HIQKIIENIEK--PLTTTIANIETISTVLANNISHIDKMMHTTQVT-PHSSDSKN 215
+ ++ +Q + P + IS L N ++ V+ P S
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVE----IS--LVNGAKNL-------VVSGPPQS---- 385
Query: 216 TFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQ 275
L +N L + S DQ
Sbjct: 386 --------------------LYGLNLTLRKAKAPSGL-----DQ---------------- 404
Query: 276 EVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISA------IREITDQRQKII 329
+I S+ K K ++ FL +++ + +D
Sbjct: 405 ---SRIPF------SERKLKFSNRFL------------PVASPFHSHLLVPASDL----- 438
Query: 330 STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRY 389
I +L ++ F +I ++ TF
Sbjct: 439 --------INKDLVKNNVSFNAKDIQI----------PVY-------DTF--D------- 464
Query: 390 IPSIGNNLQNFSQSGLNDIQNLVRKL-QETVN 420
G++L+ S + + +V + + V
Sbjct: 465 ----GSDLRVLSG---SISERIVDCIIRLPVK 489
Score = 49.2 bits (117), Expect = 2e-06
Identities = 42/303 (13%), Positives = 85/303 (28%), Gaps = 119/303 (39%)
Query: 174 KPLTTTIANIET---ISTVLANNISHIDKMMHTTQVTPHSSDSKNTFN----TITDLITS 226
+PLT + ++E + T +Q+ + FN T+ +
Sbjct: 7 RPLTLSHGSLEHVLLVPTAS-----FF----IASQL-------QEQFNKILPEPTEGFAA 50
Query: 227 LDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQT-FQEVGQKIDHLL 285
D+ +L V + L +V V + F +V ++ L
Sbjct: 51 DDEPTTPAEL--VGKFLG--------YV---------SSLVEPSKVGQFDQV---LNLCL 88
Query: 286 SDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITD----QRQKIIST-INTIENITS 340
++F + +LE +++ + + + + D + +++I I
Sbjct: 89 TEF--------ENCYLEG-----NDIHALAAKLLQENDTTLVKTKELIKNYITAR----I 131
Query: 341 NLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPSI----GNN 396
K + SAL F+ +I GN
Sbjct: 132 MAKRPFDKKSN--------SAL------FRAVG---------EGNAQLV--AIFGGQGNT 166
Query: 397 LQNFSQSGLNDIQN----LVRKLQETVNHFDDCLNNFERNPQ----------DIV-W--G 439
F + L D+ LV L + + L+ R +I+ W
Sbjct: 167 DDYFEE--LRDLYQTYHVLVGDLIKFS---AETLSELIRTTLDAEKVFTQGLNILEWLEN 221
Query: 440 REK 442
Sbjct: 222 PSN 224
>1fft_C Ubiquinol oxidase; electron transport, cytochrome oxidase,
membrane protein, oxidoreductase; HET: HEM HEO; 3.50A
{Escherichia coli} SCOP: f.25.1.1
Length = 204
Score = 33.4 bits (76), Expect = 0.11
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 12 LFVVS--ILFFSFFSIYWLSRSNQYDGPMAEVIIRIP 46
++++S ILF F+ Y + + GP + I +P
Sbjct: 31 IYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELP 67
>2d4x_A Flagellar HOOK-associated protein 3; multi-domain protein,
alpha-helical bundle, complex all- beta folds,
structural protein; 1.90A {Salmonella typhimurium}
Length = 248
Score = 32.4 bits (72), Expect = 0.18
Identities = 19/226 (8%), Positives = 53/226 (23%)
Query: 131 RNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVL 190
+A + + +S + IQ E I T+++ + S
Sbjct: 15 SQAQAQNSQYALARTFATQKVSLEESVLSQVTTAIQTAQEKIVYAGNGTLSDDDRASLAT 74
Query: 191 ANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSS 250
M + + T + Q+ +
Sbjct: 75 DLQGIRDQLMNLANSTDGNGRYIFAGYKTEAAPFDQATGGYHGGEKSVTQQVDSARTMVI 134
Query: 251 NNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSN 310
+ I + ++ + + A
Sbjct: 135 GHTGAQIFNSITSNAVPEPDGSDSEKNLFVMLDTAIAALKTPVEGNNVEKEKAAAAIDKT 194
Query: 311 MRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKI 356
R +++ + R ++ + ++ + + S +D + MS +
Sbjct: 195 NRGLKNSLNNVLTVRAELGTQLSELSTLDSLGSDRALGQKLQMSNL 240
>3bh2_A ADC, AAD, acetoacetate decarboxylase; lyase, plasmid, schiff base;
2.40A {Clostridium acetobutylicum atcc 824}
Length = 244
Score = 32.2 bits (73), Expect = 0.28
Identities = 11/54 (20%), Positives = 15/54 (27%), Gaps = 11/54 (20%)
Query: 25 IYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYP 78
G E IP V FNG+ + ++LD E
Sbjct: 61 EIMAMHDTSGLGCYTESGQAIP-----------VSFNGVKGDYLHMMYLDNEPA 103
>2ch7_A Methyl-accepting chemotaxis protein; receptor, four-helix bundle,
signal transduction, methyl-accepting receptor; 2.5A
{Thermotoga maritima} SCOP: h.4.5.1 PDB: 2ch7_B
Length = 309
Score = 31.3 bits (69), Expect = 0.40
Identities = 36/281 (12%), Positives = 83/281 (29%), Gaps = 16/281 (5%)
Query: 149 SNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTP 208
+N S +I S +Q+ E+ +++ NI + A+ ++
Sbjct: 37 KEMDNISTRIESISASVQETTAGSEE-ISSATKNIADSAQQAASFADQSTQLAKEAGDAL 95
Query: 209 HSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVR 268
+ + +++ +E I + +
Sbjct: 96 KKVIEVTRMISNSAKDVERVVESFQKGAEEITSFVETINAIAEQTNLLALNAAIEAARAG 155
Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKI 328
E + F V +I + + A + A + ++ ++
Sbjct: 156 EAGRGFAVVADEIRK--------LAEESQQASENVRRVVNEIRSIAEDAGKVSSEITARV 207
Query: 329 ISTINTIENITSNLNDSSQKFAELMSKINNI-SALKENNSLFKDAQRAMHTFRDTSEKIN 387
+ LN + + NI +A++E + + AM +E+I
Sbjct: 208 EEGTKLADEADEKLNSIVGAVERINEMLQNIAAAIEEQTAAVDEITTAMTENAKNAEEIT 267
Query: 388 RYIPSIGNNLQNFSQS------GLNDIQNLVRKLQETVNHF 422
+ + LQ S S + I+ V+ L+E V +
Sbjct: 268 NSVKEVNARLQEISASTEEVTSRVQTIRENVQMLKEIVARY 308
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomography,
contractIle protein/transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 31.0 bits (69), Expect = 0.55
Identities = 41/293 (13%), Positives = 89/293 (30%), Gaps = 31/293 (10%)
Query: 162 SRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTIT 221
R + E KP++ A + + + ++ HS+ +++F +
Sbjct: 377 HRKLATATETYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKALHSTVKQHSFIGVL 436
Query: 222 DLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTF------Q 275
D+ I + + +N E +Q N V +Q + T F
Sbjct: 437 DIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKEQIPWTLIDFYDNQPCI 496
Query: 276 EVGQKIDHLLS--DFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIS--- 330
+ + +L D KM + + + ++ N + R + II
Sbjct: 497 NLIEAKMGVLDLLDEECKMPKGSDDTWAQKLYNTHLNKCALFEKPR--LSNKAFIIKHFA 554
Query: 331 ---TINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKIN 387
+ N + ++ +++ L E LF+D ++A+ T
Sbjct: 555 DKVEYQCEGFLEKNKDTVYEEQIKVLKSSKKFKLLPE---LFQDEEKAISPTSATPSGRV 611
Query: 388 ------------RYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDCLNN 428
R + + + N + L+ L T H+ C+
Sbjct: 612 PLSRTPVKPAKARPGQTSKEHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKP 664
>3l39_A Putative PHOU-like phosphate regulatory protein; BT4638, structural
genomics, joint center for structural genomics, JCSG;
1.93A {Bacteroides thetaiotaomicron}
Length = 227
Score = 31.1 bits (70), Expect = 0.58
Identities = 26/177 (14%), Positives = 59/177 (33%), Gaps = 9/177 (5%)
Query: 145 NYFISNAENTSKKISDSSRHIQKIIENIEKPLTT---TIANIETISTVLANNISHIDKMM 201
+ + + K+I D R ++ I L+T T + E I + S +D ++
Sbjct: 52 HDLPTERADYYKQIKDMEREGDRLTHLIFDELSTTFITPFDREDIHDL----ASCMDDVI 107
Query: 202 HTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVI 261
+ N I++ L ++I + + ++ ++ N D
Sbjct: 108 DGINSSAKRIVIYN-PRPISESGKELSRLIHEEA-INIGKAMDELETFRKNPKPLRDYCT 165
Query: 262 NTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAI 318
+ ++ K+ D +K KE LE D+ ++ + +
Sbjct: 166 QLHDIENQADDVYELFITKLFEEEKDCIELIKIKEIMHELEKTTDAAEHVGKILKNL 222
>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold,
ATPase, parallel dimer, structural genomics; 2.80A
{Thermus thermophilus HB8}
Length = 997
Score = 30.5 bits (68), Expect = 0.71
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 319 REITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKE 364
REI ++++ +N +E L D + + EL K ++L E
Sbjct: 14 REIARYYKQVVEPVNRLEAEVEKLPDLAAAYRELKEKHEKGASLDE 59
>2x2e_A Dynamin-1; nitration, hydrolase, membrane fission,
nucleotide-binding, endocytosis, motor protein; HET:
GDP; 2.00A {Homo sapiens} PDB: 2x2f_A*
Length = 341
Score = 30.6 bits (68), Expect = 0.74
Identities = 23/214 (10%), Positives = 68/214 (31%), Gaps = 3/214 (1%)
Query: 147 FISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQV 206
+ T + D I+ I ++ T + + +++++ D + +V
Sbjct: 129 LVDLPGMTKVPVGDQPPDIEFQIRDMLMQFVTKENCLILAVSPANSDLANSDALKVAKEV 188
Query: 207 TPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHD 266
P + T DL+ ++ + + I V + + + T
Sbjct: 189 DPQGQRT-IGVITKLDLMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAAL 247
Query: 267 VRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISA-IREITDQR 325
E + F + ++ +I D+ +R+ + + + I +
Sbjct: 248 AAER-KFFLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKLQSQLLSIEKEV 306
Query: 326 QKIISTINTIENITSNLNDSSQKFAELMSKINNI 359
++ + S +++ + + L ++ I
Sbjct: 307 EEYKNFRPDKHGTDSRVDEMLRMYHALKEALSII 340
>2wm9_A Dedicator of cytokinesis protein 9; polymorphism, cell membrane,
phosphoprotein, nucleotide-binding, alternative
splicing; 2.20A {Homo sapiens} PDB: 2wmn_A* 2wmo_A*
Length = 428
Score = 30.4 bits (68), Expect = 0.95
Identities = 18/142 (12%), Positives = 39/142 (27%), Gaps = 19/142 (13%)
Query: 254 VKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRS 313
V +V + ++ L S M L+ N +
Sbjct: 296 VMYQHHTDLNPIEV--AIDEMSKKVAELRQLCSSAEVDMIK--LQLKLQGSVSVQVN--A 349
Query: 314 SISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQ 373
A + NT + + + F + + AL N L K+ Q
Sbjct: 350 GPLAYARA------FLDDTNTKRYPDNKVKLLKEVFRQFVEACGQ--ALAVNERLIKEDQ 401
Query: 374 RAMHT-----FRDTSEKINRYI 390
+R+ +++++ +
Sbjct: 402 LEYQEEMKANYREMAKELSEIM 423
>3c8w_A Acetoacetate decarboxylase ADC; YP_094708.1, structural genomics,
joint center for structural genomics, JCSG; HET: LCK
CIT; 1.60A {Legionella pneumophila subsp} SCOP:
d.347.1.1
Length = 255
Score = 29.9 bits (67), Expect = 1.1
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 15/62 (24%)
Query: 17 ILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQE 76
++ F F + + Y E +P VR+ G G + +FLD
Sbjct: 68 VVKFEFIRMPDSTGFGDYT----ESGQVVP-----------VRYKGEEGGFTISMFLDCH 112
Query: 77 YP 78
P
Sbjct: 113 AP 114
>1dn1_B Syntaxin 1A, syntaxin binding protein 1; protein-protein complex,
multi-subunit; 2.60A {Rattus norvegicus} SCOP: a.47.2.1
PDB: 3c98_B
Length = 267
Score = 30.1 bits (67), Expect = 1.2
Identities = 34/269 (12%), Positives = 86/269 (31%), Gaps = 26/269 (9%)
Query: 157 KISDSSRHIQKIIENIEKPLTTTIANIETISTVLA---NNISHIDKMMHTTQVTP-HSSD 212
+ + ++ + +E I + N+ + + +P
Sbjct: 11 AKDSXXXXXVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEK 70
Query: 213 SKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQ 272
+K + I +++ L+ + Q +E + + + + ++ T H ++
Sbjct: 71 TKEELEELMSDIKKTANKVRS-KLKSIEQSIEQEEGLNRS--SADLRIRKTQHST--LSR 125
Query: 273 TFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTI 332
F EV + + SD+ + K + +TS + II
Sbjct: 126 KFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASGIIMDS 185
Query: 333 NTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPS 392
+ + S + + +L + I E + +F D + E I+R
Sbjct: 186 SISKQALSEIETRHSEIIKLENSIR------ELHDMFMDMAMLVE---SQGEMIDR---- 232
Query: 393 IGNNLQNFSQSGLNDIQNLVRKLQETVNH 421
I N+++ ++ V ++ V +
Sbjct: 233 IEYNVEHAVD----YVERAVSDTKKAVKY 257
>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand
binding domain, AF-2, androgen, testosterone, DHT,
alpha-helical sandwich; HET: DHT; 1.40A {Pan
troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A*
1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A*
2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A*
2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ...
Length = 269
Score = 30.0 bits (67), Expect = 1.2
Identities = 9/90 (10%), Positives = 29/90 (32%), Gaps = 5/90 (5%)
Query: 285 LSDFSSKMKS----KETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINT-IENIT 339
+ S + + ++ + + + + + R I ++ I
Sbjct: 137 MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKR 196
Query: 340 SNLNDSSQKFAELMSKINNISALKENNSLF 369
N S++F +L ++++ + F
Sbjct: 197 KNPTSCSRRFYQLTKLLDSVQPIARELHQF 226
>1s94_A S-syntaxin; three helix bundle, structural plasticity,
endocytosis/exocytosis complex; 3.34A {Loligo pealei}
SCOP: a.47.2.1
Length = 180
Score = 29.9 bits (67), Expect = 1.3
Identities = 16/149 (10%), Positives = 49/149 (32%), Gaps = 8/149 (5%)
Query: 285 LSDFSSKMKSKETSAFLE-NIADSTSNMRSSISAIREITDQRQKIISTINTIENITSNLN 343
L+ + + +E + + M + EI KI ++ ++ S++
Sbjct: 11 LAALKAAVSDEEDVEEVAVQVDSGGGFMEEFFEQVEEIRAMIDKISDNVDAVKKKHSDIL 70
Query: 344 DSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQS 403
+ Q ++ ++ + + + + + T E+ S + +Q
Sbjct: 71 SAPQTDDQMKEELEEL--MTDIKRTANKVRGKLKTIELNIEQEEHSNKSSADLRIRKTQ- 127
Query: 404 GLNDIQNLVRKLQETVNHFDDCLNNFERN 432
+ RK E ++ ++ ++
Sbjct: 128 ----YSTISRKFVEVMSDYNTTQIDYRDR 152
>3cmg_A Putative beta-galactosidase; structural genomics, PSI-2, protein
structure initiative; 1.90A {Bacteroides fragilis nctc
9343}
Length = 667
Score = 29.9 bits (66), Expect = 1.3
Identities = 21/141 (14%), Positives = 48/141 (34%), Gaps = 6/141 (4%)
Query: 50 DGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKA------LIRPDTPLYPSTTATIRT 103
DG+++ + V N +G G + + L K L+R + +
Sbjct: 73 DGVNSIADVFINRKHIGEHRGGYGAFIFEITDLVKYGEKNSVLVRANNGEQLDIMPLVGD 132
Query: 104 QGLAGITYIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSR 163
G Y ++ L ++ I + ++ S + N S + +D +
Sbjct: 133 FNFYGGIYRDVHLLITDETCISPLDYASPGVYLVQEVVSPQEAKVCAKVNLSNRAADGTA 192
Query: 164 HIQKIIENIEKPLTTTIANIE 184
+Q ++ + K + N+
Sbjct: 193 ELQVLVTDGTKVICKESRNVS 213
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, polymorphism,
receptor, transcription, transcription regulation; HET:
DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A*
Length = 467
Score = 29.5 bits (65), Expect = 1.4
Identities = 38/237 (16%), Positives = 78/237 (32%), Gaps = 12/237 (5%)
Query: 153 NTSKKISDSSRHIQKIIENIEKPLTTTIANIETI--STVLANNISHIDKMMHTTQVTPHS 210
N ++ S SS + +E I + ET + + N S D + + Q
Sbjct: 221 NENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQ 280
Query: 211 SDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRET 270
+ + + L + I L+ L S + ++ T V
Sbjct: 281 LFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 340
Query: 271 TQTFQEVGQKIDHLLSDFSSKMKS----KETSAFLENIADSTSNMRSSISAIREITDQRQ 326
+ VG D +L++ SKM+ K L I + +S E+ R+
Sbjct: 341 SAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPD-SKGLSNPAEVEALRE 399
Query: 327 KIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTS 383
K+ +++ + +FA+L+ ++ + ++ + DT
Sbjct: 400 KVYASLE--AYCKHKYPEQPGRFAKLLLRLPALRSI---GLKCLEHLFFFKLIGDTP 451
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.2 bits (64), Expect = 2.1
Identities = 7/17 (41%), Positives = 11/17 (64%), Gaps = 2/17 (11%)
Query: 409 QNLVRKLQETVNHF-DD 424
Q L +KLQ ++ + DD
Sbjct: 20 QAL-KKLQASLKLYADD 35
>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling,
alternative DNA-binding, metal-binding, nucleus,
polymorphism, receptor transcription; HET: 965; 2.00A
{Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B*
1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A*
1pqc_A* 3kfc_A* 3l0e_A*
Length = 283
Score = 29.3 bits (65), Expect = 2.1
Identities = 27/230 (11%), Positives = 77/230 (33%), Gaps = 34/230 (14%)
Query: 149 SNAENTSKKISDSSRHIQKIIENI-EKPLTTTIANIETISTVLANNISHIDKMMHTTQVT 207
A + + + S +IE + + V ++
Sbjct: 30 PRASSPPQILPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLRVTPWPMA---------PDP 80
Query: 208 PHSSDSKNTFNTITDLIT-SLDKMI---KAI----DLQKVNQI-------LENIQVSSNN 252
+ F T+L S+ +++ K + L + +QI +E + + ++
Sbjct: 81 HSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSR 140
Query: 253 FVKSSDQVINTVHDVRETTQTFQEVGQKIDHL--LSDFSSKMKS----KETSAFLENIAD 306
+ I + D + F + G +++ + + +FS M A L I+
Sbjct: 141 RYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISI 200
Query: 307 STSNMRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKI 356
+++ R ++ ++ + + ++ ++ + F ++ K+
Sbjct: 201 FSAD-RPNVQDQLQVERLQHTYVEALH--AYVSIHHPHDRLMFPRMLMKL 247
>2zbi_A Flagellin homolog; flagellum, structural protein; 2.00A
{Sphingomonas SP}
Length = 292
Score = 28.9 bits (63), Expect = 2.5
Identities = 17/231 (7%), Positives = 58/231 (25%), Gaps = 7/231 (3%)
Query: 118 RKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLT 177
R + QR + +G + +I ++ + + +
Sbjct: 55 RDALQAEVTQLQSEIQRVAEQTSFNGQKLLDGSFNGVQFQIGANAGETIGVSKIMNAQTA 114
Query: 178 TTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQ 237
+ ++ ++ + + + + ++ +AI+
Sbjct: 115 SLGGSLTRTTSTIDATDLTKYDTAMAAGDLTINGVDVGKIDAASTAQERAAQLTEAINRV 174
Query: 238 KVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKET 297
+ + V + V + + +
Sbjct: 175 SSQTNVGASYDKTTGQVTLTSNAAIAVAGAANDATVAGWANNATTGTATTTTGINSLTVS 234
Query: 298 SAFLENIADSTSNMRSSI-SAIREITDQRQKIISTINTIENITSNLNDSSQ 347
S + + I +A+++I R + + N + +NL ++
Sbjct: 235 SF------TNAQQTITQIDNALKDINTARADLGAVQNRFTSTVANLQSMTE 279
>1fio_A SSO1 protein; four helix bundle, alpha helix, membrane protein;
2.10A {Saccharomyces cerevisiae} SCOP: a.47.2.1
Length = 196
Score = 28.5 bits (63), Expect = 2.7
Identities = 20/167 (11%), Positives = 51/167 (30%), Gaps = 2/167 (1%)
Query: 251 NNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSN 310
++FV +++ D+ + T +V LL++ + + S + +A +T
Sbjct: 2 HDFVGFMNKISQINRDLDKYDHTINQVDSLHKRLLTEVNEEQASHLRHSLDNFVAQATDL 61
Query: 311 MRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFK 370
+ I+ + EN Q + + S KE
Sbjct: 62 QFKLKNEIKSAQRDGIHDTNKQAQAENSRQRFLKLIQDYRIVDSNYK--EENKEQAKRQY 119
Query: 371 DAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQE 417
+ T + I+ + + + + + + ++Q
Sbjct: 120 MIIQPEATEDEVEAAISDVGGQQIFSQALLNANRRGEAKTALAEVQA 166
>2ot3_A RAB5 GDP/GTP exchange factor; rabex-5, VPS9 domain, vesicular
traffic, protein transport; 2.10A {Homo sapiens} SCOP:
a.222.1.1 PDB: 1txu_A
Length = 274
Score = 28.8 bits (64), Expect = 2.9
Identities = 10/73 (13%), Positives = 26/73 (35%), Gaps = 3/73 (4%)
Query: 363 KENNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHF 422
E + + K+ + TF T ++I + L+ I+ Q+ ++
Sbjct: 10 IETDRVSKEFIEFLKTFHKTGQEIYKQTKLF---LEGMHYKRDLSIEEQSECAQDFYHNV 66
Query: 423 DDCLNNFERNPQD 435
+ + + P +
Sbjct: 67 AERMQTRGKVPPE 79
>2je8_A Beta-mannosidase; glycoside hydrolase, hydrolase; HET: B3P; 1.7A
{Bacteroides thetaiotaomicron} SCOP: b.1.4.1 b.1.4.1
b.1.4.1 b.18.1.5 c.1.8.3 PDB: 2vr4_A* 2vl4_A* 2vmf_A*
2vo5_A* 2vot_A* 2vqt_A* 2vjx_A* 2vqu_A* 2wbk_A*
Length = 848
Score = 28.5 bits (62), Expect = 3.4
Identities = 24/223 (10%), Positives = 62/223 (27%), Gaps = 12/223 (5%)
Query: 50 DGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKA-----LIRPDTPLYPSTTATIRTQ 104
+GL T + V NG + + +F+ P S+ + I +P+ T+
Sbjct: 89 EGLDTYADVYLNGSLLLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQ----TLPQY 144
Query: 105 GLAGITYIELSTLRKEKKTIFQIATERNQRA--MITATPSGINYFISNAENTSKKISDSS 162
G Y + ++ ++F + I SG+ +
Sbjct: 145 ASNGFNYPADNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGV-WRPVTLRFYDIATISDY 203
Query: 163 RHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITD 222
Q + + L+ + + + + + + TT +
Sbjct: 204 YVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVTLQPGINHIT 263
Query: 223 LITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVH 265
L + ++ + L + + + + +
Sbjct: 264 LPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHRIG 306
>2oo2_A Hypothetical protein AF_1782; structural genomics, unknown
function, PSI-2, protein structure initiative; 1.80A
{Archaeoglobus fulgidus dsm 4304} SCOP: a.8.11.1
Length = 86
Score = 28.2 bits (63), Expect = 4.2
Identities = 6/57 (10%), Positives = 16/57 (28%), Gaps = 5/57 (8%)
Query: 376 MHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHF---DDCLNNF 429
M + + +++ I ++ G + +F D + F
Sbjct: 1 MSLEEELRRETLKWLERIEERVKEI--EGDEGFMRNIEAYISDSRYFLEKGDLVRAF 55
>3k8w_A Flagellin homolog; flagellum, structural protein, bacterial
flagellu; 1.70A {Sphingomonas SP} PDB: 2zbi_A 3k8v_A
Length = 326
Score = 27.8 bits (60), Expect = 5.2
Identities = 23/235 (9%), Positives = 67/235 (28%), Gaps = 15/235 (6%)
Query: 118 RKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLT 177
R + QR + +G + +I ++ + + +
Sbjct: 89 RDALQAEVTQLQSEIQRVAEQTSFNGQKLLDGSFNGVQFQIGANAGETIGVSKIMNAQTA 148
Query: 178 TTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQ 237
+ ++ ++ + + + + ++ +AI
Sbjct: 149 SLGGSLTRTTSTIDATDLTKYDTAMAAGDLTINGVDVGKIDAASTAQERAAQLTEAI--- 205
Query: 238 KVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKET 297
N S N S D+ V ++ + T
Sbjct: 206 -------NRVSSQTNVGASYDKTTGQVTLTSNAAIAVAGAANDATVAGWANNATTGTATT 258
Query: 298 SAFLENIADST-SNMRSSI----SAIREITDQRQKIISTINTIENITSNLNDSSQ 347
+ + ++ S+ +N + +I +A+++I R + + N + +NL ++
Sbjct: 259 TTGINSLTVSSFTNAQQTITQIDNALKDINTARADLGAVQNRFTSTVANLQSMTE 313
>1ucu_A Phase 1 flagellin; flagellar filament, cryo-electron microscopy,
helical reconstruction, structural protein; 4.00A
{Salmonella typhimurium} SCOP: e.32.1.1
Length = 494
Score = 27.8 bits (60), Expect = 5.4
Identities = 24/233 (10%), Positives = 61/233 (26%), Gaps = 6/233 (2%)
Query: 125 FQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIE 184
+ T + ++ + + +
Sbjct: 226 TGKYYAKVTVTGGTGKDGYYEVSVDKTNGEVTLAGGATSPLTGGLPATATEDVKNVQVAN 285
Query: 185 TISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILE 244
T ++ + V +D N TI + Q + +
Sbjct: 286 ADLTEAKAALTAAGVTGTASVVKMSYTD--NNGKTIDGGLAVKVGDDYYSATQNKDGSIS 343
Query: 245 NIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENI 304
+S +N + T+ G+ ++ + + + E
Sbjct: 344 INTTKYTADDGTSKTALNKLGGADGKTEVVSIGGKTYAASKAEGHNFKAQPDLA---EAA 400
Query: 305 ADSTSNMRSSI-SAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKI 356
A +T N I +A+ ++ R + + N + +NL ++ + S+I
Sbjct: 401 ATTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLTSVRSRI 453
>2k3r_A Ribonuclease P protein component 4; PFU RPP21, RNAse P, hydrolase,
tRNA processing; NMR {Pyrococcus furiosus} PDB: 2ki7_B
Length = 123
Score = 27.9 bits (62), Expect = 5.4
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 12/57 (21%)
Query: 118 RKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEK 174
EKK +IA ER I+ S AE + ++ ++ +++
Sbjct: 4 YNEKKEKKRIAKER------------IDILFSLAERVFPYSPELAKRYVELALLVQQ 48
>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding,
HOST-virus interaction, metal-binding, nucleus,
polymorphism, receptor, transcription, transcription
regulation; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_D* 3e00_D* 2env_A
Length = 419
Score = 27.6 bits (60), Expect = 5.5
Identities = 18/113 (15%), Positives = 43/113 (38%), Gaps = 3/113 (2%)
Query: 250 SNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTS 309
+ + S Q T ++ + F + + F++ A + S
Sbjct: 278 KDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVI-ILS 336
Query: 310 NMRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISAL 362
R + ++ I D + ++ + + N +SSQ FA+L+ K+ ++ +
Sbjct: 337 GDRPGLLNVKPIEDIQDNLLQALE--LQLKLNHPESSQLFAKLLQKMTDLRQI 387
>2j0o_A Invasin IPAD; type III secretion, cell invasion, T3SS, plasmid,
virulence; 3.00A {Shigella flexneri} SCOP: a.250.1.1
Length = 318
Score = 27.6 bits (61), Expect = 6.4
Identities = 24/163 (14%), Positives = 54/163 (33%), Gaps = 17/163 (10%)
Query: 235 DLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKS 294
L +N L NI+ ++ K Q T + E ++ ++ +
Sbjct: 29 SLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRH 88
Query: 295 KET------SAFLENIADSTSNMRSSISAIREITDQRQKIISTINT-----IENITSNLN 343
+ ++ + IS RE+ + I+ IN E+ S+
Sbjct: 89 EYPINKDARELLHSAPKEAELDGDQMIS-HRELWAKIANSINDINEQYLKVYEHAVSSYT 147
Query: 344 DSSQKFAELMSKINN--ISALKENNSL---FKDAQRAMHTFRD 381
Q F+ ++S + + NS+ ++A+ ++
Sbjct: 148 QMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKE 190
>2nrj_A HBL B protein; enterotoxin, hemolysis, transmembrane, structural
genomics, PSI-2, protein structure initiative; 2.03A
{Bacillus cereus} SCOP: h.4.4.2
Length = 346
Score = 27.2 bits (60), Expect = 6.7
Identities = 14/111 (12%), Positives = 46/111 (41%), Gaps = 13/111 (11%)
Query: 327 KIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKI 386
+++ T+N I + ++ + E ++ + + + L + Q+ + E++
Sbjct: 87 QLLDTLNGIVEYDTTFDNYYETMVEAINTGDGETLKEGITDLRGEIQQNQKYAQQLIEEL 146
Query: 387 NRYIPSIGNNLQNFS-------------QSGLNDIQNLVRKLQETVNHFDD 424
+ SIG++++ F + ++ Q + ++ +VN++
Sbjct: 147 TKLRDSIGHDVRAFGSNKELLQSILKNQGADVDADQKRLEEVLGSVNYYKQ 197
>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation,
ATPase, transmembrane transport, helicase-like motor
domain; HET: ADP; 2.60A {Mycobacterium tuberculosis}
SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB:
1nl3_A
Length = 922
Score = 26.9 bits (59), Expect = 9.5
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 15/80 (18%)
Query: 292 MKSKETSAFLENIADS--------TSNMRSSISAIREITDQR-----QKIISTINTIENI 338
MK + F DS +M +S + + + R +K+ + T+ +
Sbjct: 1 MKETAAAKFERQHMDSPDLGTLVPRGSMADILSKLLRLGEGRMVKRLKKVADYVGTLSDD 60
Query: 339 TSNLNDS--SQKFAELMSKI 356
L D+ K E ++
Sbjct: 61 VEKLTDAELRAKTDEFKRRL 80
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.314 0.129 0.350
Gapped
Lambda K H
0.267 0.0494 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,445,661
Number of extensions: 153620
Number of successful extensions: 675
Number of sequences better than 10.0: 1
Number of HSP's gapped: 668
Number of HSP's successfully gapped: 73
Length of query: 452
Length of database: 5,693,230
Length adjustment: 96
Effective length of query: 356
Effective length of database: 3,365,806
Effective search space: 1198226936
Effective search space used: 1198226936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.7 bits)