RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780837|ref|YP_003065250.1| putative restriction
endonuclease S subunit [Candidatus Liberibacter asiaticus str. psy62]
(426 letters)
>1yf2_A Type I restriction-modification enzyme, S subunit; structural
genomics, PSI, protein structure initiative; 2.40A
{Methanocaldococcus jannaschii DSM2661} SCOP: d.287.1.2
d.287.1.2
Length = 425
Score = 102 bits (254), Expect = 2e-22
Identities = 70/438 (15%), Positives = 157/438 (35%), Gaps = 40/438 (9%)
Query: 7 YPQYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGK-------DIIYIGLEDVES 58
+K + IG IP+ W++V +K K+ G T ++ I ++ +ED+ +
Sbjct: 5 EENFKKT---EIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITN 61
Query: 59 GTGKYLPKDG---NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
KYL + S I K +L+ G AI ++
Sbjct: 62 S-NKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIP 120
Query: 116 PKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
++L + + + T + + + + + +P+PPL EQ I + +
Sbjct: 121 KDNILESEFL-YYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILT 179
Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
I+ + + L+ K+ L+ ++TKG+ K +G +P+ WEV
Sbjct: 180 KIDEGIEIIEKSINK----LERIKKGLMHKLLTKGIGHSRFKKSE----IGEIPEDWEVF 231
Query: 236 PFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
+ +S N I L+ + K + + V +
Sbjct: 232 EIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCN 291
Query: 296 IDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-----------IDSTYLAWLMRSYDLCK 344
++L + S + + + G +++ + A+ ++
Sbjct: 292 LNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLL 351
Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
+ GS + L ++ + +PP++EQ I +++ +D +E +Q L+
Sbjct: 352 ENLSGGST-FKELSKSMLENFKIPLPPLEEQKQIAKILS----SVDKSIELKKQKKEKLQ 406
Query: 405 ERRSSFIAAAVTGQIDLR 422
+ + +TG++ ++
Sbjct: 407 RMKKKIMELLLTGKVRVK 424
Score = 64.8 bits (156), Expect = 4e-11
Identities = 40/218 (18%), Positives = 76/218 (34%), Gaps = 15/218 (6%)
Query: 2 KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK-------DIIYIGLE 54
K + IG IP+ W+V IK ++ TG T + K +I +I
Sbjct: 205 KLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPL 264
Query: 55 DVESGTGKYLPKDGNSRQSDT----STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110
D+ K + + +++ KG I+ P A++
Sbjct: 265 DLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTFNQGC 324
Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170
+ Q + +E + G+T + N +P+PPL EQ
Sbjct: 325 KGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQ--- 381
Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
++I +D I + + E L+ K+ ++ ++T
Sbjct: 382 -KQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELLLT 418
>1ydx_A Type I restriction enzyme specificity protein Mg438; type-I HSDS,
DNA binding protein; 2.30A {Mycoplasma genitalium} SCOP:
d.287.1.2 d.287.1.2
Length = 406
Score = 67.8 bits (164), Expect = 5e-12
Identities = 45/400 (11%), Positives = 99/400 (24%), Gaps = 39/400 (9%)
Query: 25 WKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKG 84
W I L G E ++ + GKY +G + S + K
Sbjct: 36 WTKRTIDSLFDLKKGEMLEK----------ELITPEGKYEYFNGGVKNSGRTDKFNTFKN 85
Query: 85 QILYGKLGPYLRKAIIAD--FDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICE 142
I G + F G + +L P ++ + L S +RIEA+
Sbjct: 86 TISVIVGGSCGYVRLADKNFFCGQSNCTLNLLDPLELDLKFAYYALKSQQ--ERIEALAF 143
Query: 143 GATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQAL 202
G T+ + + + +P + + I D + IE+ ++ +
Sbjct: 144 GTTIQNIRISDLKELEIPFTSNKNE---QHAIANTLSVFDERLENLASLIEINRKLRDEY 200
Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYG 262
+ + K + + + K K
Sbjct: 201 AHKLFSLDEAFLSHWKLEAL------QSQMHEITLGEIFNFKSGKYLKS--------EER 246
Query: 263 NIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA 322
K G+ + + I S +
Sbjct: 247 LEEGKFPYYGAGIDNTGFVAEPNTEKDTISIISNGYSLGNIRYHEIPWFNGT--GSIALE 304
Query: 323 VKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPV-LVPPIKEQFDITNV 381
+ I + ++ L + + V V + Q +
Sbjct: 305 PMNNEIYVPFFYCALKYLQKDIKERMKSDD-SPFLSLKLAGEIKVPYVKSFQLQRKAGKI 363
Query: 382 INVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421
+ +D +++ ++ + L R + + +
Sbjct: 364 VF----LLDQKLDQYKKELSSLTVIRDTLLKKLFPDMTER 399
Score = 50.4 bits (119), Expect = 8e-07
Identities = 21/187 (11%), Positives = 50/187 (26%), Gaps = 15/187 (8%)
Query: 17 WIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTS 76
+ A+ + + +G+ +S + + K+ +
Sbjct: 216 KLEALQSQMHEITLGEIFNFKSGKYLKSEERLEEG----------KFPYYGAGIDNTGFV 265
Query: 77 TVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQR 136
K I G L + T + L+P + + + + +
Sbjct: 266 AEPNTEKDTISIISNGYSLGNIRYHEIPWFNGTGSIALEPMNNEIYVPFFYCALKYLQKD 325
Query: 137 IEAICEGATMSHADWKGIGNIPMP-IPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
I+ + K G I +P + Q K +D + + + + L
Sbjct: 326 IKERMKSDDSPFLSLKLAGEIKVPYVKSFQLQ----RKAGKIVFLLDQKLDQYKKELSSL 381
Query: 196 KEKKQAL 202
+ L
Sbjct: 382 TVIRDTL 388
>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 = 50.3 bits (120), Expect = 7e-07
Identities = 70/439 (15%), Positives = 144/439 (32%), Gaps = 174/439 (39%)
Query: 65 PKDGNSRQSD-TSTVSIFAK--GQILY----GKLGPYLR--KAIIADFDGICSTQFLVLQ 115
P +G + + T+ + K G + K+G + + + +F+ +L +
Sbjct: 44 PTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFE----NCYL--E 97
Query: 116 PKDV------LP-----------ELLQGWLLSIDVTQR----------IEAICEGATMSH 148
D+ L EL++ ++ + + +R A+ EG
Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 149 ADWKGIGNIPMPIPPLAEQVL--IREKIIAETVR--IDTLITERI--RFIELLKEKKQAL 202
A + G GN + +R+ + +T + LI + EL++ A
Sbjct: 158 AIFGGQGNT--------DDYFEELRD--LYQTYHVLVGDLI-KFSAETLSELIRTTLDA- 205
Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGL-----VPDHWEVKPFFALVT-ELNRKNTKLIESNI 256
+ T+GL ++ +EW L PD K + + LI +
Sbjct: 206 -EKVFTQGL--NI------LEW--LENPSNTPD----KDYLLSIPISC-----PLI--GV 243
Query: 257 LSL-SYGNIIQKLET-RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSA----QV 310
+ L Y ++ T + +G PGE R L+ A Q
Sbjct: 244 IQLAHY--VV----TAKLLGF-----------TPGE--LR--------SYLKGATGHSQ- 275
Query: 311 MERGIITSAYMAVKPHGIDSTYLAWLMRS-YDLCK-----VFYAMGSGLRQSLKFEDVKR 364
G++T+ +A DS W S + + +F+ G+R +
Sbjct: 276 ---GLVTAVAIAET----DS----W--ESFFVSVRKAITVLFF---IGVRCYEAY----- 314
Query: 365 LPVL-VPPIKEQFDITN-------VINVETARIDVLVEKIEQ-----------SIVLLKE 405
P +PP + + N ++++ + + + + + I L+
Sbjct: 315 -PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNG 373
Query: 406 RRSSFIAAAVTG-QIDLRG 423
+ + + V+G L G
Sbjct: 374 AK-NLV---VSGPPQSLYG 388
Score = 47.2 bits (112), Expect = 7e-06
Identities = 83/461 (18%), Positives = 125/461 (27%), Gaps = 214/461 (46%)
Query: 60 TGKYLPKDGNS------RQSDTSTVSIFAKGQILYGKLGPY---LR------KAIIADFD 104
+ K NS + + V+IF GQ G Y LR ++ D
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFG-GQ---GNTDDYFEELRDLYQTYHVLVGDLI 188
Query: 105 GICSTQF--LVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADW-KGIGNIPMPI 161
+ L+ D QG +++ + W + P
Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQG----LNILE---------------WLEN----PSNT 225
Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRF--IELLKEKKQALVSYIVT-K--GLNPDVK 216
P D L++ I I ++ Q L Y+VT K G P +
Sbjct: 226 PD-----------------KDYLLSIPISCPLIGVI----Q-LAHYVVTAKLLGFTPG-E 262
Query: 217 MKDSGIEWV-----GLVP-------DHWEVKPFFALVTELNRKNTKLIESNILSLSYGNI 264
++ ++ GLV D WE FF V RK + L +
Sbjct: 263 LRSY-LKGATGHSQGLVTAVAIAETDSWE--SFFVSV----RKAITV-------LFF--- 305
Query: 265 IQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV---MERGIITSAYM 321
+G+ YE Y P SL + + +E + M
Sbjct: 306 --------IGV--RCYEAY----P-------------NTSLPPSILEDSLENNEGVPSPM 338
Query: 322 ---------AVKPHGIDST----------YLAWLMRS-------------YDLCKVFYAM 349
V+ + ++ T ++ L+ Y L
Sbjct: 339 LSISNLTQEQVQDY-VNKTNSHLPAGKQVEIS-LVNGAKNLVVSGPPQSLYGLNLTLRKA 396
Query: 350 G--SGLRQS--------LKFEDVKR-LPVLVP---P--------IKEQFDITNV-INVET 386
SGL QS LKF R LPV P I + NV N +
Sbjct: 397 KAPSGLDQSRIPFSERKLKF--SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKD 454
Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR--GES 425
+I V +F G DLR S
Sbjct: 455 IQIPVY---------------DTF-----DGS-DLRVLSGS 474
Score = 38.4 bits (89), Expect = 0.003
Identities = 50/277 (18%), Positives = 76/277 (27%), Gaps = 127/277 (45%)
Query: 17 WIG-----AIPKHWKVVPIKRFTKLNTGRTS----------ESGKD-------IIYIGLE 54
+IG A P TS E+ + I + E
Sbjct: 305 FIGVRCYEAYP-----------------NTSLPPSILEDSLENNEGVPSPMLSISNLTQE 347
Query: 55 DVES---GTGKYLPKDG-------NSRQSDTSTVSIFAKG--QILYGKLGPYLRKAIIAD 102
V+ T +LP N ++ VS G Q LYG L LRK A
Sbjct: 348 QVQDYVNKTNSHLPAGKQVEISLVNGAKN--LVVS----GPPQSLYG-LNLTLRK-AKAP 399
Query: 103 FDGI-------------CSTQFLVLQPKDVLP---ELLQGWLLSIDVTQRIEA--ICEGA 144
G+ S +FL P P LL + I +
Sbjct: 400 -SGLDQSRIPFSERKLKFSNRFL---PVAS-PFHSHLLV------PASDLINKDLVKNNV 448
Query: 145 TMSHADWKGIGNIPMPIPPLAEQVL-------IR---EKIIAETVRIDTLIT-ERIRFIE 193
+ + D + IP V +R I V I +++
Sbjct: 449 SFNAKDIQ----IP---------VYDTFDGSDLRVLSGSISERIVD---CIIRLPVKWET 492
Query: 194 LLKEKKQALVSYIV------TKGLNPDV-KMKD-SGI 222
+ K ++I+ GL + KD +G+
Sbjct: 493 TTQFK----ATHILDFGPGGASGLGVLTHRNKDGTGV 525
Score = 35.3 bits (81), Expect = 0.029
Identities = 46/275 (16%), Positives = 87/275 (31%), Gaps = 113/275 (41%)
Query: 257 LSLSYGNI-------------IQKL-ETRNMGLKPESYETYQIVD----PGEIVFRFI-- 296
L+LS+G++ +L E N L PE E + D P E+V +F+
Sbjct: 9 LTLSHGSLEHVLLVPTASFFIASQLQEQFNKIL-PEPTEGFAADDEPTTPAELVGKFLGY 67
Query: 297 --DLQNDKRSLRSAQVMERGI--ITSAYM--------AVKPHGIDSTYLAWLMRSYDLCK 344
L + + QV+ + + Y+ A K + T L ++ +L K
Sbjct: 68 VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLV---KTKELIK 124
Query: 345 VFY----AMG--------SGLRQSLK-------------------FEDVKRL-----PVL 368
+ S L +++ FE+++ L ++
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184
Query: 369 VPPIKEQFDITNVINVETARIDVLVEKI-EQSIVLLK-----ERR--SSFIAAA------ 414
IK ++ E R + EK+ Q + +L+ ++ +
Sbjct: 185 GDLIKF---SAETLS-ELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPL 240
Query: 415 ----------VTGQI------DLR-------GESQ 426
VT ++ +LR G SQ
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ 275
>3opc_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG, chaperone; HET: MSE; 2.09A {Bordetella pertussis}
Length = 154
Score = 30.6 bits (68), Expect = 0.66
Identities = 17/117 (14%), Positives = 36/117 (30%), Gaps = 5/117 (4%)
Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224
AE + ++ E+ + + + + L + + + GL D
Sbjct: 29 AETEALMDRRAHES--LQAAVQRKETLADDLAQLGAERDALLSGAGLASGPAGTDXXXXX 86
Query: 225 VGLVPDHW-EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY 280
+ W ++ A E N++N LI N+ + L +Y
Sbjct: 87 HPELGPLWQALQANAAQAREHNQRNGTLIAVNLRHTQ--ESLDALRQAAGTGAAATY 141
>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 = 30.0 bits (66), Expect = 0.93
Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 30/58 (51%)
Query: 198 KKQALVSYIVTKGLNPDVKM--KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIE 253
+KQAL K L +K+ DS P A+ K T +E
Sbjct: 18 EKQAL------KKLQASLKLYADDSA--------------PALAI------KAT--ME 47
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.4 bits (65), Expect = 1.6
Identities = 26/112 (23%), Positives = 47/112 (41%), Gaps = 25/112 (22%)
Query: 233 EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETR-NMGLK-PE--SYETYQIVDP 288
EV+ ++ T L K ++ N +Y + +++ R N+ L PE Y+ + + P
Sbjct: 753 EVRKAVSIETALEHK---VVNGNSADAAYAQV--EIQPRANIQLDFPELKPYKQVKQIAP 807
Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY 340
E+ +DL ER I+ + + V P G S W M ++
Sbjct: 808 AELE-GLLDL-------------ERVIVVTGFAEVGPWG--SARTRWEMEAF 843
>2r5t_A Serine/threonine-protein kinase SGK1; AGC protein kinase,
apoptosis, ATP-binding, cytoplasm, endoplasmic
reticulum, nucleotide-binding, nucleus; HET: ANP; 1.90A
{Homo sapiens} PDB: 3hdm_A* 3hdn_A*
Length = 373
Score = 27.0 bits (59), Expect = 7.9
Identities = 28/119 (23%), Positives = 45/119 (37%), Gaps = 17/119 (14%)
Query: 59 GTGKYLPKDGNSRQSDTSTVSIFAKGQILY----GKLGPYLRKAIIADFDGICSTQFLVL 114
GT +YL + +Q TV + G +LY G P+ + +D I + +
Sbjct: 201 GTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLP-PFYSRNTAEMYDNILNKPLQL- 258
Query: 115 QPKDVLPEL--LQGWLLSIDVTQRIEAICEGAT-MSHA-----DWKGIGN--IPMPIPP 163
++ L LL D T+R+ A + SH +W + N I P P
Sbjct: 259 -KPNITNSARHLLEGLLQKDRTKRLGAKDDFMEIKSHVFFSLINWDDLINKKITPPFNP 316
>2c30_A Serine/threonine-protein kinase PAK 6; STE20-like, CRIB domain,
ATP-binding, transferase, nucleotide-binding,
phosphorylation, polymorphism; HET: SEP; 1.6A {Homo
sapiens} PDB: 2f57_A* 2j0i_A* 2cdz_A* 2q0n_A* 2bva_A*
Length = 321
Score = 26.9 bits (59), Expect = 8.3
Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 59 GTGKYLPKDGNSRQSDTSTVSIFAKGQILY----GKLGPYLRKAIIADFDGICSTQFLVL 114
GT ++ + SR + V I++ G ++ G+ PY + + + + L
Sbjct: 203 GTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVDGEP-PYFSDSPVQAMKRLRDSPPPKL 261
Query: 115 QPKDVLPELLQ---GWLLSIDVTQRIEA 139
+ + +L+ +L D +R A
Sbjct: 262 KNSHKVSPVLRDFLERMLVRDPQERATA 289
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
0.319 0.138 0.400
Gapped
Lambda K H
0.267 0.0597 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,755,610
Number of extensions: 179229
Number of successful extensions: 427
Number of sequences better than 10.0: 1
Number of HSP's gapped: 419
Number of HSP's successfully gapped: 20
Length of query: 426
Length of database: 5,693,230
Length adjustment: 95
Effective length of query: 331
Effective length of database: 3,390,050
Effective search space: 1122106550
Effective search space used: 1122106550
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: 58 (26.4 bits)