RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254780423|ref|YP_003064836.1| S-adenosylmethionine
synthetase [Candidatus Liberibacter asiaticus str. psy62]
         (413 letters)



>1p7l_A S-adenosylmethionine synthetase; AMPPNP, SAM, transferase; HET: SAM
           ANP PPK; 2.50A {Escherichia coli} SCOP: d.130.1.1
           d.130.1.1 d.130.1.1 PDB: 1fug_A 1mxb_A* 1mxc_A* 1mxa_A*
           1rg9_A* 1xra_A 1xrb_A 1xrc_A
          Length = 383

 Score =  467 bits (1202), Expect = e-132
 Identities = 197/412 (47%), Positives = 248/412 (60%), Gaps = 33/412 (8%)

Query: 3   ADFLFTSESVSEGHPDKICDRISDEIVDLVYREAIESKMDVNSVRVACEVLVTKNKVIVA 62
           A  LFTSESVSEGHPDKI D+ISD ++D +  +      D  + RVACE  V    V+V 
Sbjct: 1   AKHLFTSESVSEGHPDKIADQISDAVLDAILEQ------DPKA-RVACETYVKTGMVLVG 53

Query: 63  GEVRLPHGLSKKDSITGQYVVDKEKFEKVVRSVIRSIGYEQE--GFHWETVDVEVLLHSQ 120
           GE            IT    VD    E++ R+ +R IGY     GF   +  V   +  Q
Sbjct: 54  GE------------ITTSAWVD---IEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQ 98

Query: 121 SSDIAYGVDNASDDCSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKNSG 180
           S DI  GVD    D    GAGDQG+MFGYA  ET   MPAPI YAHR+++  A+ RKN  
Sbjct: 99  SPDINQGVD--RADPLEQGAGDQGLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKN-- 154

Query: 181 GDVSKLGPDAKSQVTIRYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYILKALEDI 240
           G +  L PDAKSQVT +Y D K+  + ++VLS QH +    +    +V+E  I   L   
Sbjct: 155 GTLPWLRPDAKSQVTFQYDDGKIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAE 214

Query: 241 KISPDCSWYINPAGKFVIGGPCSDAGLTGRKIIVDTYGGASPHGGGAFSGKDITKVDRAA 300
            ++    ++INP G+FVIGGP  D GLTGRKIIVDTYGG + HGGGAFSGKD +KVDR+A
Sbjct: 215 WLTSATKFFINPTGRFVIGGPMGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSA 274

Query: 301 AYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANAINKVMD 360
           AYAARY+AKNIVAAGLADRC IQ+SYAIG++ P SI V+   + KV    +   + +  D
Sbjct: 275 AYAARYVAKNIVAAGLADRCEIQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFD 334

Query: 361 LSVSGIRDHLNLSRPIYAQTSAYGHFGRSANQDGFFPWEALDLIEPLKKAIG 412
           L   G+   L+L  PIY +T+AYGHFGR       FPWE  D  + L+ A G
Sbjct: 335 LRPYGLIQMLDLLHPIYKETAAYGHFGREH-----FPWEKTDKAQLLRDAAG 381


>3iml_A S-adenosylmethionine synthetase; structural genomics, ATP- binding,
           cobalt, cytoplasm, magnesium, metal-binding,
           nucleotide-binding; 2.35A {Burkholderia pseudomallei}
          Length = 399

 Score =  432 bits (1111), Expect = e-122
 Identities = 195/414 (47%), Positives = 252/414 (60%), Gaps = 29/414 (7%)

Query: 1   MSADFLFTSESVSEGHPDKICDRISDEIVDLVYREAIESKMDVNSVRVACEVLVTKNKVI 60
           M+ D+LFTSESVSEGHPDK+ D+ISD I+D +  +      D  S RVA E L     V+
Sbjct: 5   MANDYLFTSESVSEGHPDKVADQISDAILDAILAQ------DKYS-RVAAETLCNTGLVV 57

Query: 61  VAGEVRLPHGLSKKDSITGQYVVDKEKFEKVVRSVIRSIGYEQE--GFHWETVDVEVLLH 118
           +AGE+                      + ++ R  I+ IGY+    G  +    V V   
Sbjct: 58  LAGEITTTA---------------NIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYD 102

Query: 119 SQSSDIAYGVDNASDDCSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKN 178
            QS DIA GVD A D+    GAGDQG+MFGYAC ET + MP PI+ +HR++   A+ R++
Sbjct: 103 KQSPDIAQGVDRAHDNNLDQGAGDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRD 162

Query: 179 SGGDVSKLGPDAKSQVTIRYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYILKALE 238
             G +  L PDAKSQVT+RYVD K   + ++VLS QH           +V+E  I   L 
Sbjct: 163 --GRLPWLRPDAKSQVTVRYVDGKPHSIDTVVLSTQHAPEIDLPALREAVIEEVIKPTLP 220

Query: 239 DIKISPDCSWYINPAGKFVIGGPCSDAGLTGRKIIVDTYGGASPHGGGAFSGKDITKVDR 298
              I  D  + +NP G+FVIGGP  D GLTGRKIIVDTYGGA+PHGGGAFSGKD +KVDR
Sbjct: 221 ADLIKGDIKFLVNPTGRFVIGGPQGDCGLTGRKIIVDTYGGAAPHGGGAFSGKDPSKVDR 280

Query: 299 AAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANAINKV 358
           +AAYA RY+AKNIVAAGLA R  IQ+SYAIG++ P S+ V+   +G+VS+  +   + + 
Sbjct: 281 SAAYAGRYVAKNIVAAGLASRALIQVSYAIGVAEPTSVMVNTFGTGRVSDETITKLVREH 340

Query: 359 MDLSVSGIRDHLNLSRPIYAQTSAYGHFGRSANQDGFFPWEALDLIEPLKKAIG 412
            DL   GI   L+L RPIY +T+AYGHFGR   ++  F WEA D    L +A G
Sbjct: 341 FDLRPKGIIQMLDLLRPIYEKTAAYGHFGR---EEPEFSWEAADKALALAEAAG 391


>2p02_A S-adenosylmethionine synthetase isoform type-2; structural
           genomics, structural genomics consortium, SGC,
           transferase; HET: SAM; 1.21A {Homo sapiens} SCOP:
           d.130.1.1 d.130.1.1 d.130.1.1 PDB: 1qm4_A 1o92_A*
           1o93_A* 1o90_A* 1o9t_A 2obv_A*
          Length = 396

 Score =  397 bits (1021), Expect = e-111
 Identities = 174/411 (42%), Positives = 248/411 (60%), Gaps = 36/411 (8%)

Query: 1   MSADFLFTSESVSEGHPDKICDRISDEIVDLVYREAIESKMDVNSVRVACEVLVTKNKVI 60
               FLFTSESV EGHPDKICD+ISD ++D   ++      D ++ +VACE +     ++
Sbjct: 15  EEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQ------DPDA-KVACETVAKTGMIL 67

Query: 61  VAGEVRLPHGLSKKDSITGQYVVDKEKFEKVVRSVIRSIGY--EQEGFHWETVDVEVLLH 118
           +AGE+                 VD   ++KVVR  ++ IGY    +GF ++T +V V L 
Sbjct: 68  LAGEITSRA------------AVD---YQKVVREAVKHIGYDDSSKGFDYKTCNVLVALE 112

Query: 119 SQSSDIAYGVDNASDDCSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKN 178
            QS DIA GV    ++   +GAGDQG+MFGYA  ET + MP  I  AH++   LA+ R+N
Sbjct: 113 QQSPDIAQGVHLDRNE-EDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRN 171

Query: 179 SGGDVSKLGPDAKSQVTIRYVDNKVCEVKSIVLSIQHF---DPTWDRGKVRSVVEPYILK 235
             G +  L PD+K+QVT++Y+ ++   +   V +I      D      ++R  ++  ++K
Sbjct: 172 --GTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIK 229

Query: 236 A-LEDIKISPDCSWYINPAGKFVIGGPCSDAGLTGRKIIVDTYGGASPHGGGAFSGKDIT 294
           A +    +  D  +++ P+G+FVIGGP  DAGLTGRKIIVDTYGG   HGGGAFSGKD T
Sbjct: 230 AVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYT 289

Query: 295 KVDRAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANA 354
           KVDR+AAYAAR++AK++V  GL  R  +Q+SYAIG+S PLSI +  + + + SE  +   
Sbjct: 290 KVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEI 349

Query: 355 INKVMDLSVSGIRDHLNLSRPIYAQTSAYGHFGRSANQDGFFPWEALDLIE 405
           + K  DL    I   L+L +PIY +T+AYGHFGR +     FPWE    ++
Sbjct: 350 VKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDS-----FPWEVPKKLK 395


>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 = 64.2 bits (156), Expect = 5e-11
 Identities = 79/502 (15%), Positives = 136/502 (27%), Gaps = 230/502 (45%)

Query: 3   ADFL-FTSESVSEGHPDKICDRISDEIVDLVYREAIESKM----DVNSVRVACE-----V 52
             FL + S  V      +      D++++L   E  E+      D++++           
Sbjct: 62  GKFLGYVSSLVEPSKVGQ-----FDQVLNLCLTE-FENCYLEGNDIHALAAKLLQENDTT 115

Query: 53  LVTKNKVI--------VAGEVRLPHGLSK--KDSITGQ---YVV------DKEKFEK--- 90
           LV   ++I        +A         S   +    G      +        + FE+   
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD 175

Query: 91  -------VVRSVIRSIG---------------YEQEGF---HW----ETV-DVEVLLHSQ 120
                  +V  +I+                     +G     W        D + LL   
Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP 235

Query: 121 SS-------DIA-YGVDNASDDCSTLG-------------AG-DQGI------------- 145
            S        +A Y V         LG              G  QG+             
Sbjct: 236 ISCPLIGVIQLAHYVVT-----AKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE 290

Query: 146 ------------MF--GYACRETADFMPAPIYYAHRILR--TLADARKNSGGDVSKLGPD 189
                       +F  G  C E          Y +  L    L D+ +N+ G  S   P 
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEA---------YPNTSLPPSILEDSLENNEGVPS---P- 337

Query: 190 AKSQVTIRYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYI------LKALEDIKIS 243
                               +LSI            +  V+ Y+      L A + ++IS
Sbjct: 338 --------------------MLSI--------SNLTQEQVQDYVNKTNSHLPAGKQVEIS 369

Query: 244 PDCSWYINPAGKFVIGGPCSD-AGLTG--RKIIVDTYGGASPHGGGAFSGKDITKV---D 297
                 +N A   V+ GP     GL    RK               A SG D +++   +
Sbjct: 370 -----LVNGAKNLVVSGPPQSLYGLNLTLRKA-------------KAPSGLDQSRIPFSE 411

Query: 298 RAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSESCVANAINK 357
           R   ++ R+L                      ++ P   F   H S       +  A + 
Sbjct: 412 RKLKFSNRFLP---------------------VASP---F---H-S-----HLLVPASDL 438

Query: 358 VM-DLSVSGIR-DHLNLSRPIY 377
           +  DL  + +  +  ++  P+Y
Sbjct: 439 INKDLVKNNVSFNAKDIQIPVY 460



 Score = 52.3 bits (125), Expect = 2e-07
 Identities = 62/443 (13%), Positives = 116/443 (26%), Gaps = 182/443 (41%)

Query: 41  MDVNSVR--------VACEVLVTKNKVIVAGEVR------LPHGLSKKDSITGQYVVDKE 86
           MD  S R        +   +LV      +A +++      LP      +          +
Sbjct: 1   MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILP---EPTEGFAAD-----D 52

Query: 87  KFEKVVRSVIRSIGY----EQEGFHWETVDV-EVLLHS------QSSDI-AYGVDNASDD 134
           +       V + +GY     +     +   V  + L        + +DI A       ++
Sbjct: 53  EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEN 112

Query: 135 CSTLGAGDQGIMFGYACRETADFMPAPIYYAHRILRTLADARKNSGGDVSKLGPDA---- 190
            +TL                             +++    AR  +     K    A    
Sbjct: 113 DTTLVK------------------------TKELIKNYITARIMAKRPFDKKSNSALFRA 148

Query: 191 --KSQVTI-----------RYVDNKVCEVKSIVLSIQHFDPTWDRGKVRSVVEPYILKA- 236
             +    +            Y +    E++ +      +  T+       +V   I  + 
Sbjct: 149 VGEGNAQLVAIFGGQGNTDDYFE----ELRDL------YQ-TY-----HVLVGDLIKFSA 192

Query: 237 --LEDIKISPDC------------SWYINPAGK----FVIGGP----------------- 261
             L ++  +                W  NP+      +++  P                 
Sbjct: 193 ETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVT 252

Query: 262 CSDAGLT-GRKIIVDTYGGASPHGGGAFSGKDITKVDRAAAYAA-------RYLAKNIVA 313
               G T G   +     GA+ H  G      +T    A A A            +  + 
Sbjct: 253 AKLLGFTPGE--LRSYLKGATGHSQGL-----VT----AVAIAETDSWESFFVSVRKAIT 301

Query: 314 A----GLADRCTIQLSYAIGISRPLSIFVDLHDS---GKVSESCVANAINKVMDLSVSGI 366
                G+  RC    +Y    S P SI   L DS    +   S         M LS+S +
Sbjct: 302 VLFFIGV--RC--YEAYPN-TSLPPSI---LEDSLENNEGVPSP--------M-LSISNL 344

Query: 367 -RD-----------HLNLSRPIY 377
            ++           HL   + + 
Sbjct: 345 TQEQVQDYVNKTNSHLPAGKQVE 367



 Score = 28.4 bits (63), Expect = 3.2
 Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 6/20 (30%)

Query: 52  VLVTKNK------VIVAGEV 65
           VL  +NK      VIVAG +
Sbjct: 514 VLTHRNKDGTGVRVIVAGTL 533


>2o9u_X Monellin chain B and monellin chain A; alternative conformations,
           3-10 polyproline II helix, plant protein; 1.15A
           {Dioscoreophyllum cumminsii} SCOP: d.17.1.1 PDB: 1m9g_A
           1fa3_A 1iv7_A 1iv9_A 1mnl_A 1mol_A 1fuw_A 4mon_B 3mon_B
           1krl_B 4mon_A 1krl_A 3mon_A 2q33_B* 2q33_A*
          Length = 97

 Score = 30.8 bits (69), Expect = 0.65
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 11/70 (15%)

Query: 79  GQYVVDKEK---------FEKVVRSVIRSIGYEQEGFHWETVDVEVLLHSQSSDIAYGVD 129
           G++ VD+E          F KV+R  ++   YE EGF  E    E  L+  +SD  +  D
Sbjct: 17  GKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFR-EIKGYEYQLYVYASDKLFRAD 75

Query: 130 NASDDCSTLG 139
             S+D  T G
Sbjct: 76  -ISEDYKTRG 84


>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCSG,
           protein structure initiative, PSI, joint center for
           structural genomics; HET: CIT; 1.60A {Thermotoga
           maritima} SCOP: a.24.13.1 c.37.1.10
          Length = 306

 Score = 29.8 bits (66), Expect = 1.1
 Identities = 22/156 (14%), Positives = 41/156 (26%), Gaps = 2/156 (1%)

Query: 206 VKSIVLSIQHFDPTWDRGKVRSVVEPYI-LKALEDIKISPDCSWYINPAGKFVIGGPCSD 264
           +K I+L I +FD   +       V   + +            +      GK V+      
Sbjct: 83  LKEIILEILNFDTKLNVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADT 142

Query: 265 AGLTGRKIIVDTYGGASPHGGGAFSGKDITKVDRAAAYAARYLAKNIVAAGLADRCTIQL 324
                 + +                G D   V   A   A    K++V    A R   + 
Sbjct: 143 FRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAHALARNKDVVIIDTAGRLHTKK 202

Query: 325 SYAIGISRPLSIFVDLHDSGKVSESCVANAINKVMD 360
           +  +   R +   V         E+ +        +
Sbjct: 203 NL-MEELRKVHRVVKKKIPDAPHETLLVIDATTGQN 237


>3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, plasmid; 2.60A
           {Thermus thermophilus HB27} PDB: 3dlb_A* 3dlh_A* 3f73_A*
           3hm9_A 3hvr_A 3hxm_A* 3hk2_A 3hjf_A
          Length = 685

 Score = 28.0 bits (62), Expect = 4.2
 Identities = 5/15 (33%), Positives = 12/15 (80%)

Query: 158 MPAPIYYAHRILRTL 172
           +PAP++ A R+++ +
Sbjct: 652 LPAPLHLADRLVKEV 666


>1yvu_A Hypothetical protein AQ_1447; RNAse H fold, RNA binding protein,
           gene regulation; 2.90A {Aquifex aeolicus VF5} SCOP:
           b.34.14.1 c.55.3.10 PDB: 2f8s_A 2f8t_A 2nub_A
          Length = 706

 Score = 27.6 bits (61), Expect = 4.7
 Identities = 4/11 (36%), Positives = 9/11 (81%)

Query: 158 MPAPIYYAHRI 168
           +PA ++Y+ +I
Sbjct: 675 LPATVHYSDKI 685


>2w42_A PIWI, putative uncharacterized protein; RNAI, RISC, argonaute, PIWI
           domain, protein/DNA complex; 1.90A {Archaeoglobus
           fulgidus} PDB: 1ytu_A 2bgg_A 1w9h_A
          Length = 427

 Score = 27.7 bits (61), Expect = 5.0
 Identities = 2/11 (18%), Positives = 5/11 (45%)

Query: 158 MPAPIYYAHRI 168
           +P  + Y   +
Sbjct: 387 LPVTVNYPKLV 397


>3b7k_A Acyl-coenzyme A thioesterase 12; hotdog fold, structural genomics,
           structural genomics consortium, SGC, cytoplasm, fatty
           acid metabolism, hydrolase; HET: COA; 2.70A {Homo
           sapiens}
          Length = 333

 Score = 27.7 bits (61), Expect = 5.1
 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 2/65 (3%)

Query: 283 HGGGAFSGKDITKVDRAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHD 342
             G   +G+ +  +D  A  AA   A         D   IQ      + + ++I   +  
Sbjct: 39  ARGELSAGQLLKWIDTTACLAAEKHAGVSCVTASVDD--IQFEETARVGQVITIKAKVTR 96

Query: 343 SGKVS 347
           +   S
Sbjct: 97  AFSTS 101


>2v4n_A Multifunctional protein SUR E; hydrolase, surviVal protein,
           stationary phase, phosphatase, mononucleotidase,
           divalent metal ION; 1.7A {Salmonella typhimurium} PDB:
           2v4o_A
          Length = 254

 Score = 27.3 bits (60), Expect = 6.0
 Identities = 25/119 (21%), Positives = 41/119 (34%), Gaps = 18/119 (15%)

Query: 298 RAAAYAARYLAKNIVAAGLADRCTIQLSYAIGISRPLSIFVDLHDSGKVSES----CVAN 353
           +  A A R  A   V A   +R     S ++ +   L  F   +    V       CV  
Sbjct: 18  QTLAKALREFADVQVVAPDRNRSGA--SNSLTLESSLRTFTFDNGDIAVQMGTPTDCVYL 75

Query: 354 AINKVM----DLSVSGIRDHLNLSRPIY-------AQTSA-YGHFGRSANQDGFFPWEA 400
            +N +M    D+ VSGI    NL   +        A      G    + + +G+  ++ 
Sbjct: 76  GVNALMRPRPDIVVSGINAGPNLGDDVIYSGTVAAAMEGRHLGFPALAVSLNGYQHYDT 134


  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    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0716    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,612,722
Number of extensions: 167024
Number of successful extensions: 490
Number of sequences better than 10.0: 1
Number of HSP's gapped: 471
Number of HSP's successfully gapped: 17
Length of query: 413
Length of database: 5,693,230
Length adjustment: 95
Effective length of query: 318
Effective length of database: 3,390,050
Effective search space: 1078035900
Effective search space used: 1078035900
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 (21.7 bits)
S2: 58 (26.1 bits)