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)