RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780683|ref|YP_003065096.1| lipoprotein [Candidatus Liberibacter asiaticus str. psy62] (84 letters) >1qwy_A Peptidoglycan hydrolase; LYTM lysostaphin metalloprotease asparagine switch; 1.30A {Staphylococcus aureus subsp} SCOP: b.84.3.2 PDB: 2b0p_A 2b13_A* 2b44_A Length = 291 Score = 79.7 bits (196), Expect = 1e-16 Identities = 27/86 (31%), Positives = 39/86 (45%), Gaps = 5/86 (5%) Query: 2 VIYVGNDLVELGNTILIRHDDS-IVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHP 60 V+ G GN + I+ +S Y H + V G KV G I SG +GN+ P Sbjct: 206 VVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAP 265 Query: 61 QVHFELRKNAI----AMDPIKFLEEK 82 VHF+ I A+DP +L+ + Sbjct: 266 HVHFQRMSGGIGNQYAVDPTSYLQSR 291 >2hsi_A Putative peptidase M23; structural genomics, PSI, protein structure initiative, NEW YORK SGX research center for structural genomics; 1.90A {Pseudomonas aeruginosa PAO1} Length = 282 Score = 73.3 bits (179), Expect = 1e-14 Identities = 20/71 (28%), Positives = 36/71 (50%) Query: 14 NTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIAM 73 T+ + H ++++ H+ V+ GQ+V RG +G G +G A P +H+ + N + Sbjct: 212 KTVFVDHGQGFISMFCHLSKIDVKLGQQVPRGGVLGKVGATGRATGPHMHWNVSLNDARV 271 Query: 74 DPIKFLEEKIP 84 DP F+ P Sbjct: 272 DPAIFIGAFQP 282 >3nyy_A Putative glycyl-glycine endopeptidase LYTM; structural genomics, joint center for structural genomics, J protein structure initiative, PSI; HET: MSE 2PE SO4; 1.60A {Ruminococcus gnavus} Length = 252 Score = 70.1 bits (171), Expect = 1e-13 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 12/79 (15%) Query: 13 GNTILIRHDDSIVTVYSHIDT-PYVQKGQKVSRGHTIGLSGKSGNAQH-------PQVHF 64 G I I Y+H+D+ ++KG V G +G G SG + +H Sbjct: 160 GWRIGITAPTGAYFYYAHLDSYAELEKGDPVKAGDLLGYMGDSGYGEEGTTGEFPVHLHL 219 Query: 65 ELRKN----AIAMDPIKFL 79 + I+++P L Sbjct: 220 GIYLKEGTEEISVNPYPVL 238 >3csq_A Morphogenesis protein 1; hydrolase, infection, late protein; 1.80A {Bacteriophage phi-29} Length = 334 Score = 68.6 bits (167), Expect = 4e-13 Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 6/75 (8%) Query: 2 VIYVG--NDLVELGNTILIRHDDSIVT----VYSHIDTPYVQKGQKVSRGHTIGLSGKSG 55 ++ G + + + + D V V H G+K+ +G +G +G G Sbjct: 213 CVWRGDASAYLAWTSDKEVMCADGSVRYITWVNVHESPLPFDVGKKLKKGDLMGHTGIGG 272 Query: 56 NAQHPQVHFELRKNA 70 N HF + Sbjct: 273 NVTGDHWHFNVIDGK 287 >2gu1_A Zinc peptidase; alpha/beta, beta barrel, structural genomics, PSI, protein structure initiative; 1.90A {Vibrio cholerae} Length = 361 Score = 65.1 bits (157), Expect = 4e-12 Identities = 25/67 (37%), Positives = 36/67 (53%) Query: 13 GNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIA 72 GN ++I H+ T Y H+D V+KGQ V RG I L+G +G P +HFE+ Sbjct: 263 GNYLVIEHNSVYKTRYLHLDKILVKKGQLVKRGQKIALAGATGRLTGPHLHFEVLVRNRP 322 Query: 73 MDPIKFL 79 +D +K Sbjct: 323 VDAMKAD 329 >3it5_A Protease LASA; metallopeptidase, beta-protein, cell membrane, cell outer membrane, hydrolase, membrane, metal-binding; 2.00A {Pseudomonas aeruginosa PAO1} PDB: 3it7_A* Length = 182 Score = 48.7 bits (115), Expect = 3e-07 Identities = 19/87 (21%), Positives = 32/87 (36%), Gaps = 10/87 (11%) Query: 2 VIYVGNDLVEL--GNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGL--------S 51 V+ V + + + H T Y H+D V GQ+VS +G+ Sbjct: 51 VVAAHAGTVRVLSRCQVRVTHPSGWATNYYHMDQIQVSNGQQVSADTKLGVYAGNINTAL 110 Query: 52 GKSGNAQHPQVHFELRKNAIAMDPIKF 78 + G++ P +HF L N + Sbjct: 111 CEGGSSTGPHLHFSLLYNGAFVSLQGA 137 >2hcn_A RNA-directed RNA polymerase (NS5); WEST-NIle virus RNA polymerase, structural genomics, marseilles structural genomics program @ AFMB, MSGP; 2.35A {Kunjin virus} PDB: 2hcs_A 2hfz_A Length = 595 Score = 29.0 bits (65), Expect = 0.26 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 3/50 (6%) Query: 8 DLVELGNTILI---RHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKS 54 D++E+ N + I + V D PY K + + G IG ++ Sbjct: 503 DMLEVWNRVWIEENEWMEDKTPVEKWSDVPYSGKREDIWCGSLIGTRARA 552 >2j7u_A RNA dependent RNA polymerase; nucleoside binding site, flavivirus, high-throughput assay, viral protein; HET: PGE; 1.85A {Dengue virus} PDB: 2j7w_A* Length = 635 Score = 27.8 bits (62), Expect = 0.58 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 3/50 (6%) Query: 8 DLVELGNTILIR---HDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKS 54 D++ + N + I + V + + PY+ K + G IGL+ ++ Sbjct: 543 DMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCGSLIGLTSRA 592 >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 = 27.5 bits (60), Expect = 0.78 Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 9/61 (14%) Query: 31 IDTPYVQKGQKVSRG--HTIGLSGKSGNAQHPQVHFELRKNAIAMD-----PIKFLEEKI 83 ++T V+K + H + ++G S +A + QV + R N I +D P K +++ Sbjct: 749 VETSEVRKAVSIETALEHKV-VNGNSADAAYAQVEIQPRAN-IQLDFPELKPYKQVKQIA 806 Query: 84 P 84 P Sbjct: 807 P 807 >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 = 24.9 bits (54), Expect = 4.7 Identities = 23/124 (18%), Positives = 33/124 (26%), Gaps = 69/124 (55%) Query: 3 IYV-----GN------DLVELGNT--------I---------LIRHDDSIVTVYSH-ID- 32 + GN +L +L T I LIR V++ ++ Sbjct: 156 LVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215 Query: 33 ---------TP---Y-------------VQKGQ-----KVSRGHTIG-----LSGKSGNA 57 TP Y +Q K+ G T G L G +G Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLL-GFTPGELRSYLKGATG-- 272 Query: 58 QHPQ 61 H Q Sbjct: 273 -HSQ 275 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 0.398 Gapped Lambda K H 0.267 0.0517 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 712,053 Number of extensions: 26036 Number of successful extensions: 73 Number of sequences better than 10.0: 1 Number of HSP's gapped: 67 Number of HSP's successfully gapped: 14 Length of query: 84 Length of database: 5,693,230 Length adjustment: 52 Effective length of query: 32 Effective length of database: 4,432,542 Effective search space: 141841344 Effective search space used: 141841344 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: 50 (23.5 bits)