RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus str. psy62] (354 letters) >1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Length = 234 Score = 161 bits (409), Expect = 2e-40 Identities = 58/226 (25%), Positives = 100/226 (44%), Gaps = 3/226 (1%) Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74 R+ K IA+ SR R I RV V+G ++ AA ++ + DG PL + R Sbjct: 5 RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 64 Query: 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134 ++ +KP G V + DPD + ++ + ++ + GRLDI+T GL+L+T+DG + + Sbjct: 65 YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 124 Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194 P + Y V V D KG+ + + + V + + Sbjct: 125 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPA--VLEVITPTQVRLTIS 182 Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239 EG+ ++K++F V L R G L L G R ++++ Sbjct: 183 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 228 >3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Length = 290 Score = 157 bits (398), Expect = 3e-39 Identities = 58/234 (24%), Positives = 103/234 (44%), Gaps = 5/234 (2%) Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71 + R++K I+ +GI SRRE +R I Q V +NG V D ++V+G + E Sbjct: 5 SSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPRE 63 Query: 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131 L L + + DG + + RV +GRLD +++GL+ LTN G L Sbjct: 64 AEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLV 123 Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191 + + Y V + ++ + + G+ I G +V +K + + Sbjct: 124 NKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKV----KKEAPFVFRI 179 Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245 L +G NR+I+++ E F ++V +L R L + G R+++ L + Sbjct: 180 TLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF 233 >2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Length = 237 Score = 125 bits (316), Expect = 1e-29 Identities = 51/235 (21%), Positives = 101/235 (42%), Gaps = 19/235 (8%) Query: 77 LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136 +KP+G+V+T D + R + D + RV +GRLD +++GL+ LTN G L + Sbjct: 18 ALNKPVGIVSTTEDGE-RDNIVDFVNH-SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR 75 Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196 + Y V + ++ + + G+ I G + +K + + L +G Sbjct: 76 AGNDHEKEYLVTVDKPITEEFIRGMSAGVPI----LGTVTKKCKVKKEAPFVFRITLVQG 131 Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256 NR+I+++ E F ++V +L R L + G R+++ L + L+E + Sbjct: 132 LNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFK--LIENS--- 186 Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG--LSKQKKLATPVHRRN 309 SSE + + + + +++K G S K+ +P ++ Sbjct: 187 ------SSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 235 >2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Length = 217 Score = 124 bits (312), Expect = 3e-29 Identities = 53/200 (26%), Positives = 90/200 (45%), Gaps = 18/200 (9%) Query: 53 NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112 V + + TR+ L++KP ++ +D GR T+ + +P V + G Sbjct: 20 QVKRFSSQRSTRRKP-ENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAG 76 Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172 RLD ++EGLL+LTN+G L L P + ++Y V+ G QD L L+ G+ + Sbjct: 77 RLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPT 136 Query: 173 GDMQVTLDTQK---------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217 L + +W+ + L EG+NR+++++ + RLIR Sbjct: 137 LPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIR 196 Query: 218 ISYGPFQLGTLLAGSTREVS 237 + G + L L G REV+ Sbjct: 197 YAMGDYSLDNLANGEWREVT 216 >2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Length = 189 Score = 119 bits (300), Expect = 8e-28 Identities = 52/184 (28%), Positives = 89/184 (48%), Gaps = 17/184 (9%) Query: 69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128 + + TR+ L++KP ++ +D GR T+ + +P V + GRLD ++EGLL+LTN+G Sbjct: 7 ENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNG 64 Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----- 183 L L P + ++Y V+ G QD L L+ G+ + L + Sbjct: 65 ALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWP 124 Query: 184 ----------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233 +W+ + L EG+NR+++++ + RLIR + G + L L G Sbjct: 125 RNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEW 184 Query: 234 REVS 237 REV+ Sbjct: 185 REVT 188 >1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Length = 243 Score = 116 bits (291), Expect = 6e-27 Identities = 58/226 (25%), Positives = 104/226 (46%), Gaps = 3/226 (1%) Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74 R+ K IA +R + + I Q VK+NG +++ +V + D I + L E + Sbjct: 4 RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 63 Query: 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134 ++ +KP G V ++ D D + + ++ S GRLD++T GL+LLT+DG + + Sbjct: 64 YFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRI 123 Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194 P + Y V V+++ +GI+++G L+ N +T+ Sbjct: 124 TSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNLTI--S 181 Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239 EG+ ++K++F KV L R G L L G R +++ Sbjct: 182 EGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQS 227 >1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} SCOP: d.66.1.6 Length = 79 Score = 52.8 bits (127), Expect = 1e-07 Identities = 11/69 (15%), Positives = 30/69 (43%), Gaps = 3/69 (4%) Query: 1 MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59 M ++ + + ++ G + S + + IA+ +VKV+G + R +++ Sbjct: 10 MATFSLGKHPHV--ELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQT 67 Query: 60 IEVDGVPLR 68 + G ++ Sbjct: 68 VSFAGHSVQ 76 >1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325 Score = 47.7 bits (112), Expect = 4e-06 Identities = 49/311 (15%), Positives = 92/311 (29%), Gaps = 43/311 (13%) Query: 6 IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 V EN QR+ + +A SR ++ I QRV VNG + ++ V+ + + ++ Sbjct: 9 TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 68 Query: 65 VPLRKAERT-------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110 +A + + +KP LV + TV + L + + Sbjct: 69 EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 128 Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165 V RLD +T GL+++ L + + + I Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 188 Query: 166 VIQGICYGDMQVT-----------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214 M V + + + + L G+ +I+ + Sbjct: 189 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV- 247 Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274 YG A + + Q L + L PI S + Sbjct: 248 -GDPVYGGRPRPPKGASEAFISTLRKFDRQ----ALHATMLRLYHPI-SGIEM-----EW 296 Query: 275 ISEVPDDFTRM 285 + +P D + Sbjct: 297 HAPIPQDMVEL 307 >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 = 44.9 bits (106), Expect = 3e-05 Identities = 38/243 (15%), Positives = 75/243 (30%), Gaps = 100/243 (41%) Query: 56 STDHIEVDGVP-----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110 S ++ E GVP + + ++ + +H LP+ + + Sbjct: 327 SLENNE--GVPSPMLSISNLTQEQV---QDYVNKTNSH------------LPA--GKQVE 367 Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170 + L +N L+++ G + L +G LNL Sbjct: 368 IS-L-VNGAKNLVVS---GPPQSL---------------YG------LNL---------- 391 Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLG 226 TL K + GL + +R E K F NR + ++ PF Sbjct: 392 -------TLRKAKAPS-----GLDQ--SRIPFSERKLKF------SNRFLPVA-SPFH-S 429 Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD-R---PNIISEVPDDF 282 LL ++ ++ + L + + ++ P+Y + D R +I + Sbjct: 430 HLLVPAS-----DLINKDLVKNNVSFNAKDIQIPVYDTFD-GSDLRVLSGSIS----ERI 479 Query: 283 TRM 285 Sbjct: 480 VDC 482 Score = 41.9 bits (98), Expect = 3e-04 Identities = 24/92 (26%), Positives = 29/92 (31%), Gaps = 39/92 (42%) Query: 33 RMIAQQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRKAERTRLWLYHKPIGL-VTT 87 I + VK E +T HI +D G GL V T Sbjct: 481 DCIIRLPVK-----WE-TTTQFKAT-HI-LDFGPGGAS----------------GLGVLT 516 Query: 88 HSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119 H + DG RVI G LDIN + Sbjct: 517 HRNKDGTGV----------RVIVAGTLDINPD 538 Score = 32.6 bits (74), Expect = 0.14 Identities = 24/140 (17%), Positives = 48/140 (34%), Gaps = 46/140 (32%) Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAP----IYSSETLVRDRPNIISEV---PDDF-- 282 S ++ +EQ+ ++ + N P + S LV N++ V P Sbjct: 340 SISNLT----QEQVQDYV---NKTNSHLPAGKQVEIS--LVNGAKNLV--VSGPPQSLYG 388 Query: 283 --TRMKKNSSQKNGLS------KQKKLATPVHRRNLASNVWMAKGI----HSSFLSDSGQ 330 ++K + GL ++KL R L + HS L + Sbjct: 389 LNLTLRKAKAPS-GLDQSRIPFSERKLK--FSNRFLP--------VASPFHSHLLVPASD 437 Query: 331 R--EENHRRSPSFPSKRSLR 348 ++ + + SF +K ++ Sbjct: 438 LINKDLVKNNVSFNAK-DIQ 456 >1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Length = 133 Score = 39.6 bits (92), Expect = 0.001 Identities = 16/112 (14%), Positives = 31/112 (27%), Gaps = 9/112 (8%) Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRK 69 R+ K + A +R MI +V NG + + V + + G R Sbjct: 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNG-QRSKPSKIVELNATLTLRQGNDERT 65 Query: 70 AERTRLWLYHKPIG----LVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLD 115 + +P L ++ + + + R D Sbjct: 66 VIVKAITEQRRPASEAALLYEETAESVEKREKMALARKLNALTMPHPDRRPD 117 >3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} Length = 291 Score = 36.8 bits (85), Expect = 0.008 Identities = 12/62 (19%), Positives = 27/62 (43%), Gaps = 3/62 (4%) Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRV--KVNGILLERAAVNVMSTDHIEVDGVPLRKA 70 +RV + + G+ +R + +R + V +NG ++ + +++ G LR Sbjct: 7 ERVDVLAYKQGLFETREQAKRGVMAGLVVNVINGERYDKPGEKIDDGTELKLKGEKLRYV 66 Query: 71 ER 72 R Sbjct: 67 SR 68 >1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Length = 420 Score = 31.9 bits (72), Expect = 0.20 Identities = 10/55 (18%), Positives = 25/55 (45%), Gaps = 1/55 (1%) Query: 16 VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 + +V+ GI+ S+R+ + + +NG + + D I+ + +R+ Sbjct: 355 IVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKIDGEFTIIRR 409 >2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Length = 432 Score = 31.3 bits (70), Expect = 0.36 Identities = 13/62 (20%), Positives = 29/62 (46%), Gaps = 1/62 (1%) Query: 9 ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67 + +P + ++ +G++ S+ R I + V VN I ++ S+D + + L Sbjct: 351 KPGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDFLHGRWLVL 410 Query: 68 RK 69 R+ Sbjct: 411 RR 412 >1eje_A FMN-binding protein; structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; HET: FMN; 2.20A {Methanothermobacterthermautotrophicus} SCOP: b.45.1.2 Length = 192 Score = 30.7 bits (69), Expect = 0.52 Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 4/36 (11%) Query: 59 HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94 ++ + P+ A R L +P +VTT D +G Sbjct: 9 SMDFEDFPVESAHR---ILTPRPTVMVTTV-DEEGN 40 >2vk9_A Alpha-toxin; glycosyltransferase; 2.85A {Clostridium novyi} SCOP: c.68.1.22 Length = 551 Score = 30.3 bits (68), Expect = 0.66 Identities = 6/52 (11%), Positives = 20/52 (38%), Gaps = 3/52 (5%) Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV---HRRNLASNVWMAKGIH 321 + ++E+ D++ +S + L + +N ++ +K + Sbjct: 50 SKLNELVDNYQTKYPSSGRNLALENFRDSLYSELRELIKNSRTSTIASKNLS 101 >3e4v_A NADH:FMN oxidoreductase like protein; YP_544701.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE FMN; 1.40A {Methylobacillus flagellatus KT} Length = 186 Score = 30.1 bits (67), Expect = 0.71 Identities = 12/30 (40%), Positives = 14/30 (46%), Gaps = 4/30 (13%) Query: 65 VPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94 +P A R L PI LV+T DGR Sbjct: 6 LPPENAYRI---LESGPIVLVSTR-GADGR 31 >2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A Length = 419 Score = 29.7 bits (66), Expect = 1.0 Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 1/55 (1%) Query: 16 VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 + +++ AGI+ S+R+ I + VNG L+ + + +E +R+ Sbjct: 354 LVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRLEGRFTVIRR 408 >3hmz_A Flavin reductase domain protein, FMN-binding; YP_001049024.1, FMN-binding domain of flavin reductases-like enzyme, structural genomics; HET: MSE FMN; 1.50A {Shewanella baltica OS155} Length = 199 Score = 29.3 bits (65), Expect = 1.5 Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 3/30 (10%) Query: 61 EVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90 + V L KA R L H P LV+ S Sbjct: 13 NIAAVELAKAYRL---LNHGPTVLVSARSQ 39 >1rkd_A Ribokinase; carbohydrate kinase, ribose, nucleotide binding, transferase; HET: RIB ADP; 1.84A {Escherichia coli K12} SCOP: c.72.1.1 PDB: 1gqt_A* 1rka_A 1rk2_A* 1rks_A* Length = 309 Score = 28.6 bits (62), Expect = 2.2 Identities = 6/24 (25%), Positives = 14/24 (58%) Query: 16 VSKVIARAGIASRREVERMIAQQR 39 V++ A+ + R E++ + +QR Sbjct: 286 VTRKGAQPSVPWREEIDAFLDRQR 309 >3epu_A STM2138 virulence chaperone; TYPEIII secretion system, SRCA (SSRB-regulated chaperone A); 2.50A {Salmonella typhimurium} Length = 144 Score = 28.3 bits (63), Expect = 2.7 Identities = 8/51 (15%), Positives = 20/51 (39%) Query: 95 STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145 + D L FS ++ + + L D +L +++++ +Y Sbjct: 2 YSRADRLLRQFSLKLNTDSIVFDENRLCSFIIDNRYRILLTSTNSEYIMIY 52 >1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* Length = 432 Score = 28.2 bits (62), Expect = 2.8 Identities = 9/34 (26%), Positives = 20/34 (58%), Gaps = 1/34 (2%) Query: 16 VSKVIARAGIA-SRREVERMIAQQRVKVNGILLE 48 V+++ AG+ S E R+I + ++++G +L Sbjct: 371 VARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLT 404 >3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A* Length = 1706 Score = 27.9 bits (62), Expect = 3.1 Identities = 8/73 (10%), Positives = 21/73 (28%), Gaps = 5/73 (6%) Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272 +LI + + G + + L++ P +E + + + S+ Sbjct: 1304 EKLIEKAGAWYSYKGEKIGQGKANATAWLKDN--PETAKEIEKKVRELLLSN---PNSTT 1358 Query: 273 NIISEVPDDFTRM 285 + M Sbjct: 1359 GSTGSMSGRTGSM 1371 >1vjj_A Protein-glutamine glutamyltransferase E; transglutaminase 3, X-RAY crystallography, metalloenzyme, calcium ION; HET: GDP; 1.90A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1sgx_A* 1l9m_A 1l9n_A* 1nud_A 1nuf_A 1nug_A 1rle_A* Length = 692 Score = 27.9 bits (62), Expect = 3.5 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 8/63 (12%) Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDA--------PIYSSETLVRDRPNIISEV 278 +L E KI Q +L + + + A + ++ D P + EV Sbjct: 541 SLDPEEEAEHPIKISYAQYERYLKSDNMIRITAVCKVPDESEVVVERDIILDNPTLTLEV 600 Query: 279 PDD 281 ++ Sbjct: 601 LNE 603 >2d5m_A Flavoredoxin; flavoprotein, FMN binding, electron transport; HET: FMN MES; 1.05A {Desulfovibrio vulgaris str} Length = 190 Score = 27.1 bits (59), Expect = 5.7 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%) Query: 67 LRKAERTRLWLYHKPIGLVTTHSDPDGR 94 ++K+ R Y P+ LV T+ D D R Sbjct: 1 MKKSLGARTLAYPTPLFLVGTY-DRDSR 27 >2jgs_A Circular permutant of avidin; biotin, D-biotin, beta-barrel, protein engineering, nanobiotechnology, biotin-binding protein, glycoprotein; HET: BTN; 1.9A {Gallus gallus} Length = 130 Score = 27.2 bits (60), Expect = 6.3 Identities = 10/34 (29%), Positives = 15/34 (44%) Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313 FTR++ +G S +K T +L SN Sbjct: 76 MIFTRLRTQKEGGSGGSARKCSLTGKWTNDLGSN 109 >1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A* Length = 353 Score = 26.7 bits (59), Expect = 7.3 Identities = 7/43 (16%), Positives = 15/43 (34%) Query: 59 HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101 + D + + + + IG+V T F+N+ Sbjct: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENI 103 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 0.318 0.134 0.385 Gapped Lambda K H 0.267 0.0676 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,975,492 Number of extensions: 140609 Number of successful extensions: 382 Number of sequences better than 10.0: 1 Number of HSP's gapped: 372 Number of HSP's successfully gapped: 35 Length of query: 354 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 261 Effective length of database: 3,438,538 Effective search space: 897458418 Effective search space used: 897458418 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 (21.7 bits) S2: 57 (25.8 bits)