RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus str. psy62] (340 letters) >1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} (A:) Length = 228 Score = 179 bits (453), Expect = 7e-46 Identities = 73/251 (29%), Positives = 104/251 (41%), Gaps = 25/251 (9%) Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLD 149 I YEDD I+V+NKP+G VH G G + +VHRLD Sbjct: 2 DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEAR--------FLELVHRLD 53 Query: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKS 209 +DT+GV++VAK A + L EQ + G Y A+V G + APL + Sbjct: 54 RDTSGVLLVAKKRSALRSLHEQLREKGXQKD----YLALVRGQWQSHVKSVQAPLLKNIL 109 Query: 210 NRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGN 269 R V + + T ++ E Y + +C TGRTHQIRVH + G+ Sbjct: 110 QSGERIV--RVSQEGKPSETRFKVEERYAFATLV-----RCSPVTGRTHQIRVHTQYAGH 162 Query: 270 PLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPED 329 P+ D YG + A L R LHA +L F+HP + + P E Sbjct: 163 PIAFDDRYGDREFDRQL------TEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEG 216 Query: 330 MLTVIRKLNEK 340 + ++K Sbjct: 217 LKRCLQKXRNA 227 >1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} (A:) Length = 325 Score = 164 bits (416), Expect = 1e-41 Identities = 114/330 (34%), Positives = 159/330 (48%), Gaps = 21/330 (6%) Query: 9 SSIKISLLSDSTAEG-RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVP 67 ++++ G R+D+ LA + +SRS +K IL+ + +NG V P KV+ Sbjct: 2 QRVQLTATVSENQLGQRLDQALAEMFPD-YSRSRIKEWILDQRVLVNGKVCDKPKEKVLG 60 Query: 68 GDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLY 127 G+ I ++ ++IPLDI+YED+DII+INKP LVVHP GN GT++NALL+ Sbjct: 61 GEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLH 120 Query: 128 HCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYA 187 + I V R GIVHRLDKDTTG+MVVAK A +L E R Y A Sbjct: 121 YYPP----IADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREI----TREYEA 172 Query: 188 MVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSL 247 + G + + Sbjct: 173 VAIGHMTAGGTVDEPISRHPTKRTHMAVHPM----------GKPAVTHYRIMEHFRVHTR 222 Query: 248 LKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAH 307 L+ LETGRTHQIRVHMAH +PL+GDP+YG + + S + RQALHA Sbjct: 223 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGA-SEAFISTLRKFDRQALHAT 281 Query: 308 SLSFSHPRNNQDMDFQVPIPEDMLTVIRKL 337 L HP + +M++ PIP+DM+ +I + Sbjct: 282 MLRLYHPISGIEMEWHAPIPQDMVELIEVM 311 >2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} (A:) Length = 217 Score = 158 bits (401), Expect = 8e-40 Identities = 68/242 (28%), Positives = 98/242 (40%), Gaps = 33/242 (13%) Query: 86 ENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIV 145 + L ILY+DD I V+NKP+GL+ P V + + + V Sbjct: 8 QEPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDY---------PQAESV 58 Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205 HRLD T+GV+VVA A ++L QF + K+ Y A VWG P P G+++ PL Sbjct: 59 HRLDXATSGVIVVALTKAAERELKRQFREREP----KKQYVARVWGHPSPAEGLVDLPLI 114 Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265 NR ++ V K A + + + TGR+HQ+RVH Sbjct: 115 CDWPNRPKQKVCYETGKPA--QTEYEVVEYAADNTARV-----VLKPITGRSHQLRVHXL 167 Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVP 325 G+P++GD Y R LHA L+ +HP F+ P Sbjct: 168 ALGHPILGDRFYASPEAR-------------AXAPRLLLHAEXLTITHPAYGNSXTFKAP 214 Query: 326 IP 327 Sbjct: 215 AD 216 >2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} (A:) Length = 237 Score = 145 bits (365), Expect = 9e-36 Identities = 32/263 (12%), Positives = 64/263 (24%), Gaps = 49/263 (18%) Query: 86 ENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIV 145 + D +I +NKP G+V G + + H R + Sbjct: 3 SSHHHHHHGSDLVLIALNKPVGIVSTTEDGERDN--IVDFVNHSK----------RVFPI 50 Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205 RLDKD+ G++ + + K+ DH ++ Y V + + Sbjct: 51 GRLDKDSQGLIFLTNHGDLVNKILRAGNDH------EKEYLVTVDKPITEEFIRGXSAGV 104 Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265 + F + L G QIR Sbjct: 105 PILGTV------------------TKKCKVKKEAPFVF-----RITLVQGLNRQIRRXCE 141 Query: 266 HKGNPLIGDPLYGKGFKTKAN--------IVNNNAKSAILSLARQALHAHSLSFSHPRNN 317 H G + + + + ++ + + + + P+ Sbjct: 142 HFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTA 201 Query: 318 QDMDFQVPIPEDMLTVIRKLNEK 340 V + R + Sbjct: 202 GIKRPVVKXEKTAEKGGRPASNG 224 >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} (A:64-290) Length = 227 Score = 138 bits (349), Expect = 7e-34 Identities = 36/251 (14%), Positives = 70/251 (27%), Gaps = 49/251 (19%) Query: 95 EDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTG 154 ED +I +NKP G+V G +V+ + + KR + RLDKD+ G Sbjct: 2 EDLVLIALNKPVGIVSTTEDGERD-NIVDFVNHS-----------KRVFPIGRLDKDSQG 49 Query: 155 VMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRR 214 ++ + + K+ DH ++ Y V + + Sbjct: 50 LIFLTNHGDLVNKILRAGNDH------EKEYLVTVDKPITEEFIRGMSAGVPI------- 96 Query: 215 AVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGD 274 T+ K A + + L G QIR H G + Sbjct: 97 ----------------LGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKL 140 Query: 275 PLYGKGFKTKAN--------IVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPI 326 + + + ++ + + + + P+ V + Sbjct: 141 ERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKM 200 Query: 327 PEDMLTVIRKL 337 + R Sbjct: 201 EKTAEKGGRPA 211 >2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} (A:) Length = 189 Score = 130 bits (328), Expect = 2e-31 Identities = 39/222 (17%), Positives = 60/222 (27%), Gaps = 39/222 (17%) Query: 87 NIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVH 146 + + +I+ NKP ++ TL + Sbjct: 1 STRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQG------------VYAAG 48 Query: 147 RLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGR 206 RLD+D+ G++V+ N +L++ + YY V GIP D+ Sbjct: 49 RLDRDSEGLLVLTNNGALQARLTQPGKRT------GKIYYVQVEGIPTQDALEALRNGVT 102 Query: 207 CKSNRLRRAVKG-IDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265 A +D+ S K L GR Q+R A Sbjct: 103 LNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWL-----KITLYEGRNRQVRRMTA 157 Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAH 307 H G P + Y G SL A Sbjct: 158 HVGFPTLRLIRYAMGD---------------YSLDNLANGEW 184 >1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:58-243) Length = 186 Score = 125 bits (313), Expect = 1e-29 Identities = 32/222 (14%), Positives = 63/222 (28%), Gaps = 40/222 (18%) Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153 E+ ++NKP G V G++ T+ Y + RLD DTT Sbjct: 2 IEEGQYFMLNKPQGCVCSNDDGDY-PTIYQFFDYPLA---------GKLHSAGRLDVDTT 51 Query: 154 GVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLR 213 G++++ + +++ K+ Y + + A + + Sbjct: 52 GLVLLTDDGQWSHRITSPKHHCEKT------YLVTLADPVEENYSAACAEGILLRGEK-- 103 Query: 214 RAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIG 273 + N + GR HQ++ A GN ++G Sbjct: 104 --------------EPTKPAKLEILDDYNV-----NLTISEGRYHQVKRMFAALGNKVVG 144 Query: 274 DPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPR 315 + G + + L + + SH Sbjct: 145 LHRWKIGDVVLD---ESLEEGEYRPLTQSEIEKLVEGGSHHH 183 >1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:59-234) Length = 176 Score = 116 bits (291), Expect = 4e-27 Identities = 27/223 (12%), Positives = 58/223 (26%), Gaps = 51/223 (22%) Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153 +NKP G V T++ L + RLD DTT Sbjct: 2 QHGPRYFXLNKPQGYVCSTDDP-DHPTVLYFLDEPV---------AWKLHAAGRLDIDTT 51 Query: 154 GVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLR 213 G+++ + +++ ++ Y + D + + Sbjct: 52 GLVLXTDDGQWSHRITSPRHHC------EKTYLVTLESPVADD-----------TAEQFA 94 Query: 214 RAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIG 273 + V+ + + + + + ++ + GR HQ++ A GN ++ Sbjct: 95 KGVQ----------LHNEKDLTKPAVLEVITPTQVRLTISEGRYHQVKRXFAAVGNHVVE 144 Query: 274 DPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRN 316 G T A + Sbjct: 145 LHRERIGGITLDA--------------DLAPGEYRPLTEEEIA 173 >2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:1-102,A:201-217) Length = 119 Score = 91.9 bits (228), Expect = 1e-19 Identities = 17/133 (12%), Positives = 35/133 (26%), Gaps = 33/133 (24%) Query: 39 RSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDD 98 R ++ S K + + + Sbjct: 2 RQFIISENTMQKTSFRNHQVKRFSSQRSTR---------------------RKPENQPTR 40 Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158 +I+ NKP ++ TL + RLD+D+ G++V+ Sbjct: 41 VILFNKPYDVLPQFTDEAGRKTLKEFIPVQ------------GVYAAGRLDRDSEGLLVL 88 Query: 159 AKNDLAHQKLSEQ 171 N +L++ Sbjct: 89 TNNGALQARLTQP 101 >2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:103-200) Length = 98 Score = 85.9 bits (212), Expect = 7e-18 Identities = 24/102 (23%), Positives = 31/102 (30%), Gaps = 6/102 (5%) Query: 180 RLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRA-VKGIDDKTADSAITHYQTIEIYN 238 R + YY V GIP D+ A + +D+ Sbjct: 2 RTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSI 61 Query: 239 KNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKG 280 S LK L GR Q+R AH G P + Y G Sbjct: 62 PTS-----WLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 98 >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} (A:) Length = 133 Score = 83.2 bits (205), Expect = 4e-17 Identities = 25/153 (16%), Positives = 49/153 (32%), Gaps = 32/153 (20%) Query: 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76 E R+D+WL + +R+ + +I G + NG SK P++ V + + Sbjct: 3 EKPAVEVRLDKWLWAARFY-KTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQG 60 Query: 77 AAQKLNIA-------QENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHC 129 ++ I + +LYE+ V + + Sbjct: 61 NDERTVIVKAITEQRRPASEAALLYEETAESVEKREKMALARK----------------- 103 Query: 130 HNNLSSINGVKRPGIVHRLDKDTTGVMVVAKND 162 +N + P R DK ++ K+ Sbjct: 104 ------LNALTMPHPDRRPDKKERRDLLRFKHG 130 >2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} (A:) Length = 92 Score = 78.9 bits (194), Expect = 9e-16 Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 3/91 (3%) Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV-PAAQKLN 82 RID++L + R + G + +NG +K +++V GD+ + ++ Sbjct: 2 RIDKFLQSVGLV-KRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLHYLKGIEEYT 59 Query: 83 IAQENIPLDILYEDDDIIVINKPAGLVVHPA 113 I Q ++ +D + + K L H Sbjct: 60 ILQIPALKNVPRKDTHLYIAPKTKELEHHHH 90 >1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:1-58) Length = 58 Score = 45.3 bits (108), Expect = 1e-05 Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 4/55 (7%) Query: 21 AEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 + R+D+++A L SR+ I ++++G + +N K++P + Sbjct: 2 SHXRLDKFIAQQLG--VSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEH--DVAY 52 >1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} (A:) Length = 79 Score = 43.6 bits (103), Expect = 4e-05 Identities = 11/58 (18%), Positives = 19/58 (32%), Gaps = 3/58 (5%) Query: 18 DSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 + L S + KI I G + ++G V K+V G ++ Sbjct: 16 GKHPHVELCDLLK-LEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQ--TVSF 70 >1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:1-57) Length = 57 Score = 41.9 bits (99), Expect = 1e-04 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 4/54 (7%) Query: 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 R+D+++A ++ +RS I + ING + K+ + ++ D I Sbjct: 2 SLRLDKFIAENV--GLTRSQATKAIRQSAVKINGEIVKSGSVQISQED--EIYF 51 >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} (A:1-63) Length = 63 Score = 41.2 bits (97), Expect = 2e-04 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 5/52 (9%) Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITV 75 R++++++ S SR I G + +NG + +V PGD ++ V Sbjct: 8 RLNKYISESG--ICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGD--VVKV 54 >3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} (A:1-65) Length = 65 Score = 35.1 bits (81), Expect = 0.013 Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 5/61 (8%) Query: 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFI--SINGMVSKNPNRKVVPGDSFLIT 74 S++ + R+D +R K + G + ING P K+ G + Sbjct: 1 SNAXPKERVDVLAY-KQGLFETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGT--ELK 57 Query: 75 V 75 + Sbjct: 58 L 58 >1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} (A:350-432) Length = 83 Score = 32.7 bits (75), Expect = 0.067 Identities = 10/68 (14%), Positives = 22/68 (32%), Gaps = 1/68 (1%) Query: 6 DNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKV 65 + + I + R S + + LI N + ++G V +P +V Sbjct: 3 EEIPEVTIPASELKEGRIWVARLFT-LAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQV 61 Query: 66 VPGDSFLI 73 ++ Sbjct: 62 DLSRPRIL 69 >2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (D:100-193) Length = 94 Score = 30.6 bits (69), Expect = 0.33 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%) Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQK-LN 82 R+D + L SR + L+ +G I++NG P+ +V PGD I V + L Sbjct: 1 RLDNVVY-RLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGD--EIAVAEKSRNLE 57 Query: 83 IAQENI 88 + ++N+ Sbjct: 58 LIRQNL 63 >2uxt_A Protein SUFI, SUFI; periplasmic, cupredoxin-like, FTS mutant suppressor, oxidoreductase; 1.9A {Escherichia coli} PDB: 2uxv_A (A:313-451) Length = 139 Score = 28.5 bits (63), Expect = 1.2 Identities = 13/112 (11%), Positives = 25/112 (22%), Gaps = 10/112 (8%) Query: 45 LILNGFISINGMV--SKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVI 102 + L ING + + G TV A + E + I + + Sbjct: 17 ISLGDDPGINGQLWDVNRIDVTAQQGTWERWTVRADEPQAFHIEGVMFQIRNVNGAMPFP 76 Query: 103 NKPAGLVVHPAPGN--------WTGTLVNALLYHCHNNLSSINGVKRPGIVH 146 G ++ + G +V+ Sbjct: 77 EDRGWKDTVWVDGQVELLVYFGQPSWAHFPFYFNSQTLEMADRGSIGQLLVN 128 >3i1m_D 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ... (D:97-190) Length = 94 Score = 28.2 bits (63), Expect = 1.5 Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 1/51 (1%) Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENI 88 +R+ + L+ + I +NG V + +V P D + A+K + + + Sbjct: 14 TRAEARQLVSHKAIMVNGRVVNIASYQVSPND-VVSIREKAKKQSRVKAAL 63 >1sdd_A Coagulation factor V; copper-binding protein, cofactor, blood clotting; HET: NAG NDG; 2.80A {Bos taurus} (A:181-306) Length = 126 Score = 27.8 bits (61), Expect = 2.0 Identities = 8/102 (7%), Positives = 24/102 (23%), Gaps = 10/102 (9%) Query: 50 FISINGMVSKNPNRKVVP-GDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGL 108 ++NG V+ V D + ++ I + + + Sbjct: 23 MYTVNGYVNGTMPDITVCAHDHISWHLI-----GMSSGPELFSIHFNGQVLEQNHHKISA 77 Query: 109 VVHPAPGNWTGTLVN----ALLYHCHNNLSSINGVKRPGIVH 146 + + + T + G++ + Sbjct: 78 ITLVSATSTTANMTVSPEGRWTIASLIPRHFQAGMQAYIDIK 119 >1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, protein structure initiative; 1.90A {Mycobacterium tuberculosis H37RV} (A:1-60,A:206-232) Length = 87 Score = 27.8 bits (62), Expect = 2.0 Identities = 17/66 (25%), Positives = 23/66 (34%), Gaps = 16/66 (24%) Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153 I+VI+KPAG+ H I +R G LD T Sbjct: 3 ATGPGIVVIDKPAGMTSH----------------DVVGRCRRIFATRRVGHAGTLDPMAT 46 Query: 154 GVMVVA 159 GV+V+ Sbjct: 47 GVLVIG 52 >2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} (A:345-432) Length = 88 Score = 27.8 bits (62), Expect = 2.1 Identities = 7/32 (21%), Positives = 12/32 (37%) Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGD 69 S+ + I G +S+N + N D Sbjct: 26 SKGAARRTIHEGGVSVNNIRVDNEEWVPQSSD 57 >1cb6_A Protein (lactoferrin); iron transport, apolactoferrin, conformational change; 2.00A {Homo sapiens} (A:90-242,A:317-333) Length = 170 Score = 27.6 bits (61), Expect = 2.4 Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 4/42 (9%) Query: 229 THYQTIEIYNKNSNFAVSLLK----CHLETGRTHQIRVHMAH 266 THY + + K +F ++ L+ CH RT V + Sbjct: 1 THYYAVAVVKKGGSFQLNELQGLKSCHTGLRRTAGWNVPIGT 42 >2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} (A:51-266) Length = 216 Score = 27.4 bits (60), Expect = 2.5 Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 16/61 (26%) Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158 ++V++KP G H + + + G LD TGV+ V Sbjct: 18 VVVVDKPRGPTSHEV--------STWVKKIL--------NLDKAGHGGTLDPKVTGVLPV 61 Query: 159 A 159 A Sbjct: 62 A 62 >1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} (A:247-420) Length = 174 Score = 27.3 bits (60), Expect = 2.6 Identities = 10/43 (23%), Positives = 17/43 (39%) Query: 29 LATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSF 71 + S+ + + NG I ING ++ N + P D Sbjct: 112 VLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI 154 >1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} (A:1-79,A:225-253) Length = 108 Score = 27.1 bits (60), Expect = 3.1 Identities = 10/66 (15%), Positives = 23/66 (34%), Gaps = 16/66 (24%) Query: 94 YEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTT 153 + + +++++KP G+ + + I R G LD T Sbjct: 22 MDINGVLLLDKPQGMSSN----------------DALQKVKRIYNANRAGHTGALDPLAT 65 Query: 154 GVMVVA 159 G++ + Sbjct: 66 GMLPIC 71 >3cvz_A S-layer protein; surface layer protein, protein binding, structural protein; 2.40A {Clostridium difficile} (A:94-236) Length = 143 Score = 27.2 bits (60), Expect = 3.2 Identities = 11/39 (28%), Positives = 14/39 (35%), Gaps = 2/39 (5%) Query: 36 QFSRSYVKILILNGFISINGMVSK--NPNRKVVPGDSFL 72 + + K LI GMVSK + K V L Sbjct: 13 KLNSLNEKTLIDIATKDTFGMVSKTQDSEGKNVAATKAL 51 >2r7e_B Coagulation factor VIII; ceruloplasmin fold, cupper protein fold, C2 domain fold, acute phase, blood coagulation, calcium, disease mutation; HET: NAG BMA MAN; 3.70A {Homo sapiens} PDB: 3cdz_B* (B:305-458) Length = 154 Score = 26.8 bits (58), Expect = 4.0 Identities = 10/105 (9%), Positives = 26/105 (24%), Gaps = 9/105 (8%) Query: 48 NGFISINGMVSKNPNRKVVP-GDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPA 106 F +ING + V+ + + + + + + Sbjct: 50 YRFHAINGYIMDTLPGLVMAQDQRIRWYL---LSMGSNENIHSIHFSGHVFTVRKKEEYK 106 Query: 107 GLVVHPAPGNWTGTLVNA-----LLYHCHNNLSSINGVKRPGIVH 146 + + PG + + C G+ +V+ Sbjct: 107 MALYNLYPGVFETVEMLPSKAGIWRVECLIGEHLHAGMSTLFLVY 151 >2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:) Length = 71 Score = 26.9 bits (60), Expect = 4.3 Identities = 9/59 (15%), Positives = 17/59 (28%), Gaps = 1/59 (1%) Query: 22 EGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQK 80 R+ L L+ + G + + V +P V +T + K Sbjct: 7 GRRLPTVLL-KLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSSK 64 >1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima} (A:1-57,A:190-224) Length = 92 Score = 26.7 bits (59), Expect = 4.8 Identities = 11/61 (18%), Positives = 19/61 (31%), Gaps = 16/61 (26%) Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158 I+V KP G H + + ++ G LD GV+++ Sbjct: 5 ILVAYKPKGPTSH----------------DVVDEVRKKLKTRKVGHGGTLDPFACGVLII 48 Query: 159 A 159 Sbjct: 49 G 49 >2cvl_A TTHA0137, protein translation initiation inhibitor; structural genomics, NPPSFA; 1.65A {Thermus thermophilus} (A:) Length = 124 Score = 26.4 bits (58), Expect = 6.2 Identities = 8/29 (27%), Positives = 16/29 (55%) Query: 41 YVKILILNGFISINGMVSKNPNRKVVPGD 69 Y + + GF+ ++G + P+ +V GD Sbjct: 16 YAQAVKAGGFVFVSGQIPLAPDGSLVEGD 44 >3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (D:82-201) Length = 120 Score = 26.4 bits (58), Expect = 6.4 Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 3/91 (3%) Query: 38 SRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDD 97 + + L+ + I +NG + P+ + P D+ + + + + Q ++ L E Sbjct: 22 TIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMAR-DEQKSIALIQNSLDLSPREELP 80 Query: 98 DIIVINKPA--GLVVHPAPGNWTGTLVNALL 126 + +N GLV W G +N LL Sbjct: 81 KHLTLNPFPYKGLVNQIIDSKWVGLKINELL 111 >3lb5_A HIT-like protein involved in cell-cycle regulation; niaid, seattle structural genomics center for infectious disease, ssgcid; 1.90A {Bartonella henselae} (A:) Length = 161 Score = 26.2 bits (57), Expect = 6.6 Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 7/41 (17%) Query: 82 NIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLV 122 + + IP +YEDDD+I + P TLV Sbjct: 34 KLIRNEIPSVRVYEDDDVIAF-------MDIMPQAPGHTLV 67 >3g5w_A Multicopper oxidase type 1; two domain, laccase, nitrifier, metal binding protein; 1.90A {Nitrosomonas europaea} (A:131-290) Length = 160 Score = 26.0 bits (56), Expect = 7.9 Identities = 16/104 (15%), Positives = 29/104 (27%), Gaps = 7/104 (6%) Query: 50 FISINGMVSKN-PNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIVINKPAGL 108 + +IN +V GD + + A A D ++KP Sbjct: 36 YYTINAKSFPETQPIRVKKGDVIRLRLIGAGDHVHAIHTHGHISQIAFKDGFPLDKPIKG 95 Query: 109 VVHPAPGNWTGTLVN------ALLYHCHNNLSSINGVKRPGIVH 146 ++ + H H + + NG K G + Sbjct: 96 DTVLIGPGERYDVILNMDNPGLWMIHDHVDTHTTNGDKPDGGIM 139 >3i7t_A RV2704, putative uncharacterized protein; siras, YJGF/YER057C/UK114, homotrimer, quick SOAK NAI derivative, unknown function; 1.93A {Mycobacterium tuberculosis} (A:) Length = 149 Score = 25.7 bits (56), Expect = 8.6 Identities = 3/13 (23%), Positives = 4/13 (30%) Query: 301 RQALHAHSLSFSH 313 + A L H Sbjct: 134 KDPSPAGGLEHHH 146 >2f68_X Collagen adhesin; beta barrel, domain SWAP, cell adhesion; 1.95A {Staphylococcus aureus} PDB: 2f6a_A 1amx_A (X:1-147,X:299-313) Length = 162 Score = 25.6 bits (56), Expect = 8.7 Identities = 7/41 (17%), Positives = 14/41 (34%), Gaps = 2/41 (4%) Query: 61 PNRKVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDIIV 101 N K+ GD + P + + I + + + V Sbjct: 42 KNGKIQNGDMIKVAWPTSGTVKIEGYSKTVPL--TVKGEQV 80 >3jq1_A SUSD superfamily protein; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: MSE; 1.55A {Bacteroides vulgatus atcc 8482} (A:1-21,A:67-217,A:462-481) Length = 192 Score = 25.7 bits (56), Expect = 8.9 Identities = 5/22 (22%), Positives = 9/22 (40%) Query: 13 ISLLSDSTAEGRIDRWLATSLK 34 SLL + G+ + A + Sbjct: 120 ASLLPITNKIGKPTQGAAYAAL 141 >1n67_A Clumping factor; DEV-IGG, IGG, immunoglobulin, IGSF, fibrinongen-binding, cell adhesion; 1.90A {Staphylococcus aureus} (A:1-169) Length = 169 Score = 25.6 bits (56), Expect = 9.0 Identities = 11/37 (29%), Positives = 16/37 (43%) Query: 64 KVVPGDSFLITVPAAQKLNIAQENIPLDILYEDDDII 100 V GD+F ITVP LN + + D ++ Sbjct: 67 SAVKGDTFKITVPKELNLNGVTSTAKVPPIMAGDQVL 103 >2wdq_D Succinate dehydrogenase hydrophobic membrane anchor subunit; succinate dehydrogenase activity, cell inner membrane, tricarboxylic acid cycle; HET: FAD HEM CBE; 2.40A {Escherichia coli} PDB: 1nen_D* 2acz_D* 1nek_D* 2wdr_D* 2wdv_D* (D:) Length = 115 Score = 25.8 bits (57), Expect = 9.2 Identities = 4/31 (12%), Positives = 10/31 (32%) Query: 106 AGLVVHPAPGNWTGTLVNALLYHCHNNLSSI 136 G +T + ++L H + + Sbjct: 49 IGFFASAFTKVFTLLALFSILIHAWIGMWQV 79 >2eo4_A 150AA long hypothetical histidine triad nucleotide-binding protein; HIT family, structural genomics, NPPSFA; 1.80A {Sulfolobus tokodaii} (A:) Length = 149 Score = 25.9 bits (56), Expect = 9.2 Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 7/41 (17%) Query: 82 NIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLV 122 +I + +YED+ I + P + TLV Sbjct: 5 SIINRELEGYFVYEDEKFAAI-------LDKYPVSLGHTLV 38 >2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase/structural protein complex; 2.10A {Pyrococcus abyssi} PDB: 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3hjw_A* 3hjy_A (C:31-245) Length = 215 Score = 25.8 bits (56), Expect = 9.2 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 18/79 (22%) Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158 +I ++KP G H +V + + +++ G LD +GV+ V Sbjct: 18 VINLDKPPGPTSH--------EVVAWIKRILN--------LEKAGHGGTLDPKVSGVLPV 61 Query: 159 AKNDLAHQKLSEQFVDHGK 177 A ++ + + GK Sbjct: 62 ALER--ATRVVQALLPAGK 78 >2hd9_A UPF0310 protein PH1033; structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: CIT; 1.35A {Pyrococcus horikoshii OT3} (A:) Length = 145 Score = 25.5 bits (56), Expect = 9.2 Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 6/49 (12%) Query: 28 WLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76 W+ + +R +++ + + KN +V PGD +I V Sbjct: 4 WICIT-----NRENWEVIKRHNVWGVP-KKHKNTLSRVKPGDKLVIYVR 46 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.318 0.134 0.395 Gapped Lambda K H 0.267 0.0542 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 2,544,006 Number of extensions: 111789 Number of successful extensions: 387 Number of sequences better than 10.0: 1 Number of HSP's gapped: 353 Number of HSP's successfully gapped: 54 Length of query: 340 Length of database: 4,956,049 Length adjustment: 89 Effective length of query: 251 Effective length of database: 1,947,404 Effective search space: 488798404 Effective search space used: 488798404 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: 55 (25.4 bits)