RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780608|ref|YP_003065021.1| ribosomal large subunit pseudouridine synthase C [Candidatus Liberibacter asiaticus str. psy62] (346 letters) >gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional. Length = 317 Score = 175 bits (446), Expect = 1e-44 Identities = 109/312 (34%), Positives = 173/312 (55%), Gaps = 16/312 (5%) Query: 7 VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66 V+ V + DE R+D + + + + +ILR G+VRV+KKR+K ++++G VR Sbjct: 8 VKIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67 Query: 67 IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126 IPPV A E++ S L K + L ++LYED I V NKP+G +V GGSG++ Sbjct: 68 IPPVRVA------EREEEAVSPKLQKVAA-LADVILYEDDHILVLNKPSGTAVHGGSGLS 120 Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 + + L++ + + + L HRLD++TSG+L+VA+ R+A + L E R + +QK Y +L Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179 Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245 V G ++ + + LLK G+ +V+ +++G + + FKV + +A F L Sbjct: 180 VRGQWQSHVKVVQAPLLKNILQSGE--RIVRVSQEGKP-SETRFKVEERYA--FATLVRA 234 Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303 P TGRTHQ+RVH + G PI D +Y F T N+L+LHA + HP G Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTGTGLNRLFLHAAALKFTHPGTGE 294 Query: 304 RLQITAPLPAHM 315 ++I APL + Sbjct: 295 VMRIEAPLDEQL 306 >gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine. Length = 299 Score = 171 bits (436), Expect = 2e-43 Identities = 91/317 (28%), Positives = 150/317 (47%), Gaps = 41/317 (12%) Query: 15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74 ++ RLD + + P ++ +QK++ +GQV+V+ K V N +++ RI + Sbjct: 2 EQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGK-VTANPKLKVKDGDRITVRVPEE 60 Query: 75 --NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130 + + + LD +L+ED I V NKP+G+ V G G + ++ Sbjct: 61 EEHEVPPQDIPLD---------------ILFEDEDIIVINKPSGLVVHPGGGNPFGTVLN 105 Query: 131 GFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189 L G ++ + HRLD++TSG++VVA+T A + L + R + K Y +LV G Sbjct: 106 ALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVHG 165 Query: 190 IPKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248 + A ++ G VH + +G A++HF+V++ F +E + Sbjct: 166 QFDSGGGTVDAPLGRVPNNRGLMAVH---PSSEGKP-AVTHFRVLERF-GNASLVECELE 220 Query: 249 TGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLPHP 300 TGRTHQ+RVH ++G P+ GD Y N NF ++ LHA + HP Sbjct: 221 TGRTHQIRVHLQYLGHPLAGDPLYGNKPVPGNNLNGLLNF-----DRQALHAYELGFIHP 275 Query: 301 EGGR-LQITAPLPAHMV 316 G L+ APLPA +V Sbjct: 276 ATGEILEFEAPLPADLV 292 >gnl|CDD|182274 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional. Length = 219 Score = 100 bits (249), Expect = 7e-22 Identities = 72/208 (34%), Positives = 110/208 (52%), Gaps = 18/208 (8%) Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158 ++LY+D I V NKP+G+ SV G + H D + + + + HRLD TSG++ Sbjct: 15 VILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71 Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218 VVA T+AA + L FR R +K Y + VWG P + + L+ D+ + KQ Sbjct: 72 VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125 Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275 E G A + ++V++ A + ++P TGR+HQLRVH L +G PI+GD Y A+ Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFY-AS 183 Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303 + +P +L LHA + + HP G Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYG 208 >gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional. Length = 257 Score = 99.4 bits (248), Expect = 1e-21 Identities = 69/247 (27%), Positives = 110/247 (44%), Gaps = 63/247 (25%) Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147 +LY+D + NKPAG V +SW+D GQ Sbjct: 4 ILYQDEWLVAVNKPAGWLVH-------------RSWLDRHETVFVMQTVRDQIGQHVFTA 50 Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207 HRLD+ TSG+L++A + A+ L + F +IQK Y ++V G WL++++ Sbjct: 51 HRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRG-----------WLMEEAV 99 Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKV---------IDCFA-QKFCWLEMQPH 248 + DY + + +K A++H++ + ++ +E++P Sbjct: 100 L--DYPLKEELDKIADKFAREDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK 157 Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQ-NKLYLHARYMDLPHP-EGGR 304 TGR HQLR H H+ PI+GD K+ + + N ++L LHA + L HP G Sbjct: 158 TGRKHQLRRHMAHLRHPIIGDTKH-GDLRQNRSLAEHFGCSRLMLHASELSLTHPFTGEP 216 Query: 305 LQITAPL 311 L ITA L Sbjct: 217 LTITAGL 223 >gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional. Length = 325 Score = 93.2 bits (232), Expect = 9e-20 Identities = 75/240 (31%), Positives = 118/240 (49%), Gaps = 31/240 (12%) Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154 ++YED I V NKP + V G+G DG L + PR + HRLD++T Sbjct: 86 IVYEDDDILVINKPRDLVVHPGAGNP---DGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142 Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211 +G++VVA+T A L E+ + R I + Y ++ G E I+ K++H+ Sbjct: 143 TGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200 Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271 VH G A++H+++++ F + L ++ TGRTHQ+RVH H+ P+VGD Sbjct: 201 -VH-----PMGKP-AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252 Query: 272 YCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322 Y F S ++ + LHA + L HP G ++ APLP MV+ ++L Sbjct: 253 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEAL 312 >gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity. Length = 217 Score = 88.4 bits (219), Expect = 2e-18 Identities = 63/213 (29%), Positives = 95/213 (44%), Gaps = 22/213 (10%) Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158 +L+ + NK GISV G + L V ++ + L HRLD+ TSGIL Sbjct: 4 ILFTHPDFLLINKHPGISVHKDDG-----ETGLLQEVATQLGVGQVWLVHRLDKMTSGIL 58 Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218 ++A +A L++ F R+I+K Y +L PK K+ I ++KS G K Sbjct: 59 LLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGD-MEKSRRG-----SWKL 112 Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278 N AI+ F A ++PHTG+THQLRV +G PI+GD Y + Sbjct: 113 VNSQENPAITRFFSASA-ATGLRLFILKPHTGKTHQLRVAMKSLGSPILGDPLYGTTDE- 170 Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311 ++ YLHA + + + +Q Sbjct: 171 ------SDRGYLHAFALRFDY-QNEVIQWLCDP 196 >gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain. Length = 60 Score = 33.3 bits (77), Expect = 0.095 Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 1/55 (1%) Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVIN 72 RLD++ + +K++ G+V+V+ K+V + ++ G V+ + Sbjct: 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55 >gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional. Length = 217 Score = 33.2 bits (75), Expect = 0.098 Identities = 42/166 (25%), Positives = 70/166 (42%), Gaps = 16/166 (9%) Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163 + +++ +FNKP + Q LK ++ +G RLD+++ G+LV+ Sbjct: 37 QPTRVILFNKPYDVLPQFTDEAGRKT---LKEFIPVQGVYA--AGRLDRDSEGLLVLTNN 91 Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECIANWL-LKKSHIGGDYVHVVKQNE- 220 A LT+ +R KIY+ V GIP ++ E + N + L +V + Sbjct: 92 GALQARLTQP--GKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAW 149 Query: 221 -KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265 N I K I WL++ + GR Q+R H+G P Sbjct: 150 LWPRNPPIRERKSIPT-----SWLKITLYEGRNRQVRRMTAHVGFP 190 >gnl|CDD|131605 TIGR02554, PrgH, type III secretion system protein PrgH/EprH. In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion, as well as being a structural component of the needle complex. Length = 389 Score = 29.5 bits (66), Expect = 1.2 Identities = 8/27 (29%), Positives = 10/27 (37%) Query: 11 VVENDEENMRLDRWFKNHYPHINFVNL 37 V E R+ RW P + F L Sbjct: 219 VAVIGAERQRVSRWLDEAGPQLAFYRL 245 >gnl|CDD|148052 pfam06218, NPR2, Nitrogen permease regulator 2. This family of regulators are involved in post-translational control of nitrogen permease. Length = 400 Score = 28.8 bits (65), Expect = 2.2 Identities = 9/29 (31%), Positives = 15/29 (51%) Query: 64 VVRIPPVINALNHIIKEQKILDSSVNLTK 92 + +I P IN +N + + + D NL K Sbjct: 199 MQKILPYINGINSVARIAALADVDYNLVK 227 >gnl|CDD|182468 PRK10446, PRK10446, ribosomal protein S6 modification protein; Provisional. Length = 300 Score = 28.3 bits (63), Expect = 2.6 Identities = 29/93 (31%), Positives = 46/93 (49%), Gaps = 13/93 (13%) Query: 84 LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143 L+ SV + + D L+S+ L I + P +GIA+ D +D G Sbjct: 88 LNESVAIARARDKLRSMQLLARQGI---DLPV-------TGIAHSPDD-TSDLIDMVGGA 136 Query: 144 PRLTHRLDQETSGI-LVVARTRAAAQHLTESFR 175 P L +L + T GI +V+A TR AA+ + ++FR Sbjct: 137 P-LVVKLVEGTQGIGVVLAETRQAAESVIDAFR 168 >gnl|CDD|139571 PRK13434, PRK13434, F0F1 ATP synthase subunit delta; Provisional. Length = 184 Score = 27.2 bits (60), Expect = 5.7 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 3/62 (4%) Query: 34 FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93 F+ L +I + V +DKK+ + +I S + P ++ L I+ E+ S L Sbjct: 84 FIYLPEIQKDFTVELDKKKGRVRAQIVSYPSLE-PAQVDKLGSILSEK--FKSEFILEVS 140 Query: 94 SD 95 D Sbjct: 141 ED 142 >gnl|CDD|148071 pfam06243, PaaB, Phenylacetic acid degradation B. Phenylacetic acid degradation protein B (PaaB) is thought to be part of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation. Length = 92 Score = 26.9 bits (60), Expect = 8.6 Identities = 8/26 (30%), Positives = 15/26 (57%) Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG 302 K +F +P +K+Y H + ++P G Sbjct: 65 KDSFFAPADDKVYRHPTFYEVPDGVG 90 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.323 0.138 0.430 Gapped Lambda K H 0.267 0.0670 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,661,891 Number of extensions: 354239 Number of successful extensions: 614 Number of sequences better than 10.0: 1 Number of HSP's gapped: 597 Number of HSP's successfully gapped: 20 Length of query: 346 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 252 Effective length of database: 3,963,321 Effective search space: 998756892 Effective search space used: 998756892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 58 (26.2 bits)