RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 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) >gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine. Length = 299 Score = 315 bits (809), Expect = 1e-86 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 24/316 (7%) Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83 R+D +LA+ L + SRS ++ LI NG + +NG V+ NP KV GD + VP ++ + Sbjct: 7 RLDDFLASLLPD-LSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEV 65 Query: 84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPG 143 ++IPLDIL+ED+DIIVINKP+GLVVHP GN GT++NALL HC I GV+R G Sbjct: 66 PPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHC----PPIAGVERVG 121 Query: 144 IVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203 IVHRLD+DT+G+MVVAK LA ++L Q + + + Y A+V G G ++AP Sbjct: 122 IVHRLDRDTSGLMVVAKTPLALRELQRQLKNRT----VTKEYVALVHGQFDSGGGTVDAP 177 Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263 LGR +NR AV A+TH++ +E N+ SL++C LETGRTHQIRVH Sbjct: 178 LGRVPNNRGLMAVH--PSSEGKPAVTHFRVLE-RFGNA----SLVECELETGRTHQIRVH 230 Query: 264 MAHKGNPLIGDPLYG-KGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDF 322 + + G+PL GDPLYG K N RQALHA+ L F HP + ++F Sbjct: 231 LQYLGHPLAGDPLYGNKPVPGNNLNGLLN-------FDRQALHAYELGFIHPATGEILEF 283 Query: 323 QVPIPEDMLTVIRKLN 338 + P+P D++ ++ L Sbjct: 284 EAPLPADLVLLLEALR 299 >gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional. Length = 325 Score = 255 bits (654), Expect = 1e-68 Identities = 128/326 (39%), Positives = 179/326 (54%), Gaps = 26/326 (7%) Query: 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76 S+S R+D+ LA L +SRS +K IL+ + +NG V P KV+ G+ I Sbjct: 12 SESQLGQRLDQALA-ELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAE 70 Query: 77 AAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSI 136 ++ ++IPLDI+YEDDDI+VINKP LVVHP GN GT++NALL++ I Sbjct: 71 IEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYY----PPI 126 Query: 137 NGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPD 196 V R GIVHRLDKDTTG+MVVAK A +L V+ + + R Y A+ G + Sbjct: 127 ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRL----VEALQKREITREYEAVAIGH-MTA 181 Query: 197 SGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGR 256 G ++ P+ R + R AV A+THY+ +E + + L+ LETGR Sbjct: 182 GGTVDEPISRHPTKRTHMAVH----PMGKPAVTHYRIMEHFR-----VHTRLRLRLETGR 232 Query: 257 THQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSL---ARQALHAHSLSFSH 313 THQIRVHMAH +PL+GD +YG + ++ I +L RQALHA L H Sbjct: 233 THQIRVHMAHITHPLVGDQVYGG----RPRPPKGASEEFISTLRKFDRQALHATMLRLYH 288 Query: 314 PRNNQDMDFQVPIPEDMLTVIRKLNE 339 P +M++ P+P+DM+ +I L Sbjct: 289 PITGIEMEWHAPLPQDMVELIEALRA 314 >gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional. Length = 317 Score = 124 bits (313), Expect = 3e-29 Identities = 107/352 (30%), Positives = 161/352 (45%), Gaps = 57/352 (16%) Query: 7 NCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVV 66 S+KI +S A RID +L T LK +S + ++ G + +N K P K+ Sbjct: 4 ETPSVKIVTISADEAGQRIDNFLRTQLK-GVPKSMIYRILRKGEVRVNKKRIK-PEYKLE 61 Query: 67 PGDSFLI---------TVPAAQKLN-IAQENIPLDILYEDDDIIVINKPAGLVVHPAPGN 116 GD I + KL +A + ILYEDD I+V+NKP+G VH G Sbjct: 62 AGDEVRIPPVRVAEREEEAVSPKLQKVAA--LADVILYEDDHILVLNKPSGTAVHGGSGL 119 Query: 117 WTGTLVNALLYHCHNNLSSINGVK--RPG-----IVHRLDKDTTGVMVVAKNDLAHQKLS 169 G I G++ RP +VHRLD+DT+GV++VAK A + L Sbjct: 120 SFGV---------------IEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLH 164 Query: 170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAIT 229 EQ + G +++ Y A+V G ++ APL + R V+ + + S T Sbjct: 165 EQLREKG----MQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVR-VSQEGKPSE-T 218 Query: 230 HYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYG-KGFKTKANIV 288 ++ E Y FA +L++ TGRTHQIRVH + G+P+ D YG + F Sbjct: 219 RFKVEERYA----FA-TLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYGDREF------- 266 Query: 289 NNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK 340 + + L R LHA +L F+HP + M + P+ E + ++KL Sbjct: 267 --DQQLTGTGLNRLFLHAAALKFTHPGTGEVMRIEAPLDEQLKRCLQKLRNA 316 >gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional. Length = 257 Score = 116 bits (293), Expect = 7e-27 Identities = 72/265 (27%), Positives = 127/265 (47%), Gaps = 47/265 (17%) Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTG---------TLVNALLYHCHNNLSSINGVK 140 L+ILY+D+ ++ +NKPAG +VH + W T+ + + H Sbjct: 2 LEILYQDEWLVAVNKPAGWLVHRS---WLDRHETVFVMQTVRDQIGQHVFT--------- 49 Query: 141 RPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGII 200 HRLD+ T+GV+++A + + L++QF H ++++ Y+A+V G L + ++ Sbjct: 50 ----AHRLDRPTSGVLLMALSSEVARLLAQQFEQH----QIQKTYHAIVRGW-LMEEAVL 100 Query: 201 NAPLGRCKSNRLRRAVKGID-DKTADSAITHYQ---TIEIYNKNSNFAV---SLLKCHLE 253 + PL K + A K DK A+THY+ T+E+ + SL++ + Sbjct: 101 DYPL---KEELDKIADKFAREDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK 157 Query: 254 TGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSH 313 TGR HQ+R HMAH +P+IGD +G ++ N + + +R LHA LS +H Sbjct: 158 TGRKHQLRRHMAHLRHPIIGDTKHG-------DLRQNRSLAEHFGCSRLMLHASELSLTH 210 Query: 314 PRNNQDMDFQVPIPEDMLTVIRKLN 338 P + + + E ++ + Sbjct: 211 PFTGEPLTITAGLDETWQQLLSQFG 235 >gnl|CDD|182274 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional. Length = 219 Score = 114 bits (287), Expect = 3e-26 Identities = 83/242 (34%), Positives = 119/242 (49%), Gaps = 43/242 (17%) Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKR--PGI--V 145 L ILY+D+ I+V+NKP+GL+ P G L H + S + ++R P V Sbjct: 14 LVILYQDEHIMVVNKPSGLLSVP------GRLEE------HKD-SVMTRIQRDYPQAESV 60 Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205 HRLD T+GV+VVA A ++L QF + K+ Y A VWG P P G+++ PL Sbjct: 61 HRLDMATSGVIVVALTKAAERELKRQF----REREPKKQYVARVWGHPSPAEGLVDLPLI 116 Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265 NR ++ V +T A T Y+ +E N+ A +LK TGR+HQ+RVHM Sbjct: 117 CDWPNRPKQKVCY---ETGKPAQTEYEVVEYAADNT--ARVVLKP--ITGRSHQLRVHML 169 Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLA-RQALHAHSLSFSHPRNNQDMDFQV 324 G+P++GD Y A ++A R LHA L+ +HP M F+ Sbjct: 170 ALGHPILGDRFY--------------ASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKA 215 Query: 325 PI 326 P Sbjct: 216 PA 217 >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 = 96.1 bits (239), Expect = 1e-20 Identities = 65/229 (28%), Positives = 107/229 (46%), Gaps = 41/229 (17%) Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLD 149 +IL+ D ++INK G+ VH G TG L +++ GV + +VHRLD Sbjct: 2 FEILFTHPDFLLINKHPGISVHKDDGE-TGLL---------QEVATQLGVGQVWLVHRLD 51 Query: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKS 209 K T+G++++A N + +LS+ F ++++ Y A+ P G+I + Sbjct: 52 KMTSGILLLALNAESASELSQGFAKR----KIEKTYLALSSKKPKKKQGLICGDM----- 102 Query: 210 NRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGN 269 + RR + + + AIT + + F +LK H TG+THQ+RV M G+ Sbjct: 103 EKSRRGSWKLVNSQENPAITRFFSASAATGLRLF---ILKPH--TGKTHQLRVAMKSLGS 157 Query: 270 PLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQ 318 P++GDPLYG ++ R LHA +L F + +N Sbjct: 158 PILGDPLYGTTDESD----------------RGYLHAFALRFDY-QNEV 189 >gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional. Length = 217 Score = 40.1 bits (93), Expect = 8e-04 Identities = 44/167 (26%), Positives = 65/167 (38%), Gaps = 27/167 (16%) Query: 136 INGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLP 195 + GV G RLD+D+ G++V+ N +L++ GK R + YY V GIP Sbjct: 69 VQGVYAAG---RLDRDSEGLLVLTNNGALQARLTQP----GK--RTGKIYYVQVEGIPTQ 119 Query: 196 DSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIE-IYNKN------SNFAVSLL 248 D+ LR V D T + ++ +N + S L Sbjct: 120 DA-----------LEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWL 168 Query: 249 KCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSA 295 K L GR Q+R AH G P + Y G + N+ N + A Sbjct: 169 KITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREA 215 >gnl|CDD|161704 TIGR00093, TIGR00093, pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. Length = 128 Score = 37.3 bits (87), Expect = 0.006 Identities = 24/127 (18%), Positives = 46/127 (36%), Gaps = 27/127 (21%) Query: 145 VHRLDKDTTGVMVVAKN-DLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203 RLD+D+ G++++ + +L H+ ++ Y V G + Sbjct: 1 AGRLDRDSEGLLLLTNDGELVHRLTHPGH-------HCEKTYLVTVEGPVTDE------- 46 Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263 LR+ V+ ++D A + I + ++L + GR Q+R Sbjct: 47 ----DLEALRKGVQ-LEDGPTKPAKL--EVITEPGFPTWLRITLSE-----GRNRQVRRM 94 Query: 264 MAHKGNP 270 A G P Sbjct: 95 FAAVGFP 101 >gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain. Length = 60 Score = 36.8 bits (86), Expect = 0.008 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 3/53 (5%) Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76 R+D++LA L SRS + LI G + +NG P+ V PGD +I+V Sbjct: 2 RLDKFLA-RLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGD--VISVR 51 >gnl|CDD|129570 TIGR00478, tly, hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479). Length = 228 Score = 31.3 bits (71), Expect = 0.34 Identities = 12/28 (42%), Positives = 15/28 (53%) Query: 38 SRSYVKILILNGFISINGMVSKNPNRKV 65 SR K LIL GF+ +NG P+ V Sbjct: 14 SREKAKRLILKGFVLVNGKKVDKPSALV 41 >gnl|CDD|178682 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional. Length = 1195 Score = 30.2 bits (68), Expect = 0.73 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%) Query: 2 QQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKN 60 ++T DNCSS K + D T R L E+FS +++ + + G S+N V K+ Sbjct: 859 KKTCDNCSSSKSLIDKDVTEIARQLVELVKLTGERFSSAHI-LEVYRG--SLNQYVKKH 914 >gnl|CDD|178017 PLN02394, PLN02394, trans-cinnamate 4-monooxygenase. Length = 503 Score = 29.7 bits (67), Expect = 1.1 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 10/81 (12%) Query: 102 INKPAGLVVHPAPGNW--TGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVA 159 + P G P GNW G +N H NL+ + K+ G V L ++VV+ Sbjct: 29 LKLPPGPAAVPIFGNWLQVGDDLN------HRNLAEMA--KKYGDVFLLRMGQRNLVVVS 80 Query: 160 KNDLAHQKLSEQFVDHGKSTR 180 +LA + L Q V+ G TR Sbjct: 81 SPELAKEVLHTQGVEFGSRTR 101 >gnl|CDD|152404 pfam11969, DcpS_C, Scavenger mRNA decapping enzyme C-term binding. This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function. Length = 113 Score = 28.7 bits (65), Expect = 2.3 Identities = 7/21 (33%), Positives = 9/21 (42%) Query: 83 IAQENIPLDILYEDDDIIVIN 103 I P I+YEDD + Sbjct: 7 IINGEEPERIVYEDDGFVAFK 27 >gnl|CDD|184908 PRK14944, PRK14944, DNA polymerase III subunit beta; Provisional. Length = 375 Score = 28.3 bits (63), Expect = 3.2 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%) Query: 53 INGMVSKNPNRKVVPGDSF-----LITVPAAQKLNIAQENIPLDILYEDDDIIVINK 104 IN SKN R ++ G + L+ A ++Q+ I LD Y + +I++ NK Sbjct: 145 INISTSKNEKRPILTGLNLIYQKNLLKALATDSFRMSQKKIKLDFNYHNFNIVIPNK 201 >gnl|CDD|179429 PRK02484, truB, tRNA pseudouridine synthase B; Provisional. Length = 294 Score = 27.3 bits (61), Expect = 5.8 Identities = 22/83 (26%), Positives = 30/83 (36%), Gaps = 31/83 (37%) Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158 II + K AG+ H A ++ L I K+ G LD D GV+ + Sbjct: 5 IINLKKEAGMTSHDA------------VFK----LRKILQTKKIGHGGTLDPDVVGVLPI 48 Query: 159 AKNDLAHQKLSEQFVDHGKSTRL 181 A GK+TRL Sbjct: 49 AV---------------GKATRL 56 >gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional. Length = 295 Score = 26.9 bits (60), Expect = 7.3 Identities = 22/82 (26%), Positives = 30/82 (36%), Gaps = 31/82 (37%) Query: 100 IVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVA 159 + ++KPAGL H C L + +KR G LD TGV+ +A Sbjct: 6 LNLDKPAGLTSH----------------DCVARLRRLLRLKRVGHGGTLDPAATGVLPIA 49 Query: 160 KNDLAHQKLSEQFVDHGKSTRL 181 GK+TRL Sbjct: 50 L---------------GKATRL 56 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 0.318 0.134 0.395 Gapped Lambda K H 0.267 0.0626 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,473,326 Number of extensions: 345636 Number of successful extensions: 726 Number of sequences better than 10.0: 1 Number of HSP's gapped: 706 Number of HSP's successfully gapped: 22 Length of query: 340 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 246 Effective length of database: 3,963,321 Effective search space: 974976966 Effective search space used: 974976966 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: 57 (26.0 bits)