RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 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) >gnl|CDD|182659 PRK10700, PRK10700, 23S rRNA pseudouridylate synthase B; Provisional. Length = 289 Score = 164 bits (417), Expect = 3e-41 Identities = 91/220 (41%), Positives = 130/220 (59%), Gaps = 10/220 (4%) Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68 +++ KV+ARAG SRRE+E +I RV V+G L +R V V I +DG + ++ Sbjct: 3 EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDR--VEVTPGLKIRIDGHLISVK 60 Query: 69 KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125 ++ R+ Y+KP G + T +DP+GR TVFD LP + +R I+VGRLD+NT GLLL T Sbjct: 61 ESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120 Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185 DG LA L PS + R Y VR GQVD KL L +G+ ++ + +G Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGVQLEDGPAAFKTIKFSGGEGI 180 Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225 N W V L EG+NRE+++++E +V+RLIR+ YG L Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220 >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 = 105 bits (263), Expect = 2e-23 Identities = 43/127 (33%), Positives = 67/127 (52%) Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170 GRLD ++EGLLLLTNDG L L P + Y V G V + L L+KG+ ++ Sbjct: 1 AGRLDRDSEGLLLLTNDGELVHRLTHPGHHCEKTYLVTVEGPVTDEDLEALRKGVQLEDG 60 Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230 ++ + T+ G W+ + L EG+NR+++++F + V RL R+ G L L Sbjct: 61 PTKPAKLEVITEPGFPTWLRITLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPP 120 Query: 231 GSTREVS 237 G R ++ Sbjct: 121 GEWRPLT 127 >gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional. Length = 217 Score = 75.2 bits (184), Expect = 3e-14 Identities = 56/187 (29%), Positives = 92/187 (49%), Gaps = 19/187 (10%) Query: 68 RKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125 RK E TR+ L++KP ++ +D GR T+ + +P V + GRLD ++EGLL+LT Sbjct: 32 RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLT 89 Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVT 178 N+G L L P + ++Y V+ G QD L L+ G+ + G D Sbjct: 90 NNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAW 149 Query: 179 L--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230 L + + +W+ + L EG+NR+++++ + RLIR + G + L L Sbjct: 150 LWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLAN 209 Query: 231 GSTREVS 237 G RE + Sbjct: 210 GEWREAT 216 >gnl|CDD|182487 PRK10475, PRK10475, 23S rRNA pseudouridine synthase F; Provisional. Length = 290 Score = 72.1 bits (177), Expect = 2e-13 Identities = 68/234 (29%), Positives = 117/234 (50%), Gaps = 15/234 (6%) Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDG--VPLRKA 70 R++K I+ +GI SRRE +R I Q V +NG +RA + V + D ++V+G + R+A Sbjct: 8 RLNKYISESGICSRREADRYIEQGNVFING---KRATIGDQVKAGDVVKVNGQLIEPREA 64 Query: 71 ERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129 E L +KP+G+V+T D + + V F N RV +GRLD +++GL+ LTN G Sbjct: 65 EDLVLIALNKPVGIVSTTEDGERDNIVDFVNHS---KRVFPIGRLDKDSQGLIFLTNHGD 121 Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189 L + + Y V + + + + G+ I G +V +K + Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTKKCKV----KKEAPFVF 177 Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243 + L +G NR+I+++ E F ++V +L R L + G R+++ L + Sbjct: 178 RITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELID 231 >gnl|CDD|182770 PRK10839, PRK10839, 16S rRNA pseudouridylate synthase A; Provisional. Length = 232 Score = 67.1 bits (164), Expect = 7e-12 Identities = 46/157 (29%), Positives = 76/157 (48%), Gaps = 4/157 (2%) Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74 R+ K I++ SR R + RV V+G +++ A ++ + DG PL + R Sbjct: 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPR 61 Query: 75 LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132 ++ +KP G V + DPD TV F + P + ++ + GRLDI+T GL+L+T+DG + Sbjct: 62 YFMLNKPQGYVCSTDDPD-HPTVLYFLDEPVAY-KLHAAGRLDIDTTGLVLMTDDGQWSH 119 Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169 + P + Y V V D KG+ + Sbjct: 120 RITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN 156 >gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain. Length = 60 Score = 44.5 bits (106), Expect = 4e-05 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 1/56 (1%) Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 +R+ K +AR G+A SR + ++I Q RVKVNG + + + V D I V G L+ Sbjct: 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56 >gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional. Length = 325 Score = 33.1 bits (76), Expect = 0.10 Identities = 40/141 (28%), Positives = 61/141 (43%), Gaps = 26/141 (18%) Query: 5 NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63 V E+ QR+ + +A SR ++ I QRV VNG ++ + V+ + + +D Sbjct: 9 ATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAID 68 Query: 64 G------------VPLRKA-ERTRLWLYHKPIGLVTTH---SDPDGRSTVFDNL----PS 103 +PL E + + +KP LV H +PDG TV + L P Sbjct: 69 AEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLV-VHPGAGNPDG--TVLNALLHYYPP 125 Query: 104 I--FSRVISVGRLDINTEGLL 122 I R V RLD +T GL+ Sbjct: 126 IADVPRAGIVHRLDKDTTGLM 146 >gnl|CDD|162665 TIGR02025, BchH, magnesium chelatase, H subunit. This model represents the H subunit of the magnesium chelatase complex responsible for magnesium insertion into the protoporphyrin IX ring in the biosynthesis of both chlorophyll and bacteriochlorophyll. In chlorophyll-utilizing species, this gene is known as ChlH, while in bacteriochlorophyll-utilizing spoecies it is called BchH. Subunit H is the largest (~140kDa) of the three subunits (the others being BchD/ChlD and BchI/ChlI), and is known to bind protoporphyrin IX. Subunit H is homologous to the CobN subunit of cobaltochelatase and by anology with that enzyme, subunit H is believed to also bind the magnesium ion which is inserted into the ring. In conjunction with the hydrolysis of ATP by subunits I and D, a conformation change is believed to happen in subunit H causing the magnesium ion insertion into the distorted protoporphyrin ring. Length = 1216 Score = 30.9 bits (70), Expect = 0.50 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 10/75 (13%) Query: 4 KNIVQENFTPQRV-SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62 +NI P R+ S + G R ++++AQ R + G E AV + TD+I+ Sbjct: 824 RNI--HALDPYRIPSPAAVKRG---TRIADKLLAQHRAENGGNYPETIAVVLWGTDNIKT 878 Query: 63 DGVPLRKAERTRLWL 77 G + +A L L Sbjct: 879 KGESVAQA----LAL 889 >gnl|CDD|183556 PRK12493, PRK12493, magnesium chelatase subunit H; Provisional. Length = 1310 Score = 29.5 bits (67), Expect = 1.4 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 9/74 (12%) Query: 4 KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63 +NI PQ + A A A +R V+ ++ +QR + G E A + TD+I+ Sbjct: 917 RNI--HALDPQSIPTAAAVA--AGKRVVDELLERQR-EEQGAWPETIACVLWGTDNIKTY 971 Query: 64 GVPLRKAERTRLWL 77 G L +A L L Sbjct: 972 GEGLAQA----LAL 981 >gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine. Length = 299 Score = 29.2 bits (66), Expect = 1.6 Identities = 46/176 (26%), Positives = 68/176 (38%), Gaps = 30/176 (17%) Query: 9 ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67 E QR+ +A SR ++++I +VKVNG + + V D I V VP Sbjct: 1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVR-VPE 59 Query: 68 RKA--------------ERTRLWLYHKPIGLVTTHSDPDGRS-TVFDNL------PSIFS 106 + E + + +KP GLV H TV + L + Sbjct: 60 EEEHEVPPQDIPLDILFEDEDIIVINKPSGLV-VHPGGGNPFGTVLNALLAHCPPIAGVE 118 Query: 107 RVISVGRLDINTEGLLLL--TNDG--GLARVLELPSTQWLRVYRVRFHGQVDQDKL 158 RV V RLD +T GL+++ T L R L+ + + Y HGQ D Sbjct: 119 RVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVT--KEYVALVHGQFDSGGG 172 >gnl|CDD|130183 TIGR01113, mtrE, N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit E. coenzyme M methyltransferase subunit E in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme methyl-coenzyme M reductase. Length = 283 Score = 29.1 bits (65), Expect = 1.7 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 1/62 (1%) Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221 K G + G+ +G + V L + + + I + +N K+ R +YG Sbjct: 223 KYGGPLTGLAFG-LIVFLSSWTTTIFDQQGLVIGIAGLIIVLILIIYNRKIEVFARNAYG 281 Query: 222 PF 223 P+ Sbjct: 282 PY 283 >gnl|CDD|183993 PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional. Length = 410 Score = 28.3 bits (64), Expect = 3.5 Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 1/55 (1%) Query: 19 VIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72 ++ G+ S+RE R+I +K+NG + + D + V LR+ ++ Sbjct: 348 LLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDAFDGKFVILRRGKK 402 >gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional. Length = 264 Score = 28.1 bits (63), Expect = 3.7 Identities = 20/77 (25%), Positives = 27/77 (35%), Gaps = 15/77 (19%) Query: 80 KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL---ARVLEL 136 K V +DP VFD F G LD+ L+ N G + E+ Sbjct: 59 KVTATVADVADPAQVERVFDTAVERF------GGLDV------LVNNAGIAGPTGGIDEI 106 Query: 137 PSTQWLRVYRVRFHGQV 153 QW + V +GQ Sbjct: 107 TPEQWEQTLAVNLNGQF 123 >gnl|CDD|179192 PRK00972, PRK00972, tetrahydromethanopterin S-methyltransferase subunit E; Provisional. Length = 292 Score = 27.6 bits (62), Expect = 5.2 Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 15/71 (21%) Query: 162 KKGIVIQGICYGDMQVTLDT------QKGSNAW--VTVGLREGKNREIKKVFEFFNWKVN 213 K G + G+C+G + V LD W + VGL I + N K+ Sbjct: 229 KFGGPLTGLCFG-LIVFLDGWRTIVFNIVGGGWGAIIVGLI------IVLILIIINRKLE 281 Query: 214 RLIRISYGPFQ 224 R YGP++ Sbjct: 282 VWARKKYGPYK 292 >gnl|CDD|163053 TIGR02871, spore_ylbJ, sporulation integral membrane protein YlbJ. Members of this protein family are found exclusively in Firmicutes (low-GC Gram-positive bacterial) and are known from studies in Bacillus subtilis to be part of the sigma-E regulon. Mutation leads to a sporulation defect, confirming that members of this protein family, YlbJ, are sporulation proteins. This protein appears to be universal among endospore-forming bacteria, but is encoded by a pair ORFs distant from eash other in Symbiobacterium thermophilum IAM14863. Length = 362 Score = 27.3 bits (61), Expect = 6.3 Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 5/55 (9%) Query: 189 VTVGL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241 +T+GL R K R+ K K I F +G L + K IL Sbjct: 153 ITMGLILRFYKRRKRKI---LSKKKKTFHIIRLKSKFPIGKTLKEAIENAVKTIL 204 >gnl|CDD|178842 PRK00074, guaA, GMP synthase; Reviewed. Length = 511 Score = 26.9 bits (61), Expect = 7.9 Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 4/26 (15%) Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQV 177 + D + L G+ + GICYG MQ+ Sbjct: 66 RADPEIFEL---GVPVLGICYG-MQL 87 >gnl|CDD|179573 PRK03372, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional. Length = 306 Score = 26.8 bits (60), Expect = 8.2 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 11/47 (23%) Query: 32 ERMIAQQRVKVNGILLERA-AVNVMSTDH----------IEVDGVPL 67 ERM V+V G ++ R A+N S + +EVDG P+ Sbjct: 134 ERMTLDVTVRVGGEIVWRGWALNEASLEKADREGMLEVVLEVDGRPV 180 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 0.385 Gapped Lambda K H 0.267 0.0711 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,779,336 Number of extensions: 374605 Number of successful extensions: 664 Number of sequences better than 10.0: 1 Number of HSP's gapped: 657 Number of HSP's successfully gapped: 25 Length of query: 354 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 260 Effective length of database: 3,963,321 Effective search space: 1030463460 Effective search space used: 1030463460 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: 58 (26.2 bits)