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)