RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780146|ref|YP_003064559.1| 50S ribosomal protein L1
[Candidatus Liberibacter asiaticus str. psy62]
         (232 letters)



>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
          Length = 230

 Score =  379 bits (975), Expect = e-106
 Identities = 142/229 (62%), Positives = 185/229 (80%)

Query: 3   SKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRG 62
           +K+SKR +  ++ +DR+ LY L +A+ ++KE ATA+FDETV++A+NLG+DPR A+Q VRG
Sbjct: 1   AKLSKRYRAAAEKVDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRG 60

Query: 63  VVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMM 122
            V +P+GTG  VRVAVFA   KA+EA+ AGADIVGGEDL E +KGG +DFD  IATPDMM
Sbjct: 61  AVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADIVGGEDLIEKIKGGWLDFDVVIATPDMM 120

Query: 123 PLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFE 182
             VG+LGRILGPRG+MPN + GTVT DVA AV+E+K+G V+FR +KAGIIHA IGKVSF+
Sbjct: 121 GKVGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVDKAGIIHAPIGKVSFD 180

Query: 183 NKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231
            +K++EN+ A + A+ KAKP+ AKG Y+K V+LSSTMG G+KVD SS +
Sbjct: 181 AEKLKENLKALIDAIKKAKPATAKGTYIKSVSLSSTMGPGVKVDPSSLA 229


>gnl|CDD|162232 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast. 
           This model describes bacterial (and chloroplast)
           ribosomal protein L1. The apparent mitochondrial L1 is
           sufficiently diverged to be the subject of a separate
           model.
          Length = 227

 Score =  335 bits (860), Expect = 8e-93
 Identities = 139/227 (61%), Positives = 178/227 (78%)

Query: 4   KISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGV 63
           K+SKR +   + +DR+ LY L +A+ +LKE ATA+FDETVE+A+ LGIDPR ++Q VRG 
Sbjct: 1   KLSKRYRAAREKVDRNKLYSLDEAIALLKETATAKFDETVEVAIRLGIDPRKSDQQVRGT 60

Query: 64  VTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMP 123
           V +P+GTG  VRVAVFA   KA+EA+ AGAD VG +DL E +K G +DFD  IATPDMM 
Sbjct: 61  VVLPHGTGKTVRVAVFAKGEKAEEAKAAGADYVGSDDLIEKIKKGWLDFDVVIATPDMMR 120

Query: 124 LVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFEN 183
           +VG+LGRILGPRG+MPN + GTVT DVA AV+ +K G V+FR++KAG IHA IGKVSF++
Sbjct: 121 VVGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRADKAGNIHASIGKVSFDS 180

Query: 184 KKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSF 230
           +K++EN+ A + A+ KAKPS AKG Y+K + LSSTMG GIKVDLSS 
Sbjct: 181 EKLKENLEALLDAIKKAKPSGAKGQYIKNIALSSTMGPGIKVDLSSL 227


>gnl|CDD|179783 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed.
          Length = 215

 Score =  109 bits (274), Expect = 8e-25
 Identities = 66/214 (30%), Positives = 104/214 (48%), Gaps = 19/214 (8%)

Query: 24  LSDAVVMLKERATAR-FDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81
           + +AV    E A  R F ++V++ +NL  ID +     +   V +P+G G  V++AV A 
Sbjct: 7   IEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAK 66

Query: 82  SSKADEAREAGADIV-GGEDLFEIVK--------GGQIDFDRCIATPDMMPLVGR-LGRI 131
              A +A+EAGAD V   E+L E+            + DF   IA  D+MPL+GR LG +
Sbjct: 67  GELALQAKEAGADYVITREELEELGGDKRAAKKLANEYDF--FIAEADLMPLIGRYLGPV 124

Query: 132 LGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVL 191
           LGPRG MP         D+   V   K+  V  R++     H  +G      +++ EN+ 
Sbjct: 125 LGPRGKMP--TPLPPNADIKPLVERLKN-TVRIRTKDQPTFHVRVGTEDMSPEELAENID 181

Query: 192 AFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKV 225
           A ++ +        +   +K V + +TMG  +KV
Sbjct: 182 AVLNRIESKLEKGRQ--NIKSVYVKTTMGPAVKV 213


>gnl|CDD|162233 TIGR01170, rplA_mito, ribosomal protein L1, mitochondrial.  This
           model represents the mitochondrial homolog of bacterial
           ribosomal protein L1. Unlike chloroplast L1, this form
           was not sufficiently similar to bacterial forms to
           include in a single bacterial/organellar L1.
          Length = 141

 Score = 91.0 bits (226), Expect = 2e-19
 Identities = 49/141 (34%), Positives = 87/141 (61%), Gaps = 2/141 (1%)

Query: 22  YGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81
           Y +  A V LK ++ + +     + +++G+      + V+G+ + P+  G   ++AVF  
Sbjct: 1   YKVIKAFVYLKTKSISMYVPKQSVNLDIGLLMELGKESVQGMFSFPHPFGKEPKIAVFTK 60

Query: 82  -SSKADEAREAGADIVGGEDLFEIVKGGQID-FDRCIATPDMMPLVGRLGRILGPRGIMP 139
            +S+ +EAREAGAD VGG+DL + ++ G+I  FD  IA PD++P + +L R+LGP+G+MP
Sbjct: 61  GASEVEEAREAGADYVGGDDLIKKIEDGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMP 120

Query: 140 NLRVGTVTTDVATAVRESKSG 160
           + + GTV  ++ + +   K G
Sbjct: 121 SPKRGTVGDNLLSMIETFKKG 141


>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
          Length = 216

 Score = 53.6 bits (129), Expect = 4e-08
 Identities = 56/227 (24%), Positives = 107/227 (47%), Gaps = 22/227 (9%)

Query: 9   MQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMP 67
           M ++S    R A+      ++   E    +F ETVE+ + L   D +  ++   G V +P
Sbjct: 1   MSKLSSEALRKAI----AEILEGSEEKKRKFVETVELQIGLKDYDTQK-DKRFSGSVKLP 55

Query: 68  NGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQI------DFDRCIATPDM 121
           N    N++V V   +   DEA++ G D +  E L +  K  ++       +D  +A+  +
Sbjct: 56  NVPKPNLKVCVLGDAVHCDEAKKLGLDFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSL 115

Query: 122 MPLVGR-LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVS 180
           +P + R LG  L   G  P L   T   D+   + E KS +V F+ +K   +   +G V 
Sbjct: 116 LPQIPRLLGPGLNKAGKFPTLI--THNDDIEDKINELKS-SVKFQLKKVLCLGVAVGNVE 172

Query: 181 FENKKIEENVLAFVSAVVKAKPSVAKGDY--VKRVTLSSTMGCGIKV 225
              +++ +N++  ++ +V    S+ K ++  +K + + STMG   ++
Sbjct: 173 MTEEQLRQNIVLSINFLV----SLLKKNWQNIKTLHIKSTMGKPQRI 215


>gnl|CDD|140252 PTZ00225, PTZ00225, 60S ribosomal protein L10a; Provisional.
          Length = 214

 Score = 37.7 bits (87), Expect = 0.003
 Identities = 49/212 (23%), Positives = 97/212 (45%), Gaps = 27/212 (12%)

Query: 24  LSDAV-VMLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81
           LS+A+  +LK     +F E++++ +NL   DP+  ++   G + +PN     + V +   
Sbjct: 9   LSEAIQAVLKVDKERKFKESIDLQVNLKNYDPQK-DKRFSGSLKLPNVCRPRMTVCLLCD 67

Query: 82  SSKADEAREAGADIVGGEDLFEIVKGGQI------DFDRCIATPDMMPLVGRLGRILGPR 135
               D A++ G   +  E+L ++ K  ++       +D  + +  ++  V RL   +GP 
Sbjct: 68  LVHEDIAKKEGVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRL---VGPH 124

Query: 136 ----GIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENV- 190
               G  P   V + +  +   V E +S  V F+ +K   +   +G V    +++ +NV 
Sbjct: 125 MHRMGKFPT--VCSPSESLPDKVVELRS-TVKFQLKKVLCLGTCVGHVEMTEEQLRQNVV 181

Query: 191 --LAFVSAVVKAKPSVAKGDYVKRVTLSSTMG 220
             + F+ +++K      K  Y+K     STMG
Sbjct: 182 MAINFLVSLLKKNWQNLKSAYIK-----STMG 208


>gnl|CDD|161874 TIGR00425, CBF5, rRNA pseudouridine synthase, putative.  This
           family, found in archaea and eukaryotes, includes the
           only archaeal proteins markedly similar to bacterial
           TruB, the tRNA pseudouridine 55 synthase. However, among
           two related yeast proteins, the archaeal set matches
           yeast YLR175w far better than YNL292w. The first, termed
           centromere/microtubule binding protein 5 (CBF5), is an
           apparent rRNA pseudouridine synthase, while the second
           is the exclusive tRNA pseudouridine 55 synthase for both
           cytosolic and mitochondrial compartments. It is unclear
           whether archaeal proteins found by this model modify
           tRNA, rRNA, or both.
          Length = 322

 Score = 30.1 bits (68), Expect = 0.52
 Identities = 19/68 (27%), Positives = 26/68 (38%), Gaps = 3/68 (4%)

Query: 56  ANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRC 115
           A+ MVRG+  +  G      VAV        EA   G  ++  +D+    KG   D  R 
Sbjct: 254 ADLMVRGIARLEKGIEKGDTVAVITLKG---EAVAVGIALMSTKDIANADKGVVADVKRV 310

Query: 116 IATPDMMP 123
           I      P
Sbjct: 311 IMERGTYP 318


>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
          Length = 202

 Score = 29.4 bits (66), Expect = 0.73
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 14/77 (18%)

Query: 44  EIAMNLGIDPRHANQMVRGVVTM-PNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLF 102
           E+A    +   ++   VRGV  + PN     VR  ++  +       E G +I   +++ 
Sbjct: 101 ELAREYNLIDENSGATVRGVFIIDPNQI---VRWMIYYPA-------ETGRNI---DEII 147

Query: 103 EIVKGGQIDFDRCIATP 119
            I K  Q+++ R +ATP
Sbjct: 148 RITKALQVNWKRKVATP 164


>gnl|CDD|183509 PRK12409, PRK12409, D-amino acid dehydrogenase small subunit;
           Provisional.
          Length = 410

 Score = 27.7 bits (62), Expect = 2.8
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 6/61 (9%)

Query: 138 MPNLRVGTV-TTDVATAVRE-----SKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVL 191
           +PN R  T+ T  +A A R+     ++   +DF  E+ GI+H    K  F++ K    +L
Sbjct: 97  IPNYRANTIETVRLAIAARKHLFDIAEREGIDFDLERRGILHIYHDKAGFDHAKRVNALL 156

Query: 192 A 192
           A
Sbjct: 157 A 157


>gnl|CDD|180244 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
          Length = 393

 Score = 27.0 bits (61), Expect = 4.6
 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 11/44 (25%)

Query: 77  AVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPD 120
           A  A ++KA E +  G D++           G+ DFD    TP+
Sbjct: 15  ATLAVTAKAKELKAQGRDVIS----LGA---GEPDFD----TPE 47


>gnl|CDD|178209 PLN02599, PLN02599, dihydroorotase.
          Length = 364

 Score = 26.6 bits (59), Expect = 5.6
 Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 11/58 (18%)

Query: 116 IATPDMMPLVGRLG-----------RILGPRGIMPNLRVGTVTTDVATAVRESKSGAV 162
           I  PD   L  R G           R  G   +MPNL+    TT  A A RE    A+
Sbjct: 25  ITRPDDWHLHLRDGAKLAAVVPHSARHFGRAIVMPNLKPPVTTTARALAYRERIMKAL 82


>gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional.
          Length = 202

 Score = 26.1 bits (58), Expect = 7.5
 Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 10/56 (17%)

Query: 115 CIAT----PDM--MPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDF 164
           C+ T    P +  + L+ RL      RG    + V T   DV  AV   K GAVDF
Sbjct: 50  CVVTDVRMPGIDGIELLRRLKA----RGSPLPVIVMTGHGDVPLAVEAMKLGAVDF 101


>gnl|CDD|180850 PRK07116, PRK07116, flavodoxin; Provisional.
          Length = 160

 Score = 26.2 bits (58), Expect = 8.2
 Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)

Query: 76  VAVFATSSKADEAREAGADIVGGEDLFEIV 105
           VA F+ +    +  E  A++ G  DLFEI 
Sbjct: 7   VAYFSATGTTKKVAEKLAEVTGA-DLFEIK 35


>gnl|CDD|132281 TIGR03237, dnd_assoc_2, dnd system-associated protein 2.  cereus
           E33L, Hahella chejuensis KCTC 2396, and
           Pseudoalteromonas haloplanktis TAC12.
          Length = 1256

 Score = 26.0 bits (57), Expect = 8.9
 Identities = 10/62 (16%), Positives = 24/62 (38%)

Query: 53  PRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDF 112
           P H N +V+ +    + + ++   ++        E         G E+L+  +  G ++F
Sbjct: 125 PWHPNSIVKLLRQEIDSSMLDKTASICLLDMIKQEQAHDQVTFFGFEELYSTIADGDLEF 184

Query: 113 DR 114
             
Sbjct: 185 QE 186


  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    0.367 

Gapped
Lambda     K      H
   0.267   0.0822    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,686,153
Number of extensions: 240626
Number of successful extensions: 559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 553
Number of HSP's successfully gapped: 40
Length of query: 232
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 142
Effective length of database: 4,049,753
Effective search space: 575064926
Effective search space used: 575064926
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: 55 (24.8 bits)