RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780144|ref|YP_003064557.1| 50S ribosomal protein L12P
[Candidatus Liberibacter asiaticus str. psy62]
         (126 letters)



>gnl|CDD|178906 PRK00157, rplL, 50S ribosomal protein L7/L12; Reviewed.
          Length = 123

 Score =  131 bits (331), Expect = 7e-32
 Identities = 76/125 (60%), Positives = 94/125 (75%), Gaps = 4/125 (3%)

Query: 1   MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEV 60
               E I+E L  +T++E +EL K LE+++GVSA+APV+  A  AA A +AA EKTEF+V
Sbjct: 2   ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAAA--AAAAAAAAEEKTEFDV 59

Query: 61  VLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAG 120
           VLK   D  KKIAVIK VR IT LGLKEAK+LVE APK +K G+SK+EA E+KKKLE+AG
Sbjct: 60  VLKSAGD--KKIAVIKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAG 117

Query: 121 ATVEL 125
           A VEL
Sbjct: 118 AKVEL 122


>gnl|CDD|162069 TIGR00855, L12, ribosomal protein L7/L12.  THis model resembles
           Pfam model pfam00542 but matches the full length of
           prokaryotic and organellar proteins rather than just the
           C-terminus.
          Length = 126

 Score =  111 bits (278), Expect = 8e-26
 Identities = 75/124 (60%), Positives = 96/124 (77%), Gaps = 2/124 (1%)

Query: 3   NIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVL 62
           + E I+E L  +T++E +EL K LE+++GVSA+APV+  A  AA A +AA EKTEF+V+L
Sbjct: 5   SKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAGAAGAAAAAAAAEEKTEFDVIL 64

Query: 63  KGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGAT 122
           KG  D   KIAVIK VR IT LGLKEAK+LVE APK LK G+SK+EA E+KKKLE+AGA 
Sbjct: 65  KGAGD--NKIAVIKVVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAK 122

Query: 123 VELR 126
           VE++
Sbjct: 123 VEVK 126


>gnl|CDD|183148 PRK11466, PRK11466, hybrid sensory histidine kinase TorS;
           Provisional.
          Length = 914

 Score = 33.3 bits (76), Expect = 0.019
 Identities = 24/92 (26%), Positives = 35/92 (38%), Gaps = 14/92 (15%)

Query: 14  LTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIA 73
           L LIE   L++R+  E   ++ A V  V   AA+A         F   L  FD P     
Sbjct: 684 LLLIEDNPLTQRITAEMLNTSGAQVVAVGN-AAQALETLQNSEPFAAALVDFDLPDYD-- 740

Query: 74  VIKEVRAITDLGLKEAKELVESAPKSLKTGLS 105
                      G+  A++L +  P  +  G S
Sbjct: 741 -----------GITLARQLAQQYPSLVLIGFS 761


>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional.
          Length = 936

 Score = 32.5 bits (74), Expect = 0.034
 Identities = 24/113 (21%), Positives = 50/113 (44%), Gaps = 4/113 (3%)

Query: 5   ESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAAS---EKTEFEVV 61
           E +++KL+++ +   +EL+ R  +    S          +  EAG        ++E    
Sbjct: 681 EELLQKLNAVHIYTVSELASREPEALAKSLGLSKKEAEKLIREAGDVLELLRRRSELRKF 740

Query: 62  LKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLK-TGLSKDEANEMK 113
           ++    P++  +  K ++A+   G+ +   L  + P  LK  GLS+ EA  + 
Sbjct: 741 VRKHVPPRRGRSHAKIMKALISSGINDIAALARADPADLKKAGLSEAEAASLL 793


>gnl|CDD|178963 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
          Length = 627

 Score = 28.1 bits (64), Expect = 0.71
 Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 3/43 (6%)

Query: 79  RAITDLGLK---EAKELVESAPKSLKTGLSKDEANEMKKKLED 118
           + + +LG K   + KE +E+A K LK  L  ++   +K K E+
Sbjct: 541 KTLKELGDKVPADEKEKIEAAIKELKEALKGEDKEAIKAKTEE 583


>gnl|CDD|184895 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
          Length = 444

 Score = 27.8 bits (63), Expect = 0.76
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 14/71 (19%)

Query: 66  DDPKKKIAV--------IKEVRAITDLGLKEAKELVES----APKSLKTGLSKDEANEMK 113
            DP K++++        +K  R I   G ++A++++ES       S++    K    E+ 
Sbjct: 137 KDPVKRLSIKYSHPVWLVK--RWIDQYGEEKAEKILESLNEPPKASIRVNTLKISVEELI 194

Query: 114 KKLEDAGATVE 124
           +KLE+ G  VE
Sbjct: 195 EKLEEEGYEVE 205


>gnl|CDD|181825 PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed.
          Length = 891

 Score = 27.4 bits (62), Expect = 1.1
 Identities = 8/18 (44%), Positives = 14/18 (77%), Gaps = 3/18 (16%)

Query: 17  IEAAELSKRLEKEWGVSA 34
           +EAAE+   L +++GV+A
Sbjct: 743 LEAAEI---LAEDYGVAA 757


>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1.  This model
           describes peptide chain release factor 1 (PrfA, RF-1),
           and excludes the related peptide chain release factor 2
           (PrfB, RF-2). RF-1 helps recognize and terminate
           translation at UAA and UAG stop codons. The
           mitochondrial release factors are prfA-like, although
           not included above the trusted cutoff for this model.
           RF-1 does not have a translational frameshift.
          Length = 360

 Score = 26.2 bits (58), Expect = 2.1
 Identities = 23/114 (20%), Positives = 47/114 (41%), Gaps = 23/114 (20%)

Query: 5   ESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKG 64
            S++EKL SL      EL   L             V++    +    + E ++ E ++  
Sbjct: 3   PSLLEKLESLL-ERYEELEALLSD---------PEVISDQD-KLRKLSKEYSQLEEIVDC 51

Query: 65  FDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLED 118
           + + ++    IKE + I +    E +E+             K+E  E+++K+E+
Sbjct: 52  YREYQQAQEDIKEAKEILEESDPEMREMA------------KEELEELEEKIEE 93


>gnl|CDD|162912 TIGR02544, III_secr_YscJ, type III secretion apparatus lipoprotein,
           YscJ/HrcJ family.  All members of this protein family
           are predicted lipoproteins with a conserved Cys near the
           N-terminus for cleavage and modification, and are part
           of known or predicted type III secretion systems.
           Members are found in both plant and animal pathogens,
           including the obligately intracellular chlamydial
           species and (non-pathogenic) root nodule bacteria. The
           most closely related proteins outside this family are
           examples of the flagellar M-ring protein FliF.
          Length = 193

 Score = 26.1 bits (58), Expect = 2.5
 Identities = 12/25 (48%), Positives = 14/25 (56%)

Query: 100 LKTGLSKDEANEMKKKLEDAGATVE 124
           L +GLS+ EANEM   L   G   E
Sbjct: 22  LYSGLSEREANEMLAVLMRHGIDAE 46


>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
          Length = 684

 Score = 25.9 bits (57), Expect = 3.4
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 12/77 (15%)

Query: 51  AASEKTEFEVVLK-GFDDPKK-KIAVIKEVRAITDLGL---KEAKELVESAPKSLKTGLS 105
           A S+K++  +V    F +P++ ++ VI   +   +LGL    + K +VE+        ++
Sbjct: 426 AHSDKSKVPLVAHEKFAEPREVEVLVIVPNK--KELGLAFKGDQKVVVEA-----LEAMN 478

Query: 106 KDEANEMKKKLEDAGAT 122
           + EA EMK KLE  G  
Sbjct: 479 EKEAMEMKAKLESKGEA 495


>gnl|CDD|183840 PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1;
           Provisional.
          Length = 896

 Score = 24.9 bits (55), Expect = 5.4
 Identities = 8/18 (44%), Positives = 10/18 (55%), Gaps = 3/18 (16%)

Query: 17  IEAAELSKRLEKEWGVSA 34
           + AA L   L  +WGV A
Sbjct: 748 LAAARL---LADDWGVDA 762


>gnl|CDD|183393 PRK12273, aspA, aspartate ammonia-lyase; Provisional.
          Length = 472

 Score = 25.1 bits (56), Expect = 5.6
 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 12/45 (26%)

Query: 74  VIKEVRAITDLGLKEAKELVE------------SAPKSLKTGLSK 106
           V++++  IT L L  A++L+E             A K L   LSK
Sbjct: 248 VVEKLAEITGLPLVPAEDLIEATQDTGAFVEVSGALKRLAVKLSK 292


>gnl|CDD|150561 pfam09902, DUF2129, Uncharacterized protein conserved in bacteria
          (DUF2129).  This domain, found in various hypothetical
          prokaryotic proteins, has no known function.
          Length = 71

 Score = 24.8 bits (55), Expect = 5.7
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 1  MSNIESIVEKLSSLTLIEAAELSKR 25
             +E IVEKLS L  ++  E S R
Sbjct: 39 QEEVEEIVEKLSKLKFVKKVEPSYR 63


>gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional.
          Length = 258

 Score = 24.9 bits (55), Expect = 5.8
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 6/53 (11%)

Query: 26  LEKEWGVS-ASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVIKE 77
           L +EW V+ A   V V A + AE  +   E       +  FDDP+ K+A I  
Sbjct: 163 LTREWAVALAKDGVRVNAVIPAEVMTPLYENW-----IATFDDPEAKLAAITA 210


>gnl|CDD|162857 TIGR02438, catachol_actin, catechol 1,2-dioxygenase,
           Actinobacterial.  Members of this family are catechol
           1,2-dioxygenases of the Actinobacteria. They are more
           closely related to actinobacterial chlorocatechol
           1,2-dioxygenases than to proteobacterial catechol
           1,2-dioxygenases, and so are built in this separate
           model. The member from Rhodococcus rhodochrous NCIMB
           13259 (GB|AAC33003.1) is described as a homodimer with
           bound Fe, similarly active on catechol, 3-methylcatechol
           and 4-methylcatechol.
          Length = 281

 Score = 24.7 bits (54), Expect = 5.9
 Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 18/85 (21%)

Query: 42  APVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVI-KEV-RAITDLGLKEAKELVESAPKS 99
           AP AA +G+AA++K + E V    D  K+++A I ++V  AI +  LK            
Sbjct: 7   APTAAASGNAATDKFKAERVSA--DTSKERVAAIARDVLGAINETILKH----------- 53

Query: 100 LKTGLSKDEANEMKKKLEDAGATVE 124
               ++ DE N +K+ L D G   E
Sbjct: 54  ---KVTYDEYNVLKQWLIDVGEDGE 75


>gnl|CDD|179714 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
          Length = 1121

 Score = 24.9 bits (55), Expect = 6.0
 Identities = 7/20 (35%), Positives = 11/20 (55%)

Query: 66  DDPKKKIAVIKEVRAITDLG 85
           DD ++   +  +V  I DLG
Sbjct: 384 DDVEEAKEIRDDVEEILDLG 403


>gnl|CDD|178670 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
          Length = 981

 Score = 24.8 bits (54), Expect = 6.8
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 103 GLSKDEANEMKKKLEDAGATV 123
           G SK++  E K K+E+AG   
Sbjct: 403 GASKEKVTEWKAKIEEAGGVF 423


>gnl|CDD|178436 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
          Length = 974

 Score = 24.7 bits (54), Expect = 7.4
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 14  LTLIEAAELSKRLEKEWGVS 33
           L LI A +L   LE +WGV 
Sbjct: 278 LFLIVATDLVPALEAKWGVK 297


>gnl|CDD|181714 PRK09231, PRK09231, fumarate reductase flavoprotein subunit;
          Validated.
          Length = 582

 Score = 24.6 bits (54), Expect = 7.9
 Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 12/41 (29%)

Query: 17 IEAAELSKRLEKEWGVSASAPVSVVAP-----VAAEAGSAA 52
          I AAE +  L+        A +S V P     VAAE GSAA
Sbjct: 21 IAAAEANPNLK-------IALISKVYPMRSHTVAAEGGSAA 54


>gnl|CDD|161728 TIGR00132, gatA, glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn)
           amidotransferase, A subunit.  This orthology group is
           more narrowly defined here than in Proc Natl Acad Aci
           USA 94, 11819-11826 (1997). In particular, a Rhodococcus
           homolog found in association with nitrile hydratase
           genes and described as an enantiomer-selective amidase
           active on several 2-aryl propionamides, is excluded
           here. It is likely, however, that the amidase subunit
           GatA is not exclusively a part of the Glu-tRNA(Gln)
           amidotransferase heterotrimer and restricted to that
           function in all species.
          Length = 460

 Score = 24.6 bits (54), Expect = 7.9
 Identities = 20/75 (26%), Positives = 27/75 (36%), Gaps = 20/75 (26%)

Query: 50  SAASEKTEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEA 109
           SA     EF   LK      K + V+KE     D   KE +E  E+A             
Sbjct: 225 SAKVPDPEFFEELKKDLKGLK-VGVVKEFSEEMD---KEVQEKFENA------------- 267

Query: 110 NEMKKKLEDAGATVE 124
               + LE+ GA + 
Sbjct: 268 ---LEVLEELGAEIV 279


>gnl|CDD|149109 pfam07859, Abhydrolase_3, alpha/beta hydrolase fold.  This
           catalytic domain is found in a very wide range of
           enzymes.
          Length = 209

 Score = 24.5 bits (54), Expect = 9.0
 Identities = 8/21 (38%), Positives = 11/21 (52%)

Query: 106 KDEANEMKKKLEDAGATVELR 126
           +DE     ++L  AG  VEL 
Sbjct: 178 RDEGEAYAERLRAAGVPVELV 198


  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
   0.304    0.122    0.305 

Gapped
Lambda     K      H
   0.267   0.0623    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,868,726
Number of extensions: 109118
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 274
Number of HSP's successfully gapped: 62
Length of query: 126
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 44
Effective length of database: 4,222,617
Effective search space: 185795148
Effective search space used: 185795148
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 51 (23.7 bits)