RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780715|ref|YP_003065128.1| 50S ribosomal protein L19
[Candidatus Liberibacter asiaticus str. psy62]
         (141 letters)



>gnl|CDD|180025 PRK05338, rplS, 50S ribosomal protein L19; Provisional.
          Length = 116

 Score =  180 bits (460), Expect = 1e-46
 Identities = 70/121 (57%), Positives = 92/121 (76%), Gaps = 5/121 (4%)

Query: 1   MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGIN 60
           MN+I E++ E++     ++ +P+F PGDT+ V   + EG+K RIQA+EGV IAR GRG+N
Sbjct: 1   MNLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLN 55

Query: 61  KNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENTGK 120
           + FTVRKISYG G+ R FPL+SP I  I V+RRGKVRR+KLYYL++LRGKAARIKE    
Sbjct: 56  ETFTVRKISYGVGVERTFPLHSPRIDSIEVVRRGKVRRAKLYYLRELRGKAARIKERRDA 115

Query: 121 R 121
           +
Sbjct: 116 K 116


>gnl|CDD|130096 TIGR01024, rplS_bact, ribosomal protein L19, bacterial type.  This
           model describes bacterial ribosomoal protein L19 and its
           chloroplast equivalent. Putative mitochondrial L19 are
           found in several species (but not Saccharomyces
           cerevisiae) and score between trusted and noise cutoffs.
          Length = 113

 Score =  145 bits (368), Expect = 4e-36
 Identities = 67/116 (57%), Positives = 84/116 (72%), Gaps = 5/116 (4%)

Query: 1   MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGIN 60
            N+I +++ E++     K+ LP F  GDT+ V   I EG K RIQ +EGV IAR G GI 
Sbjct: 1   QNLIKQIEQEQL-----KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIG 55

Query: 61  KNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKE 116
           + FTVRKISYG G+ R+FPL+SP I  I V+RRGKVRR+KLYYL++ RGKAARIKE
Sbjct: 56  ETFTVRKISYGVGVERIFPLHSPNIDSIEVVRRGKVRRAKLYYLRERRGKAARIKE 111


>gnl|CDD|167649 PRK03963, PRK03963, V-type ATP synthase subunit E; Provisional.
          Length = 198

 Score = 26.6 bits (59), Expect = 2.2
 Identities = 14/40 (35%), Positives = 24/40 (60%)

Query: 102 YYLQDLRGKAARIKENTGKRAKALNEEVRRAALPEKEMSK 141
           Y L++ + +A +IKE   KRA++  E + R A  + E+ K
Sbjct: 21  YILEEAQKEAEKIKEEARKRAESKAEWILRKAKTQAELEK 60


>gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated.
          Length = 156

 Score = 26.3 bits (59), Expect = 2.9
 Identities = 13/35 (37%), Positives = 17/35 (48%)

Query: 104 LQDLRGKAARIKENTGKRAKALNEEVRRAALPEKE 138
           L + R +AA I E   KRA  + EE +  A  E  
Sbjct: 65  LAEARAEAAEIIEQAKKRAAQIIEEAKAEAEAEAA 99


>gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b.  This model
           describes the F1/F0 ATP synthase b subunit in bacteria
           only. Scoring just below the trusted cutoff are the
           N-terminal domains of Mycobacterial b/delta fusion
           proteins and a subunit from an archaeon, Methanosarcina
           barkeri, in which the ATP synthase homolog differs in
           architecture and is not experimentally confirmed. This
           model helps resolve b from the related b' subunit.
           Within the family is an example from a
           sodium-translocating rather than proton-translocating
           ATP synthase.
          Length = 147

 Score = 26.2 bits (58), Expect = 3.0
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 104 LQDLRGKAARIKENTGKRAKALNEEVRRAALPEKE 138
           L++ + +A  I EN  KR   + EE +  A  E+E
Sbjct: 56  LKEAKDEAQEIIENANKRGSEILEEAKAEAREERE 90


>gnl|CDD|150429 pfam09754, PAC2, PAC2 family.  This PAC2 (Proteasome assembly
          chaperone) family of proteins is found in bacteria,
          archaea and eukaryotes. Proteins in this family are
          typically between 247 and 307 amino acids in length.
          These proteins function as a chaperone for the 26S
          proteasome. The 26S proteasome mediates
          ubiquitin-dependent proteolysis in eukaryotic cells. A
          number of studies including very recent ones have
          revealed that assembly of its 20S catalytic core
          particle is an ordered process that involves several
          conserved proteasome assembly chaperones (PACs). Two
          heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4,
          promote the assembly of rings composed of seven alpha
          subunits.
          Length = 177

 Score = 25.3 bits (56), Expect = 5.4
 Identities = 6/31 (19%), Positives = 13/31 (41%)

Query: 3  IIDELDHEEMVRIESKRSLPKFSPGDTLCVK 33
          +I+ L+ E++  I+S    P       +   
Sbjct: 19 LIESLEAEKVGEIDSDELFPFRGRRPQVTFD 49


>gnl|CDD|149655 pfam08670, MEKHLA, MEKHLA domain.  The MEKHLA domain shares
           similarity with the PAS domain and is found in the 3'
           end of plant HD-ZIP III homeobox genes, and bacterial
           proteins.
          Length = 148

 Score = 25.3 bits (56), Expect = 5.5
 Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 14/48 (29%)

Query: 10  EEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR 57
           EE  R E    L K           ++ +G       Y GV I+  GR
Sbjct: 83  EESGRKERCSELAK-----------VMQQG---FACLYSGVRISSMGR 116


>gnl|CDD|184421 PRK13961, PRK13961,
          phosphoribosylaminoimidazole-succinocarboxamide
          synthase; Provisional.
          Length = 296

 Score = 25.2 bits (56), Expect = 5.7
 Identities = 6/19 (31%), Positives = 10/19 (52%)

Query: 79 PLYSPMIQDITVIRRGKVR 97
           L    +  + ++ RGKVR
Sbjct: 3  TLMESDLPSLPLLGRGKVR 21


>gnl|CDD|152495 pfam12060, DUF3541, Domain of unknown function (DUF3541).  This
           presumed domain is functionally uncharacterized. This
           domain is found in bacteria. This domain is about 230
           amino acids in length.
          Length = 228

 Score = 25.0 bits (55), Expect = 6.7
 Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 6/47 (12%)

Query: 101 LYYLQDLRGKAARIKEN--TGKRAKALNEEVRRA----ALPEKEMSK 141
           LY   DL    AR  E          L E +RR      L +K M +
Sbjct: 107 LYLGDDLLRFMARADEYGLKHPCDDKLREVLRRYDFKKYLTDKAMIE 153


>gnl|CDD|128878 smart00630, Sema, semaphorin domain. 
          Length = 390

 Score = 25.0 bits (55), Expect = 6.9
 Identities = 6/25 (24%), Positives = 9/25 (36%)

Query: 78  FPLYSPMIQDITVIRRGKVRRSKLY 102
            P Y   +Q   ++  G      LY
Sbjct: 207 SPFYFNELQAAFLLPPGSESDDVLY 231


>gnl|CDD|167593 PRK03732, PRK03732, hypothetical protein; Provisional.
          Length = 114

 Score = 24.9 bits (54), Expect = 7.1
 Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 90  VIRRGKVRRSKLYYLQDLRGKAARIKENTGKRAKALNEEVRRAALPEKEM 139
           +++   + R  +  L++++G    +KE T   A+A  E +RR AL  KE+
Sbjct: 32  IVKATHLGRDIMALLRNIKG--GEVKEYTQMMAEAREEALRRMALHAKEL 79


>gnl|CDD|180656 PRK06680, PRK06680, D-amino acid aminotransferase; Reviewed.
          Length = 286

 Score = 24.5 bits (54), Expect = 8.9
 Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 1/24 (4%)

Query: 90  VIRRGKVRRSKLYYLQDLRGKAAR 113
           +IRR +VR   L YLQ  RG A R
Sbjct: 78  LIRRNRVR-EGLVYLQVTRGVARR 100


>gnl|CDD|162540 TIGR01809, Shik-DH-AROM, shikimate-5-dehydrogenase, fungal
           AROM-type.  This model represents a clade of
           shikimate-5-dehydrogenases found in Corynebacterium,
           Mycobacteria and fungi. The fungal sequences are
           pentafunctional proteins known as AroM which contain the
           central five seven steps in the chorismate biosynthesis
           pathway. The Corynebacterium and Mycobacterial sequences
           represent the sole shikimate-5-dehydrogenases in species
           which otherwise have every enzyme of the chorismate
           biosynthesis pathway.
          Length = 282

 Score = 24.5 bits (53), Expect = 9.2
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 77  LFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENTGKRAKALNEEVR 130
           ++ L S  + DITVI R   + S+L  L    G   R++ ++G    A+ +   
Sbjct: 141 VYALASLGVTDITVINRNPDKLSRLVDLGVQVGVITRLEGDSG--GLAIEKAAE 192


  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    0.136    0.377 

Gapped
Lambda     K      H
   0.267   0.0705    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,325,068
Number of extensions: 138117
Number of successful extensions: 254
Number of sequences better than 10.0: 1
Number of HSP's gapped: 252
Number of HSP's successfully gapped: 26
Length of query: 141
Length of database: 5,994,473
Length adjustment: 84
Effective length of query: 57
Effective length of database: 4,179,401
Effective search space: 238225857
Effective search space used: 238225857
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: 52 (23.9 bits)