RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780236|ref|YP_003064649.1| 50S ribosomal protein L17
[Candidatus Liberibacter asiaticus str. psy62]
         (136 letters)



>gnl|CDD|180154 PRK05591, rplQ, 50S ribosomal protein L17; Validated.
          Length = 113

 Score =  191 bits (487), Expect = 6e-50
 Identities = 72/111 (64%), Positives = 88/111 (79%)

Query: 6   SGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRL 65
            GRKL RTSSHRKAM  N+A S+I HE+I TTLPKAKELR +VEKL+TL KKG LH+ R 
Sbjct: 3   KGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQ 62

Query: 66  AISKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFV 116
           A +++ D + V+KLF  IA RY+DR+GGY RI+K GFR GD+APMA+IE V
Sbjct: 63  AFARLRDKEAVHKLFDEIAPRYADRNGGYTRILKLGFRRGDNAPMAIIELV 113


>gnl|CDD|129169 TIGR00059, L17, ribosomal protein L17.  Eubacterial and
           mitochondrial. The mitochondrial form, from yeast,
           contains an additional 110 amino acids C-terminal to the
           region found by this model.
          Length = 112

 Score =  138 bits (349), Expect = 5e-34
 Identities = 62/112 (55%), Positives = 82/112 (73%)

Query: 6   SGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRL 65
           S RKL RTS+HRKA+  N+A+++I HE+I TTL KAKELR +VEKL+TL K    ++ R 
Sbjct: 1   SYRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRRE 60

Query: 66  AISKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFVD 117
           A + I + ++V+KLF  IA RY+ R GGY RI+K G R GD+A MA+IE VD
Sbjct: 61  AKAYIRNKEIVHKLFSEIAPRYAQRPGGYTRILKLGPRRGDAAEMAIIELVD 112


>gnl|CDD|173371 PTZ00076, PTZ00076, 60S ribosomal protein L17; Provisional.
          Length = 253

 Score = 59.0 bits (143), Expect = 4e-10
 Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 1/112 (0%)

Query: 8   RKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAI 67
           R+ +    HR     N    ++ + ++  TLP+AKEL+   E+L+ L KK    S     
Sbjct: 20  RRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVE 79

Query: 68  SKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKR-GFRYGDSAPMAVIEFVDR 118
           S +       KL+      Y DR   + R++ +   R  D+APMA IEFVDR
Sbjct: 80  SMLRTPQGRRKLYEKYVPLYRDRPFFFTRVVNQWRLRLRDAAPMAYIEFVDR 131


>gnl|CDD|181674 PRK09148, PRK09148, aminotransferase; Validated.
          Length = 405

 Score = 30.8 bits (70), Expect = 0.14
 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 12/83 (14%)

Query: 43  ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNK------LFGIIAKRYSDRS----- 91
           +L P  + + TLG K G  ++  AI+  GDV +          FG I      RS     
Sbjct: 88  KLNPDTQVVATLGSKEGFANMAQAITAPGDVILCPNPSYPIHAFGFIMAGGVIRSVPAEP 147

Query: 92  -GGYLRIMKRGFRYGDSAPMAVI 113
              +   ++R  R+    P+A+I
Sbjct: 148 DEEFFPALERAVRHSIPKPIALI 170


>gnl|CDD|181268 PRK08175, PRK08175, aminotransferase; Validated.
          Length = 395

 Score = 28.9 bits (65), Expect = 0.50
 Identities = 14/34 (41%), Positives = 19/34 (55%)

Query: 43  ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVV 76
           ++ P  E +VT+G K GL  L LA    GD  +V
Sbjct: 87  DIDPESEAIVTIGSKEGLAHLMLATLDHGDTVLV 120


>gnl|CDD|181511 PRK08636, PRK08636, aspartate aminotransferase; Provisional.
          Length = 403

 Score = 27.0 bits (60), Expect = 1.5
 Identities = 14/34 (41%), Positives = 19/34 (55%)

Query: 43  ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVV 76
           +L P  E + T+G K G   L  AI+  GDV +V
Sbjct: 91  DLDPETEVVATMGSKEGYVHLVQAITNPGDVAIV 124


>gnl|CDD|147801 pfam05843, Suf, Suppressor of forked protein (Suf).  This family
           consists of several eukaryotic suppressor of forked
           (Suf) like proteins. The Drosophila melanogaster
           Suppressor of forked [Su(f)] protein shares homology
           with the yeast RNA14 protein and the 77-kDa subunit of
           human cleavage stimulation factor, which are proteins
           involved in mRNA 3' end formation. This suggests a role
           for Su(f) in mRNA 3' end formation in Drosophila. The
           su(f) gene produces three transcripts; two of them are
           polyadenylated at the end of the transcription unit, and
           one is a truncated transcript, polyadenylated in intron
           4. It is thought that su(f) plays a role in the
           regulation of poly(A) site utilisation and an important
           role of the GU-rich sequence for this regulation to
           occur.
          Length = 275

 Score = 27.3 bits (61), Expect = 1.5
 Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 16/57 (28%)

Query: 32  EQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNKLFGIIAKRYS 88
           E +VT L    E +P+ +K                 SK GD+  + KL     KR  
Sbjct: 94  ETVVTKLTPEPEAKPLWKKF---------IKYE---SKYGDLSSILKL----EKRMF 134


>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 = 27.0 bits (60), Expect = 1.7
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 4/75 (5%)

Query: 30  WHEQIVTTLPKAKELRPIVE---KLVTLGKKGGLHSLRLAISKIGDVDVVNKLFGIIAKR 86
           W  ++++ +   ++   + E   +L+ L K G   ++     K G    V K+      R
Sbjct: 73  WLREVLSQIRNQEDTVVVFESMPELMKLTKLGSF-AMGKPAEKSGMPKPVKKIADKSNGR 131

Query: 87  YSDRSGGYLRIMKRG 101
             D+  GY++++K  
Sbjct: 132 GEDKLAGYMKLLKIV 146


>gnl|CDD|180317 PRK05942, PRK05942, aspartate aminotransferase; Provisional.
          Length = 394

 Score = 26.2 bits (58), Expect = 3.2
 Identities = 17/34 (50%), Positives = 18/34 (52%)

Query: 43  ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVV 76
           EL P  E L  LG K GL  L LA    GDV +V
Sbjct: 93  ELDPDSEALPLLGSKEGLTHLALAYVNPGDVVLV 126


>gnl|CDD|182898 PRK11010, ampG, muropeptide transporter; Validated.
          Length = 491

 Score = 25.8 bits (57), Expect = 3.8
 Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 2/30 (6%)

Query: 71  GDVDVVNKLFGIIAKRYSDRSGGYLRIMKR 100
           G+V +VNK  G++A       GG L  M+R
Sbjct: 258 GEVGLVNKTLGLLATIVGALYGGIL--MQR 285


>gnl|CDD|172445 PRK13932, PRK13932, stationary phase survival protein SurE;
          Provisional.
          Length = 257

 Score = 24.7 bits (54), Expect = 7.1
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 59 GLHSLRLAISKIGDVDVV 76
          G+H L  ++ KIG V VV
Sbjct: 20 GIHVLAASMKKIGRVTVV 37


>gnl|CDD|163500 TIGR03788, marine_srt_targ, marine proteobacterial sortase target
           protein.  Members of this protein family are restricted
           to the Proteobacteria. Each contains a C-terminal
           sortase-recognition motif, transmembrane domain, and
           basic residues cluster at the the C-terminus, and is
           encoded adjacent to a sortase gene. This protein is
           frequently the only sortase target in its genome, which
           is as unusual its occurrence in Gram-negative rather
           than Gram-positive genomes. Many bacteria with this
           system are marine. In addition to the LPXTG signal,
           members carry a vault protein inter-alpha-trypsin
           inhibitor domain (pfam08487) and a von Willebrand factor
           type A domain (pfam00092).
          Length = 596

 Score = 24.7 bits (54), Expect = 7.9
 Identities = 10/32 (31%), Positives = 16/32 (50%)

Query: 7   GRKLNRTSSHRKAMFSNMAASIIWHEQIVTTL 38
           G+K       R  +F+N  A+I   E +V T+
Sbjct: 77  GKKAALVEQQRPNLFTNKVANIGPGETVVVTI 108


>gnl|CDD|182374 PRK10316, PRK10316, hypothetical protein; Provisional.
          Length = 209

 Score = 24.9 bits (54), Expect = 8.2
 Identities = 15/41 (36%), Positives = 20/41 (48%)

Query: 26  ASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLA 66
           AS+   E  V T  K   ++   EK+    KKG +  LRLA
Sbjct: 113 ASVGISEDYVATPEKEAAIKIANEKMAKGDKKGAMEELRLA 153


>gnl|CDD|140343 PTZ00322, PTZ00322,
           6-phosphofructo-2-kinase/fructose-2,6-biphosphatase;
           Provisional.
          Length = 664

 Score = 24.5 bits (53), Expect = 8.4
 Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 4/36 (11%)

Query: 88  SDRSGGYLRIMKRGFRYGDSAPMAVIEFVDRDLSAK 123
           S R GG  R+ +RG  Y      A+ E+  +++S  
Sbjct: 435 SGRIGGNSRLTERGRAYSR----ALFEYFQKEISTT 466


>gnl|CDD|131381 TIGR02328, TIGR02328, conserved hypothetical protein.  Members of
          this protein are found in a small number of
          taxonomically well separated species, yet are strongly
          conserved, suggesting lateral gene transfer. Members
          are found in Treponema denticola, Clostridium
          acetobutylicum, and several of the Firmicutes. The
          function of this protein is unknown.
          Length = 120

 Score = 24.4 bits (53), Expect = 9.5
 Identities = 6/16 (37%), Positives = 12/16 (75%)

Query: 29 IWHEQIVTTLPKAKEL 44
          +WH+ ++T LP+ + L
Sbjct: 3  LWHQSLITKLPRQQLL 18


>gnl|CDD|184052 PRK13435, PRK13435, response regulator; Provisional.
          Length = 145

 Score = 24.6 bits (54), Expect = 9.8
 Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 4/36 (11%)

Query: 81  GIIAKRYSDRSG----GYLRIMKRGFRYGDSAPMAV 112
           G+IAK YS R       YL   + G R     PM V
Sbjct: 100 GVIAKPYSPRGVARALSYLSARRVGDRASGPTPMGV 135


  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
   0.321    0.135    0.382 

Gapped
Lambda     K      H
   0.267   0.0694    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,181,563
Number of extensions: 131043
Number of successful extensions: 259
Number of sequences better than 10.0: 1
Number of HSP's gapped: 258
Number of HSP's successfully gapped: 26
Length of query: 136
Length of database: 5,994,473
Length adjustment: 83
Effective length of query: 53
Effective length of database: 4,201,009
Effective search space: 222653477
Effective search space used: 222653477
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (23.9 bits)