RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780470|ref|YP_003064883.1| translation initiation factor
IF-1 [Candidatus Liberibacter asiaticus str. psy62]
         (110 letters)



>gnl|CDD|178954 PRK00276, infA, translation initiation factor IF-1; Validated.
          Length = 72

 Score =  105 bits (264), Expect = 3e-24
 Identities = 42/110 (38%), Positives = 55/110 (50%), Gaps = 38/110 (34%)

Query: 1   MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
           M KE+ +E  G V E LPNA FRV+L                      E+G E       
Sbjct: 1   MAKEDVIEMEGTVVEALPNAMFRVEL----------------------ENGHE------- 31

Query: 61  PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
                    V+A+ +G+MRK+ IRI  GDKV V ++PYD+T+ RITYR K
Sbjct: 32  ---------VLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72


>gnl|CDD|183529 PRK12442, PRK12442, translation initiation factor IF-1; Reviewed.
          Length = 87

 Score = 81.8 bits (202), Expect = 3e-17
 Identities = 41/110 (37%), Positives = 54/110 (49%), Gaps = 38/110 (34%)

Query: 1   MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
           M KEE +E  GIV E+LP++ FRV L                          E+G     
Sbjct: 1   MAKEELIELDGIVDEVLPDSRFRVTL--------------------------ENG----- 29

Query: 61  PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
                    V AY +GRMRKHRIRI  GD+V + ++PYD+T+ RI +R K
Sbjct: 30  -------VEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72


>gnl|CDD|129120 TIGR00008, infA, translation initiation factor IF-1.  This family
           consists of translation initiation factor IF-1 as found
           in bacteria and chloroplasts. This protein, about 70
           residues in length, consists largely of an S1 RNA
           binding domain (pfam00575).
          Length = 68

 Score = 73.9 bits (182), Expect = 8e-15
 Identities = 39/106 (36%), Positives = 51/106 (48%), Gaps = 38/106 (35%)

Query: 3   KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62
           KE+ +E  G V+E LPNA FRV+L  N                                 
Sbjct: 1   KEDKIEMEGKVTESLPNAMFRVEL-ENGH------------------------------- 28

Query: 63  SYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
                  V+A+ +G++R H IRI  GDKVKV ++PYD+TR RITYR
Sbjct: 29  ------EVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITYR 68


>gnl|CDD|163434 TIGR03722, arch_KAE1, universal archaeal protein Kae1.  This family
           represents the archaeal protein Kae1. Its partner Bud32
           is fused with it in about half of the known archaeal
           genomes. The pair, which appears universal in the
           archaea, corresponds to EKC/KEOPS complex in eukaryotes.
           A recent characterization of the member from Pyrococcus
           abyssi, as an iron-binding, atypical DNA-binding protein
           with an apurinic lyase activity, challenges the common
           annotation of close homologs as O-sialoglycoprotein
           endopeptidase. The latter annotation is based on a
           characterized protein from the bacterium Pasteurella
           haemolytica.
          Length = 322

 Score = 30.3 bits (69), Expect = 0.10
 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)

Query: 61  PISYL-DNAVVIAYTAGRMRKHRIRISLGD 89
           P  Y  DN  +IAYT   M KH + I + +
Sbjct: 277 PPEYAGDNGAMIAYTGLLMYKHGVTIPVEE 306


>gnl|CDD|181985 PRK09605, PRK09605, bifunctional UGMP family
           protein/serine/threonine protein kinase; Validated.
          Length = 535

 Score = 29.1 bits (66), Expect = 0.28
 Identities = 7/24 (29%), Positives = 11/24 (45%)

Query: 66  DNAVVIAYTAGRMRKHRIRISLGD 89
           DN  +IA+    M K    + + D
Sbjct: 286 DNGAMIAWLGLLMYKAGDTLDIED 309


>gnl|CDD|184878 PRK14878, PRK14878, UGMP family protein; Provisional.
          Length = 323

 Score = 28.7 bits (65), Expect = 0.35
 Identities = 9/24 (37%), Positives = 12/24 (50%)

Query: 66  DNAVVIAYTAGRMRKHRIRISLGD 89
           DN  +IAYT     KH + I   +
Sbjct: 282 DNGAMIAYTGLLAYKHGVTIPPEE 305


>gnl|CDD|180392 PRK06084, PRK06084, O-acetylhomoserine
           aminocarboxypropyltransferase; Validated.
          Length = 425

 Score = 26.0 bits (57), Expect = 2.2
 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 12  IVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSES-GSESGN 56
           +++  LP      +   +DD ++ +  +D + K+ F ES G+ +GN
Sbjct: 113 LLAHTLPRIGIETRFAAHDDIAALEALIDERTKAVFCESIGNPAGN 158


>gnl|CDD|162066 TIGR00845, caca, sodium/calcium exchanger 1.  This model is
           specific for the eukaryotic sodium ion/calcium ion
           exchangers of the Caca family.
          Length = 928

 Score = 25.9 bits (57), Expect = 2.3
 Identities = 8/26 (30%), Positives = 14/26 (53%)

Query: 4   EETLEFSGIVSELLPNANFRVKLITN 29
           EE+ EF   V +L+   N  + + T+
Sbjct: 672 EESYEFKSTVDKLIKKTNLALVVGTH 697


>gnl|CDD|179708 PRK04012, PRK04012, translation initiation factor IF-1A;
           Provisional.
          Length = 100

 Score = 25.3 bits (56), Expect = 3.2
 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 76  GRMRKHRIRISLGDKVKVAMNPYDMTRARITYRF 109
           G+M+K R+ I  GD V VA   +   +A I +R+
Sbjct: 52  GKMKK-RMWIREGDVVIVAPWDFQDEKADIIWRY 84


>gnl|CDD|181528 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional.
          Length = 477

 Score = 25.5 bits (57), Expect = 3.4
 Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 3/31 (9%)

Query: 3   KEETLEFSGIVSELLPNANFRVKLITNDDDS 33
           KEE LE++  ++E L  A  RVKL   DD S
Sbjct: 302 KEEVLEYAKELAEELKKAGIRVKL---DDRS 329


>gnl|CDD|182796 PRK10871, nlpD, lipoprotein NlpD; Provisional.
          Length = 319

 Score = 25.2 bits (55), Expect = 4.1
 Identities = 17/38 (44%), Positives = 20/38 (52%), Gaps = 3/38 (7%)

Query: 40  DSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGR 77
           D KV  NFS   SE GN G+D I+      +IA   GR
Sbjct: 205 DGKVIENFS--ASEGGNKGID-IAGSKGQAIIATADGR 239


>gnl|CDD|162469 TIGR01657, P-ATPase-V, P-type ATPase of unknown pump specificity
           (type V).  These P-type ATPases form a distinct clade
           but the substrate of their pumping activity has yet to
           be determined. This clade has been designated type V in.
          Length = 1054

 Score = 25.0 bits (55), Expect = 4.6
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 17/97 (17%)

Query: 3   KEETLEFSGIVSELLPNANFRVKLITNDDDSSA-----DCKLDSK----VKSNFSESGSE 53
           K +T E    V + L  A+ R  +IT D+  +A     +C + +     + +      S 
Sbjct: 658 KPDTKE----VIKELKRASIRTVMITGDNPLTAVHVARECGIVNPSNTLILAEAEPPESG 713

Query: 54  SGN----DGVDPISYLDNAVVIAYTAGRMRKHRIRIS 86
             N    + +D I +    V I Y  G+     +  S
Sbjct: 714 KPNQIKFEVIDSIPFASTQVEIPYPLGQDSVEDLLAS 750


>gnl|CDD|162275 TIGR01263, 4HPPD, 4-hydroxyphenylpyruvate dioxygenase.  This
           protein oxidizes 4-hydroxyphenylpyruvate, a tyrosine and
           phenylalanine catabolite, to homogentisate.
           Homogentisate can undergo a further non-enzymatic
           oxidation and polymerization into brown pigments that
           protect some bacterial species from light. A similar
           process occurs spontaneously in blood and is hemolytic
           (see PubMed:8000039). In some bacterial species, this
           enzyme has been studied as a hemolysin.
          Length = 353

 Score = 24.6 bits (54), Expect = 5.4
 Identities = 8/29 (27%), Positives = 17/29 (58%)

Query: 8   EFSGIVSELLPNANFRVKLITNDDDSSAD 36
           E+S + S ++ + + +VK+  N+  S  D
Sbjct: 195 EYSALNSIVMASPDGKVKIPLNEPASGKD 223


>gnl|CDD|163429 TIGR03717, R_switched_YjbE, integral membrane protein, YjbE
          family.  Rfam model RF00080 describes a structured RNA
          element called the yybP-ykoY leader, or SraF, which may
          precede one or several genes in a genome. Members of
          this highly hydrophobic protein family commonly are
          preceded by a yybP-ykoY leader, which may serve as a
          riboswitch. From the larger group of TerC homologs
          (pfam03741), this subfamily contains protein YjbE from
          Bacillus subtilis. A transport function is proposed.
          Length = 176

 Score = 24.8 bits (55), Expect = 5.5
 Identities = 9/16 (56%), Positives = 10/16 (62%)

Query: 66 DNAVVIAYTAGRMRKH 81
          DNAVVIA  A  +  H
Sbjct: 15 DNAVVIALAARNLPAH 30


>gnl|CDD|152593 pfam12158, DUF3592, Protein of unknown function (DUF3592).  This
           family of proteins is functionally uncharacterized.This
           family of proteins is found in bacteria, archaea,
           eukaryotes and viruses. Proteins in this family are
           typically between 150 and 242 amino acids in length.
          Length = 134

 Score = 24.7 bits (54), Expect = 5.6
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 9/50 (18%)

Query: 69  VVIAYTA--GRMRKHRIRIS-------LGDKVKVAMNPYDMTRARITYRF 109
            V+ +    GR  + R           +G++V V  +P +  +ARI  R 
Sbjct: 60  PVVEFRYDDGRRIRFRSGSGSNPPGYRVGERVPVYYDPDNPEQARIDRRG 109


>gnl|CDD|165300 PHA02999, PHA02999, Hypothetical protein; Provisional.
          Length = 382

 Score = 24.3 bits (53), Expect = 6.5
 Identities = 9/18 (50%), Positives = 14/18 (77%)

Query: 92  KVAMNPYDMTRARITYRF 109
           KV++NPY MT++ + Y F
Sbjct: 170 KVSVNPYSMTKSLMNYMF 187


>gnl|CDD|181794 PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated.
          Length = 263

 Score = 24.4 bits (54), Expect = 6.8
 Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 4/39 (10%)

Query: 43  VKSNFSE----SGSESGNDGVDPISYLDNAVVIAYTAGR 77
           ++ N SE    +G  +   GVD      +AV IA  A +
Sbjct: 116 IRGNASEIAALAGEAAETKGVDSTDGSADAVEIAKAAAK 154


  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
   0.315    0.132    0.365 

Gapped
Lambda     K      H
   0.267   0.0757    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,698,218
Number of extensions: 90843
Number of successful extensions: 185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 185
Number of HSP's successfully gapped: 32
Length of query: 110
Length of database: 5,994,473
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,352,265
Effective search space: 147977010
Effective search space used: 147977010
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 (21.5 bits)
S2: 50 (23.0 bits)