RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780496|ref|YP_003064909.1| integration host factor
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
         (114 letters)



>gnl|CDD|143973 pfam00216, Bac_DNA_binding, Bacterial DNA-binding protein. 
          Length = 90

 Score = 89.9 bits (224), Expect = 1e-19
 Identities = 31/89 (34%), Positives = 59/89 (66%)

Query: 5  ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64
          +T+ +L+K+I+++ GLS+KD+   V    + I ++  +GE +++  F TF V+++ +R G
Sbjct: 1  MTKKELIKAIAEKTGLSKKDAEAIVDAFLDVITEALKKGEKVELRGFGTFEVRERKARTG 60

Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          RN +T +E+KI  ++VV FK    LK+ +
Sbjct: 61 RNPKTGEEIKIPAKKVVKFKPGKELKEAV 89


>gnl|CDD|29683 cd00591, HU_IHF, Integration host factor (IHF) and HU are small
          heterodimeric members of the DNABII protein family that
          bind and bend DNA, functioning as architectural factors
          in many cellular processes including transcription,
          site-specific recombination, and higher-order
          nucleoprotein complex assembly. The dimer subunits
          associate to form a compact globular core from which
          two beta ribbon arms (one from each subunit) protrude.
          The beta arms track and bind the DNA minor groove.
          Despite sequence and structural similarity, IHF and HU
          can be distinguished by their different DNA substrate
          preferences..
          Length = 87

 Score = 87.4 bits (217), Expect = 7e-19
 Identities = 31/87 (35%), Positives = 57/87 (65%)

Query: 6  TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65
          T+S+L+++I+++ GLS+KD+   V    + I ++  +GE +++  F TF V+++ +R GR
Sbjct: 1  TKSELIEAIAEKTGLSKKDAEAAVDAFLDVITEALAKGEKVELPGFGTFEVRERAARTGR 60

Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKR 92
          N +T +E+KI  ++VV FK    LK  
Sbjct: 61 NPKTGEEIKIPAKKVVKFKPGKALKDA 87


>gnl|CDD|31119 COG0776, HimA, Bacterial nucleoid DNA-binding protein [DNA
          replication, recombination, and repair].
          Length = 94

 Score = 86.7 bits (215), Expect = 1e-18
 Identities = 32/90 (35%), Positives = 58/90 (64%)

Query: 4  TITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRV 63
          T+T+S+L+ +I+++ GLS+KD+   V     EI ++  +GE +++  F TF V+++ +R 
Sbjct: 1  TMTKSELIDAIAEKAGLSKKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRERAART 60

Query: 64 GRNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          GRN +T +E+KI  ++V  FK    LK  +
Sbjct: 61 GRNPKTGEEIKIPAKKVPKFKPGKALKDAV 90


>gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. 
          Length = 168

 Score = 26.4 bits (59), Expect = 1.8
 Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 30 TTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNL 67
          TTL  ++ +  ++ E +K+  F T  V++ G R+G ++
Sbjct: 13 TTLVKKVIE-LLKSEGVKVGGFYTPEVREGGRRIGFDI 49


>gnl|CDD|37330 KOG2119, KOG2119, KOG2119, Predicted bile acid beta-glucosidase
          [Carbohydrate transport and metabolism].
          Length = 879

 Score = 25.0 bits (54), Expect = 4.8
 Identities = 11/43 (25%), Positives = 19/43 (44%)

Query: 16 KEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQ 58
          +EF LS +++ + V  L+    + A  G    I  F   + K 
Sbjct: 40 REFFLSIREAIKLVPRLWLYTREEAWNGRKAFIDIFNKENHKS 82


>gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor)
            [Signal transduction mechanisms].
          Length = 5019

 Score = 25.0 bits (54), Expect = 4.9
 Identities = 16/49 (32%), Positives = 24/49 (48%)

Query: 44   EAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASSILKKR 92
            E +   + A FH++QK  RVGR      E  +  ++ V  K  S  +KR
Sbjct: 3572 ERVLDIAAALFHLEQKSKRVGRRHYCLVEHPLRSKKAVWHKLLSKQRKR 3620


>gnl|CDD|144883 pfam01454, MAGE, MAGE family.  The MAGE (melanoma
          antigen-encoding gene) family are expressed in a wide
          variety of tumours but not in normal cells, with the
          exception of the male germ cells, placenta, and,
          possibly, cells of the developing embryo. The cellular
          function of this family is unknown. This family also
          contains the yeast protein, Nse3. The Nse3 protein is
          part of the Smc5-6 complex. Nse3 has been demonstrated
          to be important for meiosis.
          Length = 171

 Score = 24.5 bits (54), Expect = 6.1
 Identities = 6/18 (33%), Positives = 13/18 (72%)

Query: 1  MSKTITRSDLVKSISKEF 18
            + ITR++++K + KE+
Sbjct: 11 KKEPITRAEILKIVIKEY 28


>gnl|CDD|144535 pfam00977, His_biosynth, Histidine biosynthesis protein.  Proteins
           involved in steps 4 and 6 of the histidine biosynthesis
           pathway are contained in this family. Histidine is
           formed by several complex and distinct biochemical
           reactions catalysed by eight enzymes. The enzymes in
           this Pfam entry are called His6 and His7 in eukaryotes
           and HisA and HisF in prokaryotes. The structure of HisA
           is known to be a TIM barrel fold. In some archaeal HisA
           proteins the TIM barrel is composed of two tandem
           repeats of a half barrel. This family belong to the
           common phosphate binding site TIM barrel family.
          Length = 229

 Score = 24.4 bits (54), Expect = 7.5
 Identities = 4/18 (22%), Positives = 11/18 (61%)

Query: 2   SKTITRSDLVKSISKEFG 19
           +  +   +L+K  +++FG
Sbjct: 103 TAAVKNPELIKEAAEKFG 120


>gnl|CDD|147677 pfam05648, PEX11, Peroxisomal biogenesis factor 11 (PEX11).  This
          family consists of several peroxisomal biogenesis
          factor 11 (PEX11) proteins from several eukaryotic
          species. The PEX11 peroxisomal membrane proteins
          promote peroxisome division in multiple eukaryotes.
          Length = 225

 Score = 24.1 bits (53), Expect = 8.2
 Identities = 7/22 (31%), Positives = 12/22 (54%)

Query: 2  SKTITRSDLVKSISKEFGLSRK 23
            +    D +K++  +F LSRK
Sbjct: 36 GSSPELIDRLKNLESQFSLSRK 57


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.318    0.131    0.355 

Gapped
Lambda     K      H
   0.267   0.0752    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,175,798
Number of extensions: 49947
Number of successful extensions: 107
Number of sequences better than 10.0: 1
Number of HSP's gapped: 107
Number of HSP's successfully gapped: 10
Length of query: 114
Length of database: 6,263,737
Length adjustment: 80
Effective length of query: 34
Effective length of database: 4,535,017
Effective search space: 154190578
Effective search space used: 154190578
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: 51 (23.4 bits)