RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780164|ref|YP_003064577.1| ATP-dependent Clp protease
adaptor protein ClpS [Candidatus Liberibacter asiaticus str. psy62]
         (138 letters)



>gnl|CDD|32310 COG2127, COG2127, Uncharacterized conserved protein [Function
           unknown].
          Length = 107

 Score =  117 bits (294), Expect = 1e-27
 Identities = 42/88 (47%), Positives = 60/88 (68%)

Query: 51  SSKVRVPKLYRVLLVNDNYTPMEFVIHVLQNFFYKDHETAKCIMLKVHHQGIGECGVYAY 110
            +K + PK+Y+V+L+ND+YTPMEFV++VLQ FF    E A  +ML+VH +G    GVY  
Sbjct: 20  KTKTKPPKMYKVILLNDDYTPMEFVVYVLQKFFGMSEERATKLMLQVHREGKAVVGVYTR 79

Query: 111 EIAEMKVNQVMNYSRQHQYPLQCIMEQK 138
           E+AE KV QV +   +  +PL C ME++
Sbjct: 80  EVAETKVAQVRDAGLEATHPLLCTMEEE 107


>gnl|CDD|145654 pfam02617, ClpS, ATP-dependent Clp protease adaptor protein ClpS.
           In the bacterial cytosol, ATP-dependent protein
           degradation is performed by several different
           chaperone-protease pairs, including ClpAP. ClpS directly
           influences the ClpAP machine by binding to the
           N-terminal domain of the chaperone ClpA. The degradation
           of ClpAP substrates, both SsrA-tagged proteins and ClpA
           itself, is specifically inhibited by ClpS. ClpS modifies
           ClpA substrate specificity, potentially redirecting
           degradation by ClpAP toward aggregated proteins.
          Length = 78

 Score =  104 bits (263), Expect = 6e-24
 Identities = 38/79 (48%), Positives = 48/79 (60%), Gaps = 4/79 (5%)

Query: 57  PKLYRVLLVNDNYTPMEFVIHVLQNFFYKDHETAKCIMLKVHHQGIGECGVYAYEIAEMK 116
           P +Y+V+L+ND+YT MEFV+ VLQ  F    E A  IML+VH +G    GV   EIAE K
Sbjct: 4   PPMYKVILLNDDYTTMEFVVEVLQKVFGMSEEQATQIMLEVHKEGRAVVGVGTREIAETK 63

Query: 117 VNQVMNYSRQHQYPLQCIM 135
           V QV  Y R    PL+  +
Sbjct: 64  VAQVHAYGR----PLRATI 78


>gnl|CDD|35442 KOG0221, KOG0221, KOG0221, Mismatch repair ATPase MSH5 (MutS
           family) [Replication, recombination and repair].
          Length = 849

 Score = 25.7 bits (56), Expect = 3.9
 Identities = 6/36 (16%), Positives = 18/36 (50%)

Query: 54  VRVPKLYRVLLVNDNYTPMEFVIHVLQNFFYKDHET 89
           + +P+L  ++  +D    ++F+    +   Y++  T
Sbjct: 462 LSIPRLPSMVEASDFENGLDFMFLSEEKLHYRNART 497


>gnl|CDD|73303 cd02062, Nitro_FMN_reductase, Proteins of this family catalyze the
           reduction of flavin or nitrocompounds using NAD(P)H as
           electron donor in a obligatory two-electron transfer,
           utilizing FMN or FAD as cofactor. They are often found
           to be homodimers. Enzymes of this family are described
           as NAD(P)H:FMN oxidoreductases, oxygen-insensitive
           nitroreductase, flavin reductase P, dihydropteridine
           reductase, NADH oxidase or NADH dehydrogenase..
          Length = 122

 Score = 25.6 bits (56), Expect = 4.7
 Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 8/76 (10%)

Query: 48  VRFSSKVRVPKLYRVLLVNDNYTPMEFVIHVLQNFFYKDHE-TAKCIMLKVHHQGIGECG 106
            RF      P L  V    D   P          +   D    A+ I+L  H  G+G C 
Sbjct: 39  WRFVVVYGAPVLIIVCADKDAARPSGP-------WAEADAGIAAQNILLAAHALGLGSCW 91

Query: 107 VYAYEIAEMKVNQVMN 122
           +   ++ E ++ +++ 
Sbjct: 92  IGGLDLVEEELRELLG 107


>gnl|CDD|173665 cd05574, STKc_phototropin_like, Catalytic domain of
           Phototropin-like Protein Serine/Threonine Kinases.
           Serine/Threonine Kinases (STKs), Phototropin-like
           subfamily, catalytic (c) domain. STKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           serine/threonine residues on protein substrates. The
           phototropin-like subfamily is part of a larger
           superfamily that includes the catalytic domains of other
           protein STKs, protein tyrosine kinases, RIO kinases,
           aminoglycoside phosphotransferase, choline kinase, and
           phosphoinositide 3-kinase. Included in this subfamily
           are plant phototropins and predominantly uncharacterized
           fungal STKs whose catalytic domains resemble the
           phototropin kinase domain. One protein from Neurospora
           crassa is called nrc-2. Phototropins are blue-light
           receptors that control responses such as phototropism,
           stromatal opening, and chloroplast movement in order to
           optimize the photosynthetic efficiency of plants. They
           are light-activated STKs that contain an N-terminal
           photosensory domain and a C-terminal catalytic domain.
           The N-terminal domain contains two LOV (Light, Oxygen or
           Voltage) domains that binds FMN. Photoexcitation of the
           LOV domains results in autophosphorylation at multiple
           sites and activation of the catalytic domain. Neurospora
           crassa nrc-2 plays a role in growth and development by
           controlling entry into the conidiation program.
          Length = 316

 Score = 24.9 bits (55), Expect = 8.2
 Identities = 13/32 (40%), Positives = 13/32 (40%), Gaps = 4/32 (12%)

Query: 40  FDNCLDSEVRFSSKVRVPK----LYRVLLVND 67
           F N L  EV F     V      L R LLV D
Sbjct: 241 FSNILKKEVTFPGSPPVSSSARDLIRKLLVKD 272


  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
   0.327    0.139    0.421 

Gapped
Lambda     K      H
   0.267   0.0850    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,662,785
Number of extensions: 79017
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 179
Number of HSP's successfully gapped: 12
Length of query: 138
Length of database: 6,263,737
Length adjustment: 84
Effective length of query: 54
Effective length of database: 4,448,581
Effective search space: 240223374
Effective search space used: 240223374
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (23.6 bits)