RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780128|ref|YP_003064541.1| VRR-NUC domain-containing
protein [Candidatus Liberibacter asiaticus str. psy62]
         (103 letters)



>gnl|CDD|37354 KOG2143, KOG2143, KOG2143, Uncharacterized conserved protein
           [Function unknown].
          Length = 854

 Score = 33.1 bits (75), Expect = 0.017
 Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 37  RRGCPDRLIITPNGG-LWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKV 84
           R G PD  +  P       +EVK P  RLS +Q   +  L   G RV+V
Sbjct: 794 RSGFPDLTLWNPETKRFKLVEVKGPNDRLSEKQRLWLALLADSGIRVEV 842


>gnl|CDD|145010 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase.  The enzyme
           methylmalonyl-CoA mutase is a member of a class of
           enzymes that uses coenzyme B12 (adenosylcobalamin) as a
           cofactor. The enzyme induces the formation of an
           adenosyl radical from the cofactor. This radical then
           initiates a free-radical rearrangement of its substrate,
           succinyl-CoA, to methylmalonyl-CoA.
          Length = 517

 Score = 28.5 bits (64), Expect = 0.43
 Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 45  IITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVS 87
           +I P GG +++E  + T R++ +     +E+   G   K +  
Sbjct: 362 VIDPWGGSYYVE--ELTDRIAEEAWKLFQEIEEAGGMAKAIED 402


>gnl|CDD|32093 COG1909, COG1909, Uncharacterized protein conserved in archaea
           [Function unknown].
          Length = 167

 Score = 27.5 bits (61), Expect = 0.80
 Identities = 12/36 (33%), Positives = 22/36 (61%)

Query: 55  IEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEE 90
           I+V+ P G ++ + +  IE+    G+RV++ V  EE
Sbjct: 82  IKVRNPPGTITFELIKAIEKALEDGKRVRIFVDGEE 117


>gnl|CDD|146188 pfam03419, Peptidase_U4, Sporulation factor SpoIIGA. 
          Length = 291

 Score = 26.8 bits (60), Expect = 1.3
 Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 2/34 (5%)

Query: 41  PDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEE 74
           PDR+ I        IEV+K    +S +++S   E
Sbjct: 250 PDRVKIEHEKE--KIEVRKVLIGISDEKLSSDGE 281


>gnl|CDD|146789 pfam04337, DUF480, Protein of unknown function, DUF480.  This
           family consists of several proteins of uncharacterized
           function.
          Length = 148

 Score = 26.4 bits (59), Expect = 1.7
 Identities = 12/26 (46%), Positives = 16/26 (61%)

Query: 74  ELRRRGQRVKVLVSMEEVDNFLEELA 99
           ELR R +R+     + EV+  LEELA
Sbjct: 107 ELRTRSERLHRFADVAEVEAVLEELA 132


>gnl|CDD|146579 pfam04019, DUF359, Protein of unknown function (DUF359).  This
          family of archaebacterial proteins are about 170 amino
          acids in length. They have no known function. The most
          conserved portion of the protein contains the sequence
          GEEDL that may be important for its function.
          Length = 121

 Score = 26.4 bits (59), Expect = 2.1
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 55 IEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEE 90
          I VK P G ++ + +  I+E    G+ V + V  EE
Sbjct: 37 ITVKNPPGTITEELIEAIKEALESGKPVVIFVDGEE 72


>gnl|CDD|146216 pfam03460, NIR_SIR_ferr, Nitrite/Sulfite reductase
          ferredoxin-like half domain.  Sulfite and Nitrite
          reductases are key to both biosynthetic assimilation of
          sulfur and nitrogen and dissimilation of oxidized
          anions for energy transduction. Two copies of this
          repeat are found in Nitrite and Sulfite reductases and
          form a single structural domain.
          Length = 67

 Score = 25.2 bits (56), Expect = 3.7
 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 11/60 (18%)

Query: 51 GLWWIEVKKPTGRLSHQQMSEIEEL-RRRG---------QRVKVL-VSMEEVDNFLEELA 99
          G + + V+ P GRL+ +Q+  + ++  + G         Q +++  V  E++   LEELA
Sbjct: 6  GDYMVRVRVPGGRLTAEQLRALADIAEKYGDGEIRLTTRQNLELHGVPEEDLPELLEELA 65


>gnl|CDD|112137 pfam03308, ArgK, ArgK protein.  The ArgK protein acts as an
          ATPase enzyme and as a kinase, and phosphorylates
          periplasmic binding proteins involved in the LAO
          (lysine, arginine, ornithine)/AO transport systems.
          Length = 267

 Score = 25.0 bits (55), Expect = 4.2
 Identities = 10/14 (71%), Positives = 10/14 (71%)

Query: 72 IEELRRRGQRVKVL 85
            ELRRRG RV VL
Sbjct: 50 GMELRRRGHRVAVL 63


>gnl|CDD|31172 COG0830, UreF, Urease accessory protein UreF [Posttranslational
           modification, protein turnover, chaperones].
          Length = 229

 Score = 24.8 bits (54), Expect = 4.6
 Identities = 20/103 (19%), Positives = 36/103 (34%), Gaps = 20/103 (19%)

Query: 4   YSFHYQTEKDVEKRLVTGAKKLDCWVRKASFVG------------RRGCPDRLIITPNGG 51
           +S+ +  E  ++  +VT A  L+ W++     G             R   D         
Sbjct: 23  FSYSFGLETAIQAGIVTDAATLEAWLKTQLNQGLLYNDALLLALAYRALLDDDAEALLEA 82

Query: 52  LWWIEVKKPTGRLSHQQMSEIEELRRRGQR-VKVLVSMEEVDN 93
              +  +K   R         EE RR G+  +K+  ++ E D 
Sbjct: 83  DELLFAQKLA-RELR------EESRRMGRALLKLARALWEDDP 118


>gnl|CDD|31678 COG1489, SfsA, DNA-binding protein, stimulates sugar fermentation
           [General function prediction only].
          Length = 235

 Score = 24.8 bits (54), Expect = 4.9
 Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 17/69 (24%)

Query: 42  DRLIITPNGGLWWIEVKK--------------PTGRLSHQQMSEIEELRRRGQRVKVL-- 85
           D L+        ++EVK               PT R   + + E+E L + G R  VL  
Sbjct: 117 DFLLDDDERPDCYVEVKSVTLVENGVAMFPDAPTAR-GQKHLRELERLAKEGYRAVVLFL 175

Query: 86  VSMEEVDNF 94
           V   ++  F
Sbjct: 176 VLRSDITRF 184


>gnl|CDD|119349 cd00598, GH18_chitinase-like, The GH18 (glycosyl hydrolase,
          family 18) type II chitinases hydrolyze chitin, an
          abundant polymer of beta-1,4-linked N-acetylglucosamine
          (GlcNAc) which is a major component of the cell wall of
          fungi and the exoskeleton of arthropods.  Chitinases
          have been identified in viruses, bacteria, fungi,
          protozoan parasites, insects, and plants. The structure
          of the GH18 domain is an eight-stranded beta/alpha
          barrel with a pronounced active-site cleft at the
          C-terminal end of the beta-barrel.  The GH18 family
          includes chitotriosidase, chitobiase, hevamine,
          zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting
          chitinase-like protein), IDGF (imaginal disc growth
          factor), CFLE (cortical fragment-lytic enzyme) spore
          hydrolase, the type III and type V plant chitinases,
          the endo-beta-N-acetylglucosaminidases, and the
          chitolectins.  The GH85 (glycosyl hydrolase, family 85)
          ENGases (endo-beta-N-acetylglucosaminidases) are
          closely related to the GH18 chitinases and are included
          in this alignment model..
          Length = 210

 Score = 25.0 bits (55), Expect = 5.1
 Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 5/45 (11%)

Query: 44 LIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSM 88
            I+ +G L     K             +EEL  +   +KVL+S+
Sbjct: 32 AEISSDGSLNLFGDKSEE-----PLKGALEELASKKPGLKVLISI 71


>gnl|CDD|88453 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is
          a trans-acting factor important for biogenesis of both
          the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
          two distinct regions, an N-terminal region containing
          tandemly repeated S1 RNA-binding domains (12 S1 repeats
          in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
          Homo sapiens Rrp5) and a C-terminal region containing
          tetratricopeptide repeat (TPR) motifs thought to be
          involved in protein-protein interactions. Mutational
          studies have shown that each region represents a
          specific functional domain. Deletions within the
          S1-containing region inhibit pre-rRNA processing at
          either site A3 or A2, whereas deletions within the TPR
          region confer an inability to support cleavage of
          A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6)
          and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in
          eukaryotes but not in prokaryotes or archaea..
          Length = 70

 Score = 24.7 bits (54), Expect = 6.1
 Identities = 12/27 (44%), Positives = 14/27 (51%)

Query: 60 PTGRLSHQQMSEIEELRRRGQRVKVLV 86
          P   LS   + + EE  R GQ VKV V
Sbjct: 29 PKSELSEAFIKDPEEHFRVGQVVKVKV 55


>gnl|CDD|114509 pfam05787, DUF839, Bacterial protein of unknown function (DUF839). 
           This family consists of several bacterial proteins of
           unknown function that contain a predicted beta-propeller
           repeats.
          Length = 515

 Score = 24.4 bits (53), Expect = 6.3
 Identities = 6/15 (40%), Positives = 7/15 (46%)

Query: 39  GCPDRLIITPNGGLW 53
             PD +   P G LW
Sbjct: 429 ESPDNITFDPAGRLW 443


>gnl|CDD|145596 pfam02540, NAD_synthase, NAD synthase.  NAD synthase (EC:6.3.5.1)
           is involved in the de novo synthesis of NAD and is
           induced by stress factors such as heat shock and glucose
           limitation.
          Length = 243

 Score = 24.6 bits (54), Expect = 6.6
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 23/71 (32%)

Query: 28  WVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVS 87
            V + +   R   P+R+I            K P+  L   Q  E +EL          ++
Sbjct: 158 QVYELA--KRLNVPERII-----------KKPPSADLWPGQTDE-DELG---------IT 194

Query: 88  MEEVDNFLEEL 98
            +E+D  L+ L
Sbjct: 195 YDELDQILKGL 205


>gnl|CDD|34143 COG4465, CodY, Pleiotropic transcriptional repressor
           [Transcription].
          Length = 261

 Score = 24.4 bits (53), Expect = 6.8
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 6/41 (14%)

Query: 64  LSHQQMSEIEELRRRGQRVKVLVS------MEEVDNFLEEL 98
           +  +++ EIEE  R+   V++ +S      +E V++  EEL
Sbjct: 158 ILREKLEEIEEEARKRTVVQMAISTLSYSELEAVEHIFEEL 198


>gnl|CDD|144562 pfam01019, G_glu_transpept, Gamma-glutamyltranspeptidase. 
          Length = 506

 Score = 24.5 bits (54), Expect = 6.9
 Identities = 7/22 (31%), Positives = 10/22 (45%)

Query: 70  SEIEELRRRGQRVKVLVSMEEV 91
             + EL  RG +VKV+      
Sbjct: 462 EVLAELEARGHKVKVVPVSSGG 483


>gnl|CDD|38935 KOG3731, KOG3731, KOG3731, Sulfatases [Carbohydrate transport and
           metabolism].
          Length = 541

 Score = 24.2 bits (52), Expect = 8.2
 Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 1/46 (2%)

Query: 53  WWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEEL 98
           W +    P     H   + I   +R      V  S+E + N L EL
Sbjct: 252 WILRTTGPMSN-IHIPFTNILPRKRLQTLQSVDDSVERLYNLLGEL 296


>gnl|CDD|36071 KOG0853, KOG0853, KOG0853, Glycosyltransferase [Cell
          wall/membrane/envelope biogenesis].
          Length = 495

 Score = 24.1 bits (52), Expect = 8.3
 Identities = 10/47 (21%), Positives = 16/47 (34%)

Query: 43 RLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSME 89
             I P+ G+   E       +      ++  L   G +V  L S E
Sbjct: 37 VTFIHPDLGIGGAERLVVDAAVHLLSGQDVLGLPDTGGQVVYLTSHE 83


>gnl|CDD|145985 pfam03129, HGTP_anticodon, Anticodon binding domain.  This domain
          is found in histidyl, glycyl, threonyl and prolyl tRNA
          synthetases it is probably the anticodon binding
          domain.
          Length = 93

 Score = 24.1 bits (53), Expect = 8.7
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 74 ELRRRGQRVKVLVSMEEVDNFLEEL 98
           +R R    K  VS+EE+   L+EL
Sbjct: 69 TVRDRDTGEKETVSLEELVEKLKEL 93


>gnl|CDD|30902 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
           [DNA replication, recombination, and repair].
          Length = 663

 Score = 24.0 bits (52), Expect = 8.9
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 5/48 (10%)

Query: 55  IEVKKPTGRLSHQQMSEIEELRRRGQRVKVLV---SM-EEVDNFLEEL 98
           IEV+   G++    +SEI +   + +RV V      M E++  +L+EL
Sbjct: 423 IEVRPTKGQVD-DLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKEL 469


>gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
           replication, recombination, and repair /
           Posttranslational modification, protein turnover,
           chaperones].
          Length = 366

 Score = 24.2 bits (52), Expect = 9.0
 Identities = 13/94 (13%), Positives = 30/94 (31%), Gaps = 2/94 (2%)

Query: 10  TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM 69
           T K    + V    +      +  ++          +     +     K P    S  ++
Sbjct: 53  TGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSK--ILNKLGKVPLTGDSSLEI 110

Query: 70  SEIEELRRRGQRVKVLVSMEEVDNFLEELACTLY 103
            +        +   V+V ++EVD  +++    LY
Sbjct: 111 LKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLY 144


  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
   0.322    0.137    0.428 

Gapped
Lambda     K      H
   0.267   0.0612    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,304,629
Number of extensions: 61921
Number of successful extensions: 219
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 25
Length of query: 103
Length of database: 6,263,737
Length adjustment: 70
Effective length of query: 33
Effective length of database: 4,751,107
Effective search space: 156786531
Effective search space used: 156786531
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 (21.9 bits)
S2: 51 (23.7 bits)