RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780807|ref|YP_003065220.1| glucose-inhibited division
protein B [Candidatus Liberibacter asiaticus str. psy62]
         (168 letters)



>gnl|CDD|30706 COG0357, GidB, Predicted S-adenosylmethionine-dependent
           methyltransferase involved in bacterial cell division
           [Cell envelope biogenesis, outer membrane].
          Length = 215

 Score =  133 bits (336), Expect = 2e-32
 Identities = 56/146 (38%), Positives = 80/146 (54%), Gaps = 5/146 (3%)

Query: 21  VSRETLEKLEYFYFLFLKWSKKINLVSSSTVEDFWIRHVEDSLRVFQ-LHPYPSIWIDLG 79
           V+ E LEKLE +  L LKW+K  NL +    E+ W RH+ DSL +   L       +D+G
Sbjct: 16  VTEEQLEKLEAYVELLLKWNKAYNLTAIRDPEELWQRHILDSLVLLPYLDGKAKRVLDIG 75

Query: 80  SGGGFPGIITSIQLSSIEGGLVNLIESKNKKASFLRYVVQKTAARG-KVFACRIQEAPQM 138
           SG GFPGI  +I    ++   V L+ES  KK +FLR V ++      ++   R +E  Q 
Sbjct: 76  SGAGFPGIPLAIAFPDLK---VTLLESLGKKIAFLREVKKELGLENVEIVHGRAEEFGQE 132

Query: 139 ITTCDVISARALADLDTLLEYSFPWL 164
               DV+++RA+A L+ LLE   P L
Sbjct: 133 KKQYDVVTSRAVASLNVLLELCLPLL 158


>gnl|CDD|111429 pfam02527, GidB, rRNA small subunit methyltransferase G.  This is a
           family of bacterial glucose inhibited division proteins
           these are probably involved in the regulation of cell
           devision. GidB has been shown to be a methyltransferase
           G specific to the rRNA small subunit. Previously
           identified as a glucose-inhibited division protein B
           that appears to be present and in a single copy in all
           complete eubacterial genomes so far sequenced. GidB
           specifically methylates the N7 position of a guanosine
           in 16S rRNA.
          Length = 184

 Score =  112 bits (282), Expect = 5e-26
 Identities = 49/140 (35%), Positives = 72/140 (51%), Gaps = 4/140 (2%)

Query: 26  LEKLEYFYFLFLKWSKKINLVSSSTVEDFWIRHVEDSLRVFQ-LHPYPSIWIDLGSGGGF 84
           LEKLE +  L L+W+K+ NL S +   +   RH+ DSL V + L        D+GSG GF
Sbjct: 2   LEKLELYVQLLLEWNKRYNLTSITEPNELLERHLLDSLVVLEYLDNIRIKVADVGSGAGF 61

Query: 85  PGIITSIQLSSIEGGLVNLIESKNKKASFLRYVVQKTAARGKVFACRIQEAPQMITTCDV 144
           PGI  +I     +   + L+ES  KK +FL  + ++             E  Q     DV
Sbjct: 62  PGIPLAIAFPDKK---LTLLESLLKKINFLEELKKELNLENVTIVHARAEEYQHEEQYDV 118

Query: 145 ISARALADLDTLLEYSFPWL 164
           I++RA+A L+ L E++ P L
Sbjct: 119 ITSRAVASLNELTEWALPLL 138


>gnl|CDD|36352 KOG1137, KOG1137, KOG1137, mRNA cleavage and polyadenylation factor
           II complex, BRR5 (CPSF subunit) [RNA processing and
           modification].
          Length = 668

 Score = 27.2 bits (60), Expect = 2.1
 Identities = 11/43 (25%), Positives = 18/43 (41%)

Query: 114 LRYVVQKTAARGKVFACRIQEAPQMITTCDVISARALADLDTL 156
           L + +QKT+  G+VF     +A       D +     +  D L
Sbjct: 82  LPFTLQKTSFIGRVFMTHPTKAIYKWLLSDYVRVSNRSGDDRL 124


>gnl|CDD|38004 KOG2793, KOG2793, KOG2793, Putative N2,N2-dimethylguanosine tRNA
           methyltransferase [RNA processing and modification].
          Length = 248

 Score = 26.9 bits (59), Expect = 2.5
 Identities = 23/127 (18%), Positives = 36/127 (28%), Gaps = 12/127 (9%)

Query: 45  LVSSSTVEDFWIRHVEDSLRVFQLHPYPSIWIDLGSGGGFPGIITSIQLSSIEGGLVNLI 104
             + +       R  E +  +          ++LGSG G  GI+ ++ L    G  V L 
Sbjct: 60  ATTLAQPLWERRRDSELTATLIGFKTKYINVLELGSGTGLVGILAALLL----GAEVVL- 114

Query: 105 ESKNKKASFLRYVVQKTAARGKVFACRIQ-------EAPQMITTCDVISARALADLDTLL 157
               K    L++   K           +         A  +           LA      
Sbjct: 115 TDLPKVVENLKFNRDKNNIALNQLGGSVIVAILVWGNALDVSFRLPNPFDLILASDVVYE 174

Query: 158 EYSFPWL 164
           E SF  L
Sbjct: 175 EESFEGL 181


>gnl|CDD|38897 KOG3693, KOG3693, KOG3693, Uncharacterized conserved protein
           [Function unknown].
          Length = 1117

 Score = 26.7 bits (58), Expect = 3.0
 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 37  LKWSKKINLVSSSTVEDF-WIRHVEDSLRVFQLHPYPSIWIDLGSGGG 83
           L W   ++    +T + F  +RH+  +    Q HPY  +W  LG   G
Sbjct: 432 LGWVTTVSRSIMTTPKAFSRVRHISITFGEAQHHPYNDLWAQLGDLYG 479


>gnl|CDD|35630 KOG0409, KOG0409, KOG0409, Predicted dehydrogenase [General
           function prediction only].
          Length = 327

 Score = 26.8 bits (59), Expect = 3.1
 Identities = 23/117 (19%), Positives = 47/117 (40%), Gaps = 23/117 (19%)

Query: 6   SNSILRANYLLNTYNVSRETLEKLEYFYFLFLKWSKKINLVSSSTVEDFWIRHVEDSLRV 65
            +++++A Y +  Y+ +++  ++ +          +    V++S  E       EDS  V
Sbjct: 51  VSNLIKAGYKVTVYDRTKDKCKEFQ----------EAGARVANSPAE-----VAEDSDVV 95

Query: 66  FQLHPYPSIWIDLGSG------GGFPGIITSIQLSSIEGGLVNLI--ESKNKKASFL 114
             + P P    D+  G      G  PG   ++ +S+I+      I     NK   F+
Sbjct: 96  ITMVPNPKDVKDVLLGKSGVLSGIRPGKKATVDMSTIDPDTSLEIAKAISNKGGRFV 152


>gnl|CDD|143381 cd07876, STKc_JNK2, Catalytic domain of the Serine/Threonine
           Kinase, c-Jun N-terminal Kinase 2.  Serine/Threonine
           Kinases (STKs), c-Jun N-terminal kinase 2 (JNK2)
           subfamily, catalytic (c) domain. STKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           serine/threonine residues on protein substrates. The
           JNK2 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. JNKs are mitogen-activated protein kinases
           (MAPKs) that are involved in many stress-activated
           responses including those during inflammation,
           neurodegeneration, apoptosis, and persistent pain
           sensitization, among others. Vetebrates harbor three
           different JNK genes (Jnk1, Jnk2, and Jnk3). JNK1, like
           JNK2, is expressed in every cell and tissue type.
           Initially it was thought that JNK1 and JNK2 were
           functionally redundant as mice deficient in either genes
           (Jnk1 or Jnk2) could survive but disruption of both
           genes resulted in lethality. However, recent studies
           have shown that JNK1 and JNK2 perform distinct functions
           through specific binding partners and substrates.  JNK2
           is specifically translocated to the mitochondria during
           dopaminergic cell death. Specific substrates include the
           microtubule-associated proteins DCX and Tau, as well as
           TIF-IA which is involved in ribosomal RNA synthesis
           regulation. Mice deficient in Jnk2 show protection
           against arthritis, type 1 diabetes, atherosclerosis,
           abdominal aortic aneurysm, cardiac cell death,
           TNF-induced liver damage, and tumor growth, indicating
           that JNK2 may play roles in the pathogenesis of these
           diseases.
          Length = 359

 Score = 26.1 bits (57), Expect = 4.7
 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)

Query: 37  LKWSKKINLVSSSTVEDFWIR-HVEDSLRVFQLHPYPSIWIDLGSGGGFPGIITSIQLSS 95
           LK S+  +L+S   V D   R  V+++LR    HPY ++W D       P  I   QL  
Sbjct: 286 LKTSQARDLLSKMLVIDPDKRISVDEALR----HPYITVWYDPAEAEAPPPQIYDAQLEE 341

Query: 96  IE 97
            E
Sbjct: 342 RE 343


>gnl|CDD|132840 cd07201, cPLA2_Grp-IVB-IVD-IVE-IVF, Group IVB, IVD, IVE, and IVF
           cytosolic phospholipase A2; catalytic domain;
           Ca-dependent.  Group IVB, IVD, IVE, and IVF cPLA2
           consists of two domains: the regulatory C2 domain and
           alpha/beta hydrolase PLA2 domain. Group IVB, IVD, IVE,
           and IVF cPLA2 are also referred to as cPLA2-beta,
           -delta, -epsilon, and -zeta respectively. cPLA2-beta is
           approximately 30% identical to cPLA2-alpha and it shows
           low enzymatic activity compared to cPLA2alpha.
           cPLA2-beta hydrolyzes palmitic acid from
           1-[14C]palmitoyl-2-arachidonoyl-PC and arachidonic acid
           from 1-palmitoyl-2[14C]arachidonoyl-PC, but not from
           1-O-alkyl-2[3H]arachidonoyl-PC. cPLA2-delta, -epsilon,
           and -zeta are approximately 45-50% identical to
           cPLA2-beta and 31-37% identical to cPLA2-alpha. It's
           possible that cPLA2-beta, -delta, -epsilon, and -zeta
           may have arisen by gene duplication from an ancestral
           gene. The catalytic domain of cytosolic phospholipase A2
           (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond
           of phospholipids to release arachidonic acid. At the
           active site, cPLA2 contains a serine nucleophile through
           which the catalytic mechanism is initiated. The active
           site is partially covered by a solvent-accessible
           flexible lid. cPLA2 displays interfacial activation as
           it exists in both "closed lid" and "open lid" forms.
           Movement of the cPLA2 lid possibly exposes a greater
           hydrophobic surface and the active site. cPLA2 belongs
           to the alpha-beta hydrolase family which is identified
           by a characteristic nucleophile elbow with a consensus
           sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
           residue and Nu = nucleophile). Calcium is required for
           cPLA2 to bind with membranes or phospholipids. The
           calcium-dependent phospholipid binding domain resides in
           the N-terminal region of cPLA2; it is homologous to the
           C2 domain superfamily which is not included in this
           hierarchy. It includes PLA2G4B, PLA2G4D, PLA2G4E, and
           PLA2G4F from humans.
          Length = 541

 Score = 25.4 bits (56), Expect = 8.6
 Identities = 10/51 (19%), Positives = 14/51 (27%), Gaps = 6/51 (11%)

Query: 47  SSSTVEDFWIRHVEDSLRV------FQLHPYPSIWIDLGSGGGFPGIITSI 91
            ++  EDFW R   D +            P   +   L  GG         
Sbjct: 272 LATGSEDFWHRWTRDKVNDIEDEPPLPPRPPERLTTLLTPGGPLSQAFRDF 322


>gnl|CDD|144488 pfam00909, Ammonium_transp, Ammonium Transporter Family. 
          Length = 399

 Score = 24.9 bits (55), Expect = 9.7
 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 7/46 (15%)

Query: 58  HVEDSLRVFQLHPYPSIWIDLGSGGGFPGII--TSIQLSSIEGGLV 101
            ++D L VF +H    IW     GG   GI     +  S I GGL+
Sbjct: 300 GIDDPLDVFPVHGVGGIW-----GGIAVGIFAAPYVPPSGIYGGLL 340


  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    0.412 

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: 2,023,167
Number of extensions: 97376
Number of successful extensions: 227
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 16
Length of query: 168
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 81
Effective length of database: 4,383,754
Effective search space: 355084074
Effective search space used: 355084074
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: 54 (24.5 bits)