RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781045|ref|YP_003065458.1| outer membrane lipoprotein
omp19 [Candidatus Liberibacter asiaticus str. psy62]
         (162 letters)



>gnl|CDD|145888 pfam02974, Inh, Protease inhibitor Inh.  The Inh inhibitor is
           secreted into the periplasm where its presumed
           physiological function is to protect periplasmic
           proteins against the action of secreted proteases. A
           range of proteases including A, B and C from E.
           chrysanthemi, alkaline protease from Pseudomonas
           aeruginosa and the 50 kDa protease from Serratia
           marcescens are inhibited.
          Length = 98

 Score = 48.1 bits (115), Expect = 1e-06
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 77  GAWKVSYRDVDCKMILTLTRFKKNFRGTARSCHGRLASLA--AWNIIDEDSFELKNKSGQ 134
           G W++S     C + LT T+  + +     +C G         W     D   L + SG 
Sbjct: 13  GQWQLSKGGQVCDIELTQTKLGQGYLAGDLACLGEWLGEVPSGWRP-TPDGLALTDASGS 71

Query: 135 TIIVFYKTAEQSFEG 149
           T+   Y++ E  +EG
Sbjct: 72  TVAFLYRSGEGRYEG 86


>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of
           Bacterial RNA polymerase.  The bacterial alpha subunit
           of RNA polymerase (RNAP) consists of two independently
           folded domains: an amino-terminal domain (alphaNTD) and
           a carboxy-terminal domain (alphaCTD). AlphaCTD is not
           required for RNAP assembly but interacts with
           transcription activators. AlphaNTD is essential in vivo
           and in vitro for RNAP assembly and basal transcription.
           It is similar to the eukaryotic RPB3/AC40/archaeal D
           subunit, and contains two subdomains: one subdomain is
           similar the eukaryotic Rpb11/AC19/archaeal L subunit
           which is involved in dimerization; and the other is an
           inserted beta sheet subdomain. The alphaNTDs of plant
           plastid RNAP (PEP) are also included in this subfamily.
           PEP is largely responsible for the transcription of
           photosynthetic genes and is closely related to the
           multi-subunit bacterial RNAP, which is a large
           multi-subunit complex responsible for the synthesis of
           all bacterial RNAs. The bacterial RNAP core enzyme
           consists of four subunits (beta', beta, alpha and
           omega). All residues in the alpha subunit that is
           involved in dimerization or in the interaction with
           other subunits are located within alphaNTD.
          Length = 215

 Score = 28.2 bits (64), Expect = 1.1
 Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 6/43 (13%)

Query: 7   ILLNLYMLTLFSHGCTQIDFGNIFFKKPE------ISLPPSVE 43
           ILLNL  +   S    +     +  K P       I LP  VE
Sbjct: 68  ILLNLKEIVFKSDSEDEPQVLRLKVKGPGVVTAADIELPSGVE 110


>gnl|CDD|37317 KOG2106, KOG2106, KOG2106, Uncharacterized conserved protein,
          contains HELP and WD40 domains [Function unknown].
          Length = 626

 Score = 26.9 bits (59), Expect = 3.1
 Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 4/68 (5%)

Query: 29 IFFKKPEISLPPSVESEILLPPIPEEEFDQDDISVPSKDNNAIRMGIIGAWKVSYRDVDC 88
           FF   E +         +L  +P +       + P  D       +   W   YR VDC
Sbjct: 12 CFFSNGEGNYKNFSRGRPVLVSVPVDPEH----TYPMADVELPTEKLKLEWVYGYRGVDC 67

Query: 89 KMILTLTR 96
          +  L L  
Sbjct: 68 RNNLYLLP 75


>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein. 
          Length = 219

 Score = 25.7 bits (57), Expect = 5.7
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 7/38 (18%)

Query: 54  EEFDQDDISVPSKDNNAIRMGIIGAWKVSYRDVDCKMI 91
           EEF  D +       +A+R   I A+K SYR+VD  +I
Sbjct: 73  EEFLNDFV-------DALRDNKIEAFKKSYRNVDLLLI 103


>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3. 
          Length = 199

 Score = 25.0 bits (55), Expect = 9.0
 Identities = 8/24 (33%), Positives = 12/24 (50%)

Query: 97  FKKNFRGTARSCHGRLASLAAWNI 120
           FK+  R   R  H +  S+ AW+ 
Sbjct: 124 FKRLPRKHGRGYHRKPGSIGAWHP 147


>gnl|CDD|36281 KOG1063, KOG1063, KOG1063, RNA polymerase II elongator complex,
           subunit ELP2, WD repeat superfamily [Chromatin structure
           and dynamics, Transcription].
          Length = 764

 Score = 25.0 bits (54), Expect = 9.9
 Identities = 11/70 (15%), Positives = 23/70 (32%), Gaps = 2/70 (2%)

Query: 65  SKDNNAIRMGIIGAWKVSYRDVDCKMILTLTRFKKNFRGTARSCHGRLASLAAWNIIDED 124
            K++  IR+     W          + +T   F  + R        R  SL  + + ++ 
Sbjct: 548 LKEHAVIRLWNTANWLQVQELEGHSLTVTRLAFSPDGRYLLSVSRDRTVSL--YEVQEDI 605

Query: 125 SFELKNKSGQ 134
             E +    +
Sbjct: 606 KDEFRFACLK 615


  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
   0.323    0.139    0.417 

Gapped
Lambda     K      H
   0.267   0.0775    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,060,131
Number of extensions: 104336
Number of successful extensions: 202
Number of sequences better than 10.0: 1
Number of HSP's gapped: 201
Number of HSP's successfully gapped: 9
Length of query: 162
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 76
Effective length of database: 4,405,363
Effective search space: 334807588
Effective search space used: 334807588
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: 53 (24.1 bits)