RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy873
         (141 letters)



>gnl|CDD|216358 pfam01198, Ribosomal_L31e, Ribosomal protein L31e. 
          Length = 83

 Score = 49.5 bits (119), Expect = 6e-09
 Identities = 16/25 (64%), Positives = 19/25 (76%)

Query: 91  IRSVPFRIRVRLSRRRNDDEDSPHK 115
           IR+ P R+RVR SR+RNDDED   K
Sbjct: 59  IRNPPSRVRVRASRKRNDDEDGKVK 83


>gnl|CDD|140220 PTZ00193, PTZ00193, 60S ribosomal protein L31; Provisional.
          Length = 188

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 91  IRSVPFRIRVRLSRRRNDDEDSPHK-LYTLVTWVPVPTFKELQTENVD 137
           ++ VP R+RV + R+    E    K  YT+++ VPV +FK L T+ V+
Sbjct: 140 VKGVPGRVRVLVERKSETLEGGKRKHFYTVISNVPVASFKNLTTKVVE 187


>gnl|CDD|199209 cd00463, Ribosomal_L31e, Eukaryotic/archaeal ribosomal protein L31.
            Ribosomal protein L31e, which is present in archaea and
           eukaryotes, binds the 23S rRNA and is one of six protein
           components encircling the polypeptide exit tunnel. It is
           a component of the eukaryotic 60S (large) ribosomal
           subunit, and the archaeal 50S (large) ribosomal subunit.
          Length = 83

 Score = 36.0 bits (84), Expect = 6e-04
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 91  IRSVPFRIRVRLSRRRNDDEDSPH 114
           I   P R+RVR+SR+R + ED+  
Sbjct: 60  IEKPPRRVRVRVSRKREETEDAVL 83


>gnl|CDD|177832 PLN02175, PLN02175, endoglucanase.
          Length = 484

 Score = 30.1 bits (67), Expect = 0.36
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 26  PSAATSYTIGGVKVEFPVK--AYPSQISMMTKESSKYISSMHLSVLCTVDLSCPIWFWWG 83
           PS++T YT GG+  + P     Y + I+ +    +KY+ S   +  C   +  P      
Sbjct: 312 PSSSTQYTQGGLMYKLPQSNLQYVTSITFLLTTYAKYMKSTKHTFNCGNSVIVP------ 365

Query: 84  TSLINMDIRSVPF 96
            +LI++  R V +
Sbjct: 366 NALISLSKRQVDY 378


>gnl|CDD|233351 TIGR01304, IMP_DH_rel_2, IMP dehydrogenase family protein.  This
          model represents a family of proteins, often annotated
          as a putative IMP dehydrogenase, related to IMP
          dehydrogenase and GMP reductase. Most species with a
          member of this family belong to the high GC
          Gram-positive bacteria, and these also have the IMP
          dehydrogenase described by TIGRFAMs equivalog model
          TIGR01302 [Unknown function, General].
          Length = 369

 Score = 29.4 bits (66), Expect = 0.54
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 15 AVLPSVKDKSKPSAATSYTIGGVKVEFPVKAYPS 48
          +V+PS + +S     T++ I   + E P  A+P 
Sbjct: 19 SVVPSRRTRSSKDVDTAWQIDAYRFELPFIAHPM 52


>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
          Length = 663

 Score = 27.2 bits (61), Expect = 3.1
 Identities = 7/29 (24%), Positives = 13/29 (44%)

Query: 72  VDLSCPIWFWWGTSLINMDIRSVPFRIRV 100
           ++L  P+W  W      +  R VP  ++ 
Sbjct: 584 INLDSPLWLRWRLDQRIIASREVPIEVQY 612


>gnl|CDD|218951 pfam06240, COXG, Carbon monoxide dehydrogenase subunit G (CoxG). 
          The CO dehydrogenase structural genes coxMSL are
          flanked by nine accessory genes arranged as the cox
          gene cluster. The cox genes are specifically and
          coordinately transcribed under chemolithoautotrophic
          conditions in the presence of CO as carbon and energy
          source.
          Length = 140

 Score = 26.5 bits (59), Expect = 3.8
 Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 11/63 (17%)

Query: 6  LLENSQKLQAVLPSVKDKSKPSAATSYT------IGGVKVEFPVKAYPSQISMMTKESSK 59
           L + + L   +P VK   K      Y       +G +K  +  +    + S +    S 
Sbjct: 15 FLNDPEVLARCIPGVKSVEK--NGDEYKAKVKLKVGPLKGSYTGRV---EFSDLDPPGSY 69

Query: 60 YIS 62
           IS
Sbjct: 70 TIS 72


>gnl|CDD|180284 PRK05844, PRK05844, pyruvate flavodoxin oxidoreductase subunit
           gamma; Validated.
          Length = 186

 Score = 26.3 bits (58), Expect = 4.8
 Identities = 10/26 (38%), Positives = 13/26 (50%)

Query: 42  PVKAYPSQISMMTKESSKYISSMHLS 67
           P   +   I    KE +KYI + HLS
Sbjct: 75  PGLVFIENIFANEKEDTKYIITTHLS 100


>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase.  The
           eukaryotic RPB3 subunit of RNA polymerase (RNAP), as
           well as its archaeal (D subunit) and bacterial (alpha
           subunit) counterparts, is involved in the assembly of
           RNAP subunits. RNAP is a large multi-subunit complex
           responsible for the synthesis of RNA. It is the
           principal enzyme of the transcription process, and is a
           final target in many regulatory pathways that control
           gene expression in all living cells. At least three
           distinct RNAP complexes are found in eukaryotic nuclei: 
           RNAP I, RNAP II, and RNAP III, for the synthesis of
           ribosomal RNA precursor, mRNA precursor, and 5S and
           tRNA, respectively. A single distinct RNAP complex is
           found in prokaryotes and archaea, which may be
           responsible for the synthesis of all RNAs. The RPB3
           subunit is similar to the bacterial RNAP alpha subunit
           in that it contains two subdomains: one subdomain is
           similar to the eukaryotic Rpb11/AC19/archaeal L subunit
           which is involved in dimerization; and the other is an
           inserted beta sheet subdomain. The assembly of the two
           largest eukaryotic RNAP subunits that provide most of
           the enzyme's catalytic functions depends on the presence
           of RPB3/RPB11 heterodimer subunits. This is also true
           for the archaeal (D/L subunits) and bacterial (alpha
           subunit) counterparts.
          Length = 212

 Score = 26.0 bits (57), Expect = 6.4
 Identities = 5/30 (16%), Positives = 13/30 (43%), Gaps = 1/30 (3%)

Query: 96  FRIRVRLSRRRNDDEDSPHKLYTL-VTWVP 124
            +  V L+ +   + +S   +Y+  +  V 
Sbjct: 90  DKCSVVLTLQAFAESESTTNVYSKDLVIVS 119


>gnl|CDD|180442 PRK06175, PRK06175, L-aspartate oxidase; Provisional.
          Length = 433

 Score = 26.2 bits (58), Expect = 8.2
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 5/32 (15%)

Query: 21  KDKSKPSAATSYTIGGVKVEFPVKAYPSQISM 52
           KD    S A  Y +GG+KV+       S+ SM
Sbjct: 318 KDAIPVSPAQHYFMGGIKVDL-----NSKTSM 344


>gnl|CDD|220633 pfam10214, Rrn6, RNA polymerase I-specific transcription-initiation
           factor.  RNA polymerase I-specific
           transcription-initiation factor Rrn6 and Rrn7 represent
           components of a multisubunit transcription factor
           essential for the initiation of rDNA transcription by
           Pol I. These proteins are found in fungi.
          Length = 753

 Score = 26.3 bits (58), Expect = 8.3
 Identities = 7/30 (23%), Positives = 14/30 (46%)

Query: 84  TSLINMDIRSVPFRIRVRLSRRRNDDEDSP 113
             +I +D+ S    ++  LS +   D + P
Sbjct: 268 KEIIWLDVNSSSPSLKRLLSWKHFRDPEDP 297


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.317    0.130    0.390 

Gapped
Lambda     K      H
   0.267   0.0689    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,773,084
Number of extensions: 555576
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 423
Number of HSP's successfully gapped: 15
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
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: 54 (24.7 bits)