RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6101
         (341 letters)



>gnl|CDD|225489 COG2938, COG2938, Uncharacterized conserved protein [Function
           unknown].
          Length = 94

 Score = 83.1 bits (206), Expect = 4e-20
 Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 3/93 (3%)

Query: 235 ERVGEPLELRKARLLYQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQYDQLINLPSNDW 294
            R  E  + RKARL ++SR RGM E  L+L  FA K  D+++++ L ++++L  L   D 
Sbjct: 5   TRSTEDDDARKARLRWRSR-RGMRELDLILGPFAEKEFDSLSDEELDEFERL--LECEDN 61

Query: 295 DIYYWATGVRPIPLQFNNEVMKLLQDHTKNKDR 327
           D++ W  G    P      +++ +Q   + +D 
Sbjct: 62  DLFNWIMGHGEPPDAELTPMVRKIQARRRIRDP 94



 Score = 46.5 bits (111), Expect = 8e-07
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 15/82 (18%)

Query: 43  RSRGGGRGCR-----LGDF--RHWLSNSGMNEDLLKQYDQLINLPSNDWDIYYWATGVRP 95
           RSR   RG R     LG F  + +     ++++ L ++++L  L   D D++ W  G   
Sbjct: 21  RSR---RGMRELDLILGPFAEKEF---DSLSDEELDEFERL--LECEDNDLFNWIMGHGE 72

Query: 96  IPLQFNNEVMKLLQDHTKNKDR 117
            P      +++ +Q   + +D 
Sbjct: 73  PPDAELTPMVRKIQARRRIRDP 94


>gnl|CDD|202817 pfam03937, Sdh5, Flavinator of succinate dehydrogenase.  This
           family of uncharacterized proteins. Based on personal
           observation it was previously annotated in Pfam as being
           a divergent TPR repeat but structural evidence has
           indicated this is not true.This family is now found to
           be a highly conserved mitochondrial protein, Sdh5. Both
           yeast and human Sdh5 interact with the catalytic subunit
           of the succinate dehydrogenase (SDH) complex, a
           component of both the electron transport chain and the
           tricarboxylic acid cycle. Sdh5 is required for
           SDH-dependent respiration and for Sdh1 flavination
           (incorporation of the flavin adenine dinucleotide
           cofactor). Mutational inactivation of Sdh5 confers tumor
           susceptibility in humans.
          Length = 51

 Score = 72.8 bits (180), Expect = 8e-17
 Identities = 23/53 (43%), Positives = 37/53 (69%), Gaps = 2/53 (3%)

Query: 250 YQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQYDQLINLPSNDWDIYYWATG 302
           ++S +RGMLE  LLL  FA  +LDT++E+ L  +++L++L   D D++ W TG
Sbjct: 1   WRSWRRGMLELDLLLGRFADAHLDTLSEEELDAFERLLDL--EDPDLFDWLTG 51



 Score = 37.4 bits (88), Expect = 5e-04
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 12/51 (23%)

Query: 49 RGCR-----LGDF--RHWLSNSGMNEDLLKQYDQLINLPSNDWDIYYWATG 92
          RG       LG F   H      ++E+ L  +++L++L   D D++ W TG
Sbjct: 6  RGMLELDLLLGRFADAHL---DTLSEEELDAFERLLDL--EDPDLFDWLTG 51


>gnl|CDD|202199 pfam02305, Phage_F, Capsid protein (F protein).  This is a family
           of proteins from single-stranded DNA bacteriophages.
           Protein F is the major capsid component, sixty copies of
           which are found in the virion.
          Length = 450

 Score = 28.6 bits (64), Expect = 5.1
 Identities = 31/132 (23%), Positives = 47/132 (35%), Gaps = 32/132 (24%)

Query: 188 PVYENVEEEPVLTSLVFCGSQIVKNSVRSMSKEIFPPSQEPEIPAYQERVGEPLELR--- 244
           P   N+ E+ V    +FC    V +       E F          YQER       R   
Sbjct: 334 PALANLPEQEVSNKEIFCQGSSVDS-------EKF---------GYQERYA---WYRYKP 374

Query: 245 -KARLLYQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQ---YDQLINLPSN--DW--DI 296
            K   +Y+S     L+       FA   L  ++E  L++   YD+ + +      W  D 
Sbjct: 375 SKVAGVYRSNATQSLDGWHFAQHFAN--LPDLSERFLEENTPYDRCLQVSDQLPQWNMDF 432

Query: 297 YYWATGVRPIPL 308
            +  T  RP+P 
Sbjct: 433 KFNYTVYRPMPT 444


>gnl|CDD|222784 PHA00363, PHA00363, major capsid protein.
          Length = 557

 Score = 28.7 bits (64), Expect = 5.3
 Identities = 24/129 (18%), Positives = 58/129 (44%), Gaps = 19/129 (14%)

Query: 188 PVYENVEEEPVLTSLVFCGSQIVKNSVRSMSKEIFPPSQEPEIPAYQERVGEPLELRKAR 247
           P   ++ E+ VL   ++C    VK++   +         + ++  YQER  E    + ++
Sbjct: 431 PALSHLGEQAVLNKEIYCQGPAVKDAGGVV--------VDEQVFGYQERFAE-YRYKPSK 481

Query: 248 L--LYQSRKRGMLENGLLLSTFAAKYLDTMNEDLLKQ---YDQLINLPSND---WDIYYW 299
           +   ++S   G L++  L   F    L T++ + +++    D+++ + +      D ++ 
Sbjct: 482 ITGKFRSNATGSLDSWHLAQEFEN--LPTLSPEFIEENPPMDRVLAVKTEPDFLLDFWFS 539

Query: 300 ATGVRPIPL 308
               RP+P+
Sbjct: 540 LRCARPMPV 548


>gnl|CDD|180537 PRK06348, PRK06348, aspartate aminotransferase; Provisional.
          Length = 384

 Score = 27.8 bits (62), Expect = 8.4
 Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 6/35 (17%)

Query: 268 AAKYLDTMNE------DLLKQYDQLINLPSNDWDI 296
           A KY             L K++  +I+L   D D+
Sbjct: 7   AKKYQQMEVNIMAEIATLAKKFPDIIDLSLGDPDL 41


  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
   0.318    0.135    0.411 

Gapped
Lambda     K      H
   0.267   0.0624    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,467,836
Number of extensions: 1669767
Number of successful extensions: 1448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1443
Number of HSP's successfully gapped: 14
Length of query: 341
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 243
Effective length of database: 6,590,910
Effective search space: 1601591130
Effective search space used: 1601591130
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: 59 (26.7 bits)