RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13564
         (323 letters)



>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
           factor RRN3.  This family consists of several eukaryotic
           proteins which are homologous to the yeast RRN3 protein.
           RRN3 is one of the RRN genes specifically required for
           the transcription of rDNA by RNA polymerase I (Pol I) in
           Saccharomyces cerevisiae.
          Length = 554

 Score =  174 bits (444), Expect = 2e-50
 Identities = 86/286 (30%), Positives = 133/286 (46%), Gaps = 53/286 (18%)

Query: 2   LFNELLAVFESTILPTHGITHVPFLVFYFCSLRLSIGENFIEFLWKKIANVKIYNIFRQS 61
           LFN LL++F++ ILPT+   HV FL+F+F SL   + + F+  LW    N          
Sbjct: 301 LFNTLLSLFDNHILPTYRSRHVQFLLFHFSSLSPELMDAFLGTLWDIAFNPN-------- 352

Query: 62  CCHYVSSLLIHAHFMPVSIGENFIEFLWKKIANVKIYNIFRQSCCHYVSSLLIHAHFMPV 121
                          P                        RQ+   Y++S L  A  +P+
Sbjct: 353 --------------EPAVK---------------------RQAAAAYLASFLARAKHVPL 377

Query: 122 RVIKTCLNEMSQWCHSYLDNTDLTDEEACSPVKHPVFYSVCQALFSVITYKHSILVDSKK 181
             ++  L+ +  W + Y+D  + ++       +H VFYS CQAL  +  ++   L+ S K
Sbjct: 378 EQVRFVLSLLVDWLNRYVDERE-SECRGPDLERHGVFYSACQALLYIFCFRWRDLLLSPK 436

Query: 182 NMKFLQSLN--LTRLVMSQLNPLRSCNAEIVSHFASITNTYQIVYCYNVIHQNARLNVLP 239
           ++++LQSL+  L R+VMS+LNPL+ C   +VS FA I    Q+VYCY++I +N R  +  
Sbjct: 437 DLEWLQSLDKFLQRIVMSKLNPLKYCLPSVVSEFARIARHLQLVYCYSIIERNKRERLSR 496

Query: 240 IVSTDALGNIIKLNTVNA-------LDQYSPFSTFLLVRCKSIITP 278
           +    A    ++     A       LD Y PF  +LL R K  I P
Sbjct: 497 VRGGSASDGALRERPSAAGDEKTRQLDAYFPFDPYLLKRSKKWIEP 542


>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
          Length = 1627

 Score = 32.9 bits (75), Expect = 0.27
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 253  NTVNALDQY-SPFSTFLLVRCKSIITPEIHCQADPIPVTTNTNRTQNLLIADPVSSKQAD 311
            N V   D+Y S     + VR   II PE     D    + N  +  N++I + + + Q D
Sbjct: 1324 NKVRKADKYLSENGWIVKVRRVEIIKPE-----DEFVYSLNAKKYHNVIINENIQTHQCD 1378

Query: 312  HDEDDFLMSVDS 323
             DED   + +D+
Sbjct: 1379 GDEDAVFLLLDA 1390


>gnl|CDD|107166 PHA02283, PHA02283, hypothetical protein.
          Length = 210

 Score = 29.0 bits (64), Expect = 2.9
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 208 EIVSHFASITNTYQIVYCYNVIHQNARLNVLPIVSTDALGNI 249
           ++  +    T T++  Y Y V+ +   L + P V TD  G +
Sbjct: 23  QVKVNRDGYTRTHEGQYAYKVVSEGEELFLYP-VQTDGKGTL 63


>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
           Provisional.
          Length = 846

 Score = 29.0 bits (65), Expect = 3.9
 Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 7/45 (15%)

Query: 175 ILVDSKKNMKFLQSLNLTRLVMSQLNPLRS-------CNAEIVSH 212
           + V+SK+  + + SL L R+       LRS       CN  I   
Sbjct: 232 VYVNSKEAWELVDSLGLRRIPKEGWKGLRSFLRAYFDCNGGIEKD 276


>gnl|CDD|225335 COG2710, NifD, Nitrogenase molybdenum-iron protein, alpha and beta
           chains [Energy production and conversion].
          Length = 456

 Score = 28.1 bits (63), Expect = 7.6
 Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 1/30 (3%)

Query: 103 QSCCHYVSSLLI-HAHFMPVRVIKTCLNEM 131
           Q C  YV  LL  H     + V  T L+E 
Sbjct: 58  QGCSFYVWDLLRRHFVKELIPVFTTSLDED 87


  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
   0.326    0.137    0.424 

Gapped
Lambda     K      H
   0.267   0.0670    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,909,658
Number of extensions: 1465749
Number of successful extensions: 1278
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1275
Number of HSP's successfully gapped: 10
Length of query: 323
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 226
Effective length of database: 6,635,264
Effective search space: 1499569664
Effective search space used: 1499569664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 59 (26.6 bits)