RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5991
         (223 letters)



>gnl|CDD|216981 pfam02338, OTU, OTU-like cysteine protease.  This family is
           comprised of a group of predicted cysteine proteases,
           homologous to the Ovarian Tumour (OTU) gene in
           Drosophila. Members include proteins from eukaryotes,
           viruses and pathogenic bacterium. The conserved cysteine
           and histidine, and possibly the aspartate, represent the
           catalytic residues in this putative group of proteases.
          Length = 123

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 31/121 (25%), Positives = 43/121 (35%), Gaps = 27/121 (22%)

Query: 104 RSAGDCLLDSLMQATWGVFDRENV--LRRALADSLAQASHLFYPRWKEYEDMHASLLHFS 161
              G+CL  ++         +E    LR A+ + L +                    +  
Sbjct: 1   PGDGNCLFHAVSDQLGDAGRQELHDELREAVVEYLRE--------------------NRE 40

Query: 162 LDESQWEEDWASLVSLASQPGAALEQLHVFALAHILRRPIIVYGVKYVKSFRGEDIGYAR 221
             E   EED        S+ GA    + +FALAHILR PIIVY     K   G    Y +
Sbjct: 41  DFEKFLEEDENEYYKWISKDGAWGGNIEIFALAHILRVPIIVY-----KLQGGRITVYIK 95

Query: 222 F 222
            
Sbjct: 96  I 96


>gnl|CDD|182368 PRK10306, PRK10306, zinc/cadmium-binding protein; Provisional.
          Length = 216

 Score = 29.4 bits (66), Expect = 1.3
 Identities = 16/41 (39%), Positives = 22/41 (53%)

Query: 94  VTAHLYALWNRSAGDCLLDSLMQATWGVFDRENVLRRALAD 134
           V+A  +A  + S G  L +   +A  GVFD  NV  R L+D
Sbjct: 17  VSAPAFAHGHHSHGKPLTEVEQKAANGVFDDANVQDRTLSD 57


>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC).  This
           family consists of several eukaryotic dynein light
           intermediate chain proteins. The light intermediate
           chains (LICs) of cytoplasmic dynein consist of multiple
           isoforms, which undergo post-translational modification
           to produce a large number of species. DLIC1 is known to
           be involved in assembly, organisation, and function of
           centrosomes and mitotic spindles when bound to
           pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
           that may play a role in maintaining Golgi organisation
           by binding cytoplasmic dynein 2 to its Golgi-associated
           cargo.
          Length = 490

 Score = 29.4 bits (66), Expect = 1.8
 Identities = 10/35 (28%), Positives = 15/35 (42%)

Query: 154 HASLLHFSLDESQWEEDWASLVSLASQPGAALEQL 188
           H  LL F+L+     +     V   S+P   +E L
Sbjct: 106 HKGLLKFALNAESLADTLVIFVVDMSRPWTIMESL 140


>gnl|CDD|188997 cd06459, M3B_PepF, Peptidase family M3B Oligopeptidase F (PepF).
           Peptidase family M3B Oligopeptidase F (PepF;
           Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
           includes oligoendopeptidase F from Lactococcus lactis.
           This enzyme hydrolyzes peptides containing between 7 and
           17 amino acids with fairly broad specificity. The PepF
           gene is duplicated in L. lactis on the plasmid that
           bears it, while a shortened second copy is found in
           Bacillus subtilis. Most bacterial PepFs are cytoplasmic
           endopeptidases; however, the PepF Bacillus
           amyloliquefaciens oligopeptidase is a secreted protein
           and may facilitate the process of sporulation.
           Specifically, the yjbG gene encoding the homolog of the
           PepF1 and PepF2 oligoendopeptidases of Lactococcus
           lactis has been identified in Bacillus subtilis as an
           inhibitor of sporulation initiation when over expressed
           from a multicopy plasmid.
          Length = 450

 Score = 28.6 bits (64), Expect = 3.1
 Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 11/77 (14%)

Query: 92  HEVTAHLYALWNRSAGDCLLDSLMQATWGVFDRENVLRRALADSLAQ---------ASHL 142
            E++  L   W+      L+ S     + V   E  L +  A +  Q         AS  
Sbjct: 23  VELSQKLNVAWSEYTK--LIASDKIFPFDVEGEERTLSQGQAQNFLQSPDRAVRRRASEA 80

Query: 143 FYPRWKEYEDMHASLLH 159
            +  +KEYE   A+L +
Sbjct: 81  RFKFFKEYEKTIAALYN 97


>gnl|CDD|188457 TIGR03942, sulfatase_rSAM, anaerobic sulfatase-maturating enzyme.
           Members of this protein family are radical SAM family
          enzymes, maturases that prepare the oxygen-sensitive
          radical required in the active site of anaerobic
          sulfatases. This maturase role has led to many
          misleading legacy annotations suggesting that this
          enzyme maturase is instead a sulfatase regulatory
          protein. All members of the seed alignment are radical
          SAM enzymes encoded next to or near an anaerobic
          sulfatase. Note that a single genome may encode more
          than one sulfatase/maturase pair [Protein fate, Protein
          modification and repair].
          Length = 363

 Score = 28.3 bits (64), Expect = 3.3
 Identities = 12/41 (29%), Positives = 25/41 (60%)

Query: 28 CFFSEIENLPPSIQEQLFDELLDKEAQQQLEAEPHPVINWS 68
          CF+ E E+L P  + ++ DE L+   +Q + ++  P +N++
Sbjct: 18 CFYLEKEDLYPKPKPKMSDETLETFIKQYIASQDGPEVNFA 58


>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
           (La or SS-B or LARP3), La-related protein 7 (LARP7 or
           PIP7S) and similar proteins.  This subfamily corresponds
           to the RRM2 of La and LARP7. La is a highly abundant
           nuclear phosphoprotein and well conserved in eukaryotes.
           It specifically binds the 3'-terminal UUU-OH motif of
           nascent RNA polymerase III transcripts and protects them
           from exonucleolytic degradation by 3' exonucleases. In
           addition, La can directly facilitate the translation
           and/or metabolism of many UUU-3' OH-lacking cellular and
           viral mRNAs, through binding internal RNA sequences
           within the untranslated regions of target mRNAs. LARP7
           is an oligopyrimidine-binding protein that binds to the
           highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
           of 7SK RNA. It is a stable component of the 7SK small
           nuclear ribonucleoprotein (7SK snRNP), intimately
           associates with all the nuclear 7SK and is required for
           7SK stability. LARP7 also acts as a negative
           transcriptional regulator of cellular and viral
           polymerase II genes, acting by means of the 7SK snRNP
           system. LARP7 plays an essential role in the inhibition
           of positive transcription elongation factor b
           (P-TEFb)-dependent transcription, which has been linked
           to the global control of cell growth and tumorigenesis.
           Both La and LARP7 contain an N-terminal La motif (LAM),
           followed by two RNA recognition motifs (RRMs), also
           termed RBDs (RNA binding domains) or RNPs
           (ribonucleoprotein domains). .
          Length = 75

 Score = 26.5 bits (59), Expect = 3.7
 Identities = 10/18 (55%), Positives = 11/18 (61%)

Query: 206 VKYVKSFRGEDIGYARFE 223
           VKYV    G D GY RF+
Sbjct: 28  VKYVDFTEGADTGYIRFK 45


>gnl|CDD|217033 pfam02438, Adeno_100, Late 100kD protein.  The late 100kD protein
           is a non-structural viral protein involved in the
           transport of hexon from the cytoplasm to the nucleus.
          Length = 583

 Score = 28.4 bits (64), Expect = 3.8
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 35  NLPPSIQEQLFDELLDKEAQ-QQLEAEPHPVI------NWSHELLDKEAQQQ 79
           NLPP + + L + LL K A+  +L+ E  PV+       W     D  A ++
Sbjct: 168 NLPPKVMKILMETLLGKRAEPNELDEEGEPVVSDEELARWLDPTNDPAALEE 219


>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 576

 Score = 27.4 bits (61), Expect = 7.3
 Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 6/42 (14%)

Query: 37  PPSIQEQLFDELLDKEAQQQL---EAEPHPVINWSHELLDKE 75
           PPS+ E+   +  ++E +Q     EA  HP++  +  +   E
Sbjct: 531 PPSLAEK---KAAEREQRQARLREEAREHPLVQEALRVFGGE 569


>gnl|CDD|236628 PRK09846, recT, recombination and repair protein RecT; Reviewed.
          Length = 266

 Score = 27.0 bits (60), Expect = 7.5
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 12/79 (15%)

Query: 5   WLNHYRRLQTKTSISRLTSKYFVCFFSEIENLPPSIQEQLFDELLDKEAQQQLEAEPHPV 64
           W++HY  +  KT I RL  KY          LP SI+ Q     +D++ +  ++ +   V
Sbjct: 200 WVDHYEEMAKKTVIRRL-FKY----------LPVSIEIQRAVS-MDEKVRLDIDPDDSSV 247

Query: 65  INWSHELLDKEAQQQLEAE 83
           +   + ++D  A+++   E
Sbjct: 248 LTGEYSVIDNSAEEESANE 266


  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
   0.320    0.133    0.414 

Gapped
Lambda     K      H
   0.267   0.0750    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,900,796
Number of extensions: 1120807
Number of successful extensions: 1083
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1083
Number of HSP's successfully gapped: 25
Length of query: 223
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 130
Effective length of database: 6,812,680
Effective search space: 885648400
Effective search space used: 885648400
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 (21.8 bits)
S2: 57 (25.7 bits)