RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy53
         (78 letters)



>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein.  Members of
           this family are long (~850 residue) bacterial proteins
           from the alpha Proteobacteria. Each has 2-3 predicted
           transmembrane helices near the N-terminus and a long
           C-terminal region that includes stretches of
           Gln/Gly-rich low complexity sequence, predicted by TMHMM
           to be outside the membrane. In Bradyrhizobium japonicum,
           two tandem reading frames are together homologous the
           single members found in other species; the cutoffs
           scores are set low enough that the longer scores above
           the trusted cutoff and the shorter above the noise
           cutoff for this model.
          Length = 851

 Score = 31.1 bits (70), Expect = 0.036
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 7/67 (10%)

Query: 1   MDIYFNQLRENI-----VRGQPPDKQASMV--QWFENLMNSIERNLLTKNRDRFTQNLSM 53
           M  Y  QL + +        +P D    ++  Q  +N+M+ IE    + +RD+  Q LS 
Sbjct: 536 MQTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQ 595

Query: 54  FRRDIND 60
            ++ +N+
Sbjct: 596 LQQMMNN 602


>gnl|CDD|176527 cd08585, GDPD_like_3, Glycerophosphodiester phosphodiesterase
           domain of uncharacterized bacterial
           glycerophosphodiester phosphodiesterases.  This
           subfamily corresponds to the glycerophosphodiester
           phosphodiesterase domain (GDPD) present in a group of
           uncharacterized bacterial glycerophosphodiester
           phosphodiesterase and similar proteins. They show high
           sequence similarity with Escherichia coli
           glycerophosphodiester phosphodiesterase, which catalyzes
           the degradation of glycerophosphodiesters to produce
           sn-glycerol-3-phosphate (G3P) and the corresponding
           alcohols.
          Length = 237

 Score = 30.0 bits (68), Expect = 0.079
 Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 3/41 (7%)

Query: 5   FNQLRENIVRGQ---PPDKQASMVQWFENLMNSIERNLLTK 42
           F +L   I RGQ     + +A    W E L++++  NLLT+
Sbjct: 145 FRKLAPGIPRGQLSEGSNDEADPAFWNEALLSALFSNLLTR 185


>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
          Length = 3151

 Score = 29.1 bits (65), Expect = 0.15
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 8   LRENIVRGQPPDKQASMVQWFENLMNSIERNLLT-KNRDRFTQNLSMFRRDIND 60
           LRE + RGQ  +  A +  W  +L ++  + L+  K  D   + +      IN+
Sbjct: 855 LRELLQRGQDLEAPADLAAWLASLGDAAGQGLVERKELDELARAI----HKINE 904


>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
           decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
           formyltransferase; Validated.
          Length = 660

 Score = 26.5 bits (59), Expect = 1.2
 Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 3/30 (10%)

Query: 18  PDKQASMVQWFENLMNSIERNLLTKNRDRF 47
           PD +AS+ +  E L+ S E++ L   RD F
Sbjct: 568 PDNEASIRELAEMLLASFEKHPL---RDHF 594


>gnl|CDD|234044 TIGR02872, spore_ytvI, sporulation integral membrane protein YtvI. 
           Three lines of evidence show this protein to be involved
           in sporulation. First, it is under control of a
           sporulation-specific sigma factor, sigma-E. Second,
           mutation leads to a sporulation defect. Third, it if
           found in exactly those genomes whose bacteria are
           capable of sporulation, except for being absent in
           Clostridium acetobutylicum ATCC824. This protein has
           extensive hydrophobic regions and is likely an integral
           membrane protein [Cellular processes, Sporulation and
           germination].
          Length = 341

 Score = 26.5 bits (59), Expect = 1.5
 Identities = 6/38 (15%), Positives = 17/38 (44%), Gaps = 1/38 (2%)

Query: 17  PPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMF 54
           PP +Q ++V   + L+  +   +++        ++  F
Sbjct: 114 PPGQQYTIVNNIQTLLEKLLNYVVSFAT-NLITSIPSF 150


>gnl|CDD|204170 pfam09226, Endonuc-HincII, Restriction endonuclease HincII.
           Members of this family of prokaryotic restriction
           endonucleases recognise the double-stranded sequence
           5'-GTYRAC-3' and cleave after Y-3. They catalyze the
           endonucleolytic cleavage of DNA to give specific
           double-stranded fragments with terminal 5'-phosphates.
          Length = 257

 Score = 26.2 bits (57), Expect = 1.8
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 14  RGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDINDSLKGPNMNSS 70
           RG+   +  S+   FE   N     LL K  D+F + L +  R+I+ S + PN+ S+
Sbjct: 90  RGKAATENWSIENLFEEKQNDTADILLVK--DQFYELLDVKTRNISKSAQAPNIISA 144


>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 = 26.1 bits (58), Expect = 2.0
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 1   MDIYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMF 54
           MD+ F  L      G+  + +   +  F  L++  + ++L   R R  Q L +F
Sbjct: 277 MDLLFTHLDSCFTDGELDEGKGVNL--FNTLLSLFDNHILPTYRSRHVQFL-LF 327


>gnl|CDD|220123 pfam09138, Urm1, Urm1 (Ubiquitin related modifier).  Urm1 is a
          ubiquitin related protein that modifies proteins in the
          yeast ubiquitin-like pathway urmylation. Structural
          comparisons and phylogenetic analysis of the ubiquitin
          superfamily has indicated that Urm1 has the most
          conserved structural and sequence features of the
          common ancestor of the entire superfamily.
          Length = 96

 Score = 24.9 bits (55), Expect = 2.8
 Identities = 8/49 (16%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 2  DIYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQN 50
          ++ F++ +++ V         +M     +L++ I++NL+ +  + F + 
Sbjct: 11 ELLFDKQKKHKVTLPIDSGPVNM----GDLIDYIKKNLIKERPEVFLEG 55


>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
            The family consists of the product of the rpoC2 gene, a
           subunit of DNA-directed RNA polymerase of cyanobacteria
           and chloroplasts. RpoC2 corresponds largely to the
           C-terminal region of the RpoC (the beta' subunit) of
           other bacteria. Members of this family are designated
           beta'' in chloroplasts/plastids, and beta' (confusingly)
           in Cyanobacteria, where RpoC1 is called beta' in
           chloroplasts/plastids and gamma in Cyanobacteria. We
           prefer to name this family beta'', after its organellar
           members, to emphasize that this RpoC1 and RpoC2 together
           replace RpoC in other bacteria [Transcription,
           DNA-dependent RNA polymerase].
          Length = 1227

 Score = 25.6 bits (56), Expect = 3.1
 Identities = 15/41 (36%), Positives = 22/41 (53%)

Query: 12  IVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLS 52
           I R Q   K+A +VQ  ++   SI R L+ +N DR   N+ 
Sbjct: 857 IARTQILCKEAGVVQGIDSGGESIRRLLVERNSDRLKVNIK 897


>gnl|CDD|233206 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
           Family protei.  [Transport and binding proteins,
           Carbohydrates, organic alcohols, and acids].
          Length = 659

 Score = 25.5 bits (56), Expect = 3.3
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 7   QLRENIVRGQPPDKQASMVQWFEN-----LMNSIERNLLTKNRDRFTQNLSMF 54
           Q+  +IVR  P +    + +WF        +NS  + LL + + RF   L+ +
Sbjct: 121 QIESSIVRRSPRNFAWILFKWFLIAPPASFINSAIKYLLKELKLRFRVRLTRY 173


>gnl|CDD|213919 TIGR04306, salvage_TenA, thiaminase II.  The TenA protein of
           Bacillus subtilis and Staphylococcus aurues, and the
           C-terminal region of trifunctional protein Thi20p from
           Saccharomyces cerevisiae, perform cleavages on thiamine
           and related compounds to produce
           4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), a
           substrate a salvage pathway for thiamine biosynthesis.
           The gene symbol tenA, for Transcription ENhancement A,
           reflects a misleading early characterization as a
           regulatory protein. This family is related to PqqC from
           the PQQ biosynthesis system (see TIGR02111), heme
           oxygenase (pfam01126), and CADD (Chlamydia protein
           Associating with Death Domains), a putative folate
           metabolism enzyme (see TIGR04305).
          Length = 208

 Score = 25.2 bits (55), Expect = 3.9
 Identities = 5/26 (19%), Positives = 11/26 (42%)

Query: 25  VQWFENLMNSIERNLLTKNRDRFTQN 50
           V   ENL+N +      +  ++  + 
Sbjct: 165 VNEGENLLNHLAETSSPEELEKLKEI 190


>gnl|CDD|217365 pfam03097, BRO1, BRO1-like domain.  This domain is found in a
           number proteins including Rhophilin and BRO1. It is
           known to have a role in endosomal targeting. ESCRT-III
           subunit Snf7 binds to a conserved hydrophobic patch in
           the BRO1 domain that is required for protein complex
           formation and for the protein-sorting function of BRO1.
          Length = 374

 Score = 25.3 bits (56), Expect = 4.1
 Identities = 8/29 (27%), Positives = 14/29 (48%)

Query: 4   YFNQLRENIVRGQPPDKQASMVQWFENLM 32
            F  L+EN +     D     +++ E+LM
Sbjct: 145 AFEYLKENFLHSPSVDLSPETLKFLESLM 173


>gnl|CDD|218229 pfam04722, Ssu72, Ssu72-like protein.  The highly conserved and
          essential protein Ssu72 has intrinsic phosphatase
          activity and plays an essential role in the
          transcription cycle. Ssu72 was originally identified in
          a yeast genetic screen as enhancer of a defect caused
          by a mutation in the transcription initiation factor
          TFIIB. It binds to TFIIB and is also involved in mRNA
          elongation. Ssu72 is further involved in both poly(A)
          dependent and independent termination. It is a subunit
          of the yeast cleavage and polyadenylation factor (CPF),
          which is part of the machinery for mRNA 3'-end
          formation. Ssu72 is also essential for transcription
          termination of snRNAs.
          Length = 193

 Score = 24.9 bits (55), Expect = 4.8
 Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)

Query: 33 NSIERNLLTKNRDRFTQN--LSMFRRDIN 59
          + I  +L +++ + +TQN  L M  R+  
Sbjct: 58 DEIYNDLESQDEELYTQNGLLHMLDRNRR 86


  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
   0.319    0.131    0.382 

Gapped
Lambda     K      H
   0.267   0.0701    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,737,643
Number of extensions: 269552
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 23
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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: 53 (24.3 bits)