RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5970
         (169 letters)



>gnl|CDD|216518 pfam01471, PG_binding_1, Putative peptidoglycan binding domain.
          This domain is composed of three alpha helices. This
          domain is found at the N or C terminus of a variety of
          enzymes involved in bacterial cell wall degradation.
          This domain may have a general peptidoglycan binding
          function. This family is found N-terminal to the
          catalytic domain of matrixins. The domain is found to
          bind peptidoglycan experimentally.
          Length = 57

 Score = 43.3 bits (103), Expect = 1e-06
 Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 5  LQSYLANFGYLEASSNSEIANLRTKEQVTEA-RFGNIPVTGIVDDATLALM 54
          LQ YL   GY     +       T+  V    RF  +PVTGIVD  TLA +
Sbjct: 8  LQRYLKRLGYYPGPVDGVFGP-STEAAVKAFQRFFGLPVTGIVDPETLAAL 57


>gnl|CDD|237915 PRK15123, PRK15123, lipopolysaccharide core heptose(I) kinase
          RfaP; Provisional.
          Length = 268

 Score = 31.8 bits (73), Expect = 0.13
 Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 5/28 (17%)

Query: 67 LDRRRTKRFTLDGR----KWDHTDLTWR 90
          L+ RRT RF L G+    KW H    W 
Sbjct: 33 LEGRRTLRFELAGKSYFLKW-HRGTGWG 59


>gnl|CDD|239805 cd04278, ZnMc_MMP, Zinc-dependent metalloprotease, matrix
          metalloproteinase (MMP) sub-family. MMPs are
          responsible for a great deal of pericellular
          proteolysis of extracellular matrix and cell surface
          molecules, playing crucial roles in morphogenesis, cell
          fate specification, cell migration, tissue repair,
          tumorigenesis, gain or loss of tissue-specific
          functions, and apoptosis. In many instances, they are
          anchored to cell membranes via trans-membrane domains,
          and their activity is controlled via TIMPs (tissue
          inhibitors of metalloproteinases).
          Length = 157

 Score = 28.3 bits (64), Expect = 1.4
 Identities = 7/13 (53%), Positives = 11/13 (84%)

Query: 81 KWDHTDLTWRVLS 93
          KW  T+LT+R+L+
Sbjct: 1  KWSKTNLTYRILN 13


>gnl|CDD|239562 cd03480, Rieske_RO_Alpha_PaO, Rieske non-heme iron oxygenase (RO)
          family, Pheophorbide a oxygenase (PaO) subfamily,
          N-terminal Rieske domain of the oxygenase alpha
          subunit; composed of the oxygenase alpha subunits of a
          small subfamily of enzymes found in plants as well as
          oxygenic cyanobacterial photosynthesizers including
          LLS1 (lethal leaf spot 1, also known as PaO) and ACD1
          (accelerated cell death 1). ROs comprise a large class
          of aromatic ring-hydroxylating dioxygenases that enable
          microorganisms to tolerate and utilize aromatic
          compounds for growth. The oxygenase alpha subunit
          contains an N-terminal Rieske domain with an [2Fe-2S]
          cluster and a C-terminal catalytic domain with a
          mononuclear Fe(II) binding site. The Rieske [2Fe-2S]
          cluster accepts electrons from a reductase or
          ferredoxin component and transfers them to the
          mononuclear iron for catalysis. PaO expression
          increases upon physical wounding of plant leaves and is
          thought to catalyze a key step in chlorophyll
          degradation. The Arabidopsis-accelerated cell death
          gene ACD1 is involved in oxygenation of PaO.
          Length = 138

 Score = 27.3 bits (61), Expect = 2.5
 Identities = 12/30 (40%), Positives = 12/30 (40%), Gaps = 4/30 (13%)

Query: 67 LDRRRTKRFTLDGRK----WDHTDLTWRVL 92
          LD  R   FTL GR     WD     WR  
Sbjct: 27 LDPSRPTPFTLLGRDLVIWWDRNSQQWRAF 56


>gnl|CDD|215908 pfam00413, Peptidase_M10, Matrixin.  The members of this family
          are enzymes that cleave peptides. These proteases
          require zinc for catalysis.
          Length = 159

 Score = 27.2 bits (61), Expect = 3.0
 Identities = 5/12 (41%), Positives = 9/12 (75%)

Query: 81 KWDHTDLTWRVL 92
          KW   +LT+R++
Sbjct: 1  KWKKKNLTYRIV 12


>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional.
          Length = 258

 Score = 26.7 bits (60), Expect = 6.7
 Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)

Query: 29  KEQ--VTEARFGNIPVTGIVD 47
           KE   V EAR   IPV  IVD
Sbjct: 168 KEHIAVKEARKLGIPVVAIVD 188


>gnl|CDD|213747 TIGR02869, spore_SleB, spore cortex-lytic enzyme.  Members of
          this protein family are the spore cortex-lytic enzyme
          SleB from Bacillus subtilis and other Gram-positive,
          endospore-forming bacterial species. This protein is
          stored in an inactive form in the spore and activated
          during germination [Cellular processes, Sporulation and
          germination].
          Length = 200

 Score = 26.6 bits (59), Expect = 6.8
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 4/50 (8%)

Query: 5  LQSYLANFGYLEASSNSEIANLRTKEQVT--EARFGNIPVTGIVDDATLA 52
          +Q  L  +GY     +  +    T   V   +++ G + V GIV   T A
Sbjct: 18 IQRRLKYWGYYNGKVDG-VFGWGTYWAVRNFQSKNG-LTVDGIVGPKTKA 65


>gnl|CDD|223130 COG0052, RpsB, Ribosomal protein S2 [Translation, ribosomal
           structure and biogenesis].
          Length = 252

 Score = 26.5 bits (59), Expect = 8.0
 Identities = 8/16 (50%), Positives = 9/16 (56%)

Query: 32  VTEARFGNIPVTGIVD 47
           V EA    IPV  +VD
Sbjct: 172 VKEANKLGIPVVALVD 187


>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
           D-isomer-specific 2-hydroxyacid dehydrogenases related
           repressor.  The transcriptional corepressor CtBP is a
           dehydrogenase with sequence and structural similarity to
           the d2-hydroxyacid dehydrogenase family. CtBP was
           initially identified as a protein that bound the PXDLS
           sequence at the adenovirus E1A C terminus, causing the
           loss of CR-1-mediated transactivation. CtBP binds NAD(H)
           within a deep cleft, undergoes a conformational change
           upon NAD binding, and has NAD-dependent dehydrogenase
           activity.
          Length = 312

 Score = 26.3 bits (59), Expect = 9.2
 Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 7/34 (20%)

Query: 43  TGIVDDATLALMKK-------PRCGLPDTPPLDR 69
             ++D   LALMK         R GL D   L R
Sbjct: 211 RHLIDAEALALMKPGAFLVNTARGGLVDEAALAR 244


  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    0.134    0.394 

Gapped
Lambda     K      H
   0.267   0.0818    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,114,409
Number of extensions: 706326
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 531
Number of HSP's successfully gapped: 14
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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: 55 (24.8 bits)