RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1736
         (125 letters)



>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
           motor.  This family represents the C-terminal region of
           dynein heavy chain. The chain also contains ATPase
           activity and microtubule binding ability and acts as a
           motor for the movement of organelles and vesicles along
           microtubules. Dynein is also involved in cilia and
           flagella movement. The dynein subunit consists of at
           least two heavy chains and a number of intermediate and
           light chains. The 380 kDa motor unit of dynein belongs
           to the AAA class of chaperone-like ATPases. The core of
           the 380 kDa motor unit contains a concatenated chain of
           six AAA modules, of which four correspond to the ATP
           binding sites with P-loop signatures described
           previously, and two are modules in which the P loop has
           been lost in evolution. This C-terminal domain carries
           the D6 region of the dynein motor where the P-loop has
           been lost in evolution but the general structure of a
           potential ATP binding site appears to be retained.
          Length = 706

 Score =  122 bits (307), Expect = 2e-33
 Identities = 46/117 (39%), Positives = 56/117 (47%), Gaps = 10/117 (8%)

Query: 2   TIPIDHLTFDFVVLQINKSE--SPPEDGVYCYGLFLDGARWDRTSNQLAEQFPKVLNDAL 59
             P+D L     V +  K E  S P DG Y +GLFL+GARWD  +  L E  PK L   +
Sbjct: 588 KWPLDKLCLQTDVTKKEKEEFDSAPRDGFYVHGLFLEGARWDGQNGLLLESRPKELFSPM 647

Query: 60  PIIWFVPTKKVELQIGSRYVCPLYKTSERRGTLSTTGHSTNYVIPLLLNTGLPSSHW 116
           P+IW       + +  S Y CP+YKT  R G        T YV   LL T  P S W
Sbjct: 648 PVIWVKAVPADKQEEKSVYECPVYKTETRGG--------TTYVFTFLLKTKEPPSKW 696


>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
          Length = 344

 Score = 27.6 bits (62), Expect = 1.6
 Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 4/33 (12%)

Query: 37  GARWDRTSNQLAEQFPKVLNDALPI----IWFV 65
           G  W RT +++A ++P V  D   +    I+ V
Sbjct: 194 GDLWQRTVDEVAAEYPDVTVDYQHVDAATIFMV 226


>gnl|CDD|132527 TIGR03488, cas_Cas5p, CRISPR-associated protein Cas5, subtype
           PGING.  CC Members of this protein family are cas, or
           CRISPR-associated, proteins. The two sequences in the
           alignment seed are found within cas gene clusters that
           are adjacent to CRISPR DNA repeats in two members of the
           order Bacteroidales, Porphyromonas gingivalis W83 and
           Bacteroides forsythus ATCC 43037. This cas protein
           family is unique to the Pgingi (Porphyromonas
           gingivalis) subtype, but shows some sequence similarity
           to genes of the Cas5 type (see TIGR02593).
          Length = 237

 Score = 27.2 bits (60), Expect = 2.0
 Identities = 12/42 (28%), Positives = 18/42 (42%)

Query: 41  DRTSNQLAEQFPKVLNDALPIIWFVPTKKVELQIGSRYVCPL 82
           D+  N   E+F K   D  P  +  PT +  +     Y CP+
Sbjct: 163 DKIDNHALEKFFKENIDFFPFFYATPTNREYIFFEGNYECPI 204


>gnl|CDD|235907 PRK07004, PRK07004, replicative DNA helicase; Provisional.
          Length = 460

 Score = 26.4 bits (58), Expect = 4.6
 Identities = 9/19 (47%), Positives = 13/19 (68%)

Query: 32 GLFLDGARWDRTSNQLAEQ 50
          GL LD A WDR ++ L++ 
Sbjct: 28 GLLLDNAAWDRIADFLSQS 46


>gnl|CDD|203928 pfam08390, TRAM1, TRAM1-like protein.  This family comprises
          sequences that are similar to human TRAM1. This is a
          transmembrane protein of the endoplasmic reticulum,
          thought to be involved in the membrane transfer of
          secretory proteins. The region featured in this family
          is found N-terminal to the longevity-assurance protein
          region (pfam03798).
          Length = 65

 Score = 24.4 bits (54), Expect = 6.3
 Identities = 9/24 (37%), Positives = 13/24 (54%)

Query: 9  TFDFVVLQINKSESPPEDGVYCYG 32
          T  F+ L  N + +PP  G+Y  G
Sbjct: 2  TSKFIFLSYNVTTTPPGTGLYGKG 25


>gnl|CDD|240332 PTZ00255, PTZ00255, 60S ribosomal protein L37a; Provisional.
          Length = 90

 Score = 24.7 bits (54), Expect = 7.8
 Identities = 8/23 (34%), Positives = 14/23 (60%), Gaps = 1/23 (4%)

Query: 68 KKVELQIGSRYVCPLY-KTSERR 89
          KK+E+   ++Y CP   K + +R
Sbjct: 27 KKIEISQHAKYFCPFCGKHAVKR 49


>gnl|CDD|218147 pfam04556, DpnII, DpnII restriction endonuclease.  Members of this
           family are type II restriction enzymes (EC:3.1.21.4).
           They recognise the double-stranded unmethylated sequence
           GATC and cleave before G-1.
           http://rebase.neb.com/rebase/enz/DpnII.html.
          Length = 284

 Score = 25.3 bits (56), Expect = 9.9
 Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 3/24 (12%)

Query: 36  DGARWDRTSNQLAEQF---PKVLN 56
           DG  W+   N+L E F     + N
Sbjct: 248 DGKGWNSAKNKLREAFEHIDYIYN 271


  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    0.138    0.438 

Gapped
Lambda     K      H
   0.267   0.0722    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,251,483
Number of extensions: 512683
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 9
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
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 (24.2 bits)