RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy416
         (157 letters)



>gnl|CDD|204985 pfam12624, Chorein_N, N-terminal region of Chorein, a TM
           vesicle-mediated sorter.  Although mutations in the
           full-length vacuolar protein sorting 13A (VPS13A)
           protein in vertebrates lead to the disease of
           chorea-acanthocytosis, the exact function of any of the
           regions within the protein is not yet known. This region
           is the proposed leucine zipper at the N-terminus. The
           full-length protein is a transmembrane protein with a
           presumed role in vesicle-mediated sorting and
           intracellular protein transport.
          Length = 117

 Score =  143 bits (362), Expect = 5e-45
 Identities = 58/117 (49%), Positives = 80/117 (68%)

Query: 2   LERLIAWVLNNYLGKYVENLNTDQLSVALLQGAVELENLPLKKDALRQLGIPIEIKSGFI 61
            E L+A +LN YLG+YVENL+ +QLSV++  G VELENL LKKDAL +L +PIE+KSG I
Sbjct: 1   FESLVADLLNRYLGEYVENLDKEQLSVSIWSGDVELENLRLKKDALDKLDLPIEVKSGHI 60

Query: 62  GKVKLQVPVSQFRSAPWVICIEQLYVVTGPVSMAQWDEELEERAAQEYKIMLLDALE 118
           GK+ L++P     S P VI I+ +Y++  P    ++DEE EE+  +  K   L+ LE
Sbjct: 61  GKLTLKIPWKSLGSEPVVITIDDVYILASPKDNDEYDEEEEEKREKALKKKKLEELE 117


>gnl|CDD|227376 COG5043, MRS6, Vacuolar protein sorting-associated protein
           [Intracellular trafficking and secretion].
          Length = 2552

 Score =  107 bits (269), Expect = 9e-28
 Identities = 57/155 (36%), Positives = 87/155 (56%), Gaps = 2/155 (1%)

Query: 1   MLERLIAWVLNNYLGKYVENLNTDQLSVALLQGAVELENLPLKKDALRQLGIPIEIKSGF 60
           MLE L+A +LN  LG YVEN +T QL+V +  G V L NL +K  AL +LG+PIE+ SG 
Sbjct: 1   MLEGLLANLLNRLLGSYVENFDTKQLNVGVWGGDVSLHNLRIKPSALDKLGLPIEVTSGL 60

Query: 61  IGKVKLQVPVSQFRSAPWVICIEQLYVVTGPVSMAQWDEELEERAAQEYKIMLLDALEAR 120
           IG + L++P S  ++ P  I IE +Y++  P +      E   ++ Q  K   LD+ E  
Sbjct: 61  IGTLTLEIPWSSLKNKPVEIYIEDIYLLISPQAKNSLTREELPQSQQALKQRQLDSWEIL 120

Query: 121 WRAETESACYYSSSYTSWLSYGTSFMTNIVENLQV 155
                ES+   + S     S+  S +T +++N+Q+
Sbjct: 121 RETLEESSSSPNISRKQ--SFIESLITKLIDNIQI 153


>gnl|CDD|111626 pfam02750, Synapsin_C, Synapsin, ATP binding domain.  Ca dependent
           ATP binding in this ATP grasp fold. Function unknown.
          Length = 203

 Score = 29.5 bits (66), Expect = 0.54
 Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 6/98 (6%)

Query: 35  VELENLPLKKDALRQLGIPIEIKSGF----IGKVKLQVPVSQFRSAPWVICIEQLYVVTG 90
           +E    P  K+ L     P+ +K G     +GKVK+      F+    V+ + + Y  T 
Sbjct: 34  IEQTYYPNHKEMLTTPTFPVVVKIGHAHSGMGKVKVDNH-HDFQDIASVVALTKTYATTE 92

Query: 91  PVSMAQWDEELEERAAQEYKIMLLDALEARWRAETESA 128
           P   +++D  ++ +    YK  +  ++   W+A T SA
Sbjct: 93  PFIDSKYDIRVQ-KIGNNYKAYMRTSISGNWKANTGSA 129


>gnl|CDD|238795 cd01554, EPT-like, Enol pyruvate transferases family includes
          EPSP synthases and UDP-N-acetylglucosamine enolpyruvyl
          transferase. Both enzymes catalyze the reaction of
          enolpyruvyl transfer.
          Length = 408

 Score = 28.7 bits (64), Expect = 1.2
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 6/39 (15%)

Query: 29 ALLQGAVELENLPLKKD------ALRQLGIPIEIKSGFI 61
          +L +G  ++ N+   +D       LR LG+ IE K G I
Sbjct: 22 SLAEGETKVYNILRGEDVLSTMQVLRDLGVEIEDKDGVI 60


>gnl|CDD|215834 pfam00275, EPSP_synthase, EPSP synthase (3-phosphoshikimate
          1-carboxyvinyltransferase). 
          Length = 415

 Score = 28.8 bits (65), Expect = 1.3
 Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 6/33 (18%)

Query: 29 ALLQGAVELENLPLKKD------ALRQLGIPIE 55
          AL  G   + NL    D      ALR LG  + 
Sbjct: 28 ALAAGESTITNLLDSDDTRLMLEALRALGAEVI 60


>gnl|CDD|234014 TIGR02786, addB_alphas, double-strand break repair protein AddB,
           alphaproteobacterial type.  AddAB is a system well
           described in the Firmicutes as a replacement for RecBCD
           in many prokaryotes for the repair of double stranded
           break DNA damage. More recently, a distantly related
           gene pair conserved in many alphaproteobacteria was
           shown also to function in double-stranded break repair
           in Rhizobium etli. This family consists of AddB proteins
           of the alphaproteobacteial type [DNA metabolism, DNA
           replication, recombination, and repair].
          Length = 1021

 Score = 28.9 bits (65), Expect = 1.3
 Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 8/48 (16%)

Query: 78  WVICIEQLYVVTGPVSMAQWDEELEERA---AQEYKIMLLDALEARWR 122
           W + ++ L +VT       W + L E         +  LL AL ARW 
Sbjct: 168 WQVTLKFLEIVT-----RAWPKRLAELGRSNPAARRNRLLRALAARWA 210


>gnl|CDD|235037 PRK02427, PRK02427, 3-phosphoshikimate 1-carboxyvinyltransferase;
           Provisional.
          Length = 435

 Score = 27.4 bits (62), Expect = 3.1
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 12/44 (27%)

Query: 45  DALRQLGI----------PIEIKSGFIGK-VKLQVPV-SQFRSA 76
           D LRQ+G           P+ I+ G  G  ++   PV SQF  +
Sbjct: 128 DPLRQMGAKIEGRDEGYLPLTIRGGKKGGPIEYDGPVSSQFVKS 171


>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
          Length = 485

 Score = 27.2 bits (61), Expect = 3.7
 Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 5/35 (14%)

Query: 79  VICIEQLYVVTG--PVSMAQWDEELEERAAQEYKI 111
           VIC+   YV  G    S+AQ    L+ER A EY I
Sbjct: 170 VICV---YVAIGQKASSVAQVVTTLQERGAMEYTI 201


>gnl|CDD|239033 cd02115, AAK, Amino Acid Kinases (AAK) superfamily, catalytic
           domain; present in such enzymes like N-acetylglutamate
           kinase (NAGK), carbamate kinase (CK), aspartokinase
           (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK).
           The AAK superfamily includes kinases that phosphorylate
           a variety of amino acid substrates. These kinases
           catalyze the formation of phosphoric anhydrides,
           generally with a carboxylate, and use ATP as the source
           of the phosphoryl group; are involved in amino acid
           biosynthesis. Some of these kinases control the process
           via allosteric feed-back inhibition.
          Length = 248

 Score = 27.0 bits (60), Expect = 4.1
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 2/46 (4%)

Query: 15  GKYVENLNTDQLSVALLQGAVELENLPLKKDALRQLGIPIEIKSGF 60
            K +  L  ++ +     GA+ L+  P   D   + GIP+ I +  
Sbjct: 188 AKLLSELTYEEAAELAYAGAMVLK--PKAADPAARAGIPVRIANTE 231


>gnl|CDD|238797 cd01556, EPSP_synthase, EPSP synthase domain. 3-phosphoshikimate
           1-carboxyvinyltransferase
           (5-enolpyruvylshikimate-3-phosphate synthase) (EC
           2.5.1.19) catalyses the reaction between
           shikimate-3-phosphate (S3P) and phosphoenolpyruvate
           (PEP) to form 5-enolpyruvylshkimate-3-phosphate (EPSP),
           an intermediate in the shikimate pathway leading to
           aromatic amino acid biosynthesis. The reaction is
           phosphoenolpyruvate + 3-phosphoshikimate = phosphate +
           5-O-(1-carboxyvinyl)-3-phosphoshikimate. It is found in
           bacteria and plants but not animals. The enzyme is the
           target of the widely used herbicide glyphosate, which
           has been shown to occupy the active site. In bacteria
           and plants, it is a single domain protein, while in
           fungi, the domain is found as part of a multidomain
           protein with functions that are all part of the
           shikimate pathway.
          Length = 409

 Score = 27.1 bits (61), Expect = 4.4
 Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 13/45 (28%)

Query: 45  DALRQLGIPIE----------IKSGFI--GKVKLQVPVS-QFRSA 76
           DALRQLG  IE          I  G +  G+V++   VS QF+SA
Sbjct: 117 DALRQLGAEIEGREGGGYPPLIGGGGLKGGEVEIPGAVSSQFKSA 161



 Score = 26.4 bits (59), Expect = 6.7
 Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 6/37 (16%)

Query: 29 ALLQGAVELENLPLKKD------ALRQLGIPIEIKSG 59
          AL +G   +ENL    D      ALR LG  IE + G
Sbjct: 22 ALAEGESRIENLLDSDDTLATLEALRALGAKIEEEGG 58


>gnl|CDD|223206 COG0128, AroA, 5-enolpyruvylshikimate-3-phosphate synthase [Amino
           acid transport and metabolism].
          Length = 428

 Score = 27.2 bits (61), Expect = 4.5
 Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 13/45 (28%)

Query: 45  DALRQLGI-----------PIEIKSGFIGK-VKLQVPV-SQFRSA 76
           DALRQLG            P+ IK G  G  V++  PV SQ  S+
Sbjct: 130 DALRQLGAKIDGREGEGYLPLTIKGGLKGGEVEIDGPVSSQQVSS 174


>gnl|CDD|236233 PRK08311, PRK08311, putative RNA polymerase sigma factor SigI;
          Reviewed.
          Length = 237

 Score = 26.4 bits (59), Expect = 6.2
 Identities = 10/26 (38%), Positives = 19/26 (73%)

Query: 6  IAWVLNNYLGKYVENLNTDQLSVALL 31
          IA V+++  G+Y++  N D+LS+ L+
Sbjct: 31 IAKVVSSVCGRYIDWENDDELSIGLI 56


>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 = 26.1 bits (58), Expect = 9.0
 Identities = 11/35 (31%), Positives = 15/35 (42%)

Query: 94  MAQWDEELEERAAQEYKIMLLDALEARWRAETESA 128
           M  W + LEE   +E K +L     A W   +E  
Sbjct: 323 MGVWQQCLEEENLKELKKLLTRNKRALWTLFSERT 357


  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
   0.317    0.132    0.389 

Gapped
Lambda     K      H
   0.267   0.0782    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,169,809
Number of extensions: 737051
Number of successful extensions: 768
Number of sequences better than 10.0: 1
Number of HSP's gapped: 768
Number of HSP's successfully gapped: 26
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.9 bits)