RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16001
         (318 letters)



>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6.  In yeast, 15 Apg proteins
           coordinate the formation of autophagosomes. Autophagy is
           a bulk degradation process induced by starvation in
           eukaryotic cells. Apg6/Vps30p has two distinct functions
           in the autophagic process, either associated with the
           membrane or in a retrieval step of the carboxypeptidase
           Y sorting pathway.
          Length = 356

 Score =  301 bits (772), Expect = e-101
 Identities = 143/253 (56%), Positives = 169/253 (66%), Gaps = 32/253 (12%)

Query: 93  LDMMDKELKNTKQDFQ-EYSDF----------LKTLELQLQYSLSQLNKFKSTNVFNATF 141
           L    ++L+N +  +  EY+ F          L++LELQ +YSL+QL+K + TN+FNATF
Sbjct: 103 LQEEKEQLENEELQYLREYNLFDRNNLQLEDNLQSLELQYEYSLNQLDKLRKTNIFNATF 162

Query: 142 HIWHSGHFGTINNFRLGTLPSAPVDWSEINAAWGQTALLLTALARKLNLTFQRYRIVPYG 201
           HI HSG F TIN  RLG LPS  V W EINAAWGQT LLL ALA+KL L F RYR+VP+G
Sbjct: 163 HISHSGPFATINGLRLGRLPSVVVPWKEINAAWGQTVLLLAALAKKLGLNFVRYRLVPFG 222

Query: 202 NHSYIEDTTEHKN-------------------LPLFASGGAKFFWDTKFDMAMVAFLDCL 242
           +HSYIE    +                     L L+ SGG KFFWDTKFD AMVAFLDCL
Sbjct: 223 SHSYIEKLMVNSVEYNNSTTNAPGDWLILPVELDLYFSGGLKFFWDTKFDKAMVAFLDCL 282

Query: 243 QQFKEELEKGDSEFHLPYNMD-SKGKIED-ETTGNTYSVKYQFNSQEQWTKALKFMLTNL 300
            QF  E+EK  ++F LPY M+  KGKI D E +G +YS+KYQFNS EQWTKALKFMLTNL
Sbjct: 283 SQFTREVEKIATQFLLPYQMESEKGKINDVENSGGSYSIKYQFNSDEQWTKALKFMLTNL 342

Query: 301 KWGLAWVSSQFKN 313
           KW LAWVSSQF  
Sbjct: 343 KWLLAWVSSQFSK 355



 Score = 72.6 bits (178), Expect = 2e-14
 Identities = 29/58 (50%), Positives = 39/58 (67%)

Query: 63  QMKVYANLFDFLSSNSGIDHPLCEECTDTLLDMMDKELKNTKQDFQEYSDFLKTLELQ 120
           Q+K   NLFD LSS + IDHPLCEEC D LL+ +D EL++ +++   Y  +L  LE Q
Sbjct: 1   QVKAMTNLFDILSSQTNIDHPLCEECADILLERLDSELRDAEKERDTYKQYLSKLESQ 58


>gnl|CDD|221897 pfam13017, Maelstrom, piRNA pathway germ-plasm component.
           Maelstrom is a germ-plasm component protein, that is
           shown to be functionally involved in the piRNA pathway.
           It is conserved throughout Eukaryota, though it appears
           to have been lost from all examined teleost fish
           species. The domain architecture shows that it is
           coupled with several DNA- and RNA- related domains such
           as HMG box, SR-25-like and HDAC_interact domains.
           Sequence analysis and fold recognition have found a
           distant similarity between Maelstrom domain and the DnaQ
           3'-5' exonuclease family with the RNase H fold
           (Exonuc_X-T, pfam00929); notably, that the Maelstrom
           domains from basal eukaryotes contain the conserved
           3'-5' exonuclease active site residues
           (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and
           some amoeba maelstrom contain another set of conserved
           residues (Glu-His-His-Cys-His-Cys, EHHCHC). This
           evolutionary link together with structural examinations
           leads to the hypothesis that Maelstrom domains may have
           a potential nuclease-transposase activity or RNA-binding
           ability that may be implicated in piRNA biogenesis. A
           protein function evolution mode, namely "active site
           switch", has been proposed, in which the amoeba
           Maelstrom domains are the possible evolutionary
           intermediates due to their harbouring of the specific
           characteristics of both 3'-5' exonuclease and Maelstrom
           domains.
          Length = 213

 Score = 32.0 bits (73), Expect = 0.29
 Identities = 17/68 (25%), Positives = 22/68 (32%), Gaps = 3/68 (4%)

Query: 65  KVYANLFDFLSSNSGIDHPLCEECTDTLLDMMDKELKNTKQDFQEYSDFLKTLELQLQYS 124
           ++Y  L  FL S +G D P         + M+   LK    D  E            QY 
Sbjct: 68  ELYNELLSFLKSFNGGDKPPPIFTKTEDIPMVKSCLKYLASDAGESERI---KVYDFQYL 124

Query: 125 LSQLNKFK 132
              L K  
Sbjct: 125 FFVLKKEV 132


>gnl|CDD|216833 pfam01991, vATP-synt_E, ATP synthase (E/31 kDa) subunit.  This
           family includes the vacuolar ATP synthase E subunit, as
           well as the archaebacterial ATP synthase E subunit.
          Length = 195

 Score = 30.8 bits (70), Expect = 0.67
 Identities = 14/40 (35%), Positives = 19/40 (47%)

Query: 86  EECTDTLLDMMDKELKNTKQDFQEYSDFLKTLELQLQYSL 125
           EE  D++ +   + L N  +D  EY D LK L  Q    L
Sbjct: 71  EELLDSVFEEAKERLANLSEDKDEYKDLLKDLIKQALVKL 110


>gnl|CDD|217201 pfam02722, MOSP_C, Major Outer Sheath Protein C-terminal region.
           This is a family of spirochete major outer sheath
           protein C-terminal regions. These proteins are present
           on the bacterial cell surface. In T. denticola the major
           outer sheath protein (Msp) binds immobilised laminin and
           fibronectin supporting the hypothesis that Msp mediates
           the extracellular matrix binding activity of T.
           denticola.
          Length = 201

 Score = 30.2 bits (68), Expect = 1.1
 Identities = 15/46 (32%), Positives = 19/46 (41%)

Query: 218 FASGGAKFFWDTKFDMAMVAFLDCLQQFKEELEKGDSEFHLPYNMD 263
           FA+  A  F       A+   LDC    K E + GD   HL   +D
Sbjct: 17  FATAPANVFGKRVLPAALSDHLDCAAFLKLETKSGDPYTHLVTGLD 62


>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase.  This model represents
           the threonyl-tRNA synthetase found in most organisms.
           This protein is a class II tRNA synthetase, and is
           recognized by the pfam model tRNA-synt_2b. Note that B.
           subtilis has closely related isozymes thrS and thrZ. The
           N-terminal regions are quite dissimilar between archaeal
           and eubacterial forms, while some eukaryotic forms are
           missing sequence there altogether. [Protein synthesis,
           tRNA aminoacylation].
          Length = 563

 Score = 29.2 bits (66), Expect = 3.3
 Identities = 13/70 (18%), Positives = 22/70 (31%), Gaps = 16/70 (22%)

Query: 186 RKLNLTFQRYRIV------PYGNH-------SYIEDTTEHKNLPLFASGGAKFFWDTKFD 232
                +F +Y +         G         + +E+  +   +P     G   F+  K D
Sbjct: 339 SDFGFSFDKYELSTRDPEDFIGEDELWEKAEAALEEALKELGVPYEIDPGRGAFYGPKID 398

Query: 233 MAMVAFLDCL 242
               AF D L
Sbjct: 399 ---FAFKDAL 405


>gnl|CDD|222157 pfam13473, Cupredoxin_1, Cupredoxin-like domain.  The
           cupredoxin-like fold consists of a beta-sandwich with 7
           strands in 2 beta-sheets, which is arranged in a
           Greek-key beta-barrel.
          Length = 104

 Score = 27.1 bits (61), Expect = 5.4
 Identities = 8/20 (40%), Positives = 14/20 (70%)

Query: 249 LEKGDSEFHLPYNMDSKGKI 268
           L+ G+ +F    +MD+KGK+
Sbjct: 83  LKPGEYDFFCGMHMDAKGKL 102


>gnl|CDD|237523 PRK13825, PRK13825, conjugal transfer protein TraB; Provisional.
          Length = 388

 Score = 28.1 bits (63), Expect = 7.3
 Identities = 10/33 (30%), Positives = 16/33 (48%)

Query: 159 TLPSAPVDWSEINAAWGQTALLLTALARKLNLT 191
           TLP AP  W  ++   G++     +L R+  L 
Sbjct: 180 TLPRAPAGWVGVDTQLGRSLGRDASLERRRELI 212


>gnl|CDD|233136 TIGR00805, oat, sodium-independent organic anion transporter.  The
           Organo Anion Transporter (OAT) Family (TC
           2.A.60)Proteins of the OAT family catalyze the
           Na+-independent facilitated transport of organic anions
           such as bromosulfobromophthalein and prostaglandins as
           well as conjugated and unconjugated bile acids
           (taurocholate and cholate, respectively). These
           transporters have been characterized in mammals, but
           homologues are present in C. elegans and A. thaliana.
           Some of the mammalian proteins exhibit a high degree of
           tissue specificity. For example, the rat OAT is found at
           high levels in liver and kidney and at lower levels in
           other tissues. These proteins possess 10-12 putative
           a-helical transmembrane spanners. They may catalyze
           electrogenic anion uniport or anion exchange.
          Length = 633

 Score = 28.1 bits (63), Expect = 8.1
 Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 1/22 (4%)

Query: 197 IVPYGNHSYIEDTTEHKNLPLF 218
           I P G  SYI+D  + KN PL+
Sbjct: 189 IFPLGI-SYIDDFAKSKNSPLY 209


>gnl|CDD|235389 PRK05287, PRK05287, hypothetical protein; Provisional.
          Length = 250

 Score = 27.5 bits (62), Expect = 8.8
 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 18/69 (26%)

Query: 70  LFDFLSSNSGIDHPL-CEECTDTLLDMMD----KELKNTKQDFQEYSDFLKTLELQLQYS 124
           LF  L+ N   D P        TL +++D     +LK         SD LK LE Q Q  
Sbjct: 24  LFQQLTFNLAQDDPADHHVAFRTLFELLDVLERGDLK---------SDLLKELERQRQ-- 72

Query: 125 LSQLNKFKS 133
             +L K++ 
Sbjct: 73  --KLQKWRG 79


  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
   0.318    0.132    0.402 

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: 15,539,676
Number of extensions: 1416568
Number of successful extensions: 1272
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1269
Number of HSP's successfully gapped: 17
Length of query: 318
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 221
Effective length of database: 6,635,264
Effective search space: 1466393344
Effective search space used: 1466393344
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: 59 (26.5 bits)