RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8359
         (279 letters)



>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 773

 Score =  109 bits (274), Expect = 7e-27
 Identities = 60/143 (41%), Positives = 82/143 (57%), Gaps = 5/143 (3%)

Query: 139 LTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDFTFKLFRIKINQIQMKETN 198
           L+  DL+R LQSL+C K  VL K           +F  N +F+ KL RIKIN I   E  
Sbjct: 634 LSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNT--KFYVNENFSSKLERIKINYIAESECM 691

Query: 199 EEQKATEERVFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRI 256
           ++   T E V +DRQ ++ A IVRIMK RK L H  L+ E+  Q K  F  K + +K+ I
Sbjct: 692 QDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAI 751

Query: 257 ESLIDRDYMERDKDKANSYNYMA 279
           E+LI+++Y+ER  D    Y Y+A
Sbjct: 752 ETLIEKEYLERQADD-EIYVYLA 773



 Score = 77.1 bits (190), Expect = 6e-16
 Identities = 33/57 (57%), Positives = 40/57 (70%)

Query: 62  KVDLAKRLLVGKSASVDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQ 118
           K  LAKRLL G+SAS  AE  M+S LK+ CG  FTSKLEGMF+D+ LS +   AF+ 
Sbjct: 467 KKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQH 523


>gnl|CDD|204512 pfam10557, Cullin_Nedd8, Cullin protein neddylation domain.  This
           is the neddylation site of cullin proteins which are a
           family of structurally related proteins containing an
           evolutionarily conserved cullin domain. With the
           exception of APC2, each member of the cullin family is
           modified by Nedd8 and several cullins function in
           Ubiquitin-dependent proteolysis, a process in which the
           26S proteasome recognises and subsequently degrades a
           target protein tagged with K48-linked poly-ubiquitin
           chains. Cullins are molecular scaffolds responsible for
           assembling the ROC1/Rbx1 RING-based E3 ubiquitin
           ligases, of which several play a direct role in
           tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
           protein, which was originally found to be conjugated to
           Cdc53, a cullin component of the SCF
           (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
           Saccharomyces cerevisiae, and Nedd8 modification has now
           emerged as a regulatory pathway of fundamental
           importance for cell cycle control and for embryogenesis
           in metazoans. The only identified Nedd8 substrates are
           cullins. Neddylation results in covalent conjugation of
           a Nedd8 moiety onto a conserved cullin lysine residue.
          Length = 68

 Score = 98.8 bits (247), Expect = 1e-26
 Identities = 42/68 (61%), Positives = 54/68 (79%), Gaps = 2/68 (2%)

Query: 208 VFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYM 265
           V +DR+ +I AAIVRIMK RKTLSHN L++E+  QLK  FP   AD+KKRIESLI+++Y+
Sbjct: 1   VEEDRKLEIQAAIVRIMKSRKTLSHNELVAEVIEQLKKRFPPSVADIKKRIESLIEKEYL 60

Query: 266 ERDKDKAN 273
           ERD+D  N
Sbjct: 61  ERDEDDRN 68


>gnl|CDD|214883 smart00884, Cullin_Nedd8, Cullin protein neddylation domain.  This
           is the neddylation site of cullin proteins which are a
           family of structurally related proteins containing an
           evolutionarily conserved cullin domain. With the
           exception of APC2, each member of the cullin family is
           modified by Nedd8 and several cullins function in
           Ubiquitin-dependent proteolysis, a process in which the
           26S proteasome recognises and subsequently degrades a
           target protein tagged with K48-linked poly-ubiquitin
           chains. Cullins are molecular scaffolds responsible for
           assembling the ROC1/Rbx1 RING-based E3 ubiquitin
           ligases, of which several play a direct role in
           tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
           protein, which was originally found to be conjugated to
           Cdc53, a cullin component of the SCF
           (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
           Saccharomyces cerevisiae, and Nedd8 modification has now
           emerged as a regulatory pathway of fundamental
           importance for cell cycle control and for embryogenesis
           in metazoans. The only identified Nedd8 substrates are
           cullins. Neddylation results in covalent conjugation of
           a Nedd8 moiety onto a conserved cullin lysine residue.
          Length = 68

 Score = 96.1 bits (240), Expect = 1e-25
 Identities = 41/68 (60%), Positives = 53/68 (77%), Gaps = 2/68 (2%)

Query: 208 VFQDRQYQIDAAIVRIMKMRKTLSHNLLLSELFNQLK--FPVKPADLKKRIESLIDRDYM 265
           V +DR+ +I AAIVRIMK RKTLSH+ L+SE+  QLK  F    +D+KKRIESLI+R+Y+
Sbjct: 1   VEEDRKLEIQAAIVRIMKSRKTLSHSELVSEVIEQLKKRFKPSVSDIKKRIESLIEREYL 60

Query: 266 ERDKDKAN 273
           ERD+D  N
Sbjct: 61  ERDEDDPN 68


>gnl|CDD|214545 smart00182, CULLIN, Cullin. 
          Length = 143

 Score = 97.8 bits (244), Expect = 2e-25
 Identities = 40/79 (50%), Positives = 53/79 (67%), Gaps = 7/79 (8%)

Query: 62  KVDLAKRLLVGKSASVDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMG 121
           K  LAKRL++ +SAS DAE++M++KLKQECG  FTSKLE MF+D+ LSKD+N +FK    
Sbjct: 13  KKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDM-- 70

Query: 122 NLKEDKESTSNNALGIDLT 140
                 E+  +    IDL 
Sbjct: 71  -----LENNPSAKPIIDLN 84


>gnl|CDD|216175 pfam00888, Cullin, Cullin family. 
          Length = 603

 Score = 96.5 bits (240), Expect = 2e-22
 Identities = 43/79 (54%), Positives = 54/79 (68%), Gaps = 6/79 (7%)

Query: 62  KVDLAKRLLVGKSASVDAEKSMLSKLKQECGGGFTSKLEGMFKDMELSKDINVAFKQYMG 121
           +  LAKRLL G SAS DAEK M+ KLKQECG  FTSKLE MFKD+ LSK++N +FK ++ 
Sbjct: 394 RKMLAKRLLNGTSASDDAEKKMIEKLKQECGYQFTSKLERMFKDISLSKELNNSFKNHLE 453

Query: 122 NLKEDKESTSNNALGIDLT 140
           N  +        + GIDL+
Sbjct: 454 NNLD------LLSEGIDLS 466



 Score = 44.2 bits (104), Expect = 5e-05
 Identities = 19/45 (42%), Positives = 23/45 (51%)

Query: 137 IDLTDADLRRTLQSLACGKTRVLKKTPASRDIEDCDRFRFNNDFT 181
             L+D  LRRTLQSL   K  +L K P   +      F  N+DFT
Sbjct: 559 TGLSDDLLRRTLQSLLKAKVLLLTKIPKGEEFSPNTVFSLNSDFT 603


>gnl|CDD|218602 pfam05478, Prominin, Prominin.  The prominins are an emerging
           family of proteins that among the multispan membrane
           proteins display a novel topology. Mouse prominin and
           human prominin (mouse)-like 1 (PROML1) are predicted to
           contain five membrane spanning domains, with an
           N-terminal domain exposed to the extracellular space
           followed by four, alternating small cytoplasmic and
           large extracellular, loops and a cytoplasmic C-terminal
           domain. The exact function of prominin is unknown
           although in humans defects in PROM1, the gene coding for
           prominin, cause retinal degeneration.
          Length = 807

 Score = 29.2 bits (66), Expect = 3.0
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 100 EGMFKDMELSKDINVA----FKQYMGNLKEDKESTSNNALGIDLTDADLRRTLQSLACGK 155
           E ++  ++L+   ++      KQY   + ++ ES   N   I L   + RR L+ LA   
Sbjct: 544 EPLYTVLQLNNSYDLNELLDIKQYTPEIDQELESLKVNLSTITLLTPEARRNLEDLASSG 603

Query: 156 T 156
            
Sbjct: 604 L 604


>gnl|CDD|236940 PRK11633, PRK11633, cell division protein DedD; Provisional.
          Length = 226

 Score = 28.0 bits (63), Expect = 4.0
 Identities = 11/22 (50%), Positives = 13/22 (59%)

Query: 68  RLLVGKSASVDAEKSMLSKLKQ 89
           R+ VG  AS D  K  L +LKQ
Sbjct: 191 RIYVGPDASKDKLKGSLGELKQ 212


>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
          Length = 865

 Score = 27.7 bits (63), Expect = 7.9
 Identities = 12/28 (42%), Positives = 19/28 (67%), Gaps = 2/28 (7%)

Query: 235 LLSELFNQLKFPVKPADLKKRIESLIDR 262
           LL EL   LK   KP++L +R+E+L++ 
Sbjct: 702 LLKELAALLK--AKPSELPERVEALLEE 727


>gnl|CDD|137204 PRK09310, aroDE, bifunctional 3-dehydroquinate
           dehydratase/shikimate dehydrogenase protein; Reviewed.
          Length = 477

 Score = 27.8 bits (62), Expect = 7.9
 Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 3/28 (10%)

Query: 230 LSHNLLLSEL---FNQLKFPVKPADLKK 254
           LSHN L S+L      +K P+ P +L K
Sbjct: 232 LSHNPLFSQLSLNCPYIKLPLTPQELPK 259


>gnl|CDD|213733 TIGR02720, pyruv_oxi_spxB, pyruvate oxidase.  Members of this
           family are examples of pyruvate oxidase (EC 1.2.3.3), an
           enzyme with FAD and TPP as cofactors that catalyzes the
           reaction pyruvate + phosphate + O2 + H2O = acetyl
           phosphate + CO2 + H2O2. It should not be confused with
           pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2) as in
           E. coli PoxB, although the E. coli enzyme is closely
           homologous and has pyruvate oxidase as an alternate name
           [Energy metabolism, Aerobic].
          Length = 575

 Score = 27.5 bits (61), Expect = 9.3
 Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 112 INVAF-KQYMGNLKEDKESTSNNALGIDLTDAD 143
           IN+ F     G +K+++E T+   +G+D  DAD
Sbjct: 456 INIVFSNCTYGFIKDEQEDTNQPLIGVDFNDAD 488


  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
   0.316    0.130    0.353 

Gapped
Lambda     K      H
   0.267   0.0811    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,363,127
Number of extensions: 1232509
Number of successful extensions: 1134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1127
Number of HSP's successfully gapped: 31
Length of query: 279
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 183
Effective length of database: 6,679,618
Effective search space: 1222370094
Effective search space used: 1222370094
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 (21.6 bits)
S2: 58 (26.0 bits)