RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6393
         (315 letters)



>gnl|CDD|218643 pfam05571, DUF766, Protein of unknown function (DUF766).  This
           family consists of several eukaryotic proteins of
           unknown function.
          Length = 296

 Score =  285 bits (731), Expect = 5e-96
 Identities = 135/316 (42%), Positives = 191/316 (60%), Gaps = 31/316 (9%)

Query: 6   CAGLYCGRYYL----PDGNLSACEACPRGFRANALTICEPCNDSPTFYDWLYLGFMVLFP 61
           C GLYCGR  L     +   S C ACPRG+R NA +IC PC    + YDWLYLGFM + P
Sbjct: 1   CLGLYCGRTLLFNNSSEEIYSECGACPRGYRVNAQSICSPCTTPLSLYDWLYLGFMAMLP 60

Query: 62  LICHWFAIDSTPQFTGSQNQKSAFYPIRTFKAKKKNFNKEALILHFTAFVEVSLAAVLTL 121
           L+ H F ID                    +  K + F+   +IL+ +A +EV +AAVLT+
Sbjct: 61  LLLHMFFID--------------------WARKYRKFSYYEVILYASAILEVVIAAVLTV 100

Query: 122 LLVDPVGSYQIRSCNVDKLQDWYTVFYNPNPDYEYTLHCTQEAVYPLYTMVFIFYLLNII 181
           L+  P    ++ SC V  L DWYT+FYNP+P+YE T++CTQEAVYPLYT+VF+FYL  ++
Sbjct: 101 LIYPPRWELRLNSCRVRMLSDWYTLFYNPSPNYETTVYCTQEAVYPLYTIVFVFYLFCLV 160

Query: 182 ILTSIRP-LIARFCIRTGAARTVYFGLYLFPVLALVHLICD----YSFAYITIVLSVVSM 236
           ++  +RP L+ +    +G  + +Y  LY FP+L ++H +      YSF YI++V+S+V+ 
Sbjct: 161 LMFLLRPILVCKILYVSGNMKPIYAALYFFPILTVIHAVLGGLIYYSFPYISLVISLVAN 220

Query: 237 ATHFAFKIDQSVHFLVVSTVTDLRNCLILLGHWALHAYGLVVITQPHVNPALIIL--LVP 294
           A H + K+DQ +  L+V +VT   N +IL  HW L AYG++ + +P        L  LVP
Sbjct: 221 AFHLSLKLDQPLKALIVRSVTSPTNLVILFIHWLLLAYGVISLIRPLDIEYDWSLLCLVP 280

Query: 295 TPALFYILTSRFTDPS 310
            P LFYI T +FTDP+
Sbjct: 281 VPTLFYIFTIKFTDPA 296


>gnl|CDD|219525 pfam07699, GCC2_GCC3, GCC2 and GCC3. 
          Length = 48

 Score = 28.2 bits (63), Expect = 0.69
 Identities = 12/33 (36%), Positives = 13/33 (39%), Gaps = 4/33 (12%)

Query: 12 GRYYLPDGNLSACEACPRGFRANA--LTICEPC 42
          G Y   +  L  CE CPRG          C PC
Sbjct: 1  GTYS--NSGLKPCEPCPRGTYQPEEGQDSCIPC 31



 Score = 25.5 bits (56), Expect = 6.5
 Identities = 8/22 (36%), Positives = 10/22 (45%), Gaps = 1/22 (4%)

Query: 11 CGR-YYLPDGNLSACEACPRGF 31
          C R  Y P+    +C  CP G 
Sbjct: 14 CPRGTYQPEEGQDSCIPCPPGT 35


>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
          Length = 1465

 Score = 29.4 bits (66), Expect = 3.0
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 9/51 (17%)

Query: 91  FKAKKKNFNKEALILHFTAFV---------EVSLAAVLTLLLVDPVGSYQI 132
           F + K+NF KEA +   + +V         E SLA+ +  +  D VGS  I
Sbjct: 716 FCSFKRNFVKEAKVAQLSGYVSEHSAYHHGEQSLASTIIGMAQDFVGSNNI 766


>gnl|CDD|214379 CHL00161, secY, preprotein translocase subunit SecY; Validated.
          Length = 417

 Score = 29.2 bits (66), Expect = 3.3
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 8/67 (11%)

Query: 165 VYPLYTMVFIFYLLNIIILTSIRPLIARFCIRTGAARTVYFGLYLFPVLALVHLICDYSF 224
           ++    +V   YL NI++   + PL++ F ++  + + +Y  LY         LI  +S+
Sbjct: 260 IFASALLVLPGYLTNILLNQFLLPLLSLF-LQLASFKILYLVLYFV-------LILFFSY 311

Query: 225 AYITIVL 231
            Y TIVL
Sbjct: 312 FYSTIVL 318


>gnl|CDD|227280 COG4944, COG4944, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 213

 Score = 27.4 bits (61), Expect = 7.8
 Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 4/41 (9%)

Query: 156 YTLHCTQEAVYPLYTMVFIFYLLNIIILTSIRPLIARFCIR 196
           Y  HCT++        V  +Y L I++L  I  L  R  +R
Sbjct: 176 YAWHCTEDG----PLFVATWYTLGILLLGVIGALAGRRLLR 212


>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25.  All proteins in this
           family for which functions are known are DNA-DNA
           helicases used for the initiation of nucleotide excision
           repair and transacription as part of the TFIIH
           complex.This family is based on the phylogenomic
           analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
           University) [DNA metabolism, DNA replication,
           recombination, and repair].
          Length = 732

 Score = 27.8 bits (62), Expect = 8.0
 Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 5/43 (11%)

Query: 97  NFNKEALIL-HFTAFVEVSLAAVLTLLLVDPVGSYQIRSCNVD 138
           ++ K  L+L H   FVE     VL  LL DPV    I  C +D
Sbjct: 103 SYGKVKLVLKHNRYFVESPHPEVLQRLLKDPV----IAPCRID 141


>gnl|CDD|215118 PLN02177, PLN02177, glycerol-3-phosphate acyltransferase.
          Length = 497

 Score = 27.6 bits (61), Expect = 9.8
 Identities = 12/20 (60%), Positives = 12/20 (60%)

Query: 139 KLQDWYTVFYNPNPDYEYTL 158
           KL D Y VF NP P YE T 
Sbjct: 417 KLLDPYFVFMNPRPTYEITF 436


  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
   0.331    0.143    0.466 

Gapped
Lambda     K      H
   0.267   0.0778    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,297,843
Number of extensions: 1579456
Number of successful extensions: 1996
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1988
Number of HSP's successfully gapped: 53
Length of query: 315
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 218
Effective length of database: 6,635,264
Effective search space: 1446487552
Effective search space used: 1446487552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 59 (26.4 bits)