RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17737
         (493 letters)



>gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase.
           Corresponds to Merops family A17. These proteins are
           homologous to aspartic proteinases encoded by
           retroposons and retroviruses.
          Length = 159

 Score =  135 bits (341), Expect = 1e-37
 Identities = 57/158 (36%), Positives = 85/158 (53%), Gaps = 1/158 (0%)

Query: 51  TKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIK 110
           TKR +LS   SI+D LGL  PV +  KI +Q +W++ L WDEE+  E    ++   + + 
Sbjct: 2   TKREVLSQVASIFDPLGLLAPVTVRAKIFLQEIWRQKLGWDEEIPEELSQRWLAFRKQLS 61

Query: 111 LIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAP 170
            +  + +PR +    P    +LHGF DAS  +Y+  +Y +   G  +  +LV AK R+AP
Sbjct: 62  TLQQIRVPRYV-PYSPARNIQLHGFCDASEKAYAAAVYWRVEEGEEIQVSLVAAKTRVAP 120

Query: 171 LSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLW 208
           L   ++PRLEL  AL+  R  + V     VK    Y W
Sbjct: 121 LKTVSIPRLELCAALLLTRLARAVKPEHDVKPTDTYCW 158


>gnl|CDD|233883 TIGR02475, CobW, cobalamin biosynthesis protein CobW.  The family
           of proteins identified by this model is generally found
           proximal to the trimeric cobaltochelatase subunit CobN
           which is essential for vitamin B12 (cobalamin)
           biosynthesis. The protein contains an P-loop
           nucleotide-binding loop in the N-terminal domain and a
           histidine-rich region in the C-terminal portion
           suggesting a role in metal binding, possibly as an
           intermediary between the cobalt transport and chelation
           systems. A broader CobW family is delineated by two PFAM
           models which identify the N- and C-terminal domains
           (pfam02492 and pfam07683) [Biosynthesis of cofactors,
           prosthetic groups, and carriers, Heme, porphyrin, and
           cobalamin].
          Length = 341

 Score = 33.6 bits (77), Expect = 0.24
 Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 7/55 (12%)

Query: 379 HQKFASTMQELKQ-GHKDQLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLL 432
           H +F S + +L +      L Q+L  + +E+D+LR KG F    V GK   PM L
Sbjct: 249 HDEFDSVVVDLGEVADPAALRQRLERLAEEHDVLRIKG-FAA--VPGK---PMRL 297


>gnl|CDD|216950 pfam02259, FAT, FAT domain.  The FAT domain is named after FRAP,
           ATM and TRRAP.
          Length = 350

 Score = 32.0 bits (73), Expect = 0.71
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 19/82 (23%)

Query: 345 LKFIRLCRRQK---------------ENKGNISIIEYEESKLSWIKFAQHQKFASTMQEL 389
           LKF  L R+                 + + ++  +    +K  W K  Q       +Q+L
Sbjct: 153 LKFANLARKSGRFSLAEKALLKLLTYDTREDLPNVVIAYAKYLWAKGQQQ----EAIQKL 208

Query: 390 KQGHKDQLSQQLGLVLDENDIL 411
           ++     LS+ +G   D   +L
Sbjct: 209 REFVSCYLSKPVGSSSDSELLL 230


>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
           strand of an RNA/DNA hybrid in a sequence non-specific
           manner.  Ribonuclease H (RNase H) enzymes are divided
           into two major families, Type 1 and Type 2, based on
           amino acid sequence similarities and biochemical
           properties. RNase H is an endonuclease that cleaves the
           RNA strand of an RNA/DNA hybrid in a sequence
           non-specific manner in the presence of divalent cations.
           RNase H is widely present in various organisms,
           including bacteria, archaea and eukaryotes. Most
           prokaryotic and eukaryotic genomes contain multiple
           RNase H genes. Despite the lack of amino acid sequence
           homology, Type 1 and type 2 RNase H share a main-chain
           fold and steric configurations of the four acidic
           active-site residues and have the same catalytic
           mechanism and functions in cells. RNase H is involved in
           DNA replication, repair and transcription. One of the
           important functions of RNase H is to remove Okazaki
           fragments during DNA replication. RNase H inhibitors
           have been explored as an anti-HIV drug target because
           RNase H inactivation inhibits reverse transcription.
          Length = 123

 Score = 28.5 bits (64), Expect = 3.2
 Identities = 21/105 (20%), Positives = 33/105 (31%), Gaps = 10/105 (9%)

Query: 159 SNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWI 218
               +  A    +   T    ELL  L A          L +K +      DS+ V+  I
Sbjct: 22  HEGAWLFAGSLSIPAATNNEAELLALLEALELAL----DLGLKKLIIET--DSKYVVDLI 75

Query: 219 LGNKVLPTFINNRVKEIKNRSFK---LDVHYVPTDMNP-ADIACR 259
                     N  + +I     K   +   +VP + N  AD   +
Sbjct: 76  NSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPREGNEVADRLAK 120


>gnl|CDD|153313 cd07629, BAR_Atg20p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
           Sorting Nexin Atg20p.  BAR domains are dimerization,
           lipid binding and curvature sensing modules found in
           many different proteins with diverse functions. Sorting
           nexins (SNXs) are Phox homology (PX) domain containing
           proteins that are involved in regulating membrane
           traffic and protein sorting in the endosomal system.
           SNXs differ from each other in their lipid-binding
           specificity, subcellular localization and specific
           function in the endocytic pathway. A subset of SNXs also
           contain BAR domains. The PX-BAR structural unit
           determines the specific membrane targeting of SNXs. The
           function of Atg20p is unknown but it has been shown to
           interact with Atg11p, which plays a role in linking
           cargo molecules with vesicle-forming components. BAR
           domains form dimers that bind to membranes, induce
           membrane bending and curvature, and may also be involved
           in protein-protein interactions.
          Length = 187

 Score = 28.9 bits (65), Expect = 4.0
 Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 184 ALIAYRGLKFVGESLKVKDIKYYLWIDSQ--IVIHWILGNKVLPTFINNRVKEIK 236
            L+ YR LK V   +    +     + +   +VI   +  K LP F   R  +++
Sbjct: 106 ELLKYRKLKHVQYEMTKDSLLESALVAASDDLVISSTIKQKDLPRFQREREADLR 160


>gnl|CDD|224010 COG1085, GalT, Galactose-1-phosphate uridylyltransferase [Energy
           production and conversion].
          Length = 338

 Score = 28.5 bits (64), Expect = 7.2
 Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 7/63 (11%)

Query: 286 WPQWSFTDEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVL 345
           W +W F   I P+  VS    LS   +K L++ L          +++  N   N   Y +
Sbjct: 217 WARWPFEVLIYPKEHVSFLTDLSDEELKDLAEILK-----KLLARYD--NLFGNSFPYSM 269

Query: 346 KFI 348
            F 
Sbjct: 270 GFH 272


>gnl|CDD|183252 PRK11640, PRK11640, putative transcriptional regulator;
           Provisional.
          Length = 191

 Score = 28.0 bits (63), Expect = 9.2
 Identities = 9/19 (47%), Positives = 11/19 (57%)

Query: 82  SVWQRNLSWDEELSTEDKI 100
             W+R L  DE LS E K+
Sbjct: 61  DTWRRQLLLDETLSAEQKL 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
   0.320    0.136    0.416 

Gapped
Lambda     K      H
   0.267   0.0731    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,959,145
Number of extensions: 2397250
Number of successful extensions: 1709
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1706
Number of HSP's successfully gapped: 13
Length of query: 493
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 392
Effective length of database: 6,457,848
Effective search space: 2531476416
Effective search space used: 2531476416
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: 61 (27.3 bits)