RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14430
         (497 letters)



>gnl|CDD|217788 pfam03914, CBF, CBF/Mak21 family. 
          Length = 151

 Score =  150 bits (382), Expect = 1e-43
 Identities = 60/142 (42%), Positives = 86/142 (60%), Gaps = 2/142 (1%)

Query: 286 IAVLALQGMVNLVRQYNLEYPNIYDKLYALLEPNIFYTKYKARLF-YLTDLLMMSTHLPE 344
            ++LAL  +  L+  +NL+    Y KLY LL   + ++ YK+RLF  L D  + S HLP 
Sbjct: 1   TSILALFLLFQLMSGHNLDLDRFYRKLYRLLLDKLLHSSYKSRLFLRLLDKALKSDHLPA 60

Query: 345 GLVASFIKRLSRLCLTAPPQDIAIMIYLIGNLVLRHKGLTILFQNSDATMLEDDPFDAKQ 404
             VA+F+KRL +L L APP     ++ LI NL+ RH  L  L    +    ED P+D ++
Sbjct: 61  QRVAAFVKRLLQLALHAPPSFALGILPLIRNLLKRHPNLKSLLHTEERG-GEDGPYDPEE 119

Query: 405 EDPYHTNALKSSLWEIKMLQNH 426
            DP ++NAL SSLWE+++LQNH
Sbjct: 120 RDPEYSNALNSSLWELELLQNH 141


>gnl|CDD|133460 cd06499, GT_MraY-like, Glycosyltransferase 4 (GT4) includes both
           eukaryotic and prokaryotic
           UDP-D-N-acetylhexosamine:polyprenol phosphate
           D-N-acetylhexosamine-1-phosphate transferases. They
           catalyze the transfer of a D-N-acetylhexosamine
           1-phosphate to a membrane-bound polyprenol phosphate,
           which is the initiation step of protein N-glycosylation
           in eukaryotes and peptidoglycan biosynthesis in
           bacteria. One member, D-N-acetylhexosamine 1-phosphate
           transferase (GPT) is a eukaryotic enzyme, which is
           specific for UDP-GlcNAc as donor substrate and
           dolichol-phosphate as the membrane bound acceptor. The
           bacterial members MraY, WecA, and WbpL/WbcO utilize
           undecaprenol phosphate as the acceptor substrate, but
           use different UDP-sugar donor substrates. MraY-type
           transferases are highly specific for
           UDP-N-acetylmuramate-pentapeptide, whereas WecA proteins
           are selective for UDP-N-acetylglucosamine (UDP-GlcNAc).
           The WbcO/WbpL substrate specificity has not yet been
           determined, but the structure of their biosynthetic
           endproducts implies that UDP-N-acetyl-D-fucosamine
           (UDP-FucNAc) and/or UDPN-acetyl-D-quinosamine
           (UDP-QuiNAc) are used. The eukaryotic reaction is the
           first step in the assembly of dolichol-linked
           oligosaccharide intermediates and is essential for
           N-glycosylation. The prokaryotic reactions lead to the
           formation of polyprenol-linked oligosaccharides involved
           in bacterial cell wall and peptidoglycan assembly.
           Archaeal and eukaryotic enzymes may use the same
           substrates and are evolutionarily closer than the
           bacterial enzyme. Archaea possess the same
           N-glycosylation pathway as eukaryotes. A glycosyl
           transferase gene Mv1751 in M. voltae encodes for the
           enzyme that carries out the first step in the pathway,
           the attachment of GlcNAc to a dolichol lipid carrier in
           the membrane. A lethal mutation in the alg7 (GPT) gene
           in Saccharomyces cerevisiae was successfully
           complemented with Mv1751, the archaea gene.
          Length = 185

 Score = 33.0 bits (76), Expect = 0.21
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 4/67 (5%)

Query: 236 IWEVLSKWKGHTSESTKLLLMVLIDKLMYY----HSNPIVITDFLMNALSFKGPIAVLAL 291
             + L   K   SE  KLLL +L    +      H+       F+++   F  P A++A+
Sbjct: 44  FIDDLLGLKVELSEREKLLLQILAALFLLLIGGGHTTVTTPLGFVLDLGIFYIPFAIIAI 103

Query: 292 QGMVNLV 298
            G  N V
Sbjct: 104 VGATNAV 110


>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
           ribosomal biogenesis [Translation, ribosomal structure
           and biogenesis].
          Length = 821

 Score = 33.9 bits (77), Expect = 0.23
 Identities = 17/37 (45%), Positives = 20/37 (54%)

Query: 400 FDAKQEDPYHTNALKSSLWEIKMLQNHPLYTVNVPAR 436
           +D ++ DP   NA KSSLWEI    NH   TV   A 
Sbjct: 537 YDGRKRDPKFANAEKSSLWEINNFINHFHPTVKTYAN 573


>gnl|CDD|132774 cd06864, PX_SNX4, The phosphoinositide binding Phox Homology domain
           of Sorting Nexin 4.  The PX domain is a phosphoinositide
           (PI) binding module present in many proteins with
           diverse functions. Sorting nexins (SNXs) make up the
           largest group among PX domain containing proteins. They
           are involved in regulating membrane traffic and protein
           sorting in the endosomal system. The PX domain of SNXs
           binds PIs and targets the protein to PI-enriched
           membranes. SNXs differ from each other in PI-binding
           specificity and affinity, and the presence of other
           protein-protein interaction domains, which help
           determine subcellular localization and specific function
           in the endocytic pathway. SNX4 is involved in recycling
           traffic from the sorting endosome (post-Golgi endosome)
           back to the late Golgi. It shows a similar domain
           architecture as SNX1-2, among others, containing a
           Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane
           curvature, C-terminal to the PX domain. SNX4 is
           implicated in the regulation of plasma membrane receptor
           trafficking and interacts with receptors for EGF,
           insulin, platelet-derived growth factor and the long
           form of the leptin receptor.
          Length = 129

 Score = 30.4 bits (69), Expect = 0.74
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 12/63 (19%)

Query: 118 EAKYPITLSKPFPEDKLQMLIKNILSSPFYPVFVERFKEYL-SF-----------KDVIF 165
              YP  +  P PE +   + + + S  F P FVER +  L +F           +D IF
Sbjct: 63  VVTYPYVIVPPLPEKRAMFMWQKLSSDTFDPDFVERRRAGLENFLLRVAGHPELCQDKIF 122

Query: 166 YSF 168
             F
Sbjct: 123 LEF 125


>gnl|CDD|236374 PRK09077, PRK09077, L-aspartate oxidase; Provisional.
          Length = 536

 Score = 31.0 bits (71), Expect = 1.7
 Identities = 9/20 (45%), Positives = 17/20 (85%)

Query: 7   LKKKINEFLSNRKYSNNLIE 26
           L+++I+E+ +N + SNNL+E
Sbjct: 469 LQQEIDEYYANFRVSNNLLE 488


>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal.  This model
           describes topoisomerase I from archaea. These enzymes
           are involved in the control of DNA topology. DNA
           topoisomerase I belongs to the type I topoisomerases,
           which are ATP-independent [DNA metabolism, DNA
           replication, recombination, and repair].
          Length = 618

 Score = 30.2 bits (68), Expect = 2.7
 Identities = 26/134 (19%), Positives = 45/134 (33%), Gaps = 33/134 (24%)

Query: 62  TSEDQDKKIKAAEEKYKVW--------LRDCYKSLFPKLFDIL-----------FN---- 98
           T E       A  EK+K+W          +  KS +  + ++            F+    
Sbjct: 221 TLEKGGGVFDARPEKWKIWSEEEAKSIKEELKKSPWAAVEEVRSERSILKPPPPFDLGTL 280

Query: 99  --------GESEVQIQTFSTLMHLVQGEAKYPITLSKPFPED-KLQMLIKNILSSPFYPV 149
                   G S  + Q+ +  ++  +    YP T S+  P     + ++ N+   P Y  
Sbjct: 281 QREAYRIFGFSPKKTQSIAQELYE-EALISYPRTSSQKLPPSINYRAILDNLAKGPLYRE 339

Query: 150 FVERFKEYLSFKDV 163
             ER  E    K V
Sbjct: 340 AAERLLETGVLKPV 353


>gnl|CDD|217620 pfam03572, Peptidase_S41, Peptidase family S41. 
          Length = 166

 Score = 29.1 bits (66), Expect = 3.6
 Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 6/51 (11%)

Query: 245 GHTSESTKLLLMVLIDKLMYYHSN------PIVITDFLMNALSFKGPIAVL 289
           G  S + ++  + L D  +    +          T         KGP+ VL
Sbjct: 43  GLLSAAVEIASLFLPDGTIVSTRDRIGDRPSNTTTQSSGERYLTKGPLVVL 93


>gnl|CDD|225111 COG2201, CheB, Chemotaxis response regulator containing a CheY-like
           receiver domain and a methylesterase domain [Cell
           motility and secretion / Signal transduction
           mechanisms].
          Length = 350

 Score = 29.6 bits (67), Expect = 4.3
 Identities = 10/18 (55%), Positives = 12/18 (66%)

Query: 341 HLPEGLVASFIKRLSRLC 358
           H+P G  ASF  RL+RL 
Sbjct: 192 HMPPGFTASFADRLNRLS 209


>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
           Provisional.
          Length = 1049

 Score = 29.9 bits (67), Expect = 4.4
 Identities = 40/218 (18%), Positives = 75/218 (34%), Gaps = 9/218 (4%)

Query: 1   MAGQINLKKKINEFLSNRKYSNNLIEILACLDDVNKVKPNTLLGIQRLFVELLKKHAMSS 60
           +AG +  ++K +  +      N L+ ++  L D  +     +   Q LF+   +  A   
Sbjct: 177 LAGVMFGRRKSSYEIEFTNGKNALLNLIKVLFDYPESHNIEV--PQILFLAPKELVAEFL 234

Query: 61  QTSEDQDKKIKAAEEKYKVWLRDCYKSLFPKLFDIL--FNGESEVQIQTFSTLMHLVQGE 118
           +   D D  +       ++ +          L  +L  F   S++   T           
Sbjct: 235 RGYFDADGHVN--LRSVRIEVSSASHEFIEDLSLLLLRFGIVSKIYRSTLIISGKRNLEN 292

Query: 119 AKYPITLSKPFPEDKLQMLIKNILSSPFYPVFVE--RFKEYLSFKDVIFYSFKSMSTLLS 176
            +  I  S     + L+ +I+    S  YP+  E  R +    F      S     +   
Sbjct: 293 FRKYIGFSVKEKAEALEKIIEKSKKSERYPINEELKRLRLLFGFTRNELSSNIPFYSKYE 352

Query: 177 ENFVENEEILMNVLNFIKEIPIPNNKEKLFPAEAKSEE 214
                + EILM +LN I+     N  +K+   E K  +
Sbjct: 353 SEEAPSYEILMEILNSIERGS-KNLDKKIAVLEGKIRD 389


>gnl|CDD|218110 pfam04489, DUF570, Protein of unknown function (DUF570).  Protein
           of unknown function, found in herpesvirus and
           cytomegalovirus.
          Length = 422

 Score = 29.4 bits (66), Expect = 5.3
 Identities = 22/99 (22%), Positives = 34/99 (34%), Gaps = 12/99 (12%)

Query: 90  PKLFDILFNGESE-VQIQTFSTLMHLVQGEAKYPITLSKPFPEDKLQMLIKNILSSPF-- 146
            +LF +L + E E + +Q F T      G   YP   S   P   L  +  ++   PF  
Sbjct: 100 KELFFLLASPEEENIVLQPFITKGGWRSGSFSYPSASSAAPP---LTGVSLDLTMVPFVP 156

Query: 147 --YPVFVERFKEYLSFKDVIFY----SFKSMSTLLSENF 179
              P F  RF        ++       F  +S +     
Sbjct: 157 YKIPEFYVRFIALDDPAGLMERAPGIEFGIISIVKRRGA 195


>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
           transferase subunit alpha; Provisional.
          Length = 762

 Score = 29.1 bits (65), Expect = 6.5
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 36  KVKPNTLLGIQRLFVELLKK----HAMSSQTSEDQDKKIKAAEEKYKVWLRDCYKSLFP 90
           K KP TL   ++  V+L KK      M+++T  D   +I + E KY+  L+D Y  L P
Sbjct: 91  KPKPVTL-DFEKPLVDLEKKIVDVRKMANETGLDFSDQIISLESKYQQALKDLYTHLTP 148


>gnl|CDD|223387 COG0310, CbiM, ABC-type Co2+ transport system, permease component
           [Inorganic ion transport and metabolism].
          Length = 204

 Score = 28.5 bits (64), Expect = 6.7
 Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 2/36 (5%)

Query: 366 IAIMI-YLIGNLVLRHKGLTILFQNSDATMLEDDPF 400
           +AI I  L+  L   H G+T L  N+   M    PF
Sbjct: 85  LAIAIVLLVQALFFAHGGITALGANTF-IMGIIGPF 119


>gnl|CDD|183516 PRK12416, PRK12416, protoporphyrinogen oxidase; Provisional.
          Length = 463

 Score = 29.0 bits (65), Expect = 7.2
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 12/43 (27%)

Query: 228 DFCTFSSKIWEVLSKWKGHTSESTKLLLMVLIDKLMYYHSNPI 270
           D CT++S+ W+       HTS   KLL+     ++ Y  +NP+
Sbjct: 334 DACTWTSRKWK-------HTSGKQKLLV-----RMFYKSTNPV 364


>gnl|CDD|178769 PLN03230, PLN03230, acetyl-coenzyme A carboxylase carboxyl
           transferase; Provisional.
          Length = 431

 Score = 28.8 bits (64), Expect = 7.3
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 35  NKVKPNTLLGIQRLFVELLKK----HAMSSQTSEDQDKKIKAAEEKYKVWLRDCYKSLFP 90
           NK KP TL   ++  V+L  +      ++++T  D   +I   EE+Y    R+ Y  L P
Sbjct: 69  NKPKPVTL-PFEKPIVDLENRIDEVRELANKTGVDFSAQIAELEERYDQVRRELYSRLTP 127


>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
           chromosome partitioning].
          Length = 1163

 Score = 28.9 bits (65), Expect = 8.1
 Identities = 45/262 (17%), Positives = 87/262 (33%), Gaps = 45/262 (17%)

Query: 6   NLKKKINEFLSNR-KYSNNLIEILACLDDVNKVKPNTLLGIQRLFVELLKKHAMSSQTS- 63
            L++++ E  +   +  N L E+   ++ + +        ++ L  EL +  A   +   
Sbjct: 380 ALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQT 439

Query: 64  --EDQDKKIKAAEEKYKVWLRDCYKSL---FPKLFDILFNGESEVQIQTFSTLMHLVQGE 118
             E+ +++++  EE+ +  LRD  K L     +L + L   E E+            +  
Sbjct: 440 ELEELNEELEELEEQLEE-LRDRLKELERELAELQEELQRLEKELSSL---------EAR 489

Query: 119 AKYPITLSKPFPEDKLQMLIKNILSSPFYPVFVERFK---EYLSFKDVIFYSFKSMSTLL 175
                   +     +  +          Y    E  K   +Y            ++   L
Sbjct: 490 LDRLEAEQRASQGVRAVLEALESGLPGVYGPVAELIKVKEKY----------ETALEAAL 539

Query: 176 SENF----VENEEILMNVLNFIKE------IPIPNNKEKLFPAEAKSEEFLCGNESLALN 225
                   VENEE+    + F+KE        +P ++ K  P  +   +   G   LA  
Sbjct: 540 GNRLQAVVVENEEVAKKAIEFLKENKAGRATFLPLDRIK--PLRSLKSDAAPGFLGLAS- 596

Query: 226 IKDFCTFSSKIWEVLSKWKGHT 247
             D   F  K    +    G T
Sbjct: 597 --DLIDFDPKYEPAVRFVLGDT 616


>gnl|CDD|185542 PTZ00293, PTZ00293, thymidine kinase; Provisional.
          Length = 211

 Score = 28.2 bits (63), Expect = 8.5
 Identities = 10/57 (17%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 54  KKHAMSSQTSEDQDKKIKAAEEKYKVWLRDCYKSLFPKLFDILFNGESEVQIQTFST 110
           K+ + S +  + +  ++   E+KY    R C+++      +     +  V+   FS 
Sbjct: 145 KEASFSKRIVQSEQIELIGGEDKYIATCRKCFRTKQLA--EKELEKQDLVEFADFSN 199


  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
   0.321    0.137    0.400 

Gapped
Lambda     K      H
   0.267   0.0806    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,454,792
Number of extensions: 2535575
Number of successful extensions: 2373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2368
Number of HSP's successfully gapped: 45
Length of query: 497
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 396
Effective length of database: 6,457,848
Effective search space: 2557307808
Effective search space used: 2557307808
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 (27.1 bits)