RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10508
         (555 letters)



>gnl|CDD|221339 pfam11957, efThoc1, THO complex subunit 1 transcription elongation
           factor.  The THO complex plays a role in coupling
           transcription elongation to mRNA export. It is composed
           of subunits THP2, HPR1, THO2 and MFT1. The THO complex
           is a nuclear complex that is required for transcription
           elongation through genes containing tandemly repeated
           DNA sequences. The THO complex is also part of the TREX
           (TRanscription EXport) complex that is involved in
           coupling transcription to export of mRNAs to the
           cytoplasm.
          Length = 494

 Score =  363 bits (933), Expect = e-120
 Identities = 162/494 (32%), Positives = 233/494 (47%), Gaps = 75/494 (15%)

Query: 56  KVIENYISLCVELC--MKDMCNSTLPIILLSDTFDMSTLDKCEQLFYYVEVNVNIWKQQT 113
           K + N +     L    +  C   L   LL +  D  T+D C +LF Y+E     +K+  
Sbjct: 1   KNLWNLLDFVSILSDNEQPFCEPGLLFFLLEELLDSLTIDGCRKLFDYLESRREWFKKGH 60

Query: 114 FFMSCKNN-LLRMCNDLLRRLSRSQNTVFCGRILLFLAKFFPFSERSGLNIISEFNVENI 172
           FF   KN  LLR CN+LLRRLSR+++TVFCGRIL+FL++ FP SE+S +N+  EFN EN+
Sbjct: 61  FFQPVKNGVLLRTCNELLRRLSRTEDTVFCGRILIFLSQLFPLSEKSNVNLRGEFNTENV 120

Query: 173 TEFGGDEEMDVSSNETEETDTEEVDKVKIDFNFYKKFWSLQDYFRNPVQCYN-KVSWKMF 231
           T +  +           + +T   D + +D+N Y  FWSLQDYF NP + ++    +  F
Sbjct: 121 TTWDQEI---------GKDETSSSDSIDVDYNLYPIFWSLQDYFSNPTKLFSPLEEFATF 171

Query: 232 TSYAETVLAAFKSYKLDDVQSS-------------LNP------------SGDYFAKYLT 266
            S  E  L AF   + +                  LN             S  +  KYLT
Sbjct: 172 KSGLEATLQAFLEIETELYNKIKSKTAEIKVDSRALNKRKRNPLDGEELASSFFNPKYLT 231

Query: 267 NQKLLDLQLSDTNFRRYVLLQFLILFQYFTS------------TVKSRGEGLELKSDQEK 314
           ++ L +L+LSD+NFRR VL+Q LILF +  S            T KS      L  + +K
Sbjct: 232 SRDLFELELSDSNFRRQVLVQVLILFDFLLSLTKKDKAKLAYNTNKSVIYSDVLSDEDKK 291

Query: 315 WVKDTTETVYSLIKQTPPDGEHFSQVVKLILKGEEHWNQWKNEGCPELKRPLTSITDEDK 374
           W+K T + V   +K+  P G+ F ++V+ +L  EE+W +WKNEGCP  ++P T   D+  
Sbjct: 292 WIKFTKKKVEKRLKEFYPKGKKFYRMVEHLLSREENWVRWKNEGCPSFEKPHTV--DKIS 349

Query: 375 KDEPDAKKKK-------------TPELTKLWNSKD--NLEACKSAERDFTPSLESYFEEA 419
             E +   KK                L  LW  K    L+  K  ER   P LE Y +  
Sbjct: 350 VPEAEEAFKKRGFPKRLLGIKMGNKNLNFLWEKKIDSGLDRLKDEERYRIPPLEVYLDGI 409

Query: 420 IQ---QMDPAAAVEEQYKKVNDSNYAWRALRLLSRKCPHFF--LNATPNVEKNSEFIENM 474
            +   ++DPA   E++    N     WRALRLL R     F  +N    ++      E +
Sbjct: 410 AEDKFEIDPANTDEKEEAAENKIVKTWRALRLLRRSYLFEFDKINEKTGLK---GLFEEI 466

Query: 475 VKRCVKEKPSSQIS 488
            K+  KEK   +  
Sbjct: 467 RKKAAKEKKDPREE 480


>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger.  [Transport and
           binding proteins, Cations and iron carrying compounds].
          Length = 1096

 Score = 35.4 bits (81), Expect = 0.089
 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 8/67 (11%)

Query: 489 GNGNGVDQDPAEVEVDTKSEEIQEEEKEEDWEAKADPEGDADEVMSVEYCYQRNWHKQAV 548
           G  +G D +  E E + + EE +EEE+EE      + E + +E +S+E+   R   KQA+
Sbjct: 856 GGSDGGDSEEEEEEEEEEEEEEEEEEEEE------EEEEENEEPLSLEWPETR--QKQAI 907

Query: 549 TSFIIGI 555
             F++ I
Sbjct: 908 YLFLLPI 914



 Score = 31.1 bits (70), Expect = 1.9
 Identities = 11/52 (21%), Positives = 22/52 (42%)

Query: 480 KEKPSSQISGNGNGVDQDPAEVEVDTKSEEIQEEEKEEDWEAKADPEGDADE 531
           + +   +I     G  +   E+E      + + E +E + E + + EG  DE
Sbjct: 678 ENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDE 729


>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2.  Transcripts
           harbouring premature signals for translation termination
           are recognised and rapidly degraded by eukaryotic cells
           through a pathway known as nonsense-mediated mRNA decay.
           In Saccharomyces cerevisiae, three trans-acting factors
           (Upf1 to Upf3) are required for nonsense-mediated mRNA
           decay.
          Length = 171

 Score = 30.0 bits (68), Expect = 2.1
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 488 SGNGNGVDQDPAEVEVDTKSEEIQEEEKEEDWEAKADPEGDAD-----EVMSVEYCYQR 541
           S +   VD    E + ++ SEE Q     +  E + DPE +A+     E M  E    R
Sbjct: 25  SSDEEEVDLPDDEQDEESDSEEEQIFVTRQ--EEEVDPEAEAEFDREFEKMMAESLESR 81


>gnl|CDD|223122 COG0044, PyrC, Dihydroorotase and related cyclic amidohydrolases
           [Nucleotide transport and metabolism].
          Length = 430

 Score = 29.6 bits (67), Expect = 4.8
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 312 QEKWVKDTTETVYSLIKQTPPDG-EHFSQVVKLILKGEEHWNQWKNEGCP 360
            E+W     E +YS  K +P +G E   +VV  IL+G+  +     E   
Sbjct: 381 DEEWTIRA-EELYSKAKNSPFEGFELKGRVVATILRGKVVY--EDGEVIA 427


>gnl|CDD|225148 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
           [Inorganic ion transport and metabolism].
          Length = 451

 Score = 29.5 bits (67), Expect = 5.0
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 494 VDQDPAEVEVDTKSE--EIQEEEKEEDWEAKADPEGDADEVMSV 535
           VD+D   + + T  +  ++ EEE  ED    A P    D   SV
Sbjct: 233 VDEDNRLIGIITIDDIIDVIEEEATEDILRMAGPLDVPDLFASV 276


>gnl|CDD|233743 TIGR02136, ptsS_2, phosphate binding protein.  Members of this
           family are phosphate-binding proteins. Most are found in
           phosphate ABC-transporter operons, but some are found in
           phosphate regulatory operons. This model separates
           members of the current family from the phosphate ABC
           transporter phosphate binding protein described by
           TIGRFAMs model TIGR00975 [Transport and binding
           proteins, Anions].
          Length = 287

 Score = 28.9 bits (65), Expect = 6.6
 Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 15  NVVSDKYALYKPTCDYDKKSALEQSIRQYLLKLIKTPDIDIKVIEN--YISL 64
           N+ +  Y L +P   Y      +  +    +  + + D   +++E   Y+ L
Sbjct: 236 NIANGSYPLSRPLFMYVNGKPKKPELVAEFIDFVLSDDGGERIVEELGYVPL 287


>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
           factor RRN3.  This family consists of several eukaryotic
           proteins which are homologous to the yeast RRN3 protein.
           RRN3 is one of the RRN genes specifically required for
           the transcription of rDNA by RNA polymerase I (Pol I) in
           Saccharomyces cerevisiae.
          Length = 554

 Score = 29.2 bits (66), Expect = 7.2
 Identities = 22/108 (20%), Positives = 33/108 (30%), Gaps = 15/108 (13%)

Query: 52  DIDIKVIENYISLCVELCMKDMCNSTLPIILLSDTFDMSTLDKCEQLFYYVEVNVNIWKQ 111
             D   +E YI     L       S          +    L      F  V    +  + 
Sbjct: 86  GRDESFVEAYIQFLGNLV------SAQG------KYLGEVLSMLVSHF--VPPPSSTSES 131

Query: 112 QTFFMSCKNNLLRMCNDLLRRLSRSQNTVFCGRILLFLAKFFPFSERS 159
                  +  +L   +D LR + R   +   G +L  LAK FP   +S
Sbjct: 132 PGDPPVEQREVLSRVHDALRYILRLVPSSP-GFLLPILAKNFPHKTKS 178


>gnl|CDD|214802 smart00752, HTTM, Horizontally Transferred TransMembrane Domain.
           Sequence analysis of vitamin K dependent
           gamma-carboxylases (VKGC) revealed the presence of a
           novel domain, HTTM (Horizontally Transferred
           TransMembrane) in its N-terminus. In contrast to most
           known domains, HTTM contains four transmembrane regions.
           Its occurrence in eukaryotes, bacteria and archaea is
           more likely caused by horizontal gene transfer than by
           early invention. The conservation of VKGC catalytic
           sites indicates an enzymatic function also for the other
           family members.
          Length = 271

 Score = 28.8 bits (65), Expect = 7.3
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 9/51 (17%)

Query: 283 YVLLQFLILFQYFTSTVKSRGEGLELKSDQEKWVKDTT-ETVYSLIKQTPP 332
             +L+  +   YF + +K        K D ++WV  T    + SL     P
Sbjct: 154 TFVLRIQVFIIYFFAGLK--------KLDGDEWVDGTAMYYLLSLDWFFSP 196


>gnl|CDD|182781 PRK10854, PRK10854, exopolyphosphatase; Provisional.
          Length = 513

 Score = 28.9 bits (65), Expect = 7.7
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 272 DLQLSDTNFRRYVLLQFLILFQY---FTSTVKSRGEGLELKSDQEKWVKDTTETVYS 325
           +L+LSD   R  VL +    F++    + T KS      +  +Q + V +TT  +Y 
Sbjct: 289 ELRLSDGALREGVLYEMEGRFRHQDIRSRTAKSLANHYNIDREQARRVLETTMQLYE 345


>gnl|CDD|173597 PTZ00407, PTZ00407, DNA topoisomerase IA; Provisional.
          Length = 805

 Score = 28.8 bits (64), Expect = 8.8
 Identities = 18/62 (29%), Positives = 19/62 (30%), Gaps = 13/62 (20%)

Query: 330 TPPDGEHFSQVVKLI--LKGE-EHWN----------QWKNEGCPELKRPLTSITDEDKKD 376
             P G  FSQVV +    KG   HW           QWK   C     PL          
Sbjct: 259 PSPHGTTFSQVVTITPDRKGGASHWATEAEARRCLEQWKLNNCTGFSVPLEPKPQPSVVP 318

Query: 377 EP 378
            P
Sbjct: 319 PP 320


  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    0.132    0.390 

Gapped
Lambda     K      H
   0.267   0.0721    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,814,824
Number of extensions: 2687349
Number of successful extensions: 3129
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3084
Number of HSP's successfully gapped: 41
Length of query: 555
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 453
Effective length of database: 6,413,494
Effective search space: 2905312782
Effective search space used: 2905312782
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: 62 (27.7 bits)