RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14241
         (136 letters)



>gnl|CDD|227501 COG5174, TFA2, Transcription initiation factor IIE, beta subunit
           [Transcription].
          Length = 285

 Score = 48.8 bits (116), Expect = 9e-08
 Identities = 22/110 (20%), Positives = 52/110 (47%), Gaps = 9/110 (8%)

Query: 7   EALQNNPKIEVIEGNK-YIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCE 65
             L+   +I +   +  ++FKP++ I+  + LLK+L+        G+ +  + +  P+  
Sbjct: 118 LLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLR--SQGTEEGLSMKKLMDGWPNVV 175

Query: 66  KALK-----NEIIYVTRPADKRKVMF-YNDKSAQLDLDEDFQKLWRSISV 109
             ++     NEI+ +    D   V+   N ++ +  +D +F+ LW  + +
Sbjct: 176 PFVEELEKSNEILILRTDKDGSPVVVWNNTQNLECPVDPEFKSLWNQVRI 225


>gnl|CDD|200387 TIGR04136, rSAM_FibroRumin, radical SAM peptide maturase,
           FibroRumin system.  Members of this protein family are
           radical SAM enzymes proposed to act on small, Cys-rich
           peptides encoded by tandem gene pairs. Members occur in
           enzymes Fibrobacter succinogenes subsp. succinogenes S85
           (genes for their target peptides missed) and in
           Ruminococcus albus 8. This enzyme family is similar in
           sequence to the SCIFF (Six Cysteines in Forty-Five)
           system maturase (TIGR03974).
          Length = 458

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 24/101 (23%)

Query: 31  IKDRKGLLKLLKQHDLKGIG-GILLDDVRESLPHCEKALKNEIIYVTRPADKRKVMFYND 89
           IKD++ ++ L+ ++ +KG+G  I++ D R  LP                        YND
Sbjct: 268 IKDQQDVIDLIDEYGIKGLGFNIMMGDDRFPLPAD----------------------YND 305

Query: 90  KSAQLDLDEDFQKLWRSISVDGMILRIRSFYGVD-YFSGAG 129
           K+AQ  +DE  +     I  D ++ ++++F     YFS   
Sbjct: 306 KAAQFIIDEFKELREIGIYEDRIMRKLKAFAKAQVYFSDCA 346


>gnl|CDD|153423 cd07977, TFIIE_beta_winged_helix, TFIIE_beta_winged_helix domain,
          located at the central core region of TFIIE beta, with
          double-stranded DNA binding activity.  Transcription
          Factor IIE (TFIIE) beta winged-helix (or forkhead)
          domain is located at the central core region of TFIIE
          beta. The winged-helix is a form of helix-turn-helix
          (HTH) domain which typically binds DNA with the 3rd
          helix. The winged-helix domain is distinguished by the
          presence of a C-terminal beta-strand hairpin unit (the
          wing) that packs against the cleft of the tri-helical
          core. Although most winged-helix domains are
          multi-member families, TFIIE beta winged-helix domain
          is typically found as a single orthologous group. TFIIE
          is one of the six eukaryotic general transcription
          factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH)
          that are required for transcription initiation of
          protein-coding genes. TFIIE is a heterotetramer
          consisting of two copies each of alpha and beta
          subunits. TFIIE beta contains several functional
          domains, an N-terminal serine-rich region, a central
          core domain exhibiting a winged-helix structure capable
          of binding double-stranded DNA, a leucine repeat, a
          sigma3 region, and a C-terminal domain containing two
          basic regions. The assembly of transcription
          preinitiation complex (PIC) includes the general
          transcription factors and RNA polymerase II (pol II)
          initiated by the binding of the TBP subunit of TFIID to
          the TATA box, followed by either the sequential
          assembly of other general transcription factors and pol
          II or a preassembled pol II holoenzyme pathway. TFIIE
          interacts directly with TFIIF, TFIIB, pol II, and
          promoter DNA. TFIIE recruits TFIIH and regulates its
          activities. TFIIE and TFIIH are also important for the
          transition from initiation to elongation.
          Length = 75

 Score = 34.1 bits (79), Expect = 0.003
 Identities = 15/30 (50%), Positives = 21/30 (70%), Gaps = 1/30 (3%)

Query: 3  WLSTEALQNNPKIEVIEGNKYIFKPVFKIK 32
          WL +EAL NNPKI+  +G  + FKP + I+
Sbjct: 47 WLKSEALVNNPKIDPKDG-TFSFKPKYNIR 75


>gnl|CDD|216922 pfam02186, TFIIE_beta, TFIIE beta subunit core domain.  General
          transcription factor TFIIE consists of two subunits,
          TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has
          been found to bind to the region where the promoter
          starts to open to be single-stranded upon transcription
          initiation by RNA polymerase II. The structure of the
          DNA binding core region has been solved and has a
          winged helix fold.
          Length = 65

 Score = 30.7 bits (70), Expect = 0.043
 Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 9  LQNNPKIEVI-EGNKYIFKPVFKI 31
          L+NNPKI+   +G  + FKP++ I
Sbjct: 42 LKNNPKIKFDPKGGTFAFKPLYNI 65


>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site
           selection and in elongation by RNA polymerase II
           [Transcription].
          Length = 521

 Score = 29.2 bits (65), Expect = 0.73
 Identities = 24/110 (21%), Positives = 42/110 (38%), Gaps = 11/110 (10%)

Query: 22  KYIFKPVFK-------IKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKNEIIY 74
           + +FKP+F+        + R G       + + G+G         S P+  K +K     
Sbjct: 225 RNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVGKGST----YSKPYGRKEVKTNRYL 280

Query: 75  VTRPADKRKVMFYNDKSAQLDLDEDFQKLWRSISVDGMILRIRSFYGVDY 124
                   KV   N+ S    L E++Q++WRS  V  + +   +     Y
Sbjct: 281 DVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKY 330


>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
           Validated.
          Length = 383

 Score = 28.3 bits (64), Expect = 1.2
 Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 6/50 (12%)

Query: 7   EALQNNPKIEV-IEGNKYIFKPVFKIKDRKGLLKL---LKQHDLKGIGGI 52
           EA++     EV IEGN  I  P  K    + L KL   ++   +KGI GI
Sbjct: 178 EAIEKKKGGEVEIEGNTLIISP--KEPSYRELRKLAEKIRNIKIKGIKGI 225


>gnl|CDD|182023 PRK09665, PRK09665, PTS system galactitol-specific transporter
          subunit IIA; Provisional.
          Length = 150

 Score = 27.1 bits (60), Expect = 2.2
 Identities = 21/50 (42%), Positives = 27/50 (54%), Gaps = 8/50 (16%)

Query: 51 GILLDDVRESLPHCEKA-LKNEIIYVTRPADKRKVMFYNDKSAQLDLDED 99
          GI+L+    ++PHCE    K+  IY+ RP DK KV F      Q D D D
Sbjct: 50 GIMLEQHAVAIPHCEAIHAKSPAIYLIRP-DK-KVHF-----QQADDDND 92


>gnl|CDD|233571 TIGR01778, TonB-copper, TonB-dependent copper receptor.  This model
           represents a family of proteobacterial TonB-dependent
           outer membrane receptor/transporters which bind and
           translocate copper ions. Two characterized members of
           this family exist, outer membrane protein C (OprC) from
           Pseudomonas aeruginosa and NosA from Pseudomonas
           stutzeri which is responsible for providing copper for
           the copper-containing N2O reducatse [Transport and
           binding proteins, Cations and iron carrying compounds,
           Transport and binding proteins, Porins].
          Length = 636

 Score = 27.5 bits (61), Expect = 2.3
 Identities = 14/62 (22%), Positives = 19/62 (30%)

Query: 75  VTRPADKRKVMFYNDKSAQLDLDEDFQKLWRSISVDGMILRIRSFYGVDYFSGAGEKAEK 134
               AD        +K+ QLD    +Q       V      +  +   DY   AG     
Sbjct: 418 HNNSADNAFDGIKPEKTHQLDFGTQYQGQALKAWVSLFYGVVNDYILFDYQHSAGADGTV 477

Query: 135 AT 136
           AT
Sbjct: 478 AT 479


>gnl|CDD|216543 pfam01513, NAD_kinase, ATP-NAD kinase.  Members of this family
           include ATP-NAD kinases EC:2.7.1.23, which catalyzes the
           phosphorylation of NAD to NADP utilising ATP and other
           nucleoside triphosphates as well as inorganic
           polyphosphate as a source of phosphorus. Also includes
           NADH kinases EC:2.7.1.86.
          Length = 243

 Score = 27.3 bits (61), Expect = 2.7
 Identities = 18/85 (21%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 4   LSTEALQNNPKIEVI---EGNKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDV--R 58
           L    L  +  I ++    G    F   F  ++   LL  L + + K     LLD +  R
Sbjct: 49  LDAARLLGDHDIPILGINTGTL-GFLTEFSPEEAAKLLDALLEGEYKIEKRELLDVIVRR 107

Query: 59  ESLPHCEKALKNEIIYVTRPADKRK 83
                      NE++ +  PA    
Sbjct: 108 SKRLLIVDLALNEVVIIGGPASTMI 132


>gnl|CDD|225313 COG2515, Acd, 1-aminocyclopropane-1-carboxylate deaminase [Amino
           acid transport and metabolism].
          Length = 323

 Score = 26.2 bits (58), Expect = 6.7
 Identities = 7/30 (23%), Positives = 14/30 (46%)

Query: 24  IFKPVFKIKDRKGLLKLLKQHDLKGIGGIL 53
           +  PV+  K   GL+ L ++ +      +L
Sbjct: 277 LLDPVYTGKAMYGLIDLARKGEFPDGSPVL 306


  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    0.139    0.405 

Gapped
Lambda     K      H
   0.267   0.0760    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,131,168
Number of extensions: 648621
Number of successful extensions: 591
Number of sequences better than 10.0: 1
Number of HSP's gapped: 587
Number of HSP's successfully gapped: 23
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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 (21.7 bits)
S2: 54 (24.5 bits)