RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4382
         (258 letters)



>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha
           subunit.  The alpha-subunit of the TRAP complex (TRAP
           alpha) is a single-spanning membrane protein of the
           endoplasmic reticulum (ER) which is found in proximity
           of nascent polypeptide chains translocating across the
           membrane.
          Length = 281

 Score =  248 bits (634), Expect = 2e-82
 Identities = 106/235 (45%), Positives = 133/235 (56%), Gaps = 54/235 (22%)

Query: 10  NMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHE 69
             D PAG  V+FLVGFTNKG +DF +++L+AS RYP D+ +YIQNF+ + YN +VKP H+
Sbjct: 88  PEDFPAGKPVKFLVGFTNKGSEDFVVESLEASFRYPQDYQYYIQNFTALPYNTVVKPKHQ 147

Query: 70  ATLGYSFVPAEAVAGRPFGLSVNLQYRDEHNNFFYEGIYNETVNIITLGYSFVPAEAVAG 129
           AT  YSF+PAE  AGRPFGL +NL YRD       +G                       
Sbjct: 148 ATFEYSFIPAEPFAGRPFGLVINLNYRDA------DG----------------------- 178

Query: 130 RPFGLSVNLQYRDEHNNFFYEGIYNETVNIIEIDEGLDGETFFLYVFLGACVVLLLVIGQ 189
                           N F + ++N+TV I E+DEGLDGETFFLYVFL    +LLLV G 
Sbjct: 179 ----------------NVFQDAVFNQTVTITEVDEGLDGETFFLYVFLAGLGLLLLVGGH 222

Query: 190 HFLYSVGKKRVGTAQSKKQTVETGTKNSKDIDYDWIPKESLNSLKNLTNSPK-SP 243
             L S  +KR       +Q VE GT +  D+DY WIP+E+LN L     SPK SP
Sbjct: 223 QLLESRKRKR------PRQKVEMGTSSDNDVDYSWIPQETLNQLNK--ASPKRSP 269


>gnl|CDD|222246 pfam13589, HATPase_c_3, Histidine kinase-, DNA gyrase B-, and
           HSP90-like ATPase.  This family represents,
           additionally, the structurally related ATPase domains of
           histidine kinase, DNA gyrase B and HSP90.
          Length = 134

 Score = 27.3 bits (61), Expect = 5.1
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 3/56 (5%)

Query: 193 YSVGKKRVGTAQSKKQTVET---GTKNSKDIDYDWIPKESLNSLKNLTNSPKSPSV 245
             +G K    +  +K TV +   G  ++  +D D I KE    L  LT++    S+
Sbjct: 72  KGIGMKLASLSLGRKLTVTSKKEGESSTLTLDLDDIDKEGEWDLPELTSAEIEESL 127


>gnl|CDD|238305 cd00545, MCH, Methenyltetrahydromethanopterin (methenyl-H4MPT)
           cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that
           has been identified in methanogenic archaea, sulfate-
           reducing archaea, and methylotrophic bacteria.  It
           catalyzes the reversible formation of N(5),
           N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+)
           from N(5)-formyltetrahydromethanopterin (formyl- H4MPT),
           in the third step of the reaction to reduce CO2 to CH4.
           The protein functions as a homodimer or homotrimer,
           depending on the organism.
          Length = 312

 Score = 27.7 bits (62), Expect = 6.7
 Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 11/51 (21%)

Query: 78  PAEAVAGRPFGLSVNLQYRDEHNNFFYEGIYNETVNIITLGYSFVPAEAVA 128
           PA A+A +P  L   + YRD+             V ++ L    +P E VA
Sbjct: 109 PARALALKPEELYEEIGYRDDA-----------EVAVLVLESDKLPPEEVA 148


>gnl|CDD|235622 PRK05846, PRK05846, NADH:ubiquinone oxidoreductase subunit M;
           Reviewed.
          Length = 497

 Score = 27.5 bits (62), Expect = 8.1
 Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%)

Query: 171 FFLYVFLGACVVLLLVIGQHFLYSVGKKRVGT 202
           FFLY  LG+ ++L+ +I    L  V     GT
Sbjct: 166 FFLYTLLGSLLMLVAIIY---LVVVYYNATGT 194


>gnl|CDD|200147 TIGR01972, NDH_I_M, proton-translocating NADH-quinone
           oxidoreductase, chain M.  This model describes the 13th
           (based on E. coli) structural gene, M, of bacterial NADH
           dehydrogenase I, as well as chain 4 of the corresponding
           mitochondrial complex I and of the chloroplast NAD(P)H
           dehydrogenase complex [Energy metabolism, Electron
           transport].
          Length = 481

 Score = 27.2 bits (61), Expect = 9.5
 Identities = 10/23 (43%), Positives = 16/23 (69%)

Query: 171 FFLYVFLGACVVLLLVIGQHFLY 193
           FFLY   G+ ++LL ++G +FL 
Sbjct: 161 FFLYTLAGSLLMLLAILGLYFLG 183


  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    0.409 

Gapped
Lambda     K      H
   0.267   0.0736    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,345,455
Number of extensions: 1275303
Number of successful extensions: 964
Number of sequences better than 10.0: 1
Number of HSP's gapped: 962
Number of HSP's successfully gapped: 12
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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: 58 (26.1 bits)