RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1243
         (121 letters)



>gnl|CDD|238113 cd00190, Tryp_SPc, Trypsin-like serine protease; Many of these are
           synthesized as inactive precursor zymogens that are
           cleaved during limited proteolysis to generate their
           active forms. Alignment contains also inactive enzymes
           that have substitutions of the catalytic triad residues.
          Length = 232

 Score = 75.4 bits (186), Expect = 6e-18
 Identities = 27/65 (41%), Positives = 37/65 (56%)

Query: 7   SSSASNALTLKAARVGTLSQESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPIVC 66
           S        L+   V  +S   C++  +YG  I D+M CAG  +GG D+CQGDSGGP+VC
Sbjct: 133 SEGGPLPDVLQEVNVPIVSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVC 192

Query: 67  DIQGC 71
           +  G 
Sbjct: 193 NDNGR 197


>gnl|CDD|214473 smart00020, Tryp_SPc, Trypsin-like serine protease.  Many of these
           are synthesised as inactive precursor zymogens that are
           cleaved during limited proteolysis to generate their
           active forms. A few, however, are active as single chain
           molecules, and others are inactive due to substitutions
           of the catalytic triad residues.
          Length = 229

 Score = 75.0 bits (185), Expect = 9e-18
 Identities = 27/63 (42%), Positives = 39/63 (61%)

Query: 5   IASSSASNALTLKAARVGTLSQESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPI 64
            +  + S   TL+   V  +S  +CR+  + G  I D+M CAG  +GG D+CQGDSGGP+
Sbjct: 132 TSEGAGSLPDTLQEVNVPIVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPL 191

Query: 65  VCD 67
           VC+
Sbjct: 192 VCN 194


>gnl|CDD|215708 pfam00089, Trypsin, Trypsin. 
          Length = 218

 Score = 59.8 bits (145), Expect = 5e-12
 Identities = 28/53 (52%), Positives = 37/53 (69%), Gaps = 4/53 (7%)

Query: 15  TLKAARVGTLSQESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPIVCD 67
           TL+   V  +S+E+CR   AYG  + D+M CAG+  GG D+CQGDSGGP+VC 
Sbjct: 137 TLQEVTVPVVSRETCRS--AYGGTVTDNMICAGA--GGKDACQGDSGGPLVCS 185


>gnl|CDD|227927 COG5640, COG5640, Secreted trypsin-like serine protease
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 413

 Score = 34.5 bits (79), Expect = 0.007
 Identities = 22/63 (34%), Positives = 26/63 (41%), Gaps = 4/63 (6%)

Query: 7   SSSASNALTLKAARVGTLSQESCRKEDAYGTRIKDSM--FCAGSFQGGADSCQGDSGGPI 64
           SS     L   A     LS  +  K  A  +     +  FCAG      D+CQGDSGGPI
Sbjct: 177 SSPKGTILHEVAVLFVPLSTCAQYKGCANASDGATGLTGFCAGRP--PKDACQGDSGGPI 234

Query: 65  VCD 67
              
Sbjct: 235 FHK 237


>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
          Length = 390

 Score = 26.1 bits (58), Expect = 5.1
 Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 6/43 (13%)

Query: 65  VCDIQGCDKGAS----LGTDRLS--RACYVLSKMIRFYASVGI 101
           + DI G  KGAS    LG   LS  RA   +  ++R +    I
Sbjct: 89  ITDIAGLVKGASEGEGLGNAFLSHIRAVDGIYHVVRAFEDEDI 131


>gnl|CDD|235412 PRK05329, PRK05329, anaerobic glycerol-3-phosphate dehydrogenase
           subunit B; Validated.
          Length = 422

 Score = 26.0 bits (58), Expect = 5.5
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 11/53 (20%)

Query: 27  ESCRKEDAYGTRIKDSMFCAGSFQGGADSCQGDSGGPIVCDIQGCDKGASLGT 79
            + R  D+ G  + ++++ AG+  GG D        PI    +GC  G +L T
Sbjct: 367 ATLRPLDSQGGPVIENLYAAGAVLGGYD--------PI---REGCGSGVALAT 408


>gnl|CDD|239153 cd02752, MopB_Formate-Dh-Na-like, Formate dehydrogenase N, alpha
           subunit (Formate-Dh-Na) is a major component of nitrate
           respiration in bacteria such as in the E. coli formate
           dehydrogenase N (Fdh-N). Fdh-N is a membrane protein
           that is a complex of three different subunits and is the
           major electron donor to the nitrate respiratory chain.
           Also included in this CD is the Desulfovibrio gigas
           tungsten formate dehydrogenase, DgW-FDH. In contrast to
           Fdh-N, which is a  functional heterotrimer, DgW-FDH is a
           heterodimer. The DgW-FDH complex is composed of a large
           subunit carrying the W active site and one [4Fe-4S]
           center, and a small subunit that harbors a series of
           three [4Fe-4S] clusters as well as a putative vacant
           binding site for a fourth cluster. The smaller subunit
           is not included in this alignment. Members of the
           MopB_Formate-Dh-Na-like CD belong to the
           molybdopterin_binding (MopB) superfamily of proteins.
          Length = 649

 Score = 25.8 bits (57), Expect = 7.1
 Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 68  IQGCDKGASLGTDRLS-RACYVLSKMIRFYASVGIE 102
           +   D  A LG+ +LS   CY++ K  R   +  ++
Sbjct: 102 VNRPDSIAFLGSAKLSNEECYLIRKFARALGTNNLD 137


  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    0.129    0.385 

Gapped
Lambda     K      H
   0.267   0.0738    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,535,839
Number of extensions: 432580
Number of successful extensions: 223
Number of sequences better than 10.0: 1
Number of HSP's gapped: 222
Number of HSP's successfully gapped: 13
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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: 53 (24.2 bits)