RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5692
         (98 letters)



>gnl|CDD|184603 PRK14282, PRK14282, chaperone protein DnaJ; Provisional.
          Length = 369

 Score = 30.9 bits (70), Expect = 0.059
 Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 15/94 (15%)

Query: 9   YEINVNYEHNVILGNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYL------NTDTGGKYV 62
           Y++ ++Y    ILG T  +   +P   +  + +    Q +    L      N   G +  
Sbjct: 280 YDVTIDYL-QAILGTT--VEVPLPEGGTTMLKIPPGTQPETVFRLKGKGLPNMRYGRR-- 334

Query: 63  VLSSGDLYVQIRLSITGNLSVKKMKVEEEEEKKK 96
               GDL V + + I   LS ++ K+ +E  KK+
Sbjct: 335 ----GDLIVNVHVEIPKRLSREERKLLKELAKKR 364


>gnl|CDD|139606 PRK13486, PRK13486, bifunctional enterobactin receptor/adhesin
           protein; Provisional.
          Length = 696

 Score = 27.7 bits (61), Expect = 1.1
 Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 8   KYEINVNYEHNVILGNTAVLRCQIPSYMSEYI--IVTSWIQDDVNIYLNT 55
           K E +V+YE  V   N A L   +  +M+++   IV+  I D+ N Y+N+
Sbjct: 471 KPEESVSYEAGVYYDNPAGLNANVTGFMTDFSNKIVSYSINDNTNSYVNS 520


>gnl|CDD|100063 cd05825, LbH_wcaF_like, wcaF-like: This group is composed of the
          protein product of the E. coli wcaF gene and similar
          proteins. WcaF is part of the gene cluster responsible
          for the biosynthesis of the extracellular
          polysaccharide colanic acid. The wcaF protein is
          predicted to contain a left-handed parallel beta-helix
          (LbH) domain encoded by imperfect tandem repeats of a
          hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
          Proteins containing hexapeptide repeats are often
          enzymes showing acyltransferase activity. Many are
          trimeric in their active forms.
          Length = 107

 Score = 26.0 bits (58), Expect = 2.5
 Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 1/26 (3%)

Query: 43 SWIQDDVNIY-LNTDTGGKYVVLSSG 67
          SWI + V IY L   T G    +S G
Sbjct: 10 SWIGEGVWIYNLAPVTIGSDACISQG 35


>gnl|CDD|238620 cd01295, AdeC, Adenine deaminase (AdeC) directly deaminates adenine
           to form hypoxanthine. This reaction is part of one of
           the adenine salvage pathways, as well as the degradation
           pathway. It is important for adenine utilization as a
           purine, as well as a nitrogen source in bacteria and
           archea.
          Length = 422

 Score = 26.4 bits (59), Expect = 2.7
 Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 14/70 (20%)

Query: 40  IVTSWIQDDVNIYL--NTD------------TGGKYVVLSSGDLYVQIRLSITGNLSVKK 85
           I +S   D  NI +    D             GG  VV+ +G +  ++ L I G +S + 
Sbjct: 314 IASSVAHDSHNIIVIGTNDEDMALAVNRLKEIGGGIVVVKNGKVLAELPLPIAGLMSDEP 373

Query: 86  MKVEEEEEKK 95
            +   EE KK
Sbjct: 374 AEEVAEELKK 383


>gnl|CDD|236703 PRK10502, PRK10502, putative acyl transferase; Provisional.
          Length = 182

 Score = 26.1 bits (58), Expect = 2.9
 Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)

Query: 43  SWIQDDVNIY-LNTDTGGKYVVLSSG 67
           +WI DDV +Y L   T G + V+S  
Sbjct: 78  AWIGDDVWLYNLGEITIGAHCVISQK 103


>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
          Length = 4334

 Score = 26.3 bits (58), Expect = 3.3
 Identities = 9/14 (64%), Positives = 10/14 (71%)

Query: 23   NTAVLRCQIPSYMS 36
            NT VLRCQ+   MS
Sbjct: 2019 NTQVLRCQLDGQMS 2032


>gnl|CDD|143201 cd05724, Ig2_Robo, Second immunoglobulin (Ig)-like domain in Robo
          (roundabout) receptors.  Ig2_Robo: domain similar to
          the second immunoglobulin (Ig)-like domain in Robo
          (roundabout) receptors. Robo receptors play a role in
          the development of the central nervous system (CNS),
          and are receptors of Slit protein. Slit is a repellant
          secreted by the neural cells in the midline. Slit acts
          through Robo to prevent most neurons from crossing the
          midline from either side. Three mammalian Robo homologs
          (robo1, -2, and -3), and three mammalian Slit homologs
          (Slit-1,-2, -3), have been identified. Commissural
          axons, which cross the midline, express low levels of
          Robo; longitudinal axons, which avoid the midline,
          express high levels of Robo. robo1, -2, and -3 are
          expressed by commissural neurons in the vertebrate
          spinal cord and Slits 1, -2, -3 are expressed at the
          ventral midline. Robo-3 is a divergent member of the
          Robo family which instead of being a positive regulator
          of slit responsiveness, antagonizes slit responsiveness
          in precrossing axons.  The Slit-Robo interaction is
          mediated by the second leucine-rich repeat (LRR) domain
          of Slit and the two N-terminal Ig domains of Robo, Ig1
          and Ig2. The primary Robo binding site for Slit2 has
          been shown by surface plasmon resonance experiments and
          mutational analysis to be is the Ig1 domain, while the
          Ig2 domain has been proposed to harbor a weak secondary
          binding site.
          Length = 86

 Score = 24.7 bits (54), Expect = 5.1
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 5/54 (9%)

Query: 19 VILGNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGDLYVQ 72
          V +G  AVL C  P    E  +  SW +D   +        +  ++  G+L + 
Sbjct: 8  VAVGEMAVLECSPPRGHPEPTV--SWRKDGQPL---NLDNERVRIVDDGNLLIA 56


>gnl|CDD|234483 TIGR04150, pseudo_rSAM_GG, pseudo-rSAM protein, GG-Bacteroidales
           system.  Many peptide-modifying radical SAM enzymes have
           two 4Fe4S-binding regions, an N-terminal one recognized
           by Pfam radical SAM domain-defining model pfam04055 and
           a C-terminal one recognized by TIGR04085. Members of
           this protein family occur in cassettes with such a
           radical SAM family (TIGR04148) and with a peptide
           modification target (TIGR04149). Surprisingly, members
           of this family show full-length homology to each other,
           with several scoring at least borderline hits to both
           pfam04055 and TIGR04085, and yet differ in the
           presence/absence of a signature CX(3)CX(2)CX(9)C motif.
           Instead, members are best-conserved in the
           TIGR04085-like C-terminal region. Therefore, this
           protein family is designated a pseudo-radical-SAM
           protein, which likely works in partnership with a
           TIGR04148 family protein.
          Length = 407

 Score = 25.4 bits (56), Expect = 5.5
 Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 3/46 (6%)

Query: 53  LNTDTGGKYVVLSSGDLYVQIRLSITGNL---SVKKMKVEEEEEKK 95
           LNT+  GK  +L +GD+Y  +  S  GN+   S+K++  +E EE  
Sbjct: 322 LNTNFFGKLTILPNGDVYANVNHSSIGNIQDDSIKEIVYKEIEEGT 367


>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
          Length = 371

 Score = 25.1 bits (56), Expect = 7.5
 Identities = 7/10 (70%), Positives = 9/10 (90%)

Query: 66  SGDLYVQIRL 75
           +GDLYVQI +
Sbjct: 242 AGDLYVQIHV 251


  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
   0.314    0.133    0.368 

Gapped
Lambda     K      H
   0.267   0.0781    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,876,565
Number of extensions: 399806
Number of successful extensions: 270
Number of sequences better than 10.0: 1
Number of HSP's gapped: 270
Number of HSP's successfully gapped: 18
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)