RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7627
         (158 letters)



>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW;
           Provisional.
          Length = 223

 Score = 33.3 bits (76), Expect = 0.031
 Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 39  LTLKSADYLSEIFPFAKFIFMVRDGRATVHSIISRKVTITGFDLESYRQCLKKWNEAISI 98
           L   + DYL + F F++ +  VR  +   H  ++  + I+G  ++S  Q + + N +I++
Sbjct: 90  LDSGANDYLVKPFSFSELLARVR-AQLRQHHALNSTLEISGLRMDSVSQSVSRDNISITL 148

Query: 99  MYQK 102
             ++
Sbjct: 149 TRKE 152


>gnl|CDD|235019 PRK02259, PRK02259, aspartoacylase; Provisional.
          Length = 288

 Score = 29.1 bits (66), Expect = 0.79
 Identities = 7/26 (26%), Positives = 10/26 (38%)

Query: 33  LCNKDPLTLKSADYLSEIFPFAKFIF 58
           L  + P  L  A YL    P   ++ 
Sbjct: 116 LYGRRPFDLALAAYLQSRLPLPIYLH 141


>gnl|CDD|234166 TIGR03310, matur_ygfJ, molybdenum hydroxylase accessory protein,
          YgfJ family.  Members of this protein family are
          probable accessory proteins for the biosynthesis of
          enzymes related to xanthine dehydrogenase. Comparative
          genomics suggests a role in the maturation of
          selenium-dependent molybdenum hydroxylases, although a
          tenuous alternative hypothesis is a role for this
          protein (with a requirement for SelD, the selenium
          donor protein in the selenocysteine and selenouridine
          biosynthesis pathways) metabolizing a
          selenium-containing substrate such as selenate.
          Length = 188

 Score = 28.8 bits (65), Expect = 0.87
 Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 4/38 (10%)

Query: 8  RMVINAAIAAFCLEVIA----RHGEPAERLCNKDPLTL 41
            V++ A+  F  EVI        E    L N   +TL
Sbjct: 29 EHVVDNALRLFFDEVILVLGHEADELVALLANHSNITL 66


>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
          Length = 1364

 Score = 28.0 bits (63), Expect = 2.4
 Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)

Query: 25  RHGEPAERLCNKD-PLTLKSADYLSEIFPFAKFIFMVRDG 63
           RHG PA  LC  D  +T++S D +  +    K + +V++ 
Sbjct: 373 RHGHPA-FLCKIDLYVTIESEDIIHNVNIPPKSLLLVQND 411


>gnl|CDD|234104 TIGR03086, TIGR03086, TIGR03086 family protein.  This family, like
           Pfam family pfam07398 and TIGRFAMs family TIGR030834,
           belongs to the larger set of probable enzymes defined in
           family TIGR03083. Members are found primarily in the
           Actinobacteria (Mycobacterium, Streptomyces, etc.). The
           family is uncharacterized.
          Length = 180

 Score = 27.4 bits (61), Expect = 3.1
 Identities = 7/20 (35%), Positives = 10/20 (50%)

Query: 13  AAIAAFCLEVIARHGEPAER 32
            A+A F L +    G+P  R
Sbjct: 134 PALAEFALALAEAVGDPPLR 153


>gnl|CDD|216059 pfam00685, Sulfotransfer_1, Sulfotransferase domain. 
          Length = 254

 Score = 27.3 bits (61), Expect = 3.4
 Identities = 7/29 (24%), Positives = 14/29 (48%)

Query: 108 PSRCMVVYYEQLVLHPEKWLRRILQFFDL 136
           P   + + YE L   P   +++I +F  +
Sbjct: 155 PGNILFLRYEDLKKDPRGEIKKIAEFLGI 183


>gnl|CDD|237729 PRK14491, PRK14491, putative bifunctional molybdopterin-guanine
           dinucleotide biosynthesis protein MobB/MoeA;
           Provisional.
          Length = 597

 Score = 27.3 bits (61), Expect = 4.0
 Identities = 22/72 (30%), Positives = 29/72 (40%), Gaps = 21/72 (29%)

Query: 8   RMVIN--AAIAAFCLEVIARHGEPAERL-----CNKDPLTLKSADYLSEIFPFAKFIFMV 60
           R+ IN  AAIA F LE       PA+ L     C  D L   S  +LS           V
Sbjct: 156 RLDINDVAAIADFVLEYAQNWQAPAQDLPLAPACCCDLL---SPAFLS-----------V 201

Query: 61  RDGRATVHSIIS 72
             G   + S+++
Sbjct: 202 SQGLDKILSLVT 213


>gnl|CDD|226558 COG4072, COG4072, Uncharacterized protein conserved in archaea
          [Function unknown].
          Length = 161

 Score = 26.4 bits (58), Expect = 5.0
 Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 4/52 (7%)

Query: 20 LEVIARHGEPAERLCNKDPLTLKSADYLSEIFPFAKFIFMVRDGRATVHSII 71
           EV  + G+  E     D    ++      I+    F     + + TV +II
Sbjct: 29 GEVKLKEGDKDEDFEGLD----RAKFLAQVIYDRFHFYVDQYEHKVTVDAII 76


>gnl|CDD|215416 PLN02779, PLN02779, haloacid dehalogenase-like hydrolase family
           protein.
          Length = 286

 Score = 26.6 bits (59), Expect = 5.5
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 90  KKWNEAISIMYQKCLRVGPSRCMVV 114
           KK +  I  +  + L V PSRC+VV
Sbjct: 201 KKPDPDIYNLAAETLGVDPSRCVVV 225


>gnl|CDD|130454 TIGR01387, cztR_silR_copR, heavy metal response regulator.  Members
           of this family contain a response regulator receiver
           domain (pfam00072) and an associated transcriptional
           regulatory region (pfam00486). This group is separated
           phylogenetically from related proteins with similar
           architecture and contains a number of proteins
           associated with heavy metal resistance efflux systems
           for copper, silver, cadmium, and/or zinc. Most members
           encoded by genes adjacent to genes for encoding a member
           of the heavy metal sensor histidine kinase family
           (TIGRFAMs:TIGR01386), its partner in the two-component
           response regulator system.
          Length = 218

 Score = 26.7 bits (59), Expect = 5.8
 Identities = 17/60 (28%), Positives = 30/60 (50%)

Query: 39  LTLKSADYLSEIFPFAKFIFMVRDGRATVHSIISRKVTITGFDLESYRQCLKKWNEAISI 98
           L L + DYL + F F++ +  VR      HS+ S  + I    ++S R  + + N  I++
Sbjct: 89  LDLGADDYLVKPFSFSELLARVRTLLRRSHSLNSTVLEIADLRMDSVRHRVSRGNIRITL 148


>gnl|CDD|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB
           receptor-like is composed of two C4-type zinc fingers.
           DNA-binding domain of REV-ERB receptor- like is composed
           of two C4-type zinc fingers. Each zinc finger contains a
           group of four Cys residues which coordinates a single
           zinc atom. This domain interacts with specific DNA sites
           upstream of the target gene and modulates the rate of
           transcriptional initiation. REV-ERB receptors are
           transcriptional regulators belonging to the nuclear
           receptor superfamily. They regulate a number of
           physiological functions including the circadian rhythm,
           lipid metabolism, and cellular differentiation. REV-ERB
           receptors bind as a monomer to a (A/G)GGTCA half-site
           with a 5' AT-rich extension or as a homodimer to a
           direct repeat 2 element (AGGTCA sequence with a 2-bp
           spacer), indicating functional diversity. When bound to
           the DNA, they recruit corepressors (NcoR/histone
           deacetylase 3) to the promoter, resulting in repression
           of the target genes. The porphyrin heme has been
           demonstrated to function as a ligand for REV-ERB
           receptor. Like other members of the nuclear receptor
           (NR) superfamily of ligand-activated transcription
           factors, REV-ERB receptors have a central well conserved
           DNA binding domain (DBD), a variable N-terminal domain,
           a non-conserved hinge and a C-terminal ligand binding
           domain (LBD).
          Length = 89

 Score = 25.6 bits (56), Expect = 6.4
 Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 13/42 (30%)

Query: 85  YRQCLKKWNEAISIM-----------YQKCLRVGPSRCMVVY 115
           YR+C K  NE  SIM           ++KCL VG SR  V +
Sbjct: 40  YRKCTK--NETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRF 79


>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
           A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
          Length = 809

 Score = 26.3 bits (58), Expect = 8.0
 Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 5/27 (18%)

Query: 113 VVYYEQLVLH-----PEKWLRRILQFF 134
           VV Y+ L L      PE  L  I++ F
Sbjct: 583 VVPYQPLTLAGWKREPELCLAHIVEAF 609


>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
          Length = 1094

 Score = 26.5 bits (59), Expect = 8.8
 Identities = 18/89 (20%), Positives = 28/89 (31%), Gaps = 26/89 (29%)

Query: 8   RMVINAAIAAFCLEVIAR-HGEPAERLCNKDPLTLKSADYLSEIFPFAKFIFMVRDGRAT 66
            ++ NAA AA    V+ R  G+      +           +S  +P       V     T
Sbjct: 882 ELIQNAAQAAHGAPVVMRPDGDGVLEPVD-----------ISGPWP-------VV----T 919

Query: 67  VHSIISRKV--TIT-GFDLESYRQCLKKW 92
           VH  +S  +   I     L   R+     
Sbjct: 920 VHDAVSEALGEEIDPDTPLAELRKLCDAA 948


  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
   0.328    0.141    0.446 

Gapped
Lambda     K      H
   0.267   0.0713    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,380,983
Number of extensions: 748588
Number of successful extensions: 841
Number of sequences better than 10.0: 1
Number of HSP's gapped: 841
Number of HSP's successfully gapped: 20
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 55 (25.0 bits)