RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11631
         (219 letters)



>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25.  All proteins in this
           family for which functions are known are DNA-DNA
           helicases used for the initiation of nucleotide excision
           repair and transacription as part of the TFIIH
           complex.This family is based on the phylogenomic
           analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
           University) [DNA metabolism, DNA replication,
           recombination, and repair].
          Length = 732

 Score =  295 bits (756), Expect = 4e-96
 Identities = 115/147 (78%), Positives = 126/147 (85%)

Query: 52  DYRAQMVLKPDHKSRPLWVAPNGHIFLESFSPVYRHAHDFLIAIAEPVCRPEHIHEYKLT 111
           DY  Q+ LKPDH SRPLWVAP+GHIFLESFSP+Y+ A DFL+AIAEPVCRPEHIHEYKLT
Sbjct: 1   DYSKQLELKPDHGSRPLWVAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLT 60

Query: 112 AYSLYAAVSVGLETHDIIEYLKRLSKTSVPDGIVEFINLCTLSYGKVKLVLKHNRYFIES 171
           AYSLYAAVSVGLET DIIE L RLSKT +P GI+EFI LCT SYGKVKLVLKHNRYF+ES
Sbjct: 61  AYSLYAAVSVGLETEDIIEVLGRLSKTPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVES 120

Query: 172 PFAEVLQKLLKDPVIQDCRLRRDTEDS 198
           P  EVLQ+LLKDPVI  CR+    E+S
Sbjct: 121 PHPEVLQRLLKDPVIAPCRIDPTEEES 147


>gnl|CDD|205803 pfam13625, Helicase_C_3, Helicase conserved C-terminal domain.
           This domain family is found in a wide variety of
           helicases and helicase-related proteins.
          Length = 128

 Score =  116 bits (292), Expect = 2e-33
 Identities = 44/127 (34%), Positives = 62/127 (48%), Gaps = 5/127 (3%)

Query: 67  PLWVAPNGHIFLESFSPVYRHAHDFLIAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETH 126
           PL V P+  I L    P    A   L A AE    P H H Y+LT  SL  A+  GL   
Sbjct: 1   PLIVQPDLTILL-PGPPTPELAR-ALAAFAEL-ESPGHAHTYRLTPLSLRRALDAGLTAE 57

Query: 127 DIIEYLKRLSKTSVPDGIVEFINLCTLSYGKVKLVLKHNRYFIESPFAEVLQKLLKDPVI 186
           +IIE+L+R S+T VP  ++  I      +G+++L       ++ S    VL++LL D  +
Sbjct: 58  EIIEFLERHSRTPVPQSLLYLIRDVARRHGRLRLG--KAGLYLRSDDPAVLEELLADKKL 115

Query: 187 QDCRLRR 193
               LRR
Sbjct: 116 APLLLRR 122


>gnl|CDD|224446 COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large
           subunit CoxL/CutL homologs [Energy production and
           conversion].
          Length = 731

 Score = 28.5 bits (64), Expect = 3.1
 Identities = 14/46 (30%), Positives = 19/46 (41%)

Query: 9   EVEDESYVDDPGEPLDEDGVPVAAKKNVEKDDAAVPEDEFGAKDYR 54
           E E    V DP E L ED   +  + N+ +D     +D F A    
Sbjct: 122 EYEALPPVVDPEEALAEDAPVIHDELNIARDATFGDDDAFAAAAVV 167


>gnl|CDD|235350 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9
           3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol
           methylase; Provisional.
          Length = 233

 Score = 27.4 bits (62), Expect = 4.6
 Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 10/67 (14%)

Query: 70  VAPNGHIFLESFSPVYRHAHDFLIAI--AEPVCR--PEHIHEYK--LTAYSLYAAV-SVG 122
           V P G +F   FS + R+   +L+AI  AE V R  P+  H+YK  +    L A +   G
Sbjct: 141 VKPGGLVF---FSTLNRNLKSYLLAIVGAEYVLRMLPKGTHDYKKFIKPSELAAWLRQAG 197

Query: 123 LETHDII 129
           LE  DI 
Sbjct: 198 LEVQDIT 204


>gnl|CDD|132396 TIGR03353, VI_chp_4, type VI secretion protein, VC_A0114 family.
           Work by Mougous, et al. (2006), describes IAHP-related
           loci as a type VI secretion system (PMID:16763151). This
           protein family is associated with type VI secretion
           loci, although not treated explicitly by Mougous, et al
           [Protein fate, Protein and peptide secretion and
           trafficking, Cellular processes, Pathogenesis].
          Length = 439

 Score = 27.6 bits (62), Expect = 5.4
 Identities = 13/85 (15%), Positives = 26/85 (30%), Gaps = 13/85 (15%)

Query: 79  ESFSPVYRHAHDFLIAIAEPVCRPEHIHEYKLTAYS-------------LYAAVSVGLET 125
           E F+P+     + L  + E       + E +   Y                 AV   +  
Sbjct: 292 EVFAPLEDLLRELLSTVLEQRAVSLPLEERRDGIYVARLDDDRLLESARFVLAVRADMPA 351

Query: 126 HDIIEYLKRLSKTSVPDGIVEFINL 150
            ++       +K    + I + +NL
Sbjct: 352 EELRRQFPAQAKVGAVEQIRDLVNL 376


>gnl|CDD|184038 PRK13410, PRK13410, molecular chaperone DnaK; Provisional.
          Length = 668

 Score = 27.7 bits (62), Expect = 5.5
 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 6/36 (16%)

Query: 190 RLRRDTED----SQTLINQADKKLK--APQFGLYSA 219
           R RR+  +    + TLI QA+++L+  A +FG Y A
Sbjct: 522 RRRRERIEKRNRALTLIAQAERRLRDAALEFGPYFA 557


>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit.  Subunit of G
           proteins that contains the guanine nucleotide binding
           site.
          Length = 342

 Score = 27.5 bits (62), Expect = 5.6
 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)

Query: 167 YFIESPFAEVLQKLLKDPVIQDCRLRRDTE 196
             +    A+ ++ L KD  IQ+C  RR  E
Sbjct: 107 NVLPKEIAKAIKALWKDEGIQEC-YRRRNE 135


  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
   0.317    0.136    0.399 

Gapped
Lambda     K      H
   0.267   0.0770    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,548,905
Number of extensions: 1111134
Number of successful extensions: 982
Number of sequences better than 10.0: 1
Number of HSP's gapped: 980
Number of HSP's successfully gapped: 23
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
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: 57 (25.7 bits)