RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8915
         (220 letters)



>gnl|CDD|202224 pfam02373, JmjC, JmjC domain, hydroxylase.  The JmjC domain belongs
           to the Cupin superfamily. JmjC-domain proteins may be
           protein hydroxylases that catalyze a novel histone
           modification. This is confirmed to be a hydroxylase: the
           human JmjC protein named Tyw5p unexpectedly acts in the
           biosynthesis of a hypermodified nucleoside,
           hydroxy-wybutosine, in tRNA-Phe by catalyzing
           hydroxylation.
          Length = 114

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 111 YGIPDEHSTAFRSTMMSLFPHYCRSDKTIWLSSDVAMIPPSLLTEKGVSLSRVVQEPGQF 170
           Y IP E++  F   +          D  + L++   +I P  L E G+ + R VQ+PG+F
Sbjct: 35  YIIPSEYAEKFEKVLSKHNGGEQ-PDLLLHLNT---IISPKQLLENGIPVYRFVQKPGEF 90

Query: 171 ILVFPSAFTSSIATGYLVAESVYF 194
           +  FP  +      G+ +AE+V F
Sbjct: 91  VFTFPGWYHQVFNLGFNIAEAVNF 114


>gnl|CDD|170091 PRK09778, PRK09778, putative antitoxin of the YafO-YafN
           toxin-antitoxin system; Provisional.
          Length = 97

 Score = 29.9 bits (67), Expect = 0.33
 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 152 LLTEKGVSLSRVVQEPGQFILVFPSAFTSSIAT-GYLVAESVYFARPSWLSTCE 204
           +L EK V+++ + + P ++ +  P A  S+    GYL++ S + A    L+  E
Sbjct: 4   ILAEKSVNITELRKNPAKYFIDQPVAVLSNNRPAGYLLSASAFEALMDMLAEQE 57


>gnl|CDD|145171 pfam01863, DUF45, Protein of unknown function DUF45.  This protein
           has no known function. Members are found in some
           archaebacteria, as well as Helicobacter pylori. The
           proteins are 190-240 amino acids long, with the C
           terminus being the most conserved region, containing
           three conserved histidines. This motif is similar to
           that found in Zinc proteases, suggesting that this
           family may also be proteases.
          Length = 205

 Score = 28.5 bits (64), Expect = 2.3
 Identities = 6/21 (28%), Positives = 10/21 (47%)

Query: 133 CRSDKTIWLSSDVAMIPPSLL 153
           C S   I L+  +   PP ++
Sbjct: 144 CSSKGRIRLNWRLVKAPPEVI 164


>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein.  This
           model represents a group of paralogous families in
           plasmodium species alternately annotated as reticulocyte
           binding protein, 235-kDa family protein and rhoptry
           protein. Rhoptry protein is localized on the cell
           surface and is extremely large (although apparently
           lacking in repeat structure) and is important for the
           process of invasion of the RBCs by the parasite. These
           proteins are found in P. falciparum, P. vivax and P.
           yoelii.
          Length = 2757

 Score = 28.1 bits (62), Expect = 4.4
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 6/46 (13%)

Query: 68  LKVLTNNSASILRSLNSLVDRISFGKID------FGFEIIEFLLPI 107
           L++L  +   IL + +  ++R+ F K D      F  +  EF  PI
Sbjct: 411 LEILYKHQEDILNNFHKTIERLIFEKPDPNNNNIFKDDFDEFNKPI 456


>gnl|CDD|234052 TIGR02900, spore_V_B, stage V sporulation protein B.  SpoVB is the
           stage V sporulation protein B of the bacterial endopore
           formation program in Bacillus subtilis and various other
           Firmcutes. It is nearly universal among
           endospore-formers. Paralogs with rather high sequence
           similarity to SpoVB exist, including YkvU in B. subtilis
           and a number of proteins in the genus Clostridium.
           Member sequences for the seed alignment were chosen to
           select those proteins, no more than one to a genome,
           closest to B. subtilis SpoVB in a neighbor joining tree
           [Cellular processes, Sporulation and germination].
          Length = 488

 Score = 27.6 bits (62), Expect = 5.1
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 7/71 (9%)

Query: 147 MIPPSLLTEKGVSLSRVVQEPGQF------ILVFPSAFTSSIATGYLVAESVYFARPSWL 200
           ++P  L+   GV+        G+       +L FP+  TSS++T  +   S   A+ ++ 
Sbjct: 251 LVPQRLVI-AGVTYREATSLYGKLSGMAMPLLTFPAVITSSLSTALVPDISEAMAKKNYS 309

Query: 201 STCERVFKIYK 211
           S  +R+ +  K
Sbjct: 310 SIEKRINQAIK 320


>gnl|CDD|179028 PRK00443, nagB, glucosamine-6-phosphate deaminase; Provisional.
          Length = 261

 Score = 27.1 bits (61), Expect = 7.5
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 12/55 (21%)

Query: 82  LNSLVDRISFGKIDF----GFEIIEFLLPISPRYGIPDEHSTAFRSTMMS-LFPH 131
             +L++    GK+DF     F + E++       G+P +H  ++R  M    F H
Sbjct: 49  YKALIELHKAGKVDFSRVTTFNLDEYV-------GLPADHPESYRYFMRENFFDH 96


>gnl|CDD|220555 pfam10079, DUF2317, Uncharacterized protein conserved in bacteria
           (DUF2317).  Members of this family of hypothetical
           bacterial proteins have no known function.
          Length = 541

 Score = 27.2 bits (61), Expect = 9.2
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 11/66 (16%)

Query: 70  VLTNNSASILRSLNSLVDRISFGKIDFGFEIIEFLLPISPRYGIPDEHST---AFRSTMM 126
           V   ++  +   L         G+ ++  E++E L      Y    E  T   AF   M 
Sbjct: 169 VGRLDTEGLREVLEEFFA--ELGETEYTEELLELLEEA---Y---LESETLADAFARLMN 220

Query: 127 SLFPHY 132
            LF  Y
Sbjct: 221 ELFADY 226


>gnl|CDD|221411 pfam12078, DUF3557, Domain of unknown function (DUF3557).  This
           presumed domain is functionally uncharacterized. This
           domain is found in eukaryotes. This domain is about 150
           amino acids in length.
          Length = 153

 Score = 26.1 bits (58), Expect = 9.8
 Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 67  NLKVLTNNSASILRSLNSLVDRISFGK--IDFGFEIIEFLLPI 107
           NL++  +N+  IL +L  L+D  S     ++  F++  F  PI
Sbjct: 46  NLELSGSNTDKILEALRPLLDNSSLPLKSLEVTFDVSNFDHPI 88


>gnl|CDD|152310 pfam11874, DUF3394, Domain of unknown function (DUF3394).  This
           domain is functionally uncharacterized. This domain is
           found in bacteria. This presumed domain is about 190
           amino acids in length. This domain is found associated
           with pfam06808.
          Length = 183

 Score = 26.4 bits (59), Expect = 9.9
 Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 6/28 (21%)

Query: 85  LVDRISFG------KIDFGFEIIEFLLP 106
           +VD + FG       IDF +EI+E  +P
Sbjct: 125 IVDEVEFGSPAEKAGIDFDWEIVEVEVP 152


  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
   0.321    0.134    0.415 

Gapped
Lambda     K      H
   0.267   0.0751    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,915,815
Number of extensions: 968637
Number of successful extensions: 838
Number of sequences better than 10.0: 1
Number of HSP's gapped: 838
Number of HSP's successfully gapped: 15
Length of query: 220
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 127
Effective length of database: 6,812,680
Effective search space: 865210360
Effective search space used: 865210360
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 (21.9 bits)
S2: 57 (25.7 bits)