RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3495
         (266 letters)



>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
           recombination, and repair].
          Length = 908

 Score = 34.0 bits (78), Expect = 0.079
 Identities = 21/124 (16%), Positives = 43/124 (34%), Gaps = 18/124 (14%)

Query: 24  KLENIIKTLSVNLEQLQSYNEIINKHGAALLRTLSELES-CDNPQELQCQIKEINERATL 82
           KLE+ ++ L+    +L     ++ +    L   L ELE   +   E   Q++E  +    
Sbjct: 340 KLESELEELAEEKNELAK---LLEERLKELEERLEELEKELEKALERLKQLEEAIQELKE 396

Query: 83  FRITTNAMINS--------------CGKYLEIAQTQGGKWQRMLQHERDQRLKLEELLEQ 128
                +A +                  + LE  + +  K +  +     + L + EL   
Sbjct: 397 ELAELSAALEEIQEELEELEKELEELERELEELEEEIKKLEEQINQLESKELMIAELAGA 456

Query: 129 MARC 132
             +C
Sbjct: 457 GEKC 460


>gnl|CDD|219493 pfam07638, Sigma70_ECF, ECF sigma factor.  These proteins are
           probably RNA polymerase sigma factors belonging to the
           extra-cytoplasmic function (ECF) subfamily and show
           sequence similarity to pfam04542 and pfam04545.
          Length = 185

 Score = 30.8 bits (70), Expect = 0.46
 Identities = 18/64 (28%), Positives = 22/64 (34%), Gaps = 9/64 (14%)

Query: 101 AQTQGGKWQR---------MLQHERDQRLKLEELLEQMARCSTGPPVHDSGPRLGGLPRE 151
            Q +GG  QR               D  L L+E LEQ+   S             GL  +
Sbjct: 96  RQKRGGDVQRRELDEVVDNGDSPNPDLLLDLDEALEQLFSLSPRQARLVELRFFAGLSND 155

Query: 152 EEAE 155
           E AE
Sbjct: 156 EIAE 159


>gnl|CDD|240387 PTZ00371, PTZ00371, aspartyl aminopeptidase; Provisional.
          Length = 465

 Score = 29.9 bits (68), Expect = 1.6
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 9/63 (14%)

Query: 15  EDFEVDGEVKLENIIKT-LSVNLEQLQSYNEIINKHGAALLRTLSELESCDNPQELQCQI 73
           E F+ + E  L+ II T +   L   Q  +   N H A LL+ +++        EL C +
Sbjct: 168 ESFKPNKENHLKPIISTEVYEQLNGKQDNDNSNNNHSAPLLKLIAK--------ELGCSV 219

Query: 74  KEI 76
           ++I
Sbjct: 220 EDI 222


>gnl|CDD|181867 PRK09451, glmU, bifunctional N-acetylglucosamine-1-phosphate
           uridyltransferase/glucosamine-1-phosphate
           acetyltransferase; Provisional.
          Length = 456

 Score = 28.8 bits (65), Expect = 3.1
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 5/56 (8%)

Query: 22  EVKLENIIKTLSVNLEQLQSYNEIINKHGAALLRTLSELESCDNPQELQCQIKEIN 77
           + K +  I  L+V L+    Y  I  ++G    + +  +E  D   E Q QI+EIN
Sbjct: 119 DAKPQGGIGLLTVKLDNPTGYGRITRENG----KVVGIVEQKDATDE-QRQIQEIN 169


>gnl|CDD|185696 cd09019, galactose_mutarotase_like, galactose mutarotase_like.
           Galactose mutarotase catalyzes the conversion of
           beta-D-galactose to alpha-D-galactose. Beta-D-galactose
           is produced by the degradation of lactose, a
           disaccharide composed of beta-D-glucose and
           beta-D-galactose. This epimerization reaction is the
           first step in the four-step Leloir pathway, which
           converts galactose into metabolically important glucose.
           This epimerization step is followed by the
           phosophorylation of alpha-D-galactose by galactokinase,
           an enzyme which can only act on the alpha anomer. A
           glutamate and a histidine residue of the galactose
           mutarotase have been shown to be critical for catalysis,
           the glutamate serves as the active site base to initiate
           the reaction by removing the proton from the C-1
           hydroxyl group of the sugar substrate, and the histidine
           as the active site acid to protonate the C-5 ring
           oxygen. Galactose mutarotase is a member of the
           aldose-1-epimerase superfamily.
          Length = 326

 Score = 28.2 bits (64), Expect = 3.8
 Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 7/46 (15%)

Query: 161 VFYDAN---EVMTENGGLDPAGRGL-LEPVRYPYSPH---FPSCSL 199
            FY  N         G +     G  LE   +P +P+   FPS  L
Sbjct: 267 QFYTGNFLDGTPGGGGKVYGKRSGFCLETQHFPDAPNHPNFPSIIL 312


>gnl|CDD|222067 pfam13354, Beta-lactamase2, Beta-lactamase enzyme family.  This
           family is closely related to Beta-lactamase, pfam00144,
           the serine beta-lactamase-like superfamily, which
           contains the distantly related pfam00905 and PF00768
           D-alanyl-D-alanine carboxypeptidase.
          Length = 197

 Score = 27.6 bits (62), Expect = 5.7
 Identities = 9/23 (39%), Positives = 12/23 (52%)

Query: 111 MLQHERDQRLKLEELLEQMARCS 133
           +LQ    + L L +LLE M   S
Sbjct: 53  ILQKLPGKTLTLRDLLELMIAVS 75


>gnl|CDD|233050 TIGR00609, recB, exodeoxyribonuclease V, beta subunit.  The RecBCD
           holoenzyme is a multifunctional nuclease with potent
           ATP-dependent exodeoxyribonuclease activity. Ejection of
           RecD, as occurs at chi recombinational hotspots,
           cripples exonuclease activity in favor of recombinagenic
           helicase activity. All proteins in this family for which
           functions are known are DNA-DNA helicases that are used
           as part of an exonuclease-helicase complex (made up of
           RecBCD homologs) that function to generate substrates
           for the initiation of recombination and recombinational
           repair. 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 = 1087

 Score = 27.4 bits (61), Expect = 9.0
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 7/69 (10%)

Query: 19  VDGEVKLENIIKTLSVNLEQLQSYNEIINKHGAALLRTLSELESCDNPQELQCQIKEINE 78
             GE  L N++    + L++          +  +LLR L +  S  N +E + +I  +  
Sbjct: 596 PGGERILTNLLHLAEL-LQEAAHQER----NKLSLLRWLEDQIS--NEEEEEEEIIRLES 648

Query: 79  RATLFRITT 87
            A L +I T
Sbjct: 649 DAELVKIVT 657


>gnl|CDD|224832 COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium
           transferase] [Amino acid transport and metabolism].
          Length = 395

 Score = 27.3 bits (61), Expect = 9.8
 Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 16  DFEVDGEVKLEN--IIKTLSVNLEQLQSYNEIINKHGAALLRTLSE 59
            F V   ++L    +++  + N   L+ Y   IN++ A LL+  S 
Sbjct: 121 AFRVPDIIRLAGAKLVEVGTTNRTHLKDYELAINENTALLLKVHSS 166


  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
   0.312    0.131    0.380 

Gapped
Lambda     K      H
   0.267   0.0775    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,509,686
Number of extensions: 1272325
Number of successful extensions: 1018
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1012
Number of HSP's successfully gapped: 22
Length of query: 266
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 171
Effective length of database: 6,723,972
Effective search space: 1149799212
Effective search space used: 1149799212
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 (21.8 bits)
S2: 58 (26.0 bits)