RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7694
         (317 letters)



>gnl|CDD|165802 PLN02155, PLN02155, polygalacturonase.
          Length = 394

 Score = 32.0 bits (72), Expect = 0.39
 Identities = 15/34 (44%), Positives = 19/34 (55%)

Query: 254 LTSWARPSGNYLALVFLVGLHINCEENPISNDHN 287
           + SWARPS  ++  VF   L +   ENPI  D N
Sbjct: 275 IKSWARPSTGFVRNVFFQDLVMKNVENPIIIDQN 308


>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
           function prediction only].
          Length = 368

 Score = 30.6 bits (69), Expect = 1.0
 Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 15/87 (17%)

Query: 102 IDFRLENERDRYVLTVHVYRYLDTSLLDVDVQPNYVRVT--------IKNKVLQLALDDT 153
           I+F+L N+ +R  +   +  Y     L VD    Y+           IK KVL+ AL   
Sbjct: 279 IEFKLPNDEERLEI---LEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLKTALHRA 335

Query: 154 VLTDKSYAQRSEATRHLVVTMPKESGR 180
           +  D+   +R      +   + KE  R
Sbjct: 336 IAEDREKVER----EDIEKALKKERKR 358


>gnl|CDD|213633 TIGR01504, glyox_carbo_lig, glyoxylate carboligase.  Glyoxylate
           carboligase, also called tartronate-semialdehyde
           synthase, releases CO2 while synthesizing a single
           molecule of tartronate semialdehyde from two molecules
           of glyoxylate. It is a thiamine pyrophosphate-dependent
           enzyme, closely related in sequence to the large subunit
           of acetolactate synthase. In the D-glycerate pathway,
           part of allantoin degradation in the Enterobacteriaceae,
           tartronate semialdehyde is converted to D-glycerate and
           then 3-phosphoglycerate, a product of glycolysis and
           entry point in the general metabolism.
          Length = 588

 Score = 29.2 bits (65), Expect = 3.5
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 171 VVTMPKESGRAVLGQNETVKKTSPKKDTPNQKSNPDQPPVSNQREYLEIGKSI-----HY 225
           V    K++GR +  ++E       +K T  +K++ D  PV  QR Y E+ K+      + 
Sbjct: 331 VAQELKKAGR-LPDRSEWAADCQQRKRTLLRKTHFDNVPVKPQRVYEEMNKAFGRDVCYV 389

Query: 226 ENMDFSQIYANSELPALELNSWI 248
             +  SQI     L   +   WI
Sbjct: 390 TTIGLSQIAGAQMLHVYKPRHWI 412


>gnl|CDD|183831 PRK12933, secD, preprotein translocase subunit SecD; Reviewed.
          Length = 604

 Score = 28.9 bits (65), Expect = 4.6
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 127 LLDVDVQPNYV--RVTIKNKVLQLALDDTVLTDKSYAQRSEATRHLVVTMPKESGRAVLG 184
           LLDVDV P Y   R  + + V Q   +  +   +  + R + +  L VT P    R+ + 
Sbjct: 139 LLDVDVDPVYQEQRDALVDSVRQFLREQRI---RGVSVRLDDSDQLAVTTPDNDARSAVR 195

Query: 185 Q 185
           Q
Sbjct: 196 Q 196


>gnl|CDD|205223 pfam13042, DUF3902, Protein of unknown function (DUF3902).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in bacteria. Proteins in
           this family are approximately 170 amino acids in length.
           There is a conserved LGI sequence motif.
          Length = 161

 Score = 27.8 bits (62), Expect = 5.2
 Identities = 15/50 (30%), Positives = 23/50 (46%)

Query: 227 NMDFSQIYANSELPALELNSWIKQLDWLTSWARPSGNYLALVFLVGLHIN 276
           N+  S I++   +  L  N +    DWL SW      YL+L  L+ L+  
Sbjct: 6   NIIISFIFSVVGMIWLLFNLFKGDGDWLLSWVGVLMAYLSLYILIDLYCK 55


>gnl|CDD|185716 cd08039, Adenylation_DNA_ligase_Fungal, Adenylation domain of
           uncharacterized fungal ATP-dependent DNA ligase-like
           proteins.  ATP-dependent polynucleotide ligases catalyze
           phosphodiester bond formation using nicked nucleic acid
           substrates with the high energy nucleotide of ATP as a
           cofactor in a three step reaction mechanism. DNA ligases
           play a vital role in the diverse processes of DNA
           replication, recombination and repair. ATP-dependent
           ligases are present in many organisms such as viruses,
           bacteriophages, eukarya, archaea and bacteria. This
           group is composed of uncharacterized fungal proteins
           with similarity to ATP-dependent DNA ligases. ATP
           dependent DNA ligases have a highly modular architecture
           consisting of a unique arrangement of two or more
           discrete domains including a DNA-binding domain, an
           adenylation (nucleotidyltransferase (NTase)) domain, and
           an oligonucleotide/oligosaccharide binding (OB)-fold
           domain. The adenylation domain binds ATP and contains
           many of the active-site residues. The adenylation and
           C-terminal OB-fold domains comprise a catalytic core
           unit that is common to most members of the ATP-dependent
           DNA ligase family. The catalytic core unit contains six
           conserved sequence motifs (I, III, IIIa, IV, V and VI)
           that define this family of related
           nucleotidyltransferases. This model characterizes the
           adenylation domain of this group of uncharacterized
           fungal proteins. It is not known whether these proteins
           also contain an OB-fold domain.
          Length = 235

 Score = 27.8 bits (62), Expect = 6.6
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 148 LALDDTVLTDKSYAQRSEATRHLVVTMPKESGRA 181
           L LDD  L  K Y++R +    LV  +P  +G +
Sbjct: 141 LLLDDESLLSKPYSERRDLLESLVHVIPGYAGLS 174


>gnl|CDD|237072 PRK12355, PRK12355, conjugal transfer mating pair stabilization
           protein TraN; Reviewed.
          Length = 558

 Score = 28.2 bits (63), Expect = 7.4
 Identities = 8/23 (34%), Positives = 12/23 (52%), Gaps = 4/23 (17%)

Query: 222 SIHYENMDFSQIYA----NSELP 240
            I +  +DFS+ Y     N +LP
Sbjct: 523 KIDFSRIDFSEFYEDLMNNQKLP 545


>gnl|CDD|179855 PRK04460, PRK04460, nickel responsive regulator; Provisional.
          Length = 137

 Score = 26.9 bits (60), Expect = 7.8
 Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 8/36 (22%)

Query: 152 DTVLTDKSYAQRSEATRHLVVTMPKESGRAVLGQNE 187
           D ++ +K Y  RSEA R L+        R  L ++E
Sbjct: 18  DELIEEKGYQNRSEAIRDLI--------RDFLVEHE 45


>gnl|CDD|184771 PRK14623, PRK14623, hypothetical protein; Provisional.
          Length = 106

 Score = 26.3 bits (58), Expect = 8.8
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 123 LDTSLLDVDVQPNYVRVTI--KNKVLQLALDDTVLTDKSYAQRSEATRHLVVTMPKESGR 180
           LDT L+D       ++VT+    ++  +++DD +L DK      +   +LV+T+ K   +
Sbjct: 24  LDTVLIDEQSSDGLLKVTVTANREIKSISIDDELLEDK-----EQLEDYLVLTLNKAIEK 78

Query: 181 AVLGQNETVKKTSPKKDTPN 200
           A    NE       K+  P+
Sbjct: 79  AT-EINEAELGAVAKEGMPD 97


  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    0.131    0.371 

Gapped
Lambda     K      H
   0.267   0.0644    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,610,763
Number of extensions: 1439324
Number of successful extensions: 773
Number of sequences better than 10.0: 1
Number of HSP's gapped: 773
Number of HSP's successfully gapped: 15
Length of query: 317
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 220
Effective length of database: 6,635,264
Effective search space: 1459758080
Effective search space used: 1459758080
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 (22.0 bits)
S2: 59 (26.7 bits)