RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13300
         (346 letters)



>gnl|CDD|180712 PRK06820, PRK06820, type III secretion system ATPase; Validated.
          Length = 440

 Score = 31.3 bits (71), Expect = 0.69
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 13/78 (16%)

Query: 19  ENAPWMTRIAAYTQQIIINSSEELLKDPFLPLAERVK---KRTDNLFHKEESLRGFLKSS 75
             A  + R+ A  Q+I      ELL    + + E       + D    +  ++  FL+  
Sbjct: 372 AMAQKLRRMLACYQEI------ELL----VRVGEYQAGEDLQADEALQRYPAICAFLQQD 421

Query: 76  VDDTSQIESQIQEDWQLL 93
             +T+ +E+ ++   Q++
Sbjct: 422 HSETAHLETTLEHLAQVV 439


>gnl|CDD|219945 pfam08634, Pet127, Mitochondrial protein Pet127.  Pet127 has been
           implicated in mitochondrial RNA stability and/or
           processing and is localised to the mitochondrial
           membrane. The Pet127 family is part of the PD-(D/E)XK
           nuclease superfamily including a full set of active site
           residues.
          Length = 274

 Score = 30.8 bits (70), Expect = 1.0
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 135 NIWSKSQYFLREEQNFISANEIDNMILIMPTATRRSAVVSDSS-----VAGGVGGKMKKM 189
           N  S S+ F  ++ NF  +  + + +++        A+ SD S     +   +G  ++K+
Sbjct: 46  NTSSLSKPFPPKKSNFTRSARLPSSVILRRYKDGIYAIDSDKSADREIILSNLGHSLEKL 105

Query: 190 PEYEIMEFVKTQLTLPDKIDPADEMSWQHYLYSKLG 225
              +  EF +  LT    +   ++   + Y YSK+G
Sbjct: 106 LTLDKEEFERYLLTKKPNVSDEEKKFPEAYHYSKIG 141


>gnl|CDD|221834 pfam12891, Glyco_hydro_44, Glycoside hydrolase family 44.  This is
           a family of bacterial glycoside hydrolases formerly
           known as cellulase family J, and now known as Cel44A. It
           is one of the major enzymatic components of the
           cellulosome of Clostridium thermocellum strain F1 and of
           many other Firmicutes.
          Length = 236

 Score = 30.0 bits (68), Expect = 1.7
 Identities = 24/133 (18%), Positives = 41/133 (30%), Gaps = 46/133 (34%)

Query: 205 PDKIDPADEMS-WQHYLYSKLGNKKDST-------------------EVVPHAGQTPVKP 244
           PD  D +  M  W +YL +K GN   +                    +V P        P
Sbjct: 95  PDLTDGSVYMDEWVNYLVNKYGNASGAGGVKGYSLDNEPDLWNGTHRDVHP-------NP 147

Query: 245 PTVDDVVERIVAMAKVLFGLHMKMPEYEIMEFVKTQLTLPDKIDPADEMSWQHYLYSKLG 304
            T D+++++ + +AK +  +    P  EI                     W    Y    
Sbjct: 148 VTYDELLDKSIELAKAVKAVD---PGAEIFGPA----------------EWGWCAYFNSQ 188

Query: 305 NKKDSTEVVPHAG 317
           +  D ++   H  
Sbjct: 189 DAPDWSDRKAHGN 201


>gnl|CDD|173793 cd04847, Peptidases_S8_Subtilisin_like_2, Peptidase S8 family
           domain in Subtilisin-like proteins.  This family is a
           member of the Peptidases S8 or Subtilases serine endo-
           and exo-peptidase clan. They have an Asp/His/Ser
           catalytic triad similar to that found in trypsin-like
           proteases, but do not share their three-dimensional
           structure and are not homologous to trypsin. The
           stability of subtilases may be enhanced by calcium, some
           members have been shown to bind up to 4 ions via binding
           sites with different affinity. Some members of this clan
           contain disulfide bonds. These enzymes can be intra- and
           extracellular, some function at extreme temperatures and
           pH values.
          Length = 291

 Score = 29.2 bits (66), Expect = 2.7
 Identities = 7/24 (29%), Positives = 11/24 (45%)

Query: 21  APWMTRIAAYTQQIIINSSEELLK 44
           AP   R+AA     +   S E ++
Sbjct: 260 APLAARLAAGLFAELPELSPETIR 283


>gnl|CDD|238644 cd01319, AMPD, AMP deaminase (AMPD) catalyzes the hydrolytic
           deamination of adensosine monophosphate (AMP) at
           position 6 of the adenine nucleotide ring. AMPD is a
           diverse and highly regulated eukaryotic key enzyme of
           the adenylate catabolic pathway.
          Length = 496

 Score = 28.9 bits (65), Expect = 4.6
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 14/81 (17%)

Query: 12  IKKNIGNENAPWMTRIA----AYTQQIIINSSEELLKDPFLPLAERVKKRTDNLFHKEES 67
           +  ++ + N  W+ +I      Y +  I+NS +E+L++ F PL E   K   +  H E  
Sbjct: 205 VDNDLFSPNVRWLIQIPRLYDVYKKSGIVNSFQEMLENIFEPLFE-ATKDPSS--HPE-- 259

Query: 68  LRGFLK-----SSVDDTSQIE 83
           L  FL+      SVDD S+ E
Sbjct: 260 LHVFLQQVIGFDSVDDESKSE 280


>gnl|CDD|238617 cd01292, metallo-dependent_hydrolases, Superfamily of
           metallo-dependent hydrolases (also called amidohydrolase
           superfamily) is a large group of proteins that show
           conservation in their 3-dimensional fold (TIM barrel)
           and in details of their active site. The vast majority
           of the members have a conserved metal binding site,
           involving four histidines and one aspartic acid residue.
           In the common reaction mechanism, the metal ion (or
           ions) deprotonate a water molecule for a nucleophilic
           attack on the substrate. The family includes urease
           alpha, adenosine deaminase, phosphotriesterase
           dihydroorotases, allantoinases, hydantoinases, AMP-,
           adenine and cytosine deaminases, imidazolonepropionase,
           aryldialkylphosphatase, chlorohydrolases,
           formylmethanofuran dehydrogenases and others.
          Length = 275

 Score = 28.5 bits (63), Expect = 5.1
 Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 233 VVPHAGQTPVKPPTVDDVVERIVAMAKVLFGLHMKMPEYEIME 275
           VV HAG+ P     ++D+V  +    +V+ G H+   + E++E
Sbjct: 149 VVIHAGELPDPTRALEDLVALLRLGGRVVIG-HVSHLDPELLE 190


>gnl|CDD|214383 CHL00168, pbsA, heme oxygenase; Provisional.
          Length = 238

 Score = 28.2 bits (63), Expect = 6.4
 Identities = 13/34 (38%), Positives = 20/34 (58%)

Query: 245 PTVDDVVERIVAMAKVLFGLHMKMPEYEIMEFVK 278
           P  DD ++ I+A A + F L+MKM +     F+K
Sbjct: 180 PLSDDQIQNIIAEANIAFNLNMKMFQELNSSFIK 213


>gnl|CDD|233021 TIGR00555, panK_eukar, pantothenate kinase,
           eukaryotic/staphyloccocal type.  This model describes a
           eukaryotic form of pantothenate kinase, characterized
           from the fungus Aspergillus nidulans and with similar
           forms known in several other eukaryotes. It also
           includes forms from several Gram-positive bacteria
           suggested to have originated from the eukaryotic form by
           lateral transfer. It differs in a number of biochemical
           properties (such as inhibition by acetyl-CoA) from most
           bacterial CoaA and lacks sequence similarity. This
           enzyme is the key regulatory step in the biosynthesis of
           coenzyme A (CoA) [Biosynthesis of cofactors, prosthetic
           groups, and carriers, Pantothenate and coenzyme A].
          Length = 296

 Score = 27.8 bits (62), Expect = 7.9
 Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 4/35 (11%)

Query: 116 LRNNIPEAELIYNYVSEIFNIWSKSQYFLREEQNF 150
           LRNN    +++        N WSK   FL  E   
Sbjct: 258 LRNNQLLMKVLSYAT----NFWSKKALFLEHEGYS 288


  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    0.133    0.388 

Gapped
Lambda     K      H
   0.267   0.0702    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,009,281
Number of extensions: 1737206
Number of successful extensions: 1616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1614
Number of HSP's successfully gapped: 18
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
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 (21.7 bits)
S2: 59 (26.6 bits)