RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 039682
         (107 letters)



>gnl|CDD|223257 COG0179, MhpD, 2-keto-4-pentenoate
           hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
           (catechol pathway) [Secondary metabolites biosynthesis,
           transport, and catabolism].
          Length = 266

 Score =  118 bits (299), Expect = 1e-34
 Identities = 45/92 (48%), Positives = 59/92 (64%), Gaps = 1/92 (1%)

Query: 1   AKGQDTFTPISSVLPKSA-VPDPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIM 59
           AKG DTF P+   +     + DP N  L L+V+ E+RQ+G+T DMIF IP LI+++S  M
Sbjct: 164 AKGFDTFAPVGPWIVTKDEISDPQNLPLSLRVNGEVRQRGNTSDMIFSIPELIAYLSRFM 223

Query: 60  TLFEGDVILTGSPQGVGPVKAGQKTTAGIAGL 91
           TL  GDVILTG+P GVG +K G      I G+
Sbjct: 224 TLEPGDVILTGTPSGVGFLKPGDVVEVEIEGI 255


>gnl|CDD|216570 pfam01557, FAA_hydrolase, Fumarylacetoacetate (FAA) hydrolase
           family.  This family consists of fumarylacetoacetate
           (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH)
           and it also includes HHDD isomerase/OPET decarboxylase
           from E. coli strain W. FAA is the last enzyme in the
           tyrosine catabolic pathway, it hydrolyses
           fumarylacetoacetate into fumarate and acetoacetate which
           then join the citric acid cycle. Mutations in FAA cause
           type I tyrosinemia in humans this is an inherited
           disorder mainly affecting the liver leading to liver
           cirrhosis, hepatocellular carcinoma, renal tubular
           damages and neurologic crises amongst other symptoms.
           The enzymatic defect causes the toxic accumulation of
           phenylalanine/tyrosine catabolites. The E. coli W enzyme
           HHDD isomerase/OPET decarboxylase contains two copies of
           this domain and functions in fourth and fifth steps of
           the homoprotocatechuate pathway; here it decarboxylates
           OPET to HHDD and isomerises this to OHED. The final
           products of this pathway are pyruvic acid and succinic
           semialdehyde. This family also includes various
           hydratases and 4-oxalocrotonate decarboxylases which are
           involved in the bacterial meta-cleavage pathways for
           degradation of aromatic compounds. 2-hydroxypentadienoic
           acid hydratase, encoded by mhpD in E. coli, is involved
           in the phenylpropionic acid pathway of E. coli and
           catalyzes the conversion of 2-hydroxy pentadienoate to
           4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor.
           OHED hydratase encoded by hpcG in E. coli is involved in
           the homoprotocatechuic acid (HPC) catabolism. XylI in P.
           putida is a 4-Oxalocrotonate decarboxylase.
          Length = 207

 Score =  101 bits (254), Expect = 2e-28
 Identities = 39/95 (41%), Positives = 53/95 (55%), Gaps = 4/95 (4%)

Query: 1   AKGQDTFTPISSVL-PKSAVPDPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIM 59
           AK  D F P+   +     + DP + EL L+V+ E+ Q GST DMIF    LI+H+S  +
Sbjct: 105 AKSFDGFAPLGPWIVTPDELGDPADLELRLRVNGELVQDGSTADMIFSPAELIAHLSRFL 164

Query: 60  TLFEGDVILTGSPQGVGP---VKAGQKTTAGIAGL 91
           TL  GD+ILTG+P G  P   ++ G      I GL
Sbjct: 165 TLEPGDIILTGTPSGRAPALFLQPGDVVEVEIEGL 199


>gnl|CDD|182650 PRK10691, PRK10691, hypothetical protein; Provisional.
          Length = 219

 Score = 96.3 bits (240), Expect = 3e-26
 Identities = 42/91 (46%), Positives = 57/91 (62%), Gaps = 1/91 (1%)

Query: 1   AKGQDTFTPISSVLPKSAVP-DPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIM 59
           AK  D   PIS  +P +    DP N  L L V+ E+RQQG+T DMI  I  LI+++S   
Sbjct: 121 AKAFDNSCPISGFIPVAEFTGDPQNTTLGLSVNGEVRQQGNTADMIHPIVPLIAYMSRFF 180

Query: 60  TLFEGDVILTGSPQGVGPVKAGQKTTAGIAG 90
           TL  GDV+LTG+P+GVGP+++G + T    G
Sbjct: 181 TLRAGDVVLTGTPEGVGPLQSGDELTVTFNG 211


>gnl|CDD|131356 TIGR02303, HpaG-C-term, 4-hydroxyphenylacetate degradation
           bifunctional isomerase/decarboxylase, C-terminal
           subunit.  This model represents one of two
           subunits/domains of the bifunctional
           isomerase/decarboxylase involved in
           4-hydroxyphenylacetate degradation. In E. coli and some
           other species this enzyme is encoded by a single
           polypeptide containing both this domain and the closely
           related N-terminal domain (TIGR02305). In other species
           such as Pasteurella multocida these domains are found as
           two separate proteins (usually as tandem genes).
           Together, these domains carry out the decarboxylation of
           5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to
           2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent
           isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
          Length = 245

 Score = 96.4 bits (240), Expect = 6e-26
 Identities = 42/92 (45%), Positives = 56/92 (60%), Gaps = 1/92 (1%)

Query: 1   AKGQDTFTPISS-VLPKSAVPDPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIM 59
            K +DTFTPI   ++ K  V DP N  L   V+ E+ Q+G+T DMIF +  LI ++S  M
Sbjct: 144 VKNRDTFTPIGPWIVDKEDVEDPMNLWLRTYVNGELTQEGNTSDMIFSVAELIEYLSEFM 203

Query: 60  TLFEGDVILTGSPQGVGPVKAGQKTTAGIAGL 91
           TL  GDVILTG+P+G+  VK G      I G+
Sbjct: 204 TLEPGDVILTGTPKGLSDVKPGDVVRLEIEGV 235


>gnl|CDD|185125 PRK15203, PRK15203, 4-hydroxyphenylacetate degradation bifunctional
           isomerase/decarboxylase; Provisional.
          Length = 429

 Score = 90.1 bits (223), Expect = 1e-22
 Identities = 41/91 (45%), Positives = 62/91 (68%), Gaps = 1/91 (1%)

Query: 2   KGQDTFTPISS-VLPKSAVPDPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIMT 60
           K +D  TPI S ++PK A+PDP+N  L   V+ E+RQQG+T D+IF +P+LI+++S  MT
Sbjct: 325 KSRDGLTPILSTIVPKEAIPDPHNLTLRTFVNGELRQQGTTADLIFSVPFLIAYLSEFMT 384

Query: 61  LFEGDVILTGSPQGVGPVKAGQKTTAGIAGL 91
           L  GD+I TG+P+G+  V  G +    + G+
Sbjct: 385 LNPGDMIATGTPKGLSDVVPGDEVVVEVEGV 415



 Score = 35.0 bits (80), Expect = 0.004
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 1   AKGQDTFTPISSVLPKSAVPDPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIMT 60
           AK +D F PI   +  S V    N  ++ +++       +T D+      L+S +S   T
Sbjct: 109 AKCRDGFCPIGETVALSNVD---NLTIYTEINGRPADHWNTADLQRNAAQLLSALSEFAT 165

Query: 61  LFEGDVILTGSPQGVGPVKAGQK 83
           L  GD IL G+PQ    ++ G +
Sbjct: 166 LNPGDAILLGTPQARVEIQPGDR 188


>gnl|CDD|131358 TIGR02305, HpaG-N-term, 4-hydroxyphenylacetate degradation
           bifunctional isomerase/decarboxylase, N-terminal
           subunit.  This model represents one of two
           subunits/domains of the bifunctional
           isomerase/decarboxylase involved in
           4-hydroxyphenylacetate degradation. In E. coli and some
           other species this enzyme is encoded by a single
           polypeptide containing both this domain and the closely
           related C-terminal domain (TIGR02303). In other species
           such as Pasteurella multocida these domains are found as
           two separate proteins (usually as tandem genes).
           Together, these domains carry out the decarboxylation of
           5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to
           2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent
           isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
          Length = 205

 Score = 75.2 bits (185), Expect = 4e-18
 Identities = 29/91 (31%), Positives = 47/91 (51%)

Query: 1   AKGQDTFTPISSVLPKSAVPDPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIMT 60
           AK +D F PI   +P SA+ +P    ++  ++ +  Q  +T +++     LIS +S  MT
Sbjct: 108 AKCRDGFCPIGPEVPLSAIGNPDELTIYTYINGKPAQSNNTSNLVRSAAQLISELSEFMT 167

Query: 61  LFEGDVILTGSPQGVGPVKAGQKTTAGIAGL 91
           L  GDV+L G+P+    V  G +      GL
Sbjct: 168 LNPGDVLLLGTPEARVEVGPGDRVRVEAEGL 198


>gnl|CDD|237193 PRK12764, PRK12764, hypothetical protein; Provisional.
          Length = 500

 Score = 64.4 bits (157), Expect = 1e-13
 Identities = 31/81 (38%), Positives = 46/81 (56%)

Query: 1   AKGQDTFTPISSVLPKSAVPDPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIMT 60
           +KG D FTPI   L  +   DP    +   V+ E+ Q  +T+D++F    L++ +S ++T
Sbjct: 122 SKGGDGFTPIGPALISARGVDPAQLRVRTWVNGELVQDDTTEDLLFPFAQLVADLSQLLT 181

Query: 61  LFEGDVILTGSPQGVGPVKAG 81
           L EGDVILTG+P G      G
Sbjct: 182 LEEGDVILTGTPAGSSVAAPG 202


>gnl|CDD|132264 TIGR03220, catechol_dmpE, 2-oxopent-4-enoate hydratase.  Members of
           this protein family are 2-oxopent-4-enoate hydratase,
           which is also called 2-hydroxypent-2,4-dienoate
           hydratase. It is closely related to another gene found
           in the same operon, 4-oxalocrotonate decarboxylase, with
           which it interacts closely.
          Length = 255

 Score = 28.5 bits (64), Expect = 0.51
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 2/40 (5%)

Query: 59  MTLFEGDVILTGSPQGVGPVKAGQKTTAGIAGL--LVVRF 96
           + L  G+VIL+GS   + PVKAG      I G+    VRF
Sbjct: 216 IPLKAGEVILSGSLAALVPVKAGDNLRVSIGGIGSCSVRF 255


>gnl|CDD|132996 cd00505, Glyco_transf_8, Members of glycosyltransferase family 8
           (GT-8) are involved in lipopolysaccharide biosynthesis
           and glycogen synthesis.  Members of this family are
           involved in lipopolysaccharide biosynthesis and glycogen
           synthesis. GT-8 comprises enzymes with a number of known
           activities: lipopolysaccharide galactosyltransferase,
           lipopolysaccharide glucosyltransferase 1, glycogenin
           glucosyltransferase, and
           N-acetylglucosaminyltransferase. GT-8 enzymes contains a
           conserved DXD motif which is essential in the
           coordination of a  catalytic divalent cation, most
           commonly Mn2+.
          Length = 246

 Score = 28.6 bits (64), Expect = 0.57
 Identities = 6/48 (12%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 21  DPYNFELWLKVDREIRQQGSTKDMIFKIPYLISHISSIMTLFEGDVIL 68
            P +    +  +   R           +P L+     I+   + D+++
Sbjct: 62  IPVDILDSVDSEHLKRPIKIVTLTKLHLPNLVPDYDKIL-YVDADILV 108


>gnl|CDD|211993 TIGR04270, Rama_corrin_act, methylamine methyltransferase corrinoid
           protein reductive activase.  Members of this family
           occur as paralogs in species capable of generating
           methane from mono-, di-, and tri-methylamine. Members
           include RamA (Reductive Activation of Methyltransfer,
           Amines) from Methanosarcina barkeri MS (DSM 800). Member
           proteins have two C-terminal motifs with four Cys each,
           likely to bind one 4Fe-4S cluster per motif.
          Length = 535

 Score = 27.8 bits (62), Expect = 1.3
 Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 1/29 (3%)

Query: 59  MTLFEGDVILTGSPQGVGPVKAGQKTTAG 87
           M L  G  I TGS    GP   GQ+ + G
Sbjct: 180 MALKVGGRIYTGS-AAAGPALEGQQISCG 207


>gnl|CDD|213953 TIGR04340, rSAM_ACGX, radical SAM/SPASM domain protein, ACGX
           system.  Members of this protein family are radical
           SAM/SPASM domain proteins likely to be involved in the
           modification of small, Cys-rich peptides. Members of the
           family of proposed target sequences, TIGR04341, average
           75 amino acids in length and average six instances of
           the motif ACGX, where X is A, S, or T.
          Length = 341

 Score = 27.1 bits (60), Expect = 1.6
 Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 2/28 (7%)

Query: 35  IRQQGSTKDMIFKIPYLISH--ISSIMT 60
           IR+ GS  + + KIP +      +++MT
Sbjct: 125 IRKPGSFDETLAKIPMIRKAGIRAAVMT 152


>gnl|CDD|223057 PHA03364, PHA03364, hypothetical protein; Provisional.
          Length = 264

 Score = 27.2 bits (61), Expect = 1.8
 Identities = 7/28 (25%), Positives = 15/28 (53%), Gaps = 4/28 (14%)

Query: 19  VPDPYNFELWLKVDREIRQQGSTKDMIF 46
           VP  Y    W  +   +++ G +++M+F
Sbjct: 78  VPVEY----WKLLYDALKEMGVSEEMLF 101


>gnl|CDD|180353 PRK06026, PRK06026, 5'-methylthioadenosine/S-adenosylhomocysteine
          nucleosidase; Validated.
          Length = 212

 Score = 26.2 bits (58), Expect = 3.3
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 13/43 (30%)

Query: 49 PYLISHISSIMTLFEGDVILTGSPQGVGPVKAGQKTTAGIAGL 91
          P+L +  + +MT             GVGPV+A    TA +A L
Sbjct: 25 PHLRARFTPLMT-------------GVGPVEAAVNLTAALARL 54


>gnl|CDD|145934 pfam03049, Herpes_UL79, UL79 family.  Members of this family are
          functionally uncharacterized proteins from
          herpesviruses. This family groups together HSV-6 U52,
          HVS-1 18 and HCMV UL79.
          Length = 252

 Score = 26.4 bits (59), Expect = 3.3
 Identities = 8/28 (28%), Positives = 15/28 (53%), Gaps = 4/28 (14%)

Query: 19 VPDPYNFELWLKVDREIRQQGSTKDMIF 46
          VP  Y    W  +   +++ G ++DM+F
Sbjct: 76 VPPEY----WKILYDGLKEMGPSEDMLF 99


>gnl|CDD|221370 pfam12003, DUF3497, Domain of unknown function (DUF3497).  This
          presumed domain is functionally uncharacterized. This
          domain is found in eukaryotes. This domain is typically
          between 213 to 257 amino acids in length. This domain
          is found associated with pfam02793, pfam00002,
          pfam01825. This domain has a single completely
          conserved residue W that may be functionally important.
          Length = 221

 Score = 26.2 bits (58), Expect = 3.8
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 17 SAVPDPYNFELWLKVDREIRQQGSTK 42
          S + DP N E W  + R  R +G+TK
Sbjct: 69 SNLLDPENKESWEDLQRTERIRGATK 94


>gnl|CDD|180462 PRK06198, PRK06198, short chain dehydrogenase; Provisional.
          Length = 260

 Score = 25.7 bits (57), Expect = 4.9
 Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 59 MTLFEGDVIL-TGSPQGVGPVKAGQKTTAGIAGLLVV 94
          M   +G V L TG  QG+G   A      G AGL++ 
Sbjct: 1  MGRLDGKVALVTGGTQGLGAAIARAFAERGAAGLVIC 37


>gnl|CDD|226480 COG3971, COG3971, 2-keto-4-pentenoate hydratase [Secondary
           metabolites biosynthesis, transport, and catabolism].
          Length = 264

 Score = 25.0 bits (55), Expect = 8.6
 Identities = 14/37 (37%), Positives = 17/37 (45%)

Query: 60  TLFEGDVILTGSPQGVGPVKAGQKTTAGIAGLLVVRF 96
            L  GD++LTGS  G  P + G    A   GL  V  
Sbjct: 223 PLKAGDIVLTGSFTGPVPARPGDTFHADFGGLGAVSC 259


>gnl|CDD|113971 pfam05220, MgpC, MgpC protein precursor.  This family contains
           several Mycoplasma MgpC like-proteins.
          Length = 224

 Score = 25.0 bits (54), Expect = 9.8
 Identities = 12/24 (50%), Positives = 14/24 (58%)

Query: 69  TGSPQGVGPVKAGQKTTAGIAGLL 92
           T   Q   PVK+ QK TA IA L+
Sbjct: 162 TEPVQTTYPVKSDQKATAKIASLI 185


  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
   0.318    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0699    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,480,817
Number of extensions: 456334
Number of successful extensions: 386
Number of sequences better than 10.0: 1
Number of HSP's gapped: 383
Number of HSP's successfully gapped: 28
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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: 53 (24.3 bits)