RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13603
         (133 letters)



>gnl|CDD|152015 pfam11579, DUF3238, Protein of unknown function (DUF3238).  This
           family of proteins with unknown function appears to be
           restricted to Bacillus cereus.
          Length = 193

 Score = 29.2 bits (65), Expect = 0.50
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 8/61 (13%)

Query: 22  HVAVQMRQDLGENFDSLFKKIYMSRHENLLISGKKIS--------RRGAVSLENIICTNV 73
           H     R  + +     F K  +  + N  I+ +K++        R G  S ENI+CT++
Sbjct: 41  HAVNTKRSRVEQEVVVDFYKREVFSYANTGITTEKVTNPDGSVNKRTGKASTENIVCTDI 100

Query: 74  I 74
           +
Sbjct: 101 V 101


>gnl|CDD|233646 TIGR01936, nqrA, NADH:ubiquinone oxidoreductase,
           Na(+)-translocating, A subunit.  This model represents
           the NqrA subunit of the six-protein, Na(+)-pumping
           NADH-quinone reductase of a number of marine and
           pathogenic Gram-negative bacteria. This oxidoreductase
           complex functions primarily as a sodium ion pump
           [Transport and binding proteins, Cations and iron
           carrying compounds].
          Length = 447

 Score = 27.4 bits (61), Expect = 2.5
 Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 2/51 (3%)

Query: 17  SVLPEHVAVQMRQDLGENFDSLFKKIYMSRHENLLISGKKISRRGAVSLEN 67
             + +   V  R   G N   LF     S  EN LISG  ++ R A   E 
Sbjct: 266 PAVKKPRYV--RTTKGANLSQLFPGELTSEGENRLISGSVLTGRKAKKEEA 314


>gnl|CDD|149036 pfam07746, LigA, Aromatic-ring-opening dioxygenase LigAB, LigA
           subunit.  This is a family of aromatic ring opening
           dioxygenases which catalyze the ring-opening reaction of
           protocatechuate and related compounds.
          Length = 88

 Score = 26.0 bits (58), Expect = 2.6
 Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 2/42 (4%)

Query: 82  LGQMCYHMSEKEQRTAFLETRQCL--EMRLVIEEQSAEQRFD 121
           L + C  + + E R  FL   +    E  L  E+++A +  D
Sbjct: 1   LNKFCMSLIKAENRERFLADEEAYLDEYGLTEEQKAAVRARD 42


>gnl|CDD|130895 TIGR01836, PHA_synth_III_C, poly(R)-hydroxyalkanoic acid synthase,
           class III, PhaC subunit.  This model represents the PhaC
           subunit of a heterodimeric form of polyhydroxyalkanoic
           acid (PHA) synthase. Excepting the PhaC of Bacillus
           megaterium (which needs PhaR), all members require PhaE
           (TIGR01834) for activity and are designated class III.
           This enzyme builds ester polymers for carbon and energy
           storage that accumulate in inclusions, and both this
           enzyme and the depolymerase associate with the
           inclusions. Class III enzymes polymerize
           short-chain-length hydroxyalkanoates [Fatty acid and
           phospholipid metabolism, Biosynthesis].
          Length = 350

 Score = 27.4 bits (61), Expect = 2.7
 Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 3/39 (7%)

Query: 32  GENFDSLFKKIYMSRHENLLISGKKISRRGAVSLENIIC 70
           GE F    K  Y    +N LI+G+       V L+NI  
Sbjct: 252 GEAFRQFVKDFY---QQNGLINGEVEIGGRKVDLKNIKM 287


>gnl|CDD|217646 pfam03630, Fumble, Fumble.  Fumble is required for cell division in
           Drosophila. Mutants lacking fumble exhibit abnormalities
           in bipolar spindle organisation, chromosome segregation,
           and contractile ring formation. Analyses have
           demonstrated that encodes three protein isoforms, all of
           which contain a domain with high similarity to the
           pantothenate kinases of A. nidulans and mouse. A role of
           fumble in membrane synthesis has been proposed.
          Length = 329

 Score = 26.9 bits (60), Expect = 3.2
 Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 13/72 (18%)

Query: 34  NFDSLFKKIYMSRHENLLIS--------GKKISRRGA---VSLENIICTNVILLVSANIL 82
           N D L + IY   +    +         GK           S E+ I  +++ ++S NI 
Sbjct: 206 NVDMLVRDIYGGDYSKFGLKGDLIASSFGKVFRELKRLEDFSPED-IARSLLRMISNNI- 263

Query: 83  GQMCYHMSEKEQ 94
           GQ+ Y  + +  
Sbjct: 264 GQIAYLCALRFN 275


>gnl|CDD|180958 PRK07396, PRK07396, dihydroxynaphthoic acid synthetase; Validated.
          Length = 273

 Score = 26.8 bits (60), Expect = 3.2
 Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%)

Query: 85  MCYHMSE--KEQRTAFLETRQ 103
           M ++M+E  +E R AF E RQ
Sbjct: 243 MLFYMTEEAQEGRNAFNEKRQ 263


>gnl|CDD|219549 pfam07744, SPOC, SPOC domain.  The SPOC (Spen paralogue and
          orthologue C-terminal) domain is involved in
          developmental signalling.
          Length = 109

 Score = 26.1 bits (58), Expect = 3.2
 Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 3  MKLINLRGRERLLLSVLPEHVAVQMRQDLGENFDSLFKKIYMSR 46
          ++   + G E+L+ S+LP  + ++ R DL    +   +K+  S 
Sbjct: 15 VRAHLVSGDEKLVNSLLPLRLEIRGRLDL-SQVEKYLRKLRKSS 57


>gnl|CDD|151696 pfam11254, DUF3053, Protein of unknown function (DUF3053).  Some
           members in this family of proteins are annotated as the
           membrane protein YiaF. No function is currently known.
          Length = 229

 Score = 27.0 bits (60), Expect = 3.3
 Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 3/39 (7%)

Query: 90  SEKEQRTAF---LETRQCLEMRLVIEEQSAEQRFDKGNY 125
            E EQR AF   L+TR      + +   +A+Q+   G Y
Sbjct: 22  KEPEQRKAFIDFLQTRIMRSPGVHVPTLTADQKKAFGPY 60


>gnl|CDD|136035 PRK06758, PRK06758, hypothetical protein; Provisional.
          Length = 128

 Score = 25.8 bits (56), Expect = 6.6
 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)

Query: 66 ENIICTNVILLVSANILGQMCYHM---SEKEQRTAFL 99
          ENII   +  LVSA+ILG   + +    E  Q+T  L
Sbjct: 30 ENIIFNGIETLVSASILGGYIFFLFNPEENAQKTMLL 66


>gnl|CDD|215412 PLN02769, PLN02769, Probable galacturonosyltransferase.
          Length = 629

 Score = 26.2 bits (58), Expect = 7.1
 Identities = 24/99 (24%), Positives = 37/99 (37%), Gaps = 43/99 (43%)

Query: 54  GKKISRRGAVSLENII---------CTNVILLVSANILGQMCYHMSEKE-----QRTAFL 99
            KK+ +     +E  I         C NV        L Q+   M+E E     +++AFL
Sbjct: 238 QKKLEK-----MEQTIARAKSCPVDCNNV-----DRKLRQI-LDMTEDEAHFHMKQSAFL 286

Query: 100 ---------ETRQCLEMRLVIE---------EQSAEQRF 120
                    ++  CL MRL +E         E S  ++F
Sbjct: 287 YQLGVQTMPKSHHCLSMRLTVEYFKSSSLDMEDSNSEKF 325


>gnl|CDD|153395 cd07925, LigA_like_1, The A subunit of Uncharacterized proteins
           with similarity to Protocatechuate 4,5-dioxygenase
           (LigAB).  The proteins of unknown function in this
           subfamily are similar to the A subunit of the
           Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB
           belongs to the class III extradiol dioxygenase family,
           composed of enzymes which use a non-heme Fe(II) to
           cleave aromatic rings between a hydroxylated carbon and
           an adjacent non-hydroxylated carbon. Dioxygenases play
           key roles in the degradation of aromatic compounds. PCA
           4,5-dioxygenase catalyzes the oxidization and subsequent
           ring-opening of PCA (or 3,4-dihydroxybenzoic acid),
           which is an intermediate in the breakdown of lignin and
           other compounds.
          Length = 106

 Score = 25.1 bits (55), Expect = 7.5
 Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 2/37 (5%)

Query: 82  LGQMCYHMSEKEQRTAFL--ETRQCLEMRLVIEEQSA 116
           L +MC+  ++   R AFL  E   C +  L  E++ A
Sbjct: 16  LNKMCFSFNDAANREAFLADEEAYCEKFGLTPEQKQA 52


>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
           Present in two copies in mammalian adenylyl cyclases.
          Eubacterial homologues are known. Two residues (Asn,
          Arg) are thought to be involved in catalysis. These
          cyclases have important roles in a diverse range of
          cellular processes.
          Length = 194

 Score = 25.7 bits (57), Expect = 7.7
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 12 ERLLLSVLPEHVAVQMRQ 29
          +RLL  +LP  VA Q+++
Sbjct: 7  DRLLDQLLPASVAEQLKR 24


>gnl|CDD|117990 pfam09452, Mvb12, ESCRT-I subunit Mvb12.  The endosomal sorting
          complex required for transport (ESCRT) complexes play a
          critical role in receptor down-regulation and
          retroviral budding. A new component of the ESCRT-I
          complex was identified, multivesicular body sorting
          factor of 12 kD (Mvb12), which binds to the coiled-coil
          domain of the ESCRT-I subunit vacuolar protein sorting
          23 (Vps23).
          Length = 90

 Score = 24.8 bits (54), Expect = 7.9
 Identities = 7/23 (30%), Positives = 13/23 (56%)

Query: 24 AVQMRQDLGENFDSLFKKIYMSR 46
            Q   + GE FD  +++ Y+S+
Sbjct: 52 LCQQHDESGETFDQWYQETYLSK 74


  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
   0.324    0.137    0.387 

Gapped
Lambda     K      H
   0.267   0.0756    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,513,774
Number of extensions: 561817
Number of successful extensions: 572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 571
Number of HSP's successfully gapped: 20
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.1 bits)