RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1353
         (431 letters)



>gnl|CDD|217685 pfam03712, Cu2_monoox_C, Copper type II ascorbate-dependent
           monooxygenase, C-terminal domain.  The N and C-terminal
           domains of members of this family adopt the same PNGase
           F-like fold.
          Length = 157

 Score =  192 bits (491), Expect = 3e-60
 Identities = 66/163 (40%), Positives = 86/163 (52%), Gaps = 10/163 (6%)

Query: 202 RYDAGIMELGLEYTDKMAVPPRTNYFTLSGYCTSECTTVGLPSKGIKVFGSQLHTHLTGK 261
           +YDAGIM LG  Y    A+PP    + + G C  ECT    P      F  + HTHL G+
Sbjct: 1   KYDAGIMLLGSGYF---AIPPGQTAYPVEGSCEIECTKTMFP------FAYRTHTHLLGR 51

Query: 262 RVYTRHIRNGRELAELNRDNHYSPHFQEIRLLKHPVTVLPGDALITTCVYNTQSRANITL 321
            V    +R+G E   + RD+ Y P++Q    L+ PV VLPGD L   C Y++ SR    L
Sbjct: 52  VVSGYLVRDGEEWTLIGRDDPYDPNWQAFYPLESPVEVLPGDKLAARCTYDSTSRNTPVL 111

Query: 322 GGFAITDEMCVNYIHYYPL-VDLEVCKSSVSSDNLRTFFNYMH 363
           GG   +DEMC  YI YYP   +LE CKS VS+     +F  + 
Sbjct: 112 GGETTSDEMCNFYIMYYPDQSELEPCKSCVSNGTPDDYFRNLP 154


>gnl|CDD|216290 pfam01082, Cu2_monooxygen, Copper type II ascorbate-dependent
           monooxygenase, N-terminal domain.  The N and C-terminal
           domains of members of this family adopt the same PNGase
           F-like fold.
          Length = 128

 Score =  113 bits (286), Expect = 1e-30
 Identities = 42/107 (39%), Positives = 56/107 (52%), Gaps = 6/107 (5%)

Query: 82  DENRHNSIQFESAIQPSSEGIVHHMELFHCIAPPQQDIPLYE-GPCSSPEKPPIVESCKS 140
           D  +H+ ++FE         +VHHM L+ C    +        G C +   P    +C +
Sbjct: 27  DNRKHHIVRFEPVATSGD--LVHHMLLYGCQGNGE-PGSTDNCGSCYNA--PDSALTCST 81

Query: 141 VLAAWAMGALPFRYPKEAGRPIGGPASNSYVMLEVHYNNPEHIAGII 187
           V+AAWA GA PF YPKE G PIGG     Y++LEVHYNNP    G +
Sbjct: 82  VVAAWARGAPPFVYPKEVGLPIGGSGGIRYLVLEVHYNNPNFKDGEV 128


>gnl|CDD|217508 pfam03351, DOMON, DOMON domain.  The DOMON (named after dopamine
          beta-monooxygenase N-terminal) domain is 110-125
          residues long. It is predicted to form an all beta fold
          with up to 11 strands and is secreted to the
          extracellular compartment. The beta-strand folding
          produces a hydrophobic pocket which appears to bind
          soluble haem. This is consistent with the predominant
          architectures where the protein is associated with
          cytochromes or enzymatic domains whose activity
          involves redox or electron transfer reactions
          potentially as a direct participant in the electron
          transfer process. The DOMON domain superfamily, of
          which this is just one member, shows (1) multiple
          hydrophobic residues that contribute to the hydrophobic
          core of the strands of the beta-sandwich, and small
          residues found at the boundaries of strands and loops,
          (2) a strongly conserved charged residue (usually
          arginine/lysine) at the end of strand 9, which possibly
          stabilises the loop between 9 and 10, and (3) a polar
          residue (usually histidine, lysine or arginine), that
          interacts or coordinates with ligands. The suggested
          superfamily includes both haem- and sugar-binding
          members: the haem-binding families being the
          ethyl-Benzoate dehydrogenase family EB_dh, pfam09459,
          the cellobiose dehydrogenase family CBDH and this
          family, and the sugar-binding families being the
          xylanases, CBM_4_9, pfam02018. The common feature of
          the superfamily is the 11-beta-strand structure,
          although the first and eleventh strands are not well
          conserved either within families or between families.
          Length = 124

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 29 SHGYKLFWSPNYDSGWIKFEVHLTPALNKGDWFAIGFSNYGEFSFADYCLV 79
             Y L W  + D   I+FE  L+  +N   W AIGFS  G  S AD  + 
Sbjct: 2  DGNYTLSWKVDGDGQEIEFE--LSGKVNTNGWVAIGFSPDGGMSNADVVIG 50


>gnl|CDD|219974 pfam08696, Dna2, DNA replication factor Dna2.  Dna2 is a DNA
           replication factor with single-stranded DNA-dependent
           ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease)
           and helicase activities. It is required for Okazaki
           fragment processing and is involved in DNA repair
           pathways.
          Length = 209

 Score = 37.6 bits (88), Expect = 0.005
 Identities = 12/20 (60%), Positives = 16/20 (80%)

Query: 404 NIWLPNLGIKGKVDVTVKVR 423
           NIW P  G+KGK+D TV+V+
Sbjct: 190 NIWSPRYGLKGKIDATVEVK 209


>gnl|CDD|214768 smart00664, DoH, Possible catecholamine-binding domain present in
          a variety of eukaryotic proteins.  A predominantly
          beta-sheet domain present as a regulatory N-terminal
          domain in dopamine beta-hydroxylase, mono-oxygenase X
          and SDR2. Its function remains unknown at present
          (Ponting, Human Molecular Genetics, in press).
          Length = 148

 Score = 35.1 bits (81), Expect = 0.025
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 29 SHGYKLFWSPNYDSGWIKFEVHLTPALNKGDWFAIGFSNYGEFSFADYCLVLCDENRHNS 88
          S  Y L WS + ++        L+   +   W AIGFS  G+ + AD  +   D N   +
Sbjct: 1  SCDYFLSWSVDGEN---SIAFELSGPTSTNGWVAIGFSPDGQMAGADVVVAWVDNNGRVT 57

Query: 89 IQF 91
          ++ 
Sbjct: 58 VKD 60


>gnl|CDD|187689 cd09631, DOMON_DOH, DOMON-like domain of copper-dependent
          monooxygenases and related proteins.  This diverse
          family characterizes DOMON domains found in dopamine
          beta-hydroxylase (DBH), monooxygenase X (MOX), and
          various other proteins, some of which contain DOMON
          domains exclusively; the family is not restricted to
          eukaryotes. DBH is a membrane-bound enzyme that
          converts dopamine to L-norepinephrine, and plays a
          central role in the metabolism of catecholamine
          neurotransmitters.  DOMON domains were initially
          thought to confer protein-protein interactions. They
          were subsequently found as a heme-binding motif in
          cellobiose dehydrogenase, an extracellular fungal
          oxidoreductase that degrades both lignin and cellulose,
          and in ethylbenzene dehydrogenase, an enzyme that aids
          in the anaerobic degradation of hydrocarbons. The
          domain interacts with sugars in the type 9 carbohydrate
          binding modules (CBM9), which are present in a variety
          of glycosyl hydrolases, and it can also be found at the
          N-terminus of sensor histidine kinases.
          Length = 138

 Score = 32.5 bits (74), Expect = 0.18
 Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 5/48 (10%)

Query: 31 GYKLFWSPNYDSGWIKFEVHLTPALNKGDWFAIGFSNYGEFSFADYCL 78
           + L WS + +   I FE+    A   G W  IGFS  G    AD  +
Sbjct: 8  NFSLSWSVDGEGT-ITFELS---ARTTG-WVGIGFSPDGGMVGADAVV 50


>gnl|CDD|222960 PHA03001, PHA03001, putative virion core protein; Provisional.
          Length = 132

 Score = 29.6 bits (67), Expect = 1.4
 Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 7/50 (14%)

Query: 313 TQSRANITLGGFAITDEMCVNYIHYYPLVDLEVCKSSVSSDNLRTFFNYM 362
                 IT   F +TD M    I  YP     V      S+N + F+N +
Sbjct: 90  VDDYNEITGVEFIVTDTM---PISIYPKNGYAV---ISYSNNSK-FYNGL 132


>gnl|CDD|238267 cd00480, malate_synt, Malate synthase catalyzes the Claisen
           condensation of glyoxylate and acetyl-CoA to malyl-CoA ,
           which hydrolyzes to malate and CoA. This reaction is
           part of the glyoxylate cycle, which allows certain
           organisms, like plants and fungi, to derive their carbon
           requirements from two-carbon compounds, by bypassing the
           two carboxylation steps of the citric acid cycle.
          Length = 511

 Score = 30.3 bits (69), Expect = 2.1
 Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 8/46 (17%)

Query: 354 NLRTFFNYMHDILLALRNNI--LNVSLLFYIFDKIIHSRSQILMNH 397
            L   F  M +IL  LR++   LN     YIF   I +      NH
Sbjct: 228 TLPAAFE-MDEILYELRDHSAGLNCGRWDYIFS-EIKT----FRNH 267


>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family.  The
           medium chain dehydrogenases/reductase
           (MDR)/zinc-dependent alcohol dehydrogenase-like family,
           which contains the zinc-dependent alcohol dehydrogenase
           (ADH-Zn) and related proteins, is a diverse group of
           proteins related to the first identified member, class I
           mammalian ADH.  MDRs display a broad range of activities
           and are distinguished from the smaller short chain
           dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
           acids of the MDR).  The MDR proteins have 2 domains: a
           C-terminal NAD(P)-binding Rossmann fold domain of a
           beta-alpha form and an N-terminal catalytic domain with
           distant homology to GroES.  The MDR group contains a
           host of activities, including the founding alcohol
           dehydrogenase (ADH), quinone reductase, sorbitol
           dehydrogenase, formaldehyde dehydrogenase, butanediol
           DH, ketose reductase, cinnamyl reductase, and numerous
           others. The zinc-dependent alcohol dehydrogenases (ADHs)
           catalyze the NAD(P)(H)-dependent interconversion of
           alcohols to aldehydes or ketones.  Active site zinc has
           a catalytic role, while structural zinc aids in
           stability.
          Length = 312

 Score = 29.6 bits (67), Expect = 2.7
 Identities = 11/26 (42%), Positives = 12/26 (46%)

Query: 138 CKSVLAAWAMGALPFRYPKEAGRPIG 163
           C S L A+  G   F YP E G P  
Sbjct: 32  CGSDLPAFNQGRPWFVYPAEPGGPGH 57


>gnl|CDD|111768 pfam02917, Pertussis_S1, Pertussis toxin, subunit 1. 
          Length = 239

 Score = 29.0 bits (64), Expect = 4.3
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 228 TLSGYCTSECTTVGLPSKGIKVFGSQLHTHLTGKRVYTRHIRNGRELAELNRDNH---YS 284
            L+ Y         + +  I+   + LH  + G+  +  H    R ++E  R N    ++
Sbjct: 126 ALAAYQREWFADGPIAAANIRRVSAVLHDAIPGEPGHAEH-PAARYVSEQTRANEPEMHN 184

Query: 285 PHFQEIRLLKHPVTVLP 301
           PH QE ++  +   + P
Sbjct: 185 PHRQEAQIQANDQPMAP 201


>gnl|CDD|238369 cd00727, malate_synt_A, Malate synthase A (MSA), present in some
           bacteria, plants and fungi. Prokaryotic MSAs tend to be
           monomeric, whereas eukaryotic enzymes are homomultimers.
           In general, malate synthase catalyzes the Claisen
           condensation of glyoxylate and acetyl-CoA to malyl-CoA,
           which hydrolyzes to malate and CoA. This reaction is
           part of the glyoxylate cycle, which allows certain
           organisms, like plants and fungi, to derive their carbon
           requirements from two-carbon compounds, by bypassing the
           two carboxylation steps of the citric acid cycle.
          Length = 511

 Score = 28.8 bits (65), Expect = 5.8
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 12/46 (26%)

Query: 362 MHDILLALRNNI--LNVSLLFYIF----------DKIIHSRSQILM 395
           M +IL  LR++   LN     YIF          D ++  R+Q+ M
Sbjct: 235 MDEILYELRDHSAGLNCGRWDYIFSFIKKFRNHPDFVLPDRAQVTM 280


>gnl|CDD|218909 pfam06138, Chordopox_E11, Chordopoxvirus E11 protein.  This family
           consists of several Chordopoxvirus E11 proteins. The E11
           gene of vaccinia virus encodes a 15-kDa polypeptide.
           Mutations in the E11 gene makes the virus
           temperature-sensitive due to either the fact that virus
           infectivity requires a threshold level of active E11
           protein or that E11 function is conditionally essential.
          Length = 130

 Score = 27.4 bits (61), Expect = 8.1
 Identities = 17/44 (38%), Positives = 17/44 (38%), Gaps = 6/44 (13%)

Query: 313 TQSRANITLGGFAITDEMCVNYIHYYPLVDLEVCKSSVSSDNLR 356
             S   IT   F ITD M    I  YP     V    V SDN R
Sbjct: 91  VDSYNEITGIEFIITDTM---PISIYPKNGYAV---IVYSDNSR 128


>gnl|CDD|218663 pfam05625, PAXNEB, PAXNEB protein.  PAXNEB or PAX6 neighbor is
           found in several eukaryotic organisms. PAXNED is an RNA
           polymerase II Elongator protein subunit. It is part of
           the HAP subcomplex of Elongator, which is a six-subunit
           component of the RNA polymerase II holoenzyme. The HAP
           subcomplex is required for Elongator structural
           integrity and histone acetyltransferase activity. This
           protein family has a P-loop motif. However its sequence
           has degraded in many members of the family.
          Length = 357

 Score = 28.4 bits (64), Expect = 8.3
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 99  SEGIVHHMELFHCIAPPQ--QDIP-LYEGPCSSPEKPPIVESCK 139
           +EG+V    +F    P Q  +++P  Y+G   S +K  I    K
Sbjct: 69  AEGVVQDHHVFVASLPEQWLRELPGPYKGSEKSEKKAKIANESK 112


>gnl|CDD|226305 COG3782, COG3782, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 289

 Score = 28.0 bits (62), Expect = 8.7
 Identities = 28/110 (25%), Positives = 37/110 (33%), Gaps = 21/110 (19%)

Query: 2   FLRELGLFSLVSQFLLVSGDVF-------DIPLNSHGYKLFWSPNYDSGW--IKFEVHLT 52
            LR+ GL   VS   LV G +F         P ++ GY       Y   W    FE  L 
Sbjct: 174 TLRQHGLPLGVSPVSLVRGILFFPPFFHAFEPPDNPGYGWRGI--YIQDWAEYGFERQLI 231

Query: 53  PA----LNKGDWFAIG------FSNYGEFSFADYCLVLCDENRHNSIQFE 92
                 L++  W A          N+ E    D  L+   E R +    E
Sbjct: 232 EVRYHLLDRMAWLAPARAAETPTLNHTEIRRIDQGLIAVLECRPDGFWHE 281


  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
   0.322    0.139    0.429 

Gapped
Lambda     K      H
   0.267   0.0675    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,198,178
Number of extensions: 2138610
Number of successful extensions: 1543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1538
Number of HSP's successfully gapped: 21
Length of query: 431
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 331
Effective length of database: 6,502,202
Effective search space: 2152228862
Effective search space used: 2152228862
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (27.0 bits)