RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3517
         (113 letters)



>gnl|CDD|215152 PLN02269, PLN02269, Pyruvate dehydrogenase E1 component subunit
           alpha.
          Length = 362

 Score = 30.1 bits (68), Expect = 0.22
 Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 20/62 (32%)

Query: 13  EEINMDSSLLLKYPSICIC-------------SDSSDVYYS--DYFPGIPVDLTMDSVAL 57
           E +N+  + L   P I +C             +  S  YY   DY PG+ VD  MD   L
Sbjct: 179 EALNI--AALWDLPVIFVCENNHYGMGTAEWRAAKSPAYYKRGDYVPGLKVD-GMD--VL 233

Query: 58  AV 59
           AV
Sbjct: 234 AV 235


>gnl|CDD|143465 cd07147, ALDH_F21_RNP123, Aldehyde dehydrogenase family 21A1-like. 
           Aldehyde dehydrogenase ALDH21A1 (gene name RNP123) was
           first described in the moss Tortula ruralis and is
           believed to play an important role in the detoxification
           of aldehydes generated in response to desiccation- and
           salinity-stress, and ALDH21A1 expression represents a
           unique stress tolerance mechanism. So far, of plants,
           only the bryophyte sequence has been observed, but
           similar protein sequences from bacteria and archaea are
           also present in this CD.
          Length = 452

 Score = 29.5 bits (67), Expect = 0.27
 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 16/55 (29%)

Query: 59  VATVHLAICPFTKVEESFN--------LQAMHDIFYHNMN--ISAYDHLEFPGVV 103
           V TV     P+   +E+          LQA   +F  ++   + A+D LE  GVV
Sbjct: 362 VVTVE----PYDDFDEALAAVNDSKFGLQA--GVFTRDLEKALRAWDELEVGGVV 410


>gnl|CDD|226328 COG3806, ChrR, Transcriptional activator [Transcription].
          Length = 216

 Score = 29.4 bits (66), Expect = 0.29
 Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 51 TMDSVALAVATVHLAICPFTKVE----ESFNLQAMHDIFYHNMNISAYDHL 97
           + SV   V  VHL +CP  + E    E+     + D    +    A D +
Sbjct: 17 QLHSVTSPVVAVHLVMCPRCRKEKARAEAIGGYLLADHEPSSHQHGALDEI 67


>gnl|CDD|238640 cd01315, L-HYD_ALN, L-Hydantoinases (L-HYDs) and Allantoinase
           (ALN); L-Hydantoinases are a member of the
           dihydropyrimidinase family, which catalyzes the
           reversible hydrolytic ring opening of dihydropyrimidines
           and hydantoins (five-membered cyclic diamides used in
           biotechnology). But L-HYDs differ by having an L-enantio
           specificity and by lacking activity on possible natural
           substrates such as dihydropyrimidines. Allantoinase
           catalyzes the hydrolytic cleavage of the five-member
           ring of allantoin (5-ureidohydantoin) to form allantoic
           acid.
          Length = 447

 Score = 28.4 bits (64), Expect = 0.77
 Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 2/36 (5%)

Query: 73  EESFNLQAMHDIFYHNMNISAYDHLEFPGVVPRTFL 108
           EE F + A  +  Y+   IS Y      G V  T L
Sbjct: 393 EEEFTVDA--EDLYYKNKISPYVGRTLKGRVHATIL 426


>gnl|CDD|222405 pfam13830, DUF4192, Domain of unknown function (DUF4192). 
          Length = 321

 Score = 26.5 bits (59), Expect = 2.8
 Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 6/36 (16%)

Query: 34  SSDVYYSDYFP------GIPVDLTMDSVALAVATVH 63
           ++   +S          G+PVD    SVA A A + 
Sbjct: 111 AAGRPWSYVCGPCCPQEGVPVDPVASSVAAAAAVLA 146


>gnl|CDD|176460 cd00332, PAL-HAL, Phenylalanine ammonia-lyase (PAL) and histidine
           ammonia-lyase (HAL).  PAL and HAL are members of the
           Lyase class I_like superfamily of enzymes that, catalyze
           similar beta-elimination reactions and are active as
           homotetramers. The four active sites of the
           homotetrameric enzyme are each formed by residues from
           three different subunits. PAL, present in plants and
           fungi, catalyzes the conversion of L-phenylalanine to
           E-cinnamic acid. HAL, found in several bacteria and
           animals, catalyzes the conversion of L-histidine to
           E-urocanic acid. Both PAL and HAL contain the cofactor
           3, 5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) which
           is formed by autocatalytic excision/cyclization of the
           internal tripeptide, Ala-Ser-Gly. PAL is being explored
           as enzyme substitution therapy for Phenylketonuria
           (PKU), a disorder which involves an inability to
           metabolize phenylalanine. HAL failure in humans results
           in the disease histidinemia.
          Length = 444

 Score = 26.3 bits (59), Expect = 4.4
 Identities = 12/33 (36%), Positives = 19/33 (57%)

Query: 30  ICSDSSDVYYSDYFPGIPVDLTMDSVALAVATV 62
           +  D+ +V     F G PV L MD +A+A+A +
Sbjct: 308 VDPDNGEVLSGGNFHGQPVALAMDFLAIALAEL 340


>gnl|CDD|107358 cd06363, PBP1_Taste_receptor, Ligand-binding domain of the T1R
          taste receptor.  Ligand-binding domain of the T1R taste
          receptor. The T1R is a member of the family C receptors
          within the G-protein coupled receptor superfamily,
          which also includes the metabotropic glutamate
          receptors, GABAb receptors, the calcium-sensing
          receptor (CaSR), the V2R pheromone receptors, and a
          small group of uncharacterized orphan receptors.
          Length = 410

 Score = 26.1 bits (58), Expect = 4.9
 Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 4/30 (13%)

Query: 13 EEINMDSSLL----LKYPSICICSDSSDVY 38
          EEIN  +SLL    L Y     CSDS++  
Sbjct: 53 EEINNSTSLLPGVTLGYEIFDHCSDSANFP 82


>gnl|CDD|182312 PRK10216, PRK10216, DNA-binding transcriptional regulator YidZ;
           Provisional.
          Length = 319

 Score = 25.9 bits (57), Expect = 5.0
 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 13  EEINMDSSLLLKYPSICICSDSSDVYYSD 41
           EE N+D+   L+YP I IC + SD +  D
Sbjct: 193 EEWNLDT--FLRYPHISICWEQSDTWALD 219


>gnl|CDD|178392 PLN02795, PLN02795, allantoinase.
          Length = 505

 Score = 25.9 bits (57), Expect = 6.3
 Identities = 10/37 (27%), Positives = 18/37 (48%)

Query: 73  EESFNLQAMHDIFYHNMNISAYDHLEFPGVVPRTFLG 109
           E  F L   + I++ + ++S Y   +  G V  TF+ 
Sbjct: 447 EAEFVLDESYPIYHKHKSLSPYLGTKLSGKVIATFVR 483


>gnl|CDD|233667 TIGR01982, UbiB, 2-polyprenylphenol 6-hydroxylase.  This model
           represents the enzyme (UbiB) which catalyzes the first
           hydroxylation step in the ubiquinone biosynthetic
           pathway in bacteria. It is believed that the reaction is
           2-polyprenylphenol -> 6-hydroxy-2-polyprenylphenol. This
           model finds hits primarily in the proteobacteria. The
           gene is also known as AarF in certain species
           [Biosynthesis of cofactors, prosthetic groups, and
           carriers, Menaquinone and ubiquinone].
          Length = 437

 Score = 25.7 bits (57), Expect = 6.5
 Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 6/73 (8%)

Query: 16  NMDSSLLLKYPSICICSDSSDVYYSDYFPGIPVDLTMDSVALAVATVHL-AICPFTKVEE 74
           N  +   +  P +     S  V   ++  GIP+    D  AL  A +   A+     +  
Sbjct: 213 NFKNDPGVYVPEVYWDRTSERVLTMEWIDGIPLS---DIAALDEAGLDRKALA--ENLAR 267

Query: 75  SFNLQAMHDIFYH 87
           SF  Q + D F+H
Sbjct: 268 SFLNQVLRDGFFH 280


>gnl|CDD|131015 TIGR01960, ndhF3_CO2, NAD(P)H dehydrogenase, subunit NdhF3 family. 
           This family represents a subfamily of NAD(P)H
           dehydrogenase subunit 5, or ndhF. It is restricted to
           two paralogs in each completed cyanobacterial genome, in
           which several subtypes of ndhF are found. Included in
           this family is NdhF3, shown to play a role in
           high-affinity CO2 uptake in Synechococcus sp. PCC7002.
           In all cases, neighboring genes include a paralog of
           ndhD but do include other NAD(P)H dehydrogenase
           subunits. Instead, genes related to C02 uptake tend to
           be found nearby.
          Length = 606

 Score = 25.5 bits (56), Expect = 7.9
 Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 5   QWDTLQDTEEINMDSSLLLKYPSICICSDSSDVYYSDYFPGIPVDLTMDSV 55
           QW  L D  +IN     LL    +      S +Y     P  P+ L +  V
Sbjct: 476 QWSLLPDWAQINWAVVALLIVSGLLGIGLGSFIYLGRAIPK-PIRLPLRFV 525


>gnl|CDD|215800 pfam00221, Lyase_aromatic, Aromatic amino acid lyase.  This family
           includes proteins with phenylalanine ammonia-lyase,
           EC:4.3.1.24, histidine ammonia-lyase, EC:4.3.1.3, and
           tyrosine aminomutase, EC:5.4.3.6, activities.
          Length = 477

 Score = 25.5 bits (57), Expect = 8.0
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 30  ICSDSSDVYYSDYFPGIPVDLTMDSVALAVATV 62
           I  D  +V     F G PV L MD +A+A+A +
Sbjct: 314 IFPDRGEVLSGGNFHGEPVALAMDFLAIALAEL 346


  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
   0.323    0.138    0.427 

Gapped
Lambda     K      H
   0.267   0.0718    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,630,142
Number of extensions: 458159
Number of successful extensions: 351
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 17
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)