RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8162
         (326 letters)



>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
           transcriptases.  Ribonuclease H (RNase H) is classified
           into two families, type 1 (prokaryotic RNase HI,
           eukaryotic RNase H1 and viral RNase H) and type 2
           (prokaryotic RNase HII and HIII, and eukaryotic RNase
           H2). Ribonuclease HI (RNase HI) is an endonuclease that
           cleaves the RNA strand of an RNA/DNA hybrid in a
           sequence non-specific manner. RNase H is widely present
           in various organisms, including bacteria, archaea and
           eukaryotes.  RNase HI has also been observed as an
           adjunct domain to the reverse transcriptase gene in
           retroviruses, long-term repeat (LTR)-bearing
           retrotransposons and non-LTR retrotransposons. RNase HI
           in LTR retrotransposons perform degradation of the
           original RNA template, generation of a polypurine tract
           (the primer for plus-strand DNA synthesis), and final
           removal of RNA primers from newly synthesized minus and
           plus strands. The catalytic residues for RNase H
           enzymatic activity, three aspartatic acids and one
           glutamatic acid residue (DEDD), are unvaried across all
           RNase H domains. The position of the RNase domain of
           non-LTR and LTR transposons is at the carboxyl terminal
           of the reverse transcriptase (RT) domain and their RNase
           domains group together, indicating a common evolutionary
           origin. Many non-LTR transposons have lost the RNase
           domain because their activity is at the nucleus and
           cellular RNase may suffice; however LTR retotransposons
           always encode their own RNase domain because it requires
           RNase activity in RNA-protein particles in the
           cytoplasm. RNase H inhibitors have been explored as an
           anti-HIV drug target because RNase H inactivation
           inhibits reverse transcription.
          Length = 128

 Score = 99.3 bits (248), Expect = 9e-26
 Identities = 43/165 (26%), Positives = 59/165 (35%), Gaps = 46/165 (27%)

Query: 107 ICYTDGSKTMNSTSCAYSI---NDVISSSQLNPVNSIFSAELIAIYLCLEAITV--HPSD 161
           + YTDGSK    T   ++I     +  S +L P  S+F AEL+AI   L+        + 
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 162 HFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLKTLNKDVHFVLKPSQSALAALSNVS 221
              I SDS                                         Q+AL AL +  
Sbjct: 61  KITIFSDS-----------------------------------------QAALKALRSPR 79

Query: 222 FTNPLVSKVYSCWDLLKTLNKDVHFLWCPSHCGIRGNEAVDEAAR 266
            ++PLV ++      L      V   W P H GI GNE  D  A+
Sbjct: 80  SSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 124


>gnl|CDD|215695 pfam00075, RNase_H, RNase H.  RNase H digests the RNA strand of an
           RNA/DNA hybrid. Important enzyme in retroviral
           replication cycle, and often found as a domain
           associated with reverse transcriptases. Structure is a
           mixed alpha+beta fold with three a/b/a layers.
          Length = 126

 Score = 61.5 bits (150), Expect = 7e-12
 Identities = 34/165 (20%), Positives = 51/165 (30%), Gaps = 46/165 (27%)

Query: 104 NHTICYTDGS--KTMNSTSCAYSINDVISSSQLNPVNSIFSAELIAIYLCLEAITVHPSD 161
                YTDGS           Y  +     S+  P  +   AEL+A+   LEA+      
Sbjct: 2   EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEAL---SGQ 58

Query: 162 HFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLKTLNKDVHFVLKPSQSALAALSNVS 221
              I +DS+  +                                               S
Sbjct: 59  KVNIYTDSQYVI-------------------------------------GGITNGWPTKS 81

Query: 222 FTNPLVSKVYSCWDLLKTLNKDVHFLWCPSHCGIRGNEAVDEAAR 266
            + P+ ++    W+LL      V+  W P H GI GNE  D+ A+
Sbjct: 82  ESKPIKNE---IWELL-QKKHKVYIQWVPGHSGIPGNELADKLAK 122


>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
           strand of an RNA/DNA hybrid in a sequence non-specific
           manner.  Ribonuclease H (RNase H) enzymes are divided
           into two major families, Type 1 and Type 2, based on
           amino acid sequence similarities and biochemical
           properties. RNase H is an endonuclease that cleaves the
           RNA strand of an RNA/DNA hybrid in a sequence
           non-specific manner in the presence of divalent cations.
           RNase H is widely present in various organisms,
           including bacteria, archaea and eukaryotes. Most
           prokaryotic and eukaryotic genomes contain multiple
           RNase H genes. Despite the lack of amino acid sequence
           homology, Type 1 and type 2 RNase H share a main-chain
           fold and steric configurations of the four acidic
           active-site residues and have the same catalytic
           mechanism and functions in cells. RNase H is involved in
           DNA replication, repair and transcription. One of the
           important functions of RNase H is to remove Okazaki
           fragments during DNA replication. RNase H inhibitors
           have been explored as an anti-HIV drug target because
           RNase H inactivation inhibits reverse transcription.
          Length = 123

 Score = 50.4 bits (121), Expect = 6e-08
 Identities = 21/110 (19%), Positives = 38/110 (34%), Gaps = 9/110 (8%)

Query: 109 YTDGSKTMNSTSCAY-------SINDVISSSQLNPVNSIFSAELIAIYLCLEAITVHPSD 161
            TDGS   N                 + + S   P  +   AEL+A+   LE        
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 162 HFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLKTLNKDV--HFVLKP 209
             +I +DS+  +  +++ S      + +     LL +   D+    V + 
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE 110


>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term
           repeat retroelements.  Ribonuclease H (RNase H) enzymes
           are divided into two major families, Type 1 and Type 2,
           based on amino acid sequence similarities and
           biochemical properties. RNase H is an endonuclease that
           cleaves the RNA strand of an RNA/DNA hybrid in a
           sequence non-specific manner in the presence of divalent
           cations. RNase H is widely present in various organisms,
           including bacteria, archaea and eukaryote.  RNase HI has
           also been observed as adjunct domains to the reverse
           transcriptase gene in retroviruses, in long-term repeat
           (LTR)-bearing retrotransposons and non-LTR
           retrotransposons. RNase HI in LTR retrotransposons
           perform degradation of the original RNA template,
           generation of a polypurine tract (the primer for
           plus-strand DNA synthesis), and final removal of RNA
           primers from newly synthesized minus and plus strands.
           The catalytic residues for RNase H enzymatic activity,
           three aspartatic acids and one glutamatic acid residue
           (DEDD),  are unvaried across all RNase H domains.
           Phylogenetic patterns of RNase HI of LTR retroelements
           is classified into five major families, Ty3/Gypsy,
           Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
           retroviruses.  Bel/Pao family has been described only in
           metazoan genomes.  RNase H inhibitors have been explored
           as an anti-HIV drug target because RNase H inactivation
           inhibits reverse transcription.
          Length = 135

 Score = 45.3 bits (108), Expect = 4e-06
 Identities = 34/168 (20%), Positives = 50/168 (29%), Gaps = 46/168 (27%)

Query: 108 CYTDGSKTMNSTSCA-YSINDVISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDHFLIV 166
            +TDGS  +     A  +  DV+  + L    S   AELIA+   + A+ +       I 
Sbjct: 2   VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58

Query: 167 SDSRSALAALSNVSFTNPLVSKVYSCWDLLKTLNKDVHFVLKPSQSALAALSNVSFTNPL 226
           +DS  A   L                                   +         F    
Sbjct: 59  TDSAYAFGIL----------------------------------HALETIWKERGFLTGK 84

Query: 227 VSKVYSCW-DLLKTLN--KDVHFLWCPSHCG-----IRGNEAVDEAAR 266
              + S    L K +   K V  +   +H G       GN   D+AAR
Sbjct: 85  PIALASLILQLQKAIQRPKPVAVIHIRAHSGLPGPLALGNARADQAAR 132


>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
           prokaryotes.  Ribonuclease H (RNase H) is classified
           into two evolutionarily unrelated families, type 1
           (prokaryotic RNase HI, eukaryotic RNase H1 and viral
           RNase H) and type 2 (prokaryotic RNase HII and HIII, and
           eukaryotic RNase H2). RNase H is an endonuclease that
           cleaves the RNA strand of an RNA/DNA hybrid in a
           sequence non-specific manner. RNase H is involved in DNA
           replication, repair and transcription. RNase H is widely
           present in various organisms, including bacteria,
           archaea and eukaryotes and most prokaryotic and
           eukaryotic genomes contain multiple RNase H genes.
           Despite the lack of amino acid sequence homology, Type 1
           and type 2 RNase H share a main-chain fold and steric
           configurations of the four acidic active-site (DEDD),
           residues and have the same catalytic mechanism and
           functions in cells.  One of the important functions of
           RNase H is to remove Okazaki fragments during DNA
           replication. Prokaryotic RNase H varies greatly in
           domain structures and substrate specificities.
           Prokaryotes and some single-cell eukaryotes do not
           require RNase H for viability.
          Length = 139

 Score = 36.7 bits (86), Expect = 0.003
 Identities = 13/37 (35%), Positives = 15/37 (40%), Gaps = 5/37 (13%)

Query: 235 DLLKTL-----NKDVHFLWCPSHCGIRGNEAVDEAAR 266
           DL + L        V + W   H G  GNE  DE A 
Sbjct: 99  DLWQELDALLAKHQVTWHWVKGHAGHPGNERADELAN 135


>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
           repair].
          Length = 154

 Score = 34.6 bits (80), Expect = 0.027
 Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 3/36 (8%)

Query: 234 WDLLKTLNKD---VHFLWCPSHCGIRGNEAVDEAAR 266
           W+ L  L K    V + W   H G   NE  D+ AR
Sbjct: 105 WEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140


>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and
           more complex than their prokaryotic counterparts  and
           unlike prokaryote, RNase H are essential in higher
           eukaryote.  Ribonuclease H (RNase H) is classified into
           two families, type 1 (prokaryotic RNase HI, eukaryotic
           RNase H1 and viral RNase H) and type 2 (prokaryotic
           RNase HII and HIII, and eukaryotic RNase H2). RNase H is
           an endonuclease that cleaves the RNA strand of an
           RNA/DNA hybrid in a sequence non-specific manner. RNase
           H is involved in DNA replication, repair and
           transcription. One of the important functions of RNase H
           is to remove Okazaki fragments during DNA replication.
           RNase H is widely present in various organisms,
           including bacteria, archaea and eukaryote and most
           prokaryotic and eukaryotic genomes contain multiple
           RNase H genes. Despite the lack of amino acid sequence
           homology, Type 1 and type 2 RNase H share a main-chain
           fold and steric configurations of the four acidic
           active-site (DEDD)  residues and have the same catalytic
           mechanism and functions in cells.  Eukaryotic RNase H is
           longer and more complex than in prokaryotes. Almost all
           eukaryotic RNase HI have highly conserved regions at the
           N-terminal called hybrid binding domain (HBD). It is
           speculated that the HBD contributes to binding the
           RNA/DNA hybrid. Prokaryotes and some single-cell
           eukaryotes do not require RNase H for viability, but
           RNase H is essential in higher eukaryotes. RNase H
           knockout mice lack mitochondrial DNA replication and die
           as embryos.
          Length = 150

 Score = 32.6 bits (75), Expect = 0.12
 Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 10/43 (23%)

Query: 234 WDLLKTLNK----------DVHFLWCPSHCGIRGNEAVDEAAR 266
            DL+K L+K           V F   P H GI GNE  D  A+
Sbjct: 104 KDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146


>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
           hybrid binding domain (HBD) at the N-terminus.
           Ribonuclease H (RNase H) enzymes are divided into two
           major families, Type 1 and Type 2, based on amino acid
           sequence similarities and biochemical properties. RNase
           H is an endonuclease that cleaves the RNA strand of an
           RNA/DNA hybrid in a sequence non-specific manner in the
           presence of divalent cations.  RNase H is involved in
           DNA replication, repair and transcription.  RNase H is
           widely present in various organisms, including bacteria,
           archaea and eukaryotes and most prokaryotic and
           eukaryotic genomes contain multiple RNase H genes.
           Despite the lack of amino acid sequence homology, Type 1
           and type 2 RNase H share a main-chain fold and steric
           configurations of the four acidic active-site (DEDD)
           residues and have the same catalytic mechanism and
           functions in cells.  One of the important functions of
           RNase H is to remove Okazaki fragments during DNA
           replication. Prokaryotic RNase H varies greatly in
           domain structures and substrate specificities.
           Prokaryotes and some single-cell eukaryotes do not
           require RNase H for viability. Some bacteria
           distinguished from other bacterial RNase HI in the
           presence of a hybrid binding domain (HBD) at the
           N-terminus which is commonly present at the N-termini of
           eukaryotic RNase HI. It has been reported that this
           domain is required for dimerization and processivity of
           RNase HI upon binding to RNA-DNA hybrids.
          Length = 133

 Score = 31.7 bits (73), Expect = 0.21
 Identities = 7/27 (25%), Positives = 14/27 (51%)

Query: 243 DVHFLWCPSHCGIRGNEAVDEAARNPV 269
            + F+   +H G + NE  D+ A+  +
Sbjct: 107 KISFVKVKAHSGDKYNELADKLAKKAL 133


>gnl|CDD|191937 pfam08069, Ribosomal_S13_N, Ribosomal S13/S15 N-terminal domain. 
          This domain is found at the N-terminus of ribosomal S13
          and S15 proteins. This domain is also identified as
          NUC021.
          Length = 60

 Score = 28.3 bits (64), Expect = 0.79
 Identities = 11/21 (52%), Positives = 11/21 (52%), Gaps = 1/21 (4%)

Query: 51 ISSSDIAPYVRTVPPWSSSSP 71
          IS S   PY RT P W   SP
Sbjct: 11 ISGSAR-PYRRTPPEWLKYSP 30


>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
          Length = 150

 Score = 29.8 bits (68), Expect = 0.91
 Identities = 14/48 (29%), Positives = 17/48 (35%), Gaps = 2/48 (4%)

Query: 234 WDLLKTLNK--DVHFLWCPSHCGIRGNEAVDEAARNPVNPARLKLCSP 279
           W  L    K   + + W   H G   NE  DE AR     A L+    
Sbjct: 103 WQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTGY 150


>gnl|CDD|132300 TIGR03256, met_CoM_red_alp, methyl-coenzyme M reductase, alpha
           subunit.  Members of this protein family are the alpha
           subunit of methyl coenzyme M reductase, also called
           coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This
           enzyme, with alpha, beta, and gamma subunits, catalyzes
           the last step in methanogenesis. Several methanogens
           have encode two such enzymes, designated I and II; this
           model does not separate the isozymes [Energy metabolism,
           Methanogenesis].
          Length = 548

 Score = 29.1 bits (65), Expect = 3.8
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 3   YVAKVGASPFNPVQKVLFDQDLTPYNFT 30
           + A+  A   NP+ KV F  D  P++FT
Sbjct: 495 HAARGDAFTVNPLVKVAFADDNLPFDFT 522


>gnl|CDD|173882 cd08517, PBP2_NikA_DppA_OppA_like_13, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This CD
           represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 480

 Score = 29.1 bits (66), Expect = 3.9
 Identities = 18/73 (24%), Positives = 23/73 (31%), Gaps = 12/73 (16%)

Query: 1   MNYVAKVGASPFNPVQKVLFDQDLTPYNFTTNKPKPLL-----------SRF-LSLPNFP 48
                K    P +P     +D D+  Y F   K + LL            RF L L   P
Sbjct: 283 FFGYGKPATGPISPSLPFFYDDDVPTYPFDVAKAEALLDEAGYPRGADGIRFKLRLDPLP 342

Query: 49  NLISSSDIAPYVR 61
                   A YV+
Sbjct: 343 YGEFWKRTAEYVK 355


>gnl|CDD|234325 TIGR03713, acc_sec_asp1, accessory Sec system protein Asp1.  This
           protein is designated Asp1 because, along with SecY2,
           SecA2, and other proteins it is part of the accessory
           secretory protein system. The system is involved in the
           export of serine-rich glycoproteins important for
           virulence in a number of Gram-positive species,
           including Streptococcus gordonii and Staphylococcus
           aureus. This protein family is assigned to transport
           rather than glycosylation function, but the specific
           molecular role is unknown [Protein fate, Protein and
           peptide secretion and trafficking, Cellular processes,
           Pathogenesis].
          Length = 519

 Score = 28.9 bits (65), Expect = 4.7
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 7/71 (9%)

Query: 143 AELIA-IYLCLEAITVHPSDHFLIVSDSRSALAALSNVSFTNPLVS------KVYSCWDL 195
            ELI   +     + V   D  ++ SD R            N + S      + ++  DL
Sbjct: 207 DELIREKFQRYLKVEVKDDDEIIVASDDRHNFLVADTFPAKNLIFSLFSERNRHHTYLDL 266

Query: 196 LKTLNKDVHFV 206
            ++L++    +
Sbjct: 267 YESLSRADLII 277


>gnl|CDD|216417 pfam01293, PEPCK_ATP, Phosphoenolpyruvate carboxykinase. 
          Length = 467

 Score = 28.6 bits (65), Expect = 5.2
 Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 5/42 (11%)

Query: 104 NHTICYTDGSKTMNSTSCAYSI----NDVISSSQLNPVNSIF 141
              + + D S T N T  AY I    N V      +P N IF
Sbjct: 289 TREVDFDDTSLTEN-TRVAYPIEHIPNAVEPGVGGHPKNIIF 329


>gnl|CDD|237444 PRK13607, PRK13607, proline dipeptidase; Provisional.
          Length = 443

 Score = 28.3 bits (64), Expect = 5.6
 Identities = 9/39 (23%), Positives = 16/39 (41%)

Query: 267 NPVNPARLKLCSPDDFKPIAASMVKKEWQNQWDIIPITN 305
           + VN  +L    P D+      + +  W  + DI  +T 
Sbjct: 73  DGVNKPKLWFYQPVDYWHNVEPLPESFWTEEVDIKALTK 111


>gnl|CDD|235978 PRK07234, PRK07234, putative monovalent cation/H+ antiporter
           subunit D; Reviewed.
          Length = 470

 Score = 28.4 bits (64), Expect = 6.2
 Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 4/36 (11%)

Query: 137 VNSIF-SAELIAIYLCLEAITVHPSDHFLIVSDSRS 171
           VN+ F  A+LI++Y+ LE +++     FL+V+  R+
Sbjct: 107 VNAAFVCADLISLYVALEVLSIAT---FLLVAYPRT 139


>gnl|CDD|224779 COG1866, PckA, Phosphoenolpyruvate carboxykinase (ATP) [Energy
           production and conversion].
          Length = 529

 Score = 28.1 bits (63), Expect = 8.3
 Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 5/42 (11%)

Query: 104 NHTICYTDGSKTMNSTSCAYS---INDVISSSQL-NPVNSIF 141
           + T  + DGS T N T  AY    I +V  S +  +P N IF
Sbjct: 304 DGTPDFDDGSLTEN-TRAAYPIEHIPNVSPSVKAGHPKNVIF 344


>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
          Length = 161

 Score = 27.1 bits (59), Expect = 9.6
 Identities = 44/169 (26%), Positives = 65/169 (38%), Gaps = 33/169 (19%)

Query: 104 NHTICYTDGSKTMNS--TSCAYSINDVISSSQLNPVNSIFSAELIAIYLCLEAITVHPSD 161
           N  I  TDGS   N   +  A+ +++    S    + +   AEL A+   L A T H   
Sbjct: 4   NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIA-TRHTDR 62

Query: 162 HFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLKTLNKDVHFVLKPSQSALAALSNVS 221
             LI+SDS+  +         N L   VYS W + K    D   VL              
Sbjct: 63  PILILSDSKYVI---------NSLTKWVYS-WKMRKWRKADGKPVL-------------- 98

Query: 222 FTNPLVSKVYSCWDLLKTLNKDVHFLWCPSHCGIRGNEAVDEAARNPVN 270
               ++ ++ S  +     N+++   W  +H G   NEA D  AR   N
Sbjct: 99  -NQEIIQEIDSLME-----NRNIRMSWVNAHTGHPLNEAADSLARQAAN 141


  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    0.132    0.408 

Gapped
Lambda     K      H
   0.267   0.0643    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,200,728
Number of extensions: 1484011
Number of successful extensions: 1152
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1148
Number of HSP's successfully gapped: 24
Length of query: 326
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 229
Effective length of database: 6,635,264
Effective search space: 1519475456
Effective search space used: 1519475456
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 (26.7 bits)