RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780828|ref|YP_003065241.1| ATP-dependent protease
peptidase subunit [Candidatus Liberibacter asiaticus str. psy62]
         (190 letters)



>gnl|CDD|48442 cd01913, protease_HslV, Protease HslV and the ATPase/chaperone HslU
           are part of an ATP-dependent proteolytic system that is
           the prokaryotic homolog of the proteasome. HslV is a
           dimer of hexamers (a dodecamer) that forms a central
           proteolytic chamber with active sites on the interior
           walls of the cavity. HslV shares significant sequence
           and structural similarity with the proteasomal
           beta-subunit and both are members of the Ntn-family of
           hydrolases.  HslV has a nucleophilic threonine residue
           at its N-terminus that is exposed after processing of
           the propeptide and is directly involved in active site
           catalysis..
          Length = 171

 Score =  276 bits (708), Expect = 2e-75
 Identities = 124/171 (72%), Positives = 146/171 (85%), Gaps = 1/171 (0%)

Query: 16  TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
           TTIL VRK+G VVIAGDGQV+LG TVMK NARKVRRL  G +IAGFAGS+ADAFTL ER 
Sbjct: 1   TTILAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVIAGFAGSTADAFTLFERF 60

Query: 76  EKKLEQYPNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPENGVM 135
           E KLEQYP  LLR++VELAKDWR D+YLR LEAM+++ADK  TL+I+G GDV+EP++G+ 
Sbjct: 61  EAKLEQYPGNLLRAAVELAKDWRTDRYLRRLEAMLIVADKEHTLLISGNGDVIEPDDGIA 120

Query: 136 AIGSGGSYALSAARALM-STQNSAEEIARKAMSIAADICVYTNHNIVLETL 185
           AIGSGG+YAL+AARAL+  T  SAEEIARKA+ IAADIC+YTNHNI +E L
Sbjct: 121 AIGSGGNYALAAARALLDHTDLSAEEIARKALKIAADICIYTNHNITVEEL 171


>gnl|CDD|34964 COG5405, HslV, ATP-dependent protease HslVU (ClpYQ), peptidase
           subunit [Posttranslational modification, protein
           turnover, chaperones].
          Length = 178

 Score =  263 bits (675), Expect = 1e-71
 Identities = 123/175 (70%), Positives = 144/175 (82%), Gaps = 1/175 (0%)

Query: 12  KMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTL 71
             H TTI+ VRK+G VVIAGDGQV+LG TVMK NARKVRRL  G ++AGFAGS+ADAFTL
Sbjct: 1   TFHMTTIVAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTL 60

Query: 72  LERLEKKLEQYPNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPE 131
            ER E KLEQY   L R++VELAKDWR DKYLR LEAM+L+ADKT  L+ITG GDV+EPE
Sbjct: 61  FERFEAKLEQYQGDLFRAAVELAKDWRTDKYLRKLEAMLLVADKTHILIITGNGDVIEPE 120

Query: 132 NGVMAIGSGGSYALSAARALMS-TQNSAEEIARKAMSIAADICVYTNHNIVLETL 185
           + ++AIGSGG+YALSAARALM  T+ SA EIA K++ IA DIC+YTNHNIV+E L
Sbjct: 121 DDIIAIGSGGNYALSAARALMENTELSAREIAEKSLKIAGDICIYTNHNIVVEEL 175


>gnl|CDD|143982 pfam00227, Proteasome, Proteasome subunit.  The proteasome is a
           multisubunit structure that degrades proteins. Protein
           degradation is an essential component of regulation
           because proteins can become misfolded, damaged, or
           unnecessary. Proteasomes and their homologues vary
           greatly in complexity: from HslV (heat shock locus v),
           which is encoded by 1 gene in bacteria, to the
           eukaryotic 20S proteasome, which is encoded by more than
           14 genes. Recently evidence of two novel groups of
           bacterial proteasomes was proposed. The first is Anbu,
           which is sparsely distributed among cyanobacteria and
           proteobacteria. The second is call beta-proteobacteria
           proteasome homologue (BPH).
          Length = 188

 Score =  108 bits (271), Expect = 1e-24
 Identities = 46/189 (24%), Positives = 72/189 (38%), Gaps = 20/189 (10%)

Query: 14  HATTILTVRKDGVVVIAGDGQVSLGQTV-MKANARKVRRLGKGNIIAGFAGSSADAFTLL 72
             TTI+ ++    VV+A D + + G  +  K    K+ ++   +I   FAG +ADA TL+
Sbjct: 3   TGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDD-HIGMAFAGLAADARTLV 61

Query: 73  ERLEKKLEQY--------PNQLLRS-----SVELAKDWRMDKYLRNLEAMILIADKTITL 119
           +    + + Y          +L +              R    +  L A           
Sbjct: 62  DYARAEAQLYRLRYGRPISVELAKRIADKLQAYTQYSGRRPYGVSLLIAGYDEDGGPHLY 121

Query: 120 VITGMGDVLEPENGVMAIGSGGSYALSAARALMS---TQNSAEEIARKAMSIAADICVYT 176
            I   G V+E +    AIGSG  YA      L     T   A E+A KA+  A D    +
Sbjct: 122 SIDPSGSVIEYK--ATAIGSGSQYAYGFLEKLYKPDMTLEEAVELAVKALKEAIDRDALS 179

Query: 177 NHNIVLETL 185
             NI +  +
Sbjct: 180 GGNIEVAVI 188


>gnl|CDD|48439 cd01906, proteasome_protease_HslV, proteasome_protease_HslV. This
           group contains the eukaryotic proteosome alpha and beta
           subunits and the prokaryotic protease hslV subunit.
           Proteasomes are large multimeric self-compartmentalizing
           proteases, involved in the clearance of misfolded
           proteins, the breakdown of regulatory proteins, and the
           processing of proteins such as the preparation of
           peptides for immune presentation. Two main proteasomal
           types are distinguished by their different tertiary
           structures: the eukaryotic/archeal 20S proteasome and
           the prokaryotic proteasome-like heat shock protein
           encoded by heat shock locus V, hslV.  The proteasome
           core particle is a highly conserved cylindrical
           structure made up of non-identical subunits that have
           their active sites on the inner walls of a large central
           cavity. The proteasome subunits of bacteria, archaea,
           and eukaryotes all share a conserved Ntn (N terminal
           nucleophile) hydrolase fold and a catalytic mechanism
           involving an N-terminal nucleophilic threonine that is
           exposed by post-translational processing of an inactive
           propeptide..
          Length = 182

 Score =  107 bits (268), Expect = 2e-24
 Identities = 54/185 (29%), Positives = 82/185 (44%), Gaps = 18/185 (9%)

Query: 16  TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
           TTI+ ++    VV+A D +V+ G  V  +   K+ ++   +I   FAG +ADA TL+ERL
Sbjct: 1   TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDD-HIGCAFAGLAADAQTLVERL 59

Query: 76  EKKLEQY------PNQLLRSSVELAKDWRMDK-YLRNLEAMILIA-----DKTITLVITG 123
            K+ + Y      P  +   +  LA         LR L   +L+A            +  
Sbjct: 60  RKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQSLRPLGVSLLVAGVDEEGGPQLYSVDP 119

Query: 124 MGDVLEPENGVMAIGSGGSYALSAARALM---STQNSAEEIARKAMSIAADICVYTNHNI 180
            G  +E      AIGSG  YAL     L     T   A E+A KA+  A +  +Y+  NI
Sbjct: 120 SGSYIEY--KATAIGSGSQYALGILEKLYKPDMTLEEAIELALKALKSALERDLYSGGNI 177

Query: 181 VLETL 185
            +  +
Sbjct: 178 EVAVI 182


>gnl|CDD|48436 cd01901, Ntn_hydrolase, The Ntn hydrolases (N-terminal nucleophile)
           are a diverse superfamily of of enzymes that are
           activated autocatalytically via an N-terminally lcated
           nucleophilic amino acid.  N-terminal nucleophile (NTN-)
           hydrolase superfamily, which contains a four-layered
           alpha, beta, beta, alpha core structure. This family of
           hydrolases includes penicillin acylase, the 20S
           proteasome alpha and beta subunits, and glutamate
           synthase. The mechanism of activation of these proteins
           is conserved, although they differ in their substrate
           specificities. All known members catalyze the hydrolysis
           of amide bonds in either proteins or small molecules,
           and each one of them is synthesized as a preprotein. For
           each, an autocatalytic endoproteolytic process generates
           a new N-terminal residue. This mature N-terminal residue
           is central to catalysis and acts as both a polarizing
           base and a nucleophile during the reaction. The
           N-terminal amino group acts as the proton acceptor and
           activates either the nucleophilic hydroxyl in a Ser or
           Thr residue or the nucleophilic thiol in a Cys residue.
           The position of the N-terminal nucleophile in the active
           site and the mechanism of catalysis are conserved in
           this family, despite considerable variation in the
           protein sequences..
          Length = 164

 Score = 77.1 bits (189), Expect = 3e-15
 Identities = 48/166 (28%), Positives = 73/166 (43%), Gaps = 15/166 (9%)

Query: 16  TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
           +T + ++  G VV+A D ++S G  V  +   K+ +   G I  G AG +ADA TL+ RL
Sbjct: 1   STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDG-IAWGLAGLAADAQTLVRRL 59

Query: 76  EKKLEQY------PNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTIT----LVITGMG 125
            + L+ Y      P  ++  + ELAK  ++    R     +++A           I   G
Sbjct: 60  REALQLYRLRYGEPISVVALAKELAKLLQVYTQGRPFGVNLIVAGVDEGGGNLYYIDPSG 119

Query: 126 DVLEPENGVMAIGSGGSYALSAARALMS---TQNSAEEIARKAMSI 168
            V+E    V A GS    A S    L     T   A E+A KA+  
Sbjct: 120 PVIENPGAV-ATGSRSQRAKSLLEKLYKPDMTLEEAVELALKALKS 164


>gnl|CDD|48441 cd01912, proteasome_beta, proteasome beta subunit. The 20S
           proteasome, multisubunit proteolytic complex, is the
           central enzyme of nonlysosomal protein degradation in
           both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           alpha and 7 beta proteasome subunits while archaea have
           one of each..
          Length = 189

 Score = 57.8 bits (140), Expect = 2e-09
 Identities = 45/183 (24%), Positives = 74/183 (40%), Gaps = 22/183 (12%)

Query: 16  TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
           TTI+ ++    VV+A D + S G  V   N  K+ ++   NI+ G AGS+AD   L   L
Sbjct: 1   TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISD-NILLGTAGSAADTQALTRLL 59

Query: 76  EKKLEQYPNQLLRS-SVELAKDWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPENGV 134
           ++ L  Y  +  R  SV+ A        L N+          ++L++ G+     P    
Sbjct: 60  KRNLRLYELRNGRELSVKAAA-----NLLSNILYSYRGFPYYVSLIVGGVDKGGGPFLYY 114

Query: 135 M------------AIGSGGSYALSAARALMS---TQNSAEEIARKAMSIAADICVYTNHN 179
           +            A GSG  YA            T   A E+ +KA+  A +  + +   
Sbjct: 115 VDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMTLEEAVELVKKAIDSAIERDLSSGGG 174

Query: 180 IVL 182
           + +
Sbjct: 175 VDV 177


>gnl|CDD|30983 COG0638, PRE1, 20S proteasome, alpha and beta subunits
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 236

 Score = 54.9 bits (132), Expect = 1e-08
 Identities = 43/193 (22%), Positives = 72/193 (37%), Gaps = 15/193 (7%)

Query: 10  AVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
           AVK   TT + ++    VV+A D + + G  +  +N  K+ ++   +I    AG +ADA 
Sbjct: 25  AVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDD-HIGMAIAGLAADAQ 83

Query: 70  TLLERLEKKLEQYPNQLLRS-SVELAKDWRMDK------YLRNLEAMILIA---DKTITL 119
            L+     + + Y  +     SVE       +         R     +L+A   D    L
Sbjct: 84  VLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQSGRPYGVSLLVAGVDDGGPRL 143

Query: 120 VITGMGDVLEPENGVMAIGSGGSYALSAARALMS---TQNSAEEIARKAMSIAADICVYT 176
             T        E    AIGSG  +A            +   A E+A KA+  A +    +
Sbjct: 144 YSTDPSGSYN-EYKATAIGSGSQFAYGFLEKEYREDLSLEEAIELAVKALRAAIERDAAS 202

Query: 177 NHNIVLETLKVGD 189
              I +  +   +
Sbjct: 203 GGGIEVAVITKDE 215


>gnl|CDD|48460 cd03762, proteasome_beta_type_6, proteasome beta type-6 subunit.
           The 20S proteasome, multisubunit proteolytic complex, is
           the central enzyme of nonlysosomal protein degradation
           in both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           alpha and 7 beta proteasome subunits while archaea have
           one of each..
          Length = 188

 Score = 49.8 bits (119), Expect = 5e-07
 Identities = 43/171 (25%), Positives = 72/171 (42%), Gaps = 25/171 (14%)

Query: 16  TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
           TTI+ V  DG VV+  D + S G  V      K+ +L    I    +GS+AD   + + +
Sbjct: 1   TTIIAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHD-RIYCCRSGSAADTQAIADYV 59

Query: 76  EKKLEQYPNQ-----LLRSSVELAKDWRMDKYLRNLEAMILIA--DKTITLVITGMGDVL 128
              L+ +  +     L++++  L K+     Y   L A I++A  D+       G     
Sbjct: 60  RYYLDMHSIELGEPPLVKTAASLFKNL-CYNYKEMLSAGIIVAGWDEQ-----NGGQVYS 113

Query: 129 EPENGVM-----AIGSGGS-----YALSAARALMSTQNSAEEIARKAMSIA 169
            P  G++     AIG  GS     Y  +  +  M T     +  + A+S+A
Sbjct: 114 IPLGGMLIRQPFAIGGSGSTYIYGYVDANYKPGM-TLEECIKFVKNALSLA 163


>gnl|CDD|35406 KOG0185, KOG0185, KOG0185, 20S proteasome, regulatory subunit beta
           type PSMB4/PRE4 [Posttranslational modification, protein
           turnover, chaperones].
          Length = 256

 Score = 41.1 bits (96), Expect = 2e-04
 Identities = 41/178 (23%), Positives = 73/178 (41%), Gaps = 34/178 (19%)

Query: 16  TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
           T++L ++    VVIA D   S G      N  ++ ++G  N + G +G  +D F  ++R+
Sbjct: 42  TSVLALKYKDGVVIAADTLGSYGSLARYKNVERIFKVGD-NTLLGASGDISD-FQYIQRV 99

Query: 76  EKKLEQYPNQLLRSSVELAKDWRMD-KYLRNLEAMILIADKT------ITLVITGMGDVL 128
            ++L    N+       L     +  K + +    +L A ++       TLV+ G+ +  
Sbjct: 100 LEQLVIEDNR-------LDDGQSLGPKAIHSYLTRVLYARRSKMNPLWNTLVVGGVDNTG 152

Query: 129 EP------------ENGVMAIGSGGSYALSAAR------ALMSTQNSAEEIARKAMSI 168
           EP            E+ V+A G G   AL   R          ++  AE +  K M +
Sbjct: 153 EPFLGYVDLLGVAYESPVVATGFGAHLALPLLRDEWEKKGEDLSREEAEALIEKCMRV 210


>gnl|CDD|48455 cd03757, proteasome_beta_type_1, proteasome beta type-1 subunit.
          The 20S proteasome, multisubunit proteolytic complex,
          is the central enzyme of nonlysosomal protein
          degradation in both the cytosol and nucleus. It is
          composed of 28 subunits arranged as four homoheptameric
          rings that stack on top of one another forming an
          elongated alpha-beta-beta-alpha cylinder with a central
          cavity. The proteasome alpha and beta subunits are
          members of the N-terminal nucleophile (Ntn)-hydrolase
          superfamily. Their N-terminal threonine residues are
          exposed as a nucleophile in peptide bond hydrolysis.
          Mammals have 7 alpha and 7 beta proteasome subunits
          while archaea have one of each..
          Length = 212

 Score = 40.6 bits (95), Expect = 3e-04
 Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
          T+L +  +   VIAGD ++S G +++  ++ K+ +L    ++   +G  AD   L +RL+
Sbjct: 10 TVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGS-SGFQADILALTKRLK 68

Query: 77 KKLEQY 82
           +++ Y
Sbjct: 69 ARIKMY 74


>gnl|CDD|35395 KOG0174, KOG0174, KOG0174, 20S proteasome, regulatory subunit beta
           type PSMB6/PSMB9/PRE3 [Posttranslational modification,
           protein turnover, chaperones].
          Length = 224

 Score = 38.0 bits (88), Expect = 0.002
 Identities = 46/180 (25%), Positives = 74/180 (41%), Gaps = 19/180 (10%)

Query: 4   MGDKHYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAG 63
           +GD         TTI+ V  DG VV+  D + S G  V      K+  +   NI    +G
Sbjct: 8   IGDLPKEEVSTGTTIMAVEYDGGVVLGADSRTSTGAYVANRVTDKLTPI-TDNIYCCRSG 66

Query: 64  SSADAFTLLERLEKKLEQYPNQ-----LLRSSVELAKDWRMDKYLRNLEAMILIA---DK 115
           S+AD   + + +   LE Y  Q     L+ ++  L ++     Y   L A +++A   +K
Sbjct: 67  SAADTQAIADIVRYHLELYTIQENKPPLVHTAASLFREI-CYNYREMLSAGLIVAGWDEK 125

Query: 116 TITLVIT-GMGDVLEPENGVMAIGSGGS-----YALSAARALMSTQNSAEEIARKAMSIA 169
               V +  +G  L  +    AIG  GS     +  +  R  M T        + A+S+A
Sbjct: 126 EGGQVYSIPLGGSLTRQP--FAIGGSGSTFIYGFCDANWRPNM-TLEECVRFVKNAVSLA 182


>gnl|CDD|35400 KOG0179, KOG0179, KOG0179, 20S proteasome, regulatory subunit beta
           type PSMB1/PRE7 [Posttranslational modification, protein
           turnover, chaperones].
          Length = 235

 Score = 37.2 bits (86), Expect = 0.003
 Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 13  MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLL 72
            +  T + +  +   V+AGD ++S G  +   +  K+ +LG  NI+ G +G  AD   L+
Sbjct: 27  DNGGTTVAIAGEDFAVVAGDTRMSSGYNINSRDQSKIFKLGD-NIVLGSSGFYADTLALV 85

Query: 73  ERLEKKLEQYPNQLLRS 89
           + ++ +++QY +   + 
Sbjct: 86  KVIKSRIKQYEHDHNKK 102


>gnl|CDD|48457 cd03759, proteasome_beta_type_3, proteasome beta type-3 subunit.
          The 20S proteasome, multisubunit proteolytic complex,
          is the central enzyme of nonlysosomal protein
          degradation in both the cytosol and nucleus. It is
          composed of 28 subunits arranged as four homoheptameric
          rings that stack on top of one another forming an
          elongated alpha-beta-beta-alpha cylinder with a central
          cavity. The proteasome alpha and beta subunits are
          members of the N-terminal nucleophile (Ntn)-hydrolase
          superfamily. Their N-terminal threonine residues are
          exposed as a nucleophile in peptide bond hydrolysis.
          Mammals have 7 alpha and 7 beta proteasome subunits
          while archaea have one of each..
          Length = 195

 Score = 35.5 bits (82), Expect = 0.010
 Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
           ++ +     V IA D ++ + Q  +  + +KV R+G   +  G AG + D  TL ++L 
Sbjct: 5  AVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVFRIGD-RLYIGLAGLATDVQTLAQKLR 63

Query: 77 KKLEQY 82
           ++  Y
Sbjct: 64 FRVNLY 69


>gnl|CDD|48461 cd03763, proteasome_beta_type_7, proteasome beta type-7 subunit.
          The 20S proteasome, multisubunit proteolytic complex,
          is the central enzyme of nonlysosomal protein
          degradation in both the cytosol and nucleus. It is
          composed of 28 subunits arranged as four homoheptameric
          rings that stack on top of one another forming an
          elongated alpha-beta-beta-alpha cylinder with a central
          cavity. The proteasome alpha and beta subunits are
          members of the N-terminal nucleophile (Ntn)-hydrolase
          superfamily. Their N-terminal threonine residues are
          exposed as a nucleophile in peptide bond hydrolysis.
          Mammals have 7 alpha and 7 beta proteasome subunits
          while archaea have one of each..
          Length = 189

 Score = 35.1 bits (81), Expect = 0.011
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
          TTI+ V     VV+  D + + G  V   N  K+  +   NI    AG++AD   +   +
Sbjct: 1  TTIVGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAP-NIYCCGAGTAADTEAVTNMI 59

Query: 76 EKKLEQYPNQLLR 88
             LE +     R
Sbjct: 60 SSNLELHRLNTGR 72


>gnl|CDD|48458 cd03760, proteasome_beta_type_4, proteasome beta type-4 subunit.
          The 20S proteasome, multisubunit proteolytic complex,
          is the central enzyme of nonlysosomal protein
          degradation in both the cytosol and nucleus. It is
          composed of 28 subunits arranged as four homoheptameric
          rings that stack on top of one another forming an
          elongated alpha-beta-beta-alpha cylinder with a central
          cavity. The proteasome alpha and beta subunits are
          members of the N-terminal nucleophile (Ntn)-hydrolase
          superfamily. Their N-terminal threonine residues are
          exposed as a nucleophile in peptide bond
          hydrolysis.Mammals have 7 alpha and 7 beta proteasome
          subunits while archaea have one of each..
          Length = 197

 Score = 34.7 bits (80), Expect = 0.016
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
          T+++ ++    V+IA D   S G      N  ++ ++G  N + G +G  AD   L   L
Sbjct: 3  TSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGD-NTLLGASGDYADFQYLKRLL 61

Query: 76 EKK 78
          ++ 
Sbjct: 62 DQL 64


>gnl|CDD|35398 KOG0177, KOG0177, KOG0177, 20S proteasome, regulatory subunit
          beta type PSMB2/PRE1 [Posttranslational modification,
          protein turnover, chaperones].
          Length = 200

 Score = 34.4 bits (79), Expect = 0.022
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
          T+L ++    V++A D   +    V+K +  K+ RL    ++A   G + D     E ++
Sbjct: 3  TLLGIKGPDFVILASDTSAARSILVLKDDHDKIHRLSDHILMA-TVGEAGDTVQFTEYIQ 61

Query: 77 KKLEQY 82
          K ++ Y
Sbjct: 62 KNIQLY 67


>gnl|CDD|48462 cd03764, proteasome_beta_archeal, Archeal proteasome, beta
          subunit. The 20S proteasome, multisubunit proteolytic
          complex, is the central enzyme for non-lysosomal
          protein degradation in both the cytosol and the
          nucleus. It is composed of 28 subunits arranged as four
          homoheptameric rings that stack on top of one another
          forming an elongated alpha-beta-beta-alpha cylinder
          with a central cavity. The proteasome alpha and beta
          subunits are both members of the N-terminal nucleophile
          (Ntn)-hydrolase superfamily. Their N-terminal threonine
          residues are exposed as a nucleophile in peptide bond
          hydrolysis. Mammals have 7 alpha and 7 beta proteasome
          subunits while archaea have one of each..
          Length = 188

 Score = 34.0 bits (78), Expect = 0.026
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 15 ATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLER 74
           TT+  V KDGVV +A D + S+G  +   N +K+ ++    I    AGS  DA +L+  
Sbjct: 1  TTTVGIVCKDGVV-LAADKRASMGNFIASKNVKKIFQIDD-KIAMTIAGSVGDAQSLVRI 58

Query: 75 LEKKLEQY 82
          L+ +   Y
Sbjct: 59 LKAEARLY 66


>gnl|CDD|48456 cd03758, proteasome_beta_type_2, proteasome beta type-2 subunit.
          The 20S proteasome, multisubunit proteolytic complex,
          is the central enzyme of nonlysosomal protein
          degradation in both the cytosol and nucleus. It is
          composed of 28 subunits arranged as four homoheptameric
          rings that stack on top of one another forming an
          elongated alpha-beta-beta-alpha cylinder with a central
          cavity. The proteasome alpha and beta subunits are
          members of the N-terminal nucleophile (Ntn)-hydrolase
          superfamily. Their N-terminal threonine residues are
          exposed as a nucleophile in peptide bond
          hydrolysis.Mammals have 7 alpha and 7 beta proteasome
          subunits while archaea have one of each..
          Length = 193

 Score = 30.5 bits (69), Expect = 0.27
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
          T++ ++    V++A D   +    V+K +  K+ +L    ++A  +G + D     E ++
Sbjct: 3  TLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMA-CSGEAGDRLQFAEYIQ 61

Query: 77 KKLEQYPNQLLRSSVEL 93
          K ++ Y    +R+  EL
Sbjct: 62 KNIQLYK---MRNGYEL 75


>gnl|CDD|35396 KOG0175, KOG0175, KOG0175, 20S proteasome, regulatory subunit beta
           type PSMB5/PSMB8/PRE2 [Posttranslational modification,
           protein turnover, chaperones].
          Length = 285

 Score = 30.7 bits (69), Expect = 0.28
 Identities = 45/187 (24%), Positives = 73/187 (39%), Gaps = 30/187 (16%)

Query: 5   GDKHYAVKM---HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGF 61
            D+   V +   H TT L  +  G V++A D + S G  +     +KV  +    ++   
Sbjct: 58  DDETAGVLIKFAHGTTTLAFKFKGGVIVAVDSRASAGSYIASQTVKKVIEINP-YLLGTM 116

Query: 62  AGSSADAFTLLERLEKKLEQYPNQLL---RSSVELAKDWRMDKYLRNLE----------- 107
           AG +AD       L K+   +  +L    R SV  A      K L N+            
Sbjct: 117 AGGAADCQFWERVLAKECRLH--ELRNKERISVSAAS-----KLLSNMVYQYKGMGLSMG 169

Query: 108 AMILIADKTITLVITGMGDVLEPENGVMAIGSGGSYAL----SAARALMSTQNSAEEIAR 163
            MI   DK    +     +       + ++GSG +YA     S  R  +S +  A ++AR
Sbjct: 170 TMIAGWDKKGPGLYYVDSEGTRLSGDLFSVGSGSTYAYGVLDSGYRYDLSDEE-AYDLAR 228

Query: 164 KAMSIAA 170
           +A+  A 
Sbjct: 229 RAIYHAT 235


>gnl|CDD|48450 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4. The
          20S proteasome, multisubunit proteolytic complex, is
          the central enzyme of nonlysosomal protein degradation
          in both the cytosol and nucleus. It is composed of 28
          subunits arranged as four homoheptameric rings that
          stack on top of one another forming an elongated
          alpha-beta-beta-alpha cylinder with a central cavity.
          The proteasome alpha and beta subunits are members of
          the N-terminal nucleophile (Ntn)-hydrolase superfamily.
          Their N-terminal threonine residues are exposed as a
          nucleophile in peptide bond hydrolysis. Mammals have 7
          alpha and 7 beta proteasome subunits while archaea have
          one of each..
          Length = 213

 Score = 30.2 bits (68), Expect = 0.37
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 10 AVKMHATTILTVRKDGVVVIAGDGQVS--LGQTVMKANARKVRRLGKGNIIAGFAGSSAD 67
          A+    T +  + KDG+V+ A     S  L Q+    ++ K+ ++   +I    AG ++D
Sbjct: 25 AISHAGTCLGILAKDGIVLAAEKKVTSKLLDQSF---SSEKIYKIDD-HIACAVAGITSD 80

Query: 68 AFTLLERLEKKLEQY 82
          A  L+       ++Y
Sbjct: 81 ANILINYARLIAQRY 95


>gnl|CDD|48440 cd01911, proteasome_alpha, proteasome alpha subunit. The 20S
          proteasome, multisubunit proteolytic complex, is the
          central enzyme of nonlysosomal protein degradation in
          both the cytosol and nucleus. It is composed of 28
          subunits arranged as four homoheptameric rings that
          stack on top of one another forming an elongated
          alpha-beta-beta-alpha cylinder with a central cavity.
          The proteasome alpha and beta subunits are members of
          the N-terminal nucleophile (Ntn)-hydrolase superfamily.
          Their N-terminal threonine residues are exposed as a
          nucleophile in peptide bond hydrolysis. Mammals have 7
          different alpha and 10 different beta proteasome
          subunit genes while archaea have one of each..
          Length = 209

 Score = 30.0 bits (68), Expect = 0.45
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 10 AVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
          AVK  +T +    KDGVV+       S  + +  ++  K+ ++   +I    AG +ADA 
Sbjct: 23 AVKNGSTAVGIKGKDGVVLAVEKKVTS--KLLDPSSVEKIFKIDD-HIGCAVAGLTADAR 79

Query: 70 TLLERLEKKLEQY 82
           L+ R   + + Y
Sbjct: 80 VLVNRARVEAQNY 92


>gnl|CDD|48459 cd03761, proteasome_beta_type_5, proteasome beta type-5 subunit.
           The 20S proteasome, multisubunit proteolytic complex, is
           the central enzyme of nonlysosomal protein degradation
           in both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           alpha and 7 beta proteasome subunits while archaea have
           one of each..
          Length = 188

 Score = 29.8 bits (67), Expect = 0.51
 Identities = 43/173 (24%), Positives = 69/173 (39%), Gaps = 27/173 (15%)

Query: 16  TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
           TT L     G V++A D + + G  +     +KV  +    ++   AG +AD       L
Sbjct: 1   TTTLAFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINP-YLLGTMAGGAADCQYWERVL 59

Query: 76  EKKLEQYPNQLL---RSSVELAKDWRMDKYLRNL-----------EAMILIADKTITLVI 121
            ++   Y  +L    R SV  A      K L N+             MI   DKT   + 
Sbjct: 60  GRECRLY--ELRNKERISVAAAS-----KLLSNMLYQYKGMGLSMGTMICGWDKTGPGLY 112

Query: 122 TGMGDVLEPENGVMAIGSGGSYAL----SAARALMSTQNSAEEIARKAMSIAA 170
               D    +  + ++GSG +YA     S  R  +S +  A ++AR+A+  A 
Sbjct: 113 YVDSDGTRLKGDLFSVGSGSTYAYGVLDSGYRYDLSVEE-AYDLARRAIYHAT 164


>gnl|CDD|176247 cd08287, FDH_like_ADH3, formaldehyde dehydrogenase (FDH)-like.
           This group contains proteins identified as alcohol
           dehydrogenases and glutathione-dependant formaldehyde
           dehydrogenases (FDH) of the zinc-dependent/medium chain
           alcohol dehydrogenase family.  The MDR family uses
           NAD(H) as a cofactor in the interconversion of alcohols
           and aldehydes, or ketones.  FDH converts formaldehyde
           and NAD to formate and NADH. The initial step in this
           process the spontaneous formation of a
           S-(hydroxymethyl)glutathione adduct from formaldehyde
           and glutathione, followed by FDH-mediated oxidation (and
           detoxification) of the adduct to S-formylglutathione.
           The medium chain alcohol dehydrogenase family (MDR) has
           a NAD(P)(H)-binding domain in a Rossmann fold of a
           beta-alpha form. The N-terminal region typically has an
           all-beta catalytic domain. These proteins typically form
           dimers (typically higher plants, mammals) or tetramers
           (yeast, bacteria), and have 2 tightly bound zinc atoms
           per subunit.
          Length = 345

 Score = 29.6 bits (67), Expect = 0.57
 Identities = 23/57 (40%), Positives = 26/57 (45%), Gaps = 11/57 (19%)

Query: 3   VMGDKHYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIA 59
           VMG  H     HA     VR    VV+ GDG V L   V+ A     +RLG   IIA
Sbjct: 153 VMGTGH-----HAAVSAGVRPGSTVVVVGDGAVGL-CAVLAA-----KRLGAERIIA 198


>gnl|CDD|35401 KOG0180, KOG0180, KOG0180, 20S proteasome, regulatory subunit
          beta type PSMB3/PUP3 [Posttranslational modification,
          protein turnover, chaperones].
          Length = 204

 Score = 28.7 bits (64), Expect = 1.0
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
          +++ +     V IA D ++ +    +  + +K+ ++G   +  G  G + D  TLLERL 
Sbjct: 10 SVVAMAGKNCVAIASDLRLGVQSQTISTDFQKIFKIGD-RLYLGLTGLATDVQTLLERLR 68

Query: 77 KKLEQY 82
           +   Y
Sbjct: 69 FRKNLY 74


>gnl|CDD|72970 cd04498, hPOT1_OB2, hPOT1_OB2: A subfamily of OB folds similar to
           the second OB fold (OB2) of human protection of
           telomeres 1 protein (hPOT1). POT1 proteins bind to the
           single-stranded (ss) 3-prime ends of the telomere. hPOT1
           binds specifically to ss telomeric DNA repeats ending
           with the sequence GGTTAG. The hPOT1 monomer consists of
           two closely connected OB folds (OB1-OB2) which cooperate
           to bind telomeric ssDNA. OB1 makes more extensive
           contact with the ssDNA than OB2. OB2 protects the 3' end
           of the ssDNA. hPOT1 is implicated in telomere length
           regulation..
          Length = 123

 Score = 28.4 bits (63), Expect = 1.3
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 161 IARKAMSIAADICVYTNHNIVLETLKVGD 189
                  +  DI VY NH  + ++LK GD
Sbjct: 53  REEGGKQLTIDILVYDNHVELAKSLKPGD 81


>gnl|CDD|176218 cd08256, Zn_ADH2, Alcohol dehydrogenases of the MDR family.  This
           group has the characteristic catalytic and structural
           zinc-binding sites of the zinc-dependent 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 = 350

 Score = 28.1 bits (63), Expect = 1.6
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 9   YAVKMHATTILTVRKDGVVVIAGDGQVSLG--QTVMKANARKV 49
            A  +HA     ++ D VVV+AG G + LG        N +K+
Sbjct: 160 LACALHAVDRANIKFDDVVVLAGAGPLGLGMIGAARLKNPKKL 202


>gnl|CDD|48453 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7. The
          20S proteasome, multisubunit proteolytic complex, is
          the central enzyme of nonlysosomal protein degradation
          in both the cytosol and nucleus. It is composed of 28
          subunits arranged as four homoheptameric rings that
          stack on top of one another forming an elongated
          alpha-beta-beta-alpha cylinder with a central cavity.
          The proteasome alpha and beta subunits are members of
          the N-terminal nucleophile (Ntn)-hydrolase superfamily.
          Their N-terminal threonine residues are exposed as a
          nucleophile in peptide bond hydrolysis. Mammals have 7
          alpha and 7 beta proteasome subunits while archaea have
          one of each..
          Length = 207

 Score = 27.5 bits (61), Expect = 2.1
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 8  HYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGK--GNIIAGFAGSS 65
            AV+   TT + VR    VV+     V         + R VR++     ++   FAG +
Sbjct: 21 QEAVR-KGTTAVGVRGKDCVVLG----VEKKSVAKLQDPRTVRKICMLDDHVCLAFAGLT 75

Query: 66 ADAFTLLERLEKKLEQY 82
          ADA  L+ R   + + +
Sbjct: 76 ADARVLINRARLECQSH 92


>gnl|CDD|145851 pfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain.
          
          Length = 99

 Score = 27.2 bits (61), Expect = 2.7
 Identities = 9/23 (39%), Positives = 16/23 (69%)

Query: 17 TILTVRKDGVVVIAGDGQVSLGQ 39
          TI++V K G++V  GDG + + +
Sbjct: 58 TIVSVDKGGLLVACGDGALLILE 80


>gnl|CDD|35473 KOG0252, KOG0252, KOG0252, Inorganic phosphate transporter
           [Inorganic ion transport and metabolism].
          Length = 538

 Score = 26.8 bits (59), Expect = 3.5
 Identities = 20/66 (30%), Positives = 26/66 (39%), Gaps = 18/66 (27%)

Query: 97  WRMDKYLRN----LEAMILIADKTITLVITGMGDVLEPENGVMA----------IGSGGS 142
           W  DK+ R      E +I+I    I   ++G+        GVM           IG GG 
Sbjct: 106 WLGDKFGRKKVYGKELIIMI----ICSALSGLSVGTTSPLGVMMTLCFFRFLLGIGIGGD 161

Query: 143 YALSAA 148
           Y LSA 
Sbjct: 162 YPLSAT 167


>gnl|CDD|39745 KOG4545, KOG4545, KOG4545, Uncharacterized conserved protein
           [Function unknown].
          Length = 197

 Score = 25.8 bits (56), Expect = 7.5
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 9/49 (18%)

Query: 77  KKLEQYPNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTITLVITGMG 125
           K+  QY N L+R   E+  D   + Y R  +A+         +  TG+G
Sbjct: 28  KRWGQYWNGLVRDYTEVCVDVVRESYTRPKKAL---------VYGTGLG 67


>gnl|CDD|48454 cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal. The
          20S proteasome, multisubunit proteolytic complex, is
          the central enzyme of nonlysosomal protein degradation
          in both the cytosol and nucleus. It is composed of 28
          subunits arranged as four homoheptameric rings that
          stack on top of one another forming an elongated
          alpha-beta-beta-alpha cylinder with a central cavity.
          The proteasome alpha and beta subunits are members of
          the N-terminal nucleophile (Ntn)-hydrolase superfamily.
          Their N-terminal threonine residues are exposed as a
          nucleophile in peptide bond hydrolysis. Mammals have 7
          alpha and 7 beta proteasome subunits while archaea have
          one of each..
          Length = 211

 Score = 25.6 bits (56), Expect = 8.0
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 10 AVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
          AVK   T +    K+GVV+       S  + V   +  K+ ++   ++ A  +G  ADA 
Sbjct: 24 AVKRGTTALGIKCKEGVVLAVDKRITS--KLVEPESIEKIYKIDD-HVGAATSGLVADAR 80

Query: 70 TLLER 74
           L++R
Sbjct: 81 VLIDR 85


>gnl|CDD|145225 pfam01936, DUF88, Protein of unknown function DUF88.  This highly
           conserved bacterial protein has no known function. The
           alignment contains many conserved aspartates, suggesting
           an enzymatic function such as an endonuclease or
           glycosyl hydrolase (Bateman A pers. obs).
          Length = 140

 Score = 25.7 bits (57), Expect = 8.4
 Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 9/53 (16%)

Query: 18  ILTVRKDGVVVIAGDGQ-VSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
                 D  V+++GDG    L          ++R  GK   + G   S++DA 
Sbjct: 85  AYDNNPDTFVLVSGDGDFAPL--------LERLRERGKRVEVLGAEPSTSDAL 129


>gnl|CDD|114466 pfam05742, DUF833, Protein of unknown function (DUF833).  This
           family is found in eukaryotes, prokaryotes and viruses
           and has no known function. The Ser/Thr-rich protein T10
           has been found to be expressed during early
           embryogenesis in mice.
          Length = 267

 Score = 25.4 bits (56), Expect = 9.0
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 53  GKGNIIAGFAGSSADAFTLLERLEKKLEQYP 83
            +G ++A F  S+A A   LE L+K+  +Y 
Sbjct: 82  SRGELVADFLTSNASALEYLENLKKRAHEYN 112


>gnl|CDD|34546 COG4938, COG4938, Uncharacterized conserved protein [Function
           unknown].
          Length = 374

 Score = 25.4 bits (55), Expect = 9.7
 Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 7/41 (17%)

Query: 17  TILTVRKDGVVVIAG-------DGQVSLGQTVMKANARKVR 50
            +L V+K  +++I         +GQ  LG  + +  AR V+
Sbjct: 254 MLLIVKKKYLIIIENPEAHLHPEGQSKLGDLLAELAARGVQ 294


>gnl|CDD|176985 CHL00044, rpl16, ribosomal protein L16.
          Length = 135

 Score = 25.6 bits (57), Expect = 9.7
 Identities = 8/12 (66%), Positives = 9/12 (75%)

Query: 159 EEIARKAMSIAA 170
           E IAR A+ IAA
Sbjct: 111 ETIARAAIKIAA 122


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.317    0.132    0.358 

Gapped
Lambda     K      H
   0.267   0.0694    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,055,805
Number of extensions: 102390
Number of successful extensions: 379
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 55
Length of query: 190
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,362,145
Effective search space: 444938790
Effective search space used: 444938790
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: 54 (24.7 bits)