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)