RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780272|ref|YP_003064685.1| ATP-dependent Clp protease proteolytic subunit [Candidatus Liberibacter asiaticus str. psy62] (216 letters) >gnl|CDD|144241 pfam00574, CLP_protease, Clp protease. The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. A putative Clp protease from Cyanophora paradoxa has lost all of these active site residues and is therefore inactive. A member from Chlamydomonas eugametos contains two large insertions, a member from Chlamydomonas reinhardtii contains one large insertion. Length = 182 Score = 317 bits (815), Expect = 1e-87 Identities = 120/182 (65%), Positives = 151/182 (82%) Query: 27 NRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVV 86 + GER YDIYSRLL+ERI+F+ G+I+D +A LI AQLLFLE+E+P K+I LYINSPGG V Sbjct: 1 SGGERWYDIYSRLLRERIIFLGGEIDDEVANLIIAQLLFLESEDPDKDIYLYINSPGGSV 60 Query: 87 TAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSG 146 TAG+AIYDTMQFIKP +ST C+G AASMGS LL+AG KG RFALPNARI++HQP GG G Sbjct: 61 TAGLAIYDTMQFIKPDVSTICLGLAASMGSFLLAAGTKGKRFALPNARIMIHQPLGGAQG 120 Query: 147 QASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLM 206 QASDIE A++I+KI+ RLNEIY ++ G+ E++EK LDRD MSA EA ++G++D+V+ Sbjct: 121 QASDIEIQAEEILKIRERLNEIYAEHTGQPLEKIEKDLDRDTFMSAEEAKEYGLIDEVIE 180 Query: 207 SR 208 SR Sbjct: 181 SR 182 >gnl|CDD|31083 COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]. Length = 200 Score = 308 bits (790), Expect = 1e-84 Identities = 142/198 (71%), Positives = 169/198 (85%) Query: 18 LVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISL 77 LVPMV+EQT+RGERSYDIYSRLLKERI+F+ G+IEDHMA LI AQLLFLEAE+P K+I L Sbjct: 3 LVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEIEDHMANLIVAQLLFLEAEDPDKDIYL 62 Query: 78 YINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILL 137 YINSPGG VTAG+AIYDTMQFIKPP+ST CMGQAASMGS+LL AG+KG RFALPNARI++ Sbjct: 63 YINSPGGSVTAGLAIYDTMQFIKPPVSTICMGQAASMGSVLLMAGDKGKRFALPNARIMI 122 Query: 138 HQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACD 197 HQPSGG GQASDIE HA++I+KIK RLN IY ++ G+T E++EK DRD MSA EA + Sbjct: 123 HQPSGGAQGQASDIEIHAREILKIKERLNRIYAEHTGQTLEKIEKDTDRDTWMSAEEAKE 182 Query: 198 WGVVDKVLMSRIDIEEKS 215 +G++DKV+ SR + S Sbjct: 183 YGLIDKVIESREAAAKLS 200 >gnl|CDD|132928 cd07017, S14_ClpP_2, Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Length = 171 Score = 307 bits (788), Expect = 2e-84 Identities = 110/171 (64%), Positives = 143/171 (83%) Query: 34 DIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIY 93 DIYSRLLKERI+F+ G I+D +A LI AQLL+LE+E+P+K I LYINSPGG VTAG+AIY Sbjct: 1 DIYSRLLKERIIFLGGPIDDEVANLIIAQLLYLESEDPKKPIYLYINSPGGSVTAGLAIY 60 Query: 94 DTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIER 153 DTMQ+IKPP+ST C+G AASMG+LLL+AG KG R+ALPN+RI++HQP GG GQASDIE Sbjct: 61 DTMQYIKPPVSTICLGLAASMGALLLAAGTKGKRYALPNSRIMIHQPLGGAGGQASDIEI 120 Query: 154 HAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV 204 A++I++++RRLNEI K+ G+ E++EK DRD MSA EA ++G++DK+ Sbjct: 121 QAKEILRLRRRLNEILAKHTGQPLEKIEKDTDRDRYMSAEEAKEYGLIDKI 171 >gnl|CDD|36058 KOG0840, KOG0840, KOG0840, ATP-dependent Clp protease, proteolytic subunit [Posttranslational modification, protein turnover, chaperones]. Length = 275 Score = 269 bits (690), Expect = 3e-73 Identities = 111/195 (56%), Positives = 148/195 (75%), Gaps = 1/195 (0%) Query: 21 MVVEQTNRG-ERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYI 79 +E RG ER YDIYSRLL+ERIVF+ I+D +A L+ AQLL+L++E+P+K I LYI Sbjct: 70 FPIESPGRGRERPYDIYSRLLRERIVFLGQPIDDDVANLVIAQLLYLDSEDPKKPIYLYI 129 Query: 80 NSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQ 139 NSPGG VTAG+AIYDTMQ+IKP +ST C+G AASM +LLL+AG KG R+ALPN+RI++HQ Sbjct: 130 NSPGGSVTAGLAIYDTMQYIKPDVSTICVGLAASMAALLLAAGAKGKRYALPNSRIMIHQ 189 Query: 140 PSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWG 199 PSGG GQA+DI A+++++IK LNEIY K+ G+ E +EK +DRD MSA EA ++G Sbjct: 190 PSGGAGGQATDIVIQAKELMRIKEYLNEIYAKHTGQPLEVIEKDMDRDRFMSAEEAKEYG 249 Query: 200 VVDKVLMSRIDIEEK 214 ++DKV+ + Sbjct: 250 LIDKVIDHPPETRVD 264 >gnl|CDD|176969 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit. Length = 200 Score = 230 bits (589), Expect = 2e-61 Identities = 71/175 (40%), Positives = 120/175 (68%), Gaps = 1/175 (0%) Query: 34 DIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIY 93 D+Y+RL +ER++F+ +++D +A + +++L E+ K++ L+INSPGG V +G+AIY Sbjct: 22 DLYNRLYRERLLFLGQEVDDEIANQLIGLMVYLSIEDDTKDLYLFINSPGGSVISGLAIY 81 Query: 94 DTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFS-GQASDIE 152 DTMQF+KP + T C+G AASM S +L+ GE R A P+AR+++HQP+ F GQAS+ Sbjct: 82 DTMQFVKPDVHTICLGLAASMASFILAGGEITKRLAFPHARVMIHQPASSFYEGQASEFV 141 Query: 153 RHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMS 207 A++++K++ + +Y + GK + + ++RD MSA+EA +G+VD V ++ Sbjct: 142 LEAEELLKLRETITRVYAQRTGKPLWVISEDMERDVFMSATEAKAYGIVDLVAVN 196 >gnl|CDD|132924 cd07013, S14_ClpP, Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. Additionally, they are implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Length = 162 Score = 209 bits (532), Expect = 7e-55 Identities = 79/162 (48%), Positives = 108/162 (66%) Query: 43 RIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPP 102 R + +TG++ED A AQLLFL A NP+K+I LYINSPGG V AGMAIYDT++FIK Sbjct: 1 REIMLTGEVEDISANQFAAQLLFLGAVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIKAD 60 Query: 103 ISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERHAQDIVKIK 162 + T G AASMGS++ AG KG RF LPNA +++HQP GG G A+D+ +A ++K++ Sbjct: 61 VVTIIDGLAASMGSVIAMAGAKGKRFILPNAMMMIHQPWGGTLGDATDMRIYADLLLKVE 120 Query: 163 RRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV 204 L Y G++ EE+ L+RD +SA EA ++G D + Sbjct: 121 GNLVSAYAHKTGQSEEELHADLERDTWLSAREAVEYGFADTI 162 >gnl|CDD|132923 cd00394, Clp_protease_like, Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Another family included in this class of enzymes is the signal peptide peptidase A (SppA; S49) which is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Mutagenesis studies suggest that the catalytic center of SppA comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain. Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain. The third family included in this hierarchy is nodulation formation efficiency D (NfeD) which is a membrane-bound Clp-class protease and only found in bacteria and archaea. Majority of the NfeD genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named stomatin operon partner protein (STOPP). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 from Pyrococcus horikoshii has been shown to possess serine protease activity having a Ser-Lys catalytic dyad. Length = 161 Score = 155 bits (393), Expect = 1e-38 Identities = 57/163 (34%), Positives = 92/163 (56%), Gaps = 4/163 (2%) Query: 44 IVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPI 103 ++F+ G IED A + AQ+ F EA+N K I L +N+PGG V AGM I D +Q + P+ Sbjct: 1 VIFINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQASRKPV 60 Query: 104 STFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQAS--DIERHAQDIVKI 161 + GQAAS G + +A K P R+ H P GG+ G + E + I+ Sbjct: 61 IAYVGGQAASAGYYIATAANK--IVMAPGTRVGSHGPIGGYGGNGNPTAQEADQRIILYF 118 Query: 162 KRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV 204 R + +N G+T E++E+ +++D +++A EA ++G+VD + Sbjct: 119 IARFISLVAENRGQTTEKLEEDIEKDLVLTAQEALEYGLVDAL 161 >gnl|CDD|132927 cd07016, S14_ClpP_1, Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Length = 160 Score = 109 bits (276), Expect = 4e-25 Identities = 47/141 (33%), Positives = 79/141 (56%), Gaps = 4/141 (2%) Query: 65 FLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEK 124 L+A +I++ INSPGG V AG+AIY+ ++ K ++ G AAS S++ AG++ Sbjct: 23 ALDALGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIAMAGDE 82 Query: 125 -GMRFALPNARILLHQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKT 183 M PNA +++H PS G +G A D+ + A + KI + Y + G + EE+ Sbjct: 83 VEMP---PNAMLMIHNPSTGAAGNADDLRKAADLLDKIDESIANAYAEKTGLSEEEISAL 139 Query: 184 LDRDHIMSASEACDWGVVDKV 204 +D + ++A EA + G D++ Sbjct: 140 MDAETWLTAQEAVELGFADEI 160 >gnl|CDD|30961 COG0616, SppA, Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]. Length = 317 Score = 46.6 bits (110), Expect = 6e-06 Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 4/98 (4%) Query: 40 LKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFI 99 ++ IV G + I L A+ K + L INSPGG V A I ++ + Sbjct: 66 VEGAIVAGGGPLRFIGGDDIEEILRAARADPSVKAVVLRINSPGGSVVASELIARALKRL 125 Query: 100 --KPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARI 135 K P+ G AAS G + A +K A P++ Sbjct: 126 RAKKPVVVSVGGYAASGGYYIALAADK--IVADPSSIT 161 >gnl|CDD|132934 cd07023, S49_Sppa_N_C, Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain. Length = 208 Score = 40.5 bits (96), Expect = 3e-04 Identities = 45/196 (22%), Positives = 80/196 (40%), Gaps = 37/196 (18%) Query: 44 IVFVTGQIED---HMATLICAQLLFLEAENPQ-KEISLYINSPGGVVTAGMAIYDTMQFI 99 ++ + G I D A + QL E+ K + L INSPGG V A IY ++ + Sbjct: 4 VIDIEGTISDGGGIGADSLIEQLRKA-REDDSVKAVVLRINSPGGSVVASEEIYREIRRL 62 Query: 100 K---PPISTFCMGQAASMGSLLLSAGEK------------GMRFALPNARILLHQP---- 140 + P+ AAS G + +A +K G+ PN LL + Sbjct: 63 RKAKKPVVASMGDVAASGGYYIAAAADKIVANPTTITGSIGVIGQGPNLEELLDKLGIER 122 Query: 141 ----SGGFSGQAS-DIERHAQDIVKIKRRLNEIY-------VKNCGKTYEEVEKTLDRDH 188 SG + S D ++ ++ +++IY + G + E ++K L Sbjct: 123 DTIKSGPGKDKGSPDRPLTEEERAILQALVDDIYDQFVDVVAEGRGMSGERLDK-LADGR 181 Query: 189 IMSASEACDWGVVDKV 204 + + +A + G+VD++ Sbjct: 182 VWTGRQALELGLVDEL 197 >gnl|CDD|132932 cd07021, Clp_protease_NfeD_like, Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control. Length = 178 Score = 35.3 bits (82), Expect = 0.012 Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%) Query: 44 IVFVTGQIEDHMATLICAQLLFLEA-ENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPP 102 ++ + G+I+ +A + L EA E + L I++PGG V + + I D + P Sbjct: 3 VIPIEGEIDPGLAAFVERALK--EAKEEGADAVVLDIDTPGGRVDSALEIVDLILNSPIP 60 Query: 103 ISTFCMGQAASMGSLL-LSAGEKGMRFALPNARI 135 + +AAS G+L+ L+A E M P A I Sbjct: 61 TIAYVNDRAASAGALIALAADEIYMA---PGATI 91 >gnl|CDD|31233 COG1030, NfeD, Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]. Length = 436 Score = 34.9 bits (80), Expect = 0.018 Identities = 36/172 (20%), Positives = 69/172 (40%), Gaps = 13/172 (7%) Query: 44 IVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPI 103 ++ + G I+ A + L E EN + L +++PGG++ + I + P+ Sbjct: 30 VIEIDGAIDPASADYLQRALQSAEEENAAA-VVLELDTPGGLLDSMRQIVRAILNSPVPV 88 Query: 104 STFCM---GQAASMGS-LLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERHAQDIV 159 + + +AAS G+ +L++ M P I P G G ++ V Sbjct: 89 IGYVVPDGARAASAGTYILMATHIAAMA---PGTNIGAATPIAG-GGTSAKEANTTNAAV 144 Query: 160 KIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMSRIDI 211 R L E G+ E+ + + ++A EA GV+D + ++ Sbjct: 145 AYIRSLAEER----GRNPTWAERFVTENLSLTAEEALRQGVIDLIARDLNEL 192 >gnl|CDD|132926 cd07015, Clp_protease_NfeD, Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control. Length = 172 Score = 34.7 bits (79), Expect = 0.019 Identities = 41/176 (23%), Positives = 71/176 (40%), Gaps = 17/176 (9%) Query: 47 VTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPISTF 106 + GQI + + E +N + I + +++PGG A I +Q K P+ + Sbjct: 6 IKGQITSYTYDQFDRYITIAEQDNAE-AIIIELDTPGGRADAAGNIVQRIQQSKIPVIIY 64 Query: 107 CM---GQAASMGSLL-LSAGEKGMRFALPNARILLHQPSGGFSGQASDIE--RHAQD--I 158 AAS G+ + L + M P I +P G+S S IE + I Sbjct: 65 VYPPGASAASAGTYIALGSHLIAMA---PGTSIGACRPILGYSQNGSIIEAPPKITNYFI 121 Query: 159 VKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMSRIDIEEK 214 IK E G+ E+ + +D ++ EA +GV++ V ++ +K Sbjct: 122 AYIKSLAQE-----SGRNATIAEEFITKDLSLTPEEALKYGVIEVVARDINELLKK 172 >gnl|CDD|132930 cd07019, S49_SppA_1, Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppAs in this subfamily are found in all three domains of life and are involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain, similar to Arabidopsis thaliana SppA1 peptidase. Others, including sohB peptidase, protein C and archaeal signal peptide peptidase, do not contain the amino-terminal domain. Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain. Length = 211 Score = 30.0 bits (67), Expect = 0.51 Identities = 25/89 (28%), Positives = 32/89 (35%), Gaps = 17/89 (19%) Query: 44 IVFVTGQIEDHMAT-------LICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTM 96 +VF G I D T AQ+ + K I L +NSPGG VTA I + Sbjct: 4 VVFANGAIVDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAEL 63 Query: 97 QFIKP---PISTFCMGQAASMGSLLLSAG 122 + P+ S G S G Sbjct: 64 AAARAAGKPV-------VVSAGGAAASGG 85 >gnl|CDD|132933 cd07022, S49_Sppa_36K_type, Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. Length = 214 Score = 29.8 bits (68), Expect = 0.63 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 8/54 (14%) Query: 73 KEISLYINSPGGVVTAGMAIYDTMQFI-----KPPISTFCMGQAASMGSLLLSA 121 + I L I+SPGG V +++ I PI F G AAS + SA Sbjct: 44 RAIVLDIDSPGGEVA---GVFELADAIRAARAGKPIVAFVNGLAASAAYWIASA 94 >gnl|CDD|132931 cd07020, Clp_protease_NfeD_1, Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control. Length = 187 Score = 29.1 bits (66), Expect = 1.1 Identities = 40/177 (22%), Positives = 69/177 (38%), Gaps = 21/177 (11%) Query: 47 VTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPISTF 106 + G I A + + E I + +++PGG++ + I + P+ + Sbjct: 6 INGAITPATADYLERAIDQAEEGGADALI-IELDTPGGLLDSTREIVQAILASPVPVVVY 64 Query: 107 CM---GQAASMGSL-LLSAGEKGMRFALPNARILLHQP-SGGFSGQASDIERHA--QDIV 159 +AAS G+ LL+A M P I P + G G + + D V Sbjct: 65 VYPSGARAASAGTYILLAAHIAAMA---PGTNIGAAHPVAIGGGGGSDPVMEKKILNDAV 121 Query: 160 KIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV------LMSRID 210 R L E+ G+ E EK + ++A EA GV+D + L+ ++D Sbjct: 122 AYIRSLAELR----GRNAEWAEKAVRESLSLTAEEALKLGVIDLIAADLNELLKKLD 174 >gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit [Transcription]. Length = 1386 Score = 28.0 bits (62), Expect = 2.2 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 2/62 (3%) Query: 20 PMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYI 79 P V+ + G D+ +L + I+ I+ H++ L+ + + Q +++LYI Sbjct: 262 PSVMSEDKAGTNEDDLTMKLTE--IILTNDVIKKHLSKGTPINLIMEDWDFLQLQVALYI 319 Query: 80 NS 81 NS Sbjct: 320 NS 321 >gnl|CDD|153357 cd07673, F-BAR_FCHO2, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only 2 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. The specific function of FCH domain Only 2 (FCHO2) is still unknown. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCHO1 and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. Length = 269 Score = 27.7 bits (61), Expect = 2.4 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%) Query: 150 DIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDH-IMSASEA 195 ++ R Q+++K ++ E VK+ KT EEV TL+ I S ++A Sbjct: 85 ELVRKLQELIKEVQKYGEEQVKSHKKTKEEVAGTLEAVQNIQSITQA 131 >gnl|CDD|36327 KOG1111, KOG1111, KOG1111, N-acetylglucosaminyltransferase complex, subunit PIG-A/SPT14, required for phosphatidylinositol biosynthesis/Sulfolipid synthase [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones, Lipid transport and metabolism]. Length = 426 Score = 27.6 bits (61), Expect = 2.8 Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 15/98 (15%) Query: 98 FIKPPIS-TFCMG--QAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERH 154 F+ ++ FCM +AAS G ++S G+ LP I L +P D+ Sbjct: 275 FLNTSLTEAFCMVIVEAASCGLPVVSTRVGGIPEVLPEDMITLGEPG------PDDLVGA 328 Query: 155 AQDIVKIKRRLNEIYVKNCGKTY------EEVEKTLDR 186 + + R L + K Y E EK DR Sbjct: 329 VEKAITKLRTLPLEFHDRVKKMYSWKDVAERTEKVYDR 366 >gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]. Length = 604 Score = 26.0 bits (57), Expect = 7.9 Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%) Query: 116 SLLLSAGEKGMRFALPNARILLHQP 140 +LS GE+ R A AR+LLH+P Sbjct: 513 DRVLSGGEQ-QRLAF--ARLLLHKP 534 >gnl|CDD|110924 pfam01972, SDH_sah, Serine dehydrogenase proteinase. This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan. Length = 286 Score = 26.0 bits (57), Expect = 8.5 Identities = 14/52 (26%), Positives = 24/52 (46%) Query: 73 KEISLYINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEK 124 I L I++PGG+ A I ++ K + A S G+L+ A ++ Sbjct: 92 MPIDLIIHTPGGLALAATQIAKALKEHKAKTTVIVPHYAMSGGTLIALAADE 143 >gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).. Length = 166 Score = 25.9 bits (57), Expect = 8.7 Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 3/23 (13%) Query: 119 LSAGEKGMRFALPNARILLHQPS 141 LS GE+ R A AR+LLH+P Sbjct: 92 LSGGEQ-QRLAF--ARLLLHKPK 111 >gnl|CDD|37685 KOG2474, KOG2474, KOG2474, Zinc transporter and related ZIP domain-containing proteins [Inorganic ion transport and metabolism]. Length = 406 Score = 25.8 bits (56), Expect = 8.8 Identities = 8/37 (21%), Positives = 14/37 (37%) Query: 86 VTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAG 122 AG +Y + I P + AS+G++ Sbjct: 357 FAAGAMLYVVLDDIIPEAQRSDNSKLASLGTICGKWC 393 >gnl|CDD|37518 KOG2307, KOG2307, KOG2307, Low density lipoprotein receptor [Intracellular trafficking, secretion, and vesicular transport]. Length = 705 Score = 25.7 bits (56), Expect = 9.4 Identities = 9/29 (31%), Positives = 17/29 (58%) Query: 134 RILLHQPSGGFSGQASDIERHAQDIVKIK 162 ++LL PS A+ +ER A ++ ++K Sbjct: 151 KMLLSPPSKEQQDGATSLERIALELNQLK 179 >gnl|CDD|119339 cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.. Length = 195 Score = 25.6 bits (57), Expect = 9.6 Identities = 8/17 (47%), Positives = 13/17 (76%) Query: 189 IMSASEACDWGVVDKVL 205 +SA EA + G+VD+V+ Sbjct: 163 RISAEEALELGLVDEVV 179 >gnl|CDD|144097 pfam00378, ECH, Enoyl-CoA hydratase/isomerase family. This family contains a diverse set of enzymes including: Enoyl-CoA hydratase. Napthoate synthase. Carnitate racemase. 3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA delta-isomerase. Length = 169 Score = 25.7 bits (57), Expect = 9.7 Identities = 8/16 (50%), Positives = 11/16 (68%) Query: 190 MSASEACDWGVVDKVL 205 + A EA G+VDKV+ Sbjct: 153 IRAQEALKMGLVDKVV 168 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 0.319 0.135 0.387 Gapped Lambda K H 0.267 0.0623 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,543,184 Number of extensions: 128765 Number of successful extensions: 315 Number of sequences better than 10.0: 1 Number of HSP's gapped: 311 Number of HSP's successfully gapped: 28 Length of query: 216 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 126 Effective length of database: 4,318,927 Effective search space: 544184802 Effective search space used: 544184802 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.2 bits)