Citrus Sinensis ID: 041456

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90--
Protein Sequence
VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEYIF
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHcccccEEEEcccccHHHHHHHHHHHHHHccccccccEEEEEcccccccccHHHHHHHHccccccccEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHHHHHHcccEEEEEccEcHHHHHHHHHHHHHHHHHcccccEEEEEEEccccccccEEEEccHHHEcccHHHHHHHc
Coil and Loop (DISEMBL)
vipftsgtaweqpppdlasyLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLnstgttevgSFLCHALVFFQIssinaseyif
Flexible Loop (DISEMBL)
vipftsgtaweqpppdLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQissinaseyif
Low Complexity Region (SEG)
VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEYIF
Disordered region (IsUnstruct)
****************LASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINA*****
Disordered Region (DISOPRED)
VIPFTS*TAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEYIF
Disordered Region (DISEMBL)
VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEYIF
Disordered Region (DISPRO)
VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEYIF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEYIF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	92	2.2.26 [Sep-21-2011]
Q8LB10	305	ATP-dependent Clp proteas	yes	no	0.891	0.268	0.756	1e-29
Q8L770	330	ATP-dependent Clp proteas	no	no	0.597	0.166	0.618	1e-14
P74466	225	Putative ATP-dependent Cl	N/A	no	0.641	0.262	0.521	1e-12
Q9XJ35	387	ATP-dependent Clp proteas	no	no	0.608	0.144	0.559	2e-12
Q9L4P4	228	Putative ATP-dependent Cl	yes	no	0.489	0.197	0.490	4e-07
Q2JV68	200	ATP-dependent Clp proteas	no	no	0.565	0.26	0.461	4e-07
Q2JIP1	200	ATP-dependent Clp proteas	no	no	0.565	0.26	0.461	4e-07
B9DJL4	194	ATP-dependent Clp proteas	yes	no	0.619	0.293	0.438	5e-07
Q49VZ2	194	ATP-dependent Clp proteas	yes	no	0.619	0.293	0.438	6e-07
B9EAG5	194	ATP-dependent Clp proteas	yes	no	0.565	0.268	0.461	1e-06

>sp|Q8LB10|CLPR4_ARATH ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic OS=Arabidopsis thaliana GN=CLPR4 PE=1 SV=1

 Score =  127 bits (320), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 62/82 (75%), Positives = 68/82 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIPF+ G+A EQPPPDLASYL+KNRIVYLGMS VPSV ELILAEFLYLQYED EKPIYLY
Sbjct: 90  VIPFSKGSAHEQPPPDLASYLFKNRIVYLGMSLVPSVTELILAEFLYLQYEDEEKPIYLY 149

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 150 INSTGTTKNGEKLGYDTEAFAI 171

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L770|CLPR3_ARATH ATP-dependent Clp protease proteolytic subunit-related protein 3, chloroplastic OS=Arabidopsis thaliana GN=CLPR3 PE=1 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 34/55 (61%), Positives = 44/55 (80%)

Query: 13  PPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
           PPPDL S L   RIVY+GM  VP+V EL++AE +YLQ+ D ++PIY+Y+NSTGTT
Sbjct: 118 PPPDLPSMLLDGRIVYIGMPLVPAVTELVVAELMYLQWLDPKEPIYIYINSTGTT 172

Arabidopsis thaliana (taxid: 3702)

>sp|P74466|CLPR_SYNY3 Putative ATP-dependent Clp protease proteolytic subunit-like OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=clpR PE=3 SV=1

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 46/69 (66%), Gaps = 10/69 (14%)

Query: 9  AWEQPPPDLASYLYKNRIVYLGMSFVPS----------VRELILAEFLYLQYEDAEKPIY 58
          A++ PPPDL S L K RIVYLGM    S          V +LI+A+ LYLQ++D +KPIY
Sbjct: 15 AFKTPPPDLESLLLKERIVYLGMPLFSSDEVKQQVGIDVTQLIIAQLLYLQFDDPDKPIY 74

Query: 59 LYLNSTGTT 67
           Y+NSTGT+
Sbjct: 75 FYINSTGTS 83

Has lost the two conserved residues (Ser and His) proposed to be part of the active site. Therefore it could be inactive.

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q9XJ35|CLPR1_ARATH ATP-dependent Clp protease proteolytic subunit-related protein 1, chloroplastic OS=Arabidopsis thaliana GN=CLPR1 PE=1 SV=1

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/59 (55%), Positives = 43/59 (72%), Gaps = 3/59 (5%)

Query: 11  EQP---PPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGT 66
           E+P   PPDL S L   RI YLGM  VP+V EL++A+F++L Y++  KPIYLY+NS GT
Sbjct: 163 ERPRTAPPDLPSLLLDARICYLGMPIVPAVTELLVAQFMWLDYDNPTKPIYLYINSPGT 221

Required for chloroplast development and differentiation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9L4P4|CLPR_SYNE7 Putative ATP-dependent Clp protease proteolytic subunit-like OS=Synechococcus elongatus (strain PCC 7942) GN=clpR PE=3 SV=1

 Score = 53.5 bits (127), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 36/55 (65%), Gaps = 10/55 (18%)

Query: 23 KNRIVYLGMSFVPS----------VRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          K RI+YLGM    S          V ELI+A+ LYL++++ EKPIY Y+NSTGT+
Sbjct: 31 KERIIYLGMPLFSSDDVKRQVGFDVTELIIAQLLYLEFDNPEKPIYFYINSTGTS 85

Has lost the two conserved residues (Ser and His) proposed to be part of the active site. Therefore it could be inactive.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|Q2JV68|CLPP2_SYNJA ATP-dependent Clp protease proteolytic subunit 2 OS=Synechococcus sp. (strain JA-3-3Ab) GN=clpP2 PE=3 SV=1

 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 35/52 (67%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L ++RI++LG      +  LI+A+ LYL+ ED EK IYLY+NS G +
Sbjct: 17 DIYSRLLRDRIIFLGTQVDDDIANLIVAQMLYLESEDPEKDIYLYINSPGGS 68

Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.

Synechococcus sp. (strain JA-3-3Ab) (taxid: 321327)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 9

EC: 2

>sp|Q2JIP1|CLPP2_SYNJB ATP-dependent Clp protease proteolytic subunit 2 OS=Synechococcus sp. (strain JA-2-3B'a(2-13)) GN=clpP2 PE=3 SV=1

 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 35/52 (67%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L ++RI++LG      +  LI+A+ LYL+ ED EK IYLY+NS G +
Sbjct: 17 DIYSRLLRDRIIFLGTQVDDDIANLIVAQMLYLESEDPEKDIYLYINSPGGS 68

Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.

Synechococcus sp. (strain JA-2-3B'a(2-13)) (taxid: 321332)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 9

EC: 2

>sp|B9DJL4|CLPP_STACT ATP-dependent Clp protease proteolytic subunit OS=Staphylococcus carnosus (strain TM300) GN=clpP PE=3 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 37/57 (64%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
          D+ S L K+RI+ LG +   +V   I+++ L+LQ +DAEK IYLY+NS G +    F
Sbjct: 19 DIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLQAQDAEKDIYLYINSPGGSVTAGF 75

Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.

Staphylococcus carnosus (strain TM300) (taxid: 396513)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 9

EC: 2

>sp|Q49VZ2|CLPP_STAS1 ATP-dependent Clp protease proteolytic subunit OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) GN=clpP PE=3 SV=1

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
          D+ S L K+RI+ LG     +V   I+++ L+LQ +DAEK IYLY+NS G +    F
Sbjct: 19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDAEKDIYLYINSPGGSVTAGF 75

Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.

Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) (taxid: 342451)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 9

EC: 2

>sp|B9EAG5|CLPP_MACCJ ATP-dependent Clp protease proteolytic subunit OS=Macrococcus caseolyticus (strain JCSC5402) GN=clpP PE=3 SV=1

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 36/52 (69%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L K+RI+ LG +   +V   I+++ L+LQ +DAEK IYLY+NS G +
Sbjct: 19 DIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLQAQDAEKDIYLYINSPGGS 70

Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.

Macrococcus caseolyticus (strain JCSC5402) (taxid: 458233)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 9

EC: 2

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	92
255580803	314	ATP-dependent Clp protease proteolytic s	0.923	0.270	0.741	2e-29
359807363	304	uncharacterized protein LOC100785827 [Gl	0.891	0.269	0.768	2e-29
224126447	310	predicted protein [Populus trichocarpa]	0.891	0.264	0.768	4e-29
356563393	304	PREDICTED: ATP-dependent Clp protease pr	0.891	0.269	0.768	4e-29
449459004	304	PREDICTED: ATP-dependent Clp protease pr	0.891	0.269	0.756	8e-29
115435898	298	Os01g0271400 [Oryza sativa Japonica Grou	0.891	0.275	0.731	4e-28
56783783	306	putative ATP-dependent Clp protease prot	0.891	0.267	0.731	5e-28
242052591	291	hypothetical protein SORBIDRAFT_03g01087	0.793	0.250	0.808	5e-28
297800408	305	hypothetical protein ARALYDRAFT_493172 [	0.891	0.268	0.756	5e-28
18414804	305	ATP-dependent Clp protease proteolytic s	0.891	0.268	0.756	6e-28

>gi|255580803|ref|XP_002531222.1| ATP-dependent Clp protease proteolytic subunit, putative [Ricinus communis] gi|223529182|gb|EEF31158.1| ATP-dependent Clp protease proteolytic subunit, putative [Ricinus communis]

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 63/85 (74%), Positives = 70/85 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIP+T G+AWEQPPPDLASYL+KNRIVYLGMS VPSV ELILAEFLYLQYED EKPIYLY
Sbjct: 99  VIPYTRGSAWEQPPPDLASYLFKNRIVYLGMSLVPSVTELILAEFLYLQYEDEEKPIYLY 158

Query: 61  LNSTGTTEVGSFLCHALVFFQISSI 85
           +NSTGTT+ G  L +    F I  +
Sbjct: 159 INSTGTTKGGEKLGYETEAFAIHDV 183

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359807363|ref|NP_001241125.1| uncharacterized protein LOC100785827 [Glycine max] gi|255635880|gb|ACU18287.1| unknown [Glycine max]

 Score =  132 bits (332), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 63/82 (76%), Positives = 68/82 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIPF  G+AWEQPPPDLASYLYKNRIVYLGMS VPSV ELILAEFLYLQYED +KPIYLY
Sbjct: 89  VIPFQRGSAWEQPPPDLASYLYKNRIVYLGMSLVPSVTELILAEFLYLQYEDDDKPIYLY 148

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 149 INSTGTTKGGEKLGYETEAFAI 170

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224126447|ref|XP_002329556.1| predicted protein [Populus trichocarpa] gi|118483146|gb|ABK93479.1| unknown [Populus trichocarpa] gi|222870265|gb|EEF07396.1| predicted protein [Populus trichocarpa]

 Score =  132 bits (331), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 63/82 (76%), Positives = 69/82 (84%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIP+T G+AWEQPPPDLASYL+KNRIVYLGMS VPSV ELILAEFLYLQYED EKPIYLY
Sbjct: 95  VIPYTRGSAWEQPPPDLASYLFKNRIVYLGMSLVPSVTELILAEFLYLQYEDEEKPIYLY 154

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 155 INSTGTTKGGEKLGYETEAFAI 176

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356563393|ref|XP_003549948.1| PREDICTED: ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic-like [Glycine max]

 Score =  131 bits (330), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 63/82 (76%), Positives = 68/82 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIPF  G+AWEQPPPDLASYLYKNRIVYLGMS VPSV ELILAEFLYLQYED +KPIYLY
Sbjct: 89  VIPFQRGSAWEQPPPDLASYLYKNRIVYLGMSLVPSVTELILAEFLYLQYEDDDKPIYLY 148

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 149 INSTGTTKGGEKLGYETEAFAI 170

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459004|ref|XP_004147236.1| PREDICTED: ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic-like [Cucumis sativus] gi|449510487|ref|XP_004163680.1| PREDICTED: ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic-like [Cucumis sativus]

 Score =  130 bits (328), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 62/82 (75%), Positives = 67/82 (81%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIPF  G+AWEQPPPDLASYLYKNRIVYLGMS VPSV ELILAEFLYLQYED  KPIYLY
Sbjct: 89  VIPFARGSAWEQPPPDLASYLYKNRIVYLGMSLVPSVTELILAEFLYLQYEDETKPIYLY 148

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F +
Sbjct: 149 VNSTGTTKGGEKLGYETEAFAV 170

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115435898|ref|NP_001042707.1| Os01g0271400 [Oryza sativa Japonica Group] gi|113532238|dbj|BAF04621.1| Os01g0271400 [Oryza sativa Japonica Group]

 Score =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 68/82 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           V+PF  GTAW+QPPPDLAS+LYKNRIVYLGM  VPSV EL+LAEFLYLQY+DAEKPIYLY
Sbjct: 83  VVPFLRGTAWQQPPPDLASFLYKNRIVYLGMCLVPSVTELMLAEFLYLQYDDAEKPIYLY 142

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 143 INSTGTTKNGEKLGYETEAFAI 164

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|56783783|dbj|BAD81195.1| putative ATP-dependent Clp protease proteolytic subunit [Oryza sativa Japonica Group] gi|125569868|gb|EAZ11383.1| hypothetical protein OsJ_01248 [Oryza sativa Japonica Group]

 Score =  128 bits (321), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 68/82 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           V+PF  GTAW+QPPPDLAS+LYKNRIVYLGM  VPSV EL+LAEFLYLQY+DAEKPIYLY
Sbjct: 83  VVPFLRGTAWQQPPPDLASFLYKNRIVYLGMCLVPSVTELMLAEFLYLQYDDAEKPIYLY 142

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 143 INSTGTTKNGEKLGYETEAFAI 164

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242052591|ref|XP_002455441.1| hypothetical protein SORBIDRAFT_03g010870 [Sorghum bicolor] gi|241927416|gb|EES00561.1| hypothetical protein SORBIDRAFT_03g010870 [Sorghum bicolor]

 Score =  128 bits (321), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 59/73 (80%), Positives = 65/73 (89%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           V+PF  GTAWEQPPPDLAS+LYKNRIVYLGM  VPSV EL+LAEFLYLQY+DAEKPIYLY
Sbjct: 76  VVPFLRGTAWEQPPPDLASFLYKNRIVYLGMCLVPSVTELMLAEFLYLQYDDAEKPIYLY 135

Query: 61  LNSTGTTEVGSFL 73
           +NSTGTT+ G  L
Sbjct: 136 INSTGTTKNGEKL 148

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297800408|ref|XP_002868088.1| hypothetical protein ARALYDRAFT_493172 [Arabidopsis lyrata subsp. lyrata] gi|297313924|gb|EFH44347.1| hypothetical protein ARALYDRAFT_493172 [Arabidopsis lyrata subsp. lyrata]

 Score =  128 bits (321), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 62/82 (75%), Positives = 68/82 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIPF+ G+A EQPPPDLASYL+KNRIVYLGMS VPSV ELILAEFLYLQYED EKPIYLY
Sbjct: 90  VIPFSKGSAHEQPPPDLASYLFKNRIVYLGMSLVPSVTELILAEFLYLQYEDEEKPIYLY 149

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 150 INSTGTTKNGEKLGYDTEAFAI 171

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18414804|ref|NP_567521.1| ATP-dependent Clp protease proteolytic subunit-related protein 4 [Arabidopsis thaliana] gi|75301253|sp|Q8LB10.1|CLPR4_ARATH RecName: Full=ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic; Short=ClpR4; Flags: Precursor gi|21593086|gb|AAM65035.1| ATP-dependent Clp protease proteolytic subunit ClpR4, putative [Arabidopsis thaliana] gi|26450085|dbj|BAC42162.1| putative ClpP protease complex subunit ClpR4 [Arabidopsis thaliana] gi|332658442|gb|AEE83842.1| ATP-dependent Clp protease proteolytic subunit-related protein 4 [Arabidopsis thaliana]

 Score =  127 bits (320), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 62/82 (75%), Positives = 68/82 (82%)

Query: 1   VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
           VIPF+ G+A EQPPPDLASYL+KNRIVYLGMS VPSV ELILAEFLYLQYED EKPIYLY
Sbjct: 90  VIPFSKGSAHEQPPPDLASYLFKNRIVYLGMSLVPSVTELILAEFLYLQYEDEEKPIYLY 149

Query: 61  LNSTGTTEVGSFLCHALVFFQI 82
           +NSTGTT+ G  L +    F I
Sbjct: 150 INSTGTTKNGEKLGYDTEAFAI 171

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	92
TAIR|locus:2130449	305	CLPR4 "CLP protease R subunit	0.923	0.278	0.729	1e-27
TAIR|locus:2031070	387	CLPR1 "CLP protease proteolyti	0.652	0.155	0.539	7.1e-12
GENEDB_PFALCIPARUM|PF14_0348	244	PF14_0348 "ATP-dependent Clp p	0.826	0.311	0.342	7.2e-08
UNIPROTKB|Q8IL98	244	PF14_0348 "ATP-dependent Clp p	0.826	0.311	0.342	7.2e-08
TIGR_CMR|BA_2788	193	BA_2788 "ATP-dependent Clp pro	0.619	0.295	0.421	3e-07
UNIPROTKB|P63786	195	clpP "ATP-dependent Clp protea	0.619	0.292	0.421	3.2e-07
TIGR_CMR|GSU_1792	199	GSU_1792 "ATP-dependent Clp pr	0.543	0.251	0.44	1.8e-06
TIGR_CMR|BA_5380	193	BA_5380 "ATP-dependent Clp pro	0.760	0.362	0.342	4.8e-06
TIGR_CMR|CHY_0325	195	CHY_0325 "ATP-dependent Clp pr	0.543	0.256	0.42	5e-06
TIGR_CMR|DET_0710	200	DET_0710 "ATP-dependent Clp pr	0.543	0.25	0.42	9.4e-06

TAIR|locus:2130449 CLPR4 "CLP protease R subunit 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 62/85 (72%), Positives = 69/85 (81%)

Query:     1 VIPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLY 60
             VIPF+ G+A EQPPPDLASYL+KNRIVYLGMS VPSV ELILAEFLYLQYED EKPIYLY
Sbjct:    90 VIPFSKGSAHEQPPPDLASYLFKNRIVYLGMSLVPSVTELILAEFLYLQYEDEEKPIYLY 149

Query:    61 LNSTGTTEVGSFLCHALVFFQISSI 85
             +NSTGTT+ G  L +    F I  +
Sbjct:   150 INSTGTTKNGEKLGYDTEAFAIYDV 174

GO:0004252 "serine-type endopeptidase activity" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009532 "plastid stroma" evidence=IDA

GO:0000302 "response to reactive oxygen species" evidence=IMP

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0031347 "regulation of defense response" evidence=RCA

GO:0032880 "regulation of protein localization" evidence=RCA

GO:0009536 "plastid" evidence=IDA

TAIR|locus:2031070 CLPR1 "CLP protease proteolytic subunit 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 7.1e-12, P = 7.1e-12
 Identities = 34/63 (53%), Positives = 44/63 (69%)

Query:     7 GTAWEQP---PPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNS 63
             G   E+P   PPDL S L   RI YLGM  VP+V EL++A+F++L Y++  KPIYLY+NS
Sbjct:   159 GGGSERPRTAPPDLPSLLLDARICYLGMPIVPAVTELLVAQFMWLDYDNPTKPIYLYINS 218

Query:    64 TGT 66
              GT
Sbjct:   219 PGT 221

GO:0004252 "serine-type endopeptidase activity" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009840 "chloroplastic endopeptidase Clp complex" evidence=IDA

GO:0009532 "plastid stroma" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GENEDB_PFALCIPARUM|PF14_0348 PF14_0348 "ATP-dependent Clp protease proteolytic subunit, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 126 (49.4 bits), Expect = 7.2e-08, P = 7.2e-08
 Identities = 26/76 (34%), Positives = 42/76 (55%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCH 75
             ++ S L   RI++L     P + E I+++ LYL+YE   KPI+LY+NSTG  +    +  
Sbjct:    59 NIPSLLLSKRIIFLSSPIYPHISEQIISQLLYLEYESKRKPIHLYINSTGDIDNNKIINL 118

Query:    76 ALVFFQISSINASEYI 91
               +   IS ++   YI
Sbjct:   119 NGITDVISIVDVINYI 134

GO:0020011 "apicoplast" evidence=ISS

UNIPROTKB|Q8IL98 PF14_0348 "ATP-dependent Clp protease proteolytic subunit" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 126 (49.4 bits), Expect = 7.2e-08, P = 7.2e-08
 Identities = 26/76 (34%), Positives = 42/76 (55%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCH 75
             ++ S L   RI++L     P + E I+++ LYL+YE   KPI+LY+NSTG  +    +  
Sbjct:    59 NIPSLLLSKRIIFLSSPIYPHISEQIISQLLYLEYESKRKPIHLYINSTGDIDNNKIINL 118

Query:    76 ALVFFQISSINASEYI 91
               +   IS ++   YI
Sbjct:   119 NGITDVISIVDVINYI 134

GO:0020011 "apicoplast" evidence=ISS

TIGR_CMR|BA_2788 BA_2788 "ATP-dependent Clp protease, proteolytic subunit ClpP" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 117 (46.2 bits), Expect = 3.0e-07, P = 3.0e-07
 Identities = 24/57 (42%), Positives = 35/57 (61%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
             D+ S L K+RIV +G      V   ++A+ L+L+ EDAEK I+LY+NS G +    F
Sbjct:    19 DIYSRLLKDRIVIIGSEINDQVASSVVAQLLFLEAEDAEKDIFLYINSPGGSTTAGF 75

GO:0006508 "proteolysis" evidence=ISS

GO:0009368 "endopeptidase Clp complex" evidence=ISS

UNIPROTKB|P63786 clpP "ATP-dependent Clp protease proteolytic subunit" [Staphylococcus aureus subsp. aureus MW2 (taxid:196620)]

 Score = 117 (46.2 bits), Expect = 3.2e-07, P = 3.2e-07
 Identities = 24/57 (42%), Positives = 36/57 (63%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
             D+ S L K+RI+ LG     +V   I+++ L+LQ +D+EK IYLY+NS G +    F
Sbjct:    19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGF 75

GO:0042802 "identical protein binding" evidence=IPI

TIGR_CMR|GSU_1792 GSU_1792 "ATP-dependent Clp protease, proteolytic subunit ClpP" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 111 (44.1 bits), Expect = 1.8e-06, P = 1.8e-06
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
             D+ S L K+RI++LG      V  L++A+ L+L+ ED +K I+LY+NS G
Sbjct:    18 DIYSRLLKDRIIFLGGPVDDHVANLVIAQMLFLEAEDPDKDIHLYINSPG 67

GO:0009368 "endopeptidase Clp complex" evidence=ISS

TIGR_CMR|BA_5380 BA_5380 "ATP-dependent Clp protease, proteolytic subunit ClpP" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 107 (42.7 bits), Expect = 4.8e-06, P = 4.8e-06
 Identities = 25/73 (34%), Positives = 44/73 (60%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG-TTEVGSFLC 74
             D+ S L K+RI+ LG +   +V   I+++ L+L+ +D EK I++Y+NS G +   G  + 
Sbjct:    19 DIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLESQDPEKDIHIYINSPGGSITAGMAIY 78

Query:    75 HALVFF--QISSI 85
               + F   Q+S+I
Sbjct:    79 DTMQFIKPQVSTI 91

GO:0006508 "proteolysis" evidence=ISS

GO:0009368 "endopeptidase Clp complex" evidence=ISS

TIGR_CMR|CHY_0325 CHY_0325 "ATP-dependent Clp protease, proteolytic subunit ClpP" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 107 (42.7 bits), Expect = 5.0e-06, P = 5.0e-06
 Identities = 21/50 (42%), Positives = 33/50 (66%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
             D+ S L K+R +++G      V  L++A+ L+L+ ED EK I+LY+NS G
Sbjct:    20 DIWSRLLKDRTIFIGGPIDDHVANLVIAQMLFLEAEDPEKDIHLYINSPG 69

GO:0009368 "endopeptidase Clp complex" evidence=ISS

TIGR_CMR|DET_0710 DET_0710 "ATP-dependent Clp protease, proteolytic subunit ClpP" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 105 (42.0 bits), Expect = 9.4e-06, P = 9.4e-06
 Identities = 21/50 (42%), Positives = 31/50 (62%)

Query:    16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
             D+ S L K RI++LG      V  L++A+ L+L  ED +K I LY++S G
Sbjct:    23 DIYSLLLKERIIFLGSQINDQVANLVIAQLLFLDREDPDKDISLYIHSPG 72

GO:0009368 "endopeptidase Clp complex" evidence=ISS

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8LB10	CLPR4_ARATH	No assigned EC number	0.7560	0.8913	0.2688	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	92
PRK12552	222	PRK12552, PRK12552, ATP-dependent Clp protease-lik	4e-23
cd07017	171	cd07017, S14_ClpP_2, Caseinolytic protease (ClpP)	5e-18
COG0740	200	COG0740, ClpP, Protease subunit of ATP-dependent C	2e-10
TIGR00493	192	TIGR00493, clpP, ATP-dependent Clp endopeptidase,	7e-10
PRK12551	196	PRK12551, PRK12551, ATP-dependent Clp protease pro	1e-08
pfam00574	182	pfam00574, CLP_protease, Clp protease	1e-08
PRK00277	200	PRK00277, clpP, ATP-dependent Clp protease proteol	2e-08
PRK12553	207	PRK12553, PRK12553, ATP-dependent Clp protease pro	2e-06
CHL00028	200	CHL00028, clpP, ATP-dependent Clp protease proteol	1e-05
PRK14513	201	PRK14513, PRK14513, ATP-dependent Clp protease pro	7e-04
PRK14514	221	PRK14514, PRK14514, ATP-dependent Clp protease pro	0.001

>gnl|CDD|183588 PRK12552, PRK12552, ATP-dependent Clp protease-like protein; Reviewed

 Score = 87.9 bits (218), Expect = 4e-23
 Identities = 35/75 (46%), Positives = 44/75 (58%), Gaps = 10/75 (13%)

Query: 3  PFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPS----------VRELILAEFLYLQYED 52
          P+        PPPDL S L K RIVYLG+               V ELI+A+ LYL+++D
Sbjct: 9  PYYGDAVMRTPPPDLPSLLLKERIVYLGLPLFSDDDAKRQVGMDVTELIIAQLLYLEFDD 68

Query: 53 AEKPIYLYLNSTGTT 67
           EKPIY Y+NSTGT+
Sbjct: 69 PEKPIYFYINSTGTS 83

Length = 222

>gnl|CDD|132928 cd07017, S14_ClpP_2, Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease

 Score = 73.2 bits (181), Expect = 5e-18
 Identities = 26/51 (50%), Positives = 34/51 (66%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGT 66
          D+ S L K RI++LG      V  LI+A+ LYL+ ED +KPIYLY+NS G 
Sbjct: 1  DIYSRLLKERIIFLGGPIDDEVANLIIAQLLYLESEDPKKPIYLYINSPGG 51

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

>gnl|CDD|223811 COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 12 QPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          +   D+ S L K RI++LG      +  LI+A+ L+L+ ED +K IYLY+NS G
Sbjct: 15 ERSYDIYSRLLKERIIFLGGEIEDHMANLIVAQLLFLEAEDPDKDIYLYINSPG 68

Length = 200

>gnl|CDD|188055 TIGR00493, clpP, ATP-dependent Clp endopeptidase, proteolytic subunit ClpP

 Score = 52.5 bits (126), Expect = 7e-10
 Identities = 23/50 (46%), Positives = 32/50 (64%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K RI++L      +V   I+A+ L+L+ ED EK IYLY+NS G
Sbjct: 19 DIYSRLLKERIIFLSGEVNDNVANSIVAQLLFLEAEDPEKDIYLYINSPG 68

This model for the proteolytic subunit ClpP has been rebuilt to a higher stringency. In every bacterial genome with the ClpXP machine, a ClpP protein will be found that scores at least 370 by This model. In general, this ClpP member will be encoded adjacent to the clpX gene, as were all examples used in the seed alignment. A large fraction of genomes have one or more additional ClpP paralogs, sometimes encoded nearby and sometimes elsewhere. The stringency of the trusted cutoff used here excludes the more divergent ClpP paralogs from being called authentic ClpP by this model [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 192

>gnl|CDD|139060 PRK12551, PRK12551, ATP-dependent Clp protease proteolytic subunit; Reviewed

 Score = 49.4 bits (118), Expect = 1e-08
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L + RI++LG          I+A+ L+L+ ED EK IYLY+NS G
Sbjct: 17 DIYSRLLRERIIFLGEPVTSDSANRIVAQLLFLEAEDPEKDIYLYINSPG 66

Length = 196

>gnl|CDD|201316 pfam00574, CLP_protease, Clp protease

 Score = 48.7 bits (117), Expect = 1e-08
 Identities = 24/50 (48%), Positives = 33/50 (66%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K RI++LG      V  LI+A+ L+L+ ED +K IYLY+NS G
Sbjct: 8  DIYSRLLKERIIFLGGEIDDEVANLIIAQLLFLEAEDPDKDIYLYINSPG 57

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. Cyanophora parodoxa clpP-B has lost all of these active site residues and is therefore inactive. Some members contain one or two large insertions. Length = 182

>gnl|CDD|178955 PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed

 Score = 48.6 bits (117), Expect = 2e-08
 Identities = 23/50 (46%), Positives = 33/50 (66%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K RI++LG      +  LI+A+ L+L+ ED +K IYLY+NS G
Sbjct: 23 DIYSRLLKERIIFLGGEVEDHMANLIVAQLLFLEAEDPDKDIYLYINSPG 72

Length = 200

>gnl|CDD|237133 PRK12553, PRK12553, ATP-dependent Clp protease proteolytic subunit; Reviewed

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 1  VIP-FTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYL 59
          ++P F   T++     D  + L++ RI++LG     +    ++A+ L L+  D ++ I L
Sbjct: 11 ILPSFIERTSYGVKESDPYNKLFEERIIFLGGQVDDASANDVMAQLLVLESIDPDRDITL 70

Query: 60 YLNSTGTTEVGSF 72
          Y+NS G    GS 
Sbjct: 71 YINSPG----GSV 79

Length = 207

>gnl|CDD|214340 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit

 Score = 41.4 bits (98), Expect = 1e-05
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLC 74
          DL + LY+ R+++LG      +   ++   +YL  ED  K +YL++NS G    GS + 
Sbjct: 22 DLYNRLYRERLLFLGQEVDDEIANQLIGLMVYLSIEDDTKDLYLFINSPG----GSVIS 76

Length = 200

>gnl|CDD|237742 PRK14513, PRK14513, ATP-dependent Clp protease proteolytic subunit; Provisional

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 16/50 (32%), Positives = 29/50 (58%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K+RI+++G      +   I+A+ L L  ++ E+ I +Y+N  G
Sbjct: 19 DIYSRLLKDRIIFVGTPIESQMANTIVAQLLLLDSQNPEQEIQMYINCPG 68

Length = 201

>gnl|CDD|184722 PRK14514, PRK14514, ATP-dependent Clp protease proteolytic subunit; Provisional

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 19/52 (36%), Positives = 27/52 (51%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L  +RI++LG          I A+ LYL   D  K I +Y+NS G +
Sbjct: 46 DVFSRLMMDRIIFLGTQIDDYTANTIQAQLLYLDSVDPGKDISIYINSPGGS 97

Length = 221

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	92
KOG0840	275	consensus ATP-dependent Clp protease, proteolytic	100.0
COG0740	200	ClpP Protease subunit of ATP-dependent Clp proteas	99.97
PRK14513	201	ATP-dependent Clp protease proteolytic subunit; Pr	99.97
PRK14514	221	ATP-dependent Clp protease proteolytic subunit; Pr	99.97
PRK12552	222	ATP-dependent Clp protease-like protein; Reviewed	99.97
CHL00028	200	clpP ATP-dependent Clp protease proteolytic subuni	99.96
PRK12551	196	ATP-dependent Clp protease proteolytic subunit; Re	99.96
TIGR00493	191	clpP ATP-dependent Clp protease, proteolytic subun	99.93
PRK00277	200	clpP ATP-dependent Clp protease proteolytic subuni	99.92
PRK12553	207	ATP-dependent Clp protease proteolytic subunit; Re	99.9
PRK14512	197	ATP-dependent Clp protease proteolytic subunit; Pr	99.9
PF00574	182	CLP_protease: Clp protease; InterPro: IPR001907 In	99.9
cd07017	171	S14_ClpP_2 Caseinolytic protease (ClpP) is an ATP-	99.85
cd07013	162	S14_ClpP Caseinolytic protease (ClpP) is an ATP-de	99.78
cd07016	160	S14_ClpP_1 Caseinolytic protease (ClpP) is an ATP-	99.39
cd07020	187	Clp_protease_NfeD_1 Nodulation formation efficienc	99.09
cd07015	172	Clp_protease_NfeD Nodulation formation efficiency	99.08
cd00394	161	Clp_protease_like Caseinolytic protease (ClpP) is	99.05
cd07021	178	Clp_protease_NfeD_like Nodulation formation effici	98.46
cd07023	208	S49_Sppa_N_C Signal peptide peptidase A (SppA), a	98.01
COG0616	317	SppA Periplasmic serine proteases (ClpP class) [Po	97.71
TIGR00706	207	SppA_dom signal peptide peptidase SppA, 36K type.	97.53
TIGR00705	584	SppA_67K signal peptide peptidase SppA, 67K type.	97.29
PF01972	285	SDH_sah: Serine dehydrogenase proteinase; InterPro	96.94
cd07022	214	S49_Sppa_36K_type Signal peptide peptidase A (SppA	96.68
cd07019	211	S49_SppA_1 Signal peptide peptidase A (SppA), a se	96.55
PRK10949	618	protease 4; Provisional	96.3
PRK11778	330	putative inner membrane peptidase; Provisional	96.09
cd07014	177	S49_SppA Signal peptide peptidase A. Signal peptid	95.93
COG1030	436	NfeD Membrane-bound serine protease (ClpP class) [	95.77
cd07018	222	S49_SppA_67K_type Signal peptide peptidase A (SppA	94.75

>KOG0840 consensus ATP-dependent Clp protease, proteolytic subunit [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.5e-35  Score=222.66  Aligned_cols=82  Identities=32%  Similarity=0.524  Sum_probs=79.2

Q ss_pred             CCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhccccccee
Q 041456            9 AWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINAS   88 (92)
Q Consensus         9 ~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~   88 (92)
                      .+.++|.|++++|||+|||||+++|||++|+.+++|||||+++|++|||++|||||||++++|+||||||+|+++||.|+
T Consensus        77 rG~~~~~Di~s~LlreRIi~lg~~Idd~va~~viaqlL~Ld~ed~~K~I~lyINSPGG~vtaglAIYDtMq~ik~~V~Ti  156 (275)
T KOG0840|consen   77 RGRERPYDIYSRLLRERIVFLGQPIDDDVANLVIAQLLYLDSEDPKKPIYLYINSPGGSVTAGLAIYDTMQYIKPDVSTI  156 (275)
T ss_pred             cCCCCcccHHHHHHHhheeeeCCcCcHHHHHHHHHHHHHhhccCCCCCeEEEEeCCCCccchhhhHHHHHHhhCCCceee
Confidence            33489999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ee
Q 041456           89 EY   90 (92)
Q Consensus        89 ~~   90 (92)
                      |-
T Consensus       157 c~  158 (275)
T KOG0840|consen  157 CV  158 (275)
T ss_pred             eh
Confidence            94

>COG0740 ClpP Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=99.97  E-value=6.3e-31  Score=193.38  Aligned_cols=88  Identities=30%  Similarity=0.486  Sum_probs=83.2

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|.. +.++.+.++.|+|++|+++|+|||+|+|++.+++.+++||++|++++|+|||+||||||||+|+||++|||+|++
T Consensus         4 ~~~~~e~~~~~~~~~di~s~llk~riI~l~g~I~~~~a~~i~aqll~Lea~~~~k~I~lyINSpGG~V~aG~AIydtm~~   83 (200)
T COG0740           4 VPMVIEQTSRGERSYDIYSRLLKERIIFLGGEIEDHMANLIVAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYDTMQF   83 (200)
T ss_pred             CccccCcccCCCChhhHHHHhhhccEEEEeeeechHHHHHHHHHHHHHHhcCCCCCeEEEEeCCCcccchhHHHHHHHHh
Confidence            4555 555677888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceee
Q 041456           81 QISSINASE   89 (92)
Q Consensus        81 v~~~v~t~~   89 (92)
                      +++||.|+|
T Consensus        84 ik~~V~ti~   92 (200)
T COG0740          84 IKPPVSTIC   92 (200)
T ss_pred             cCCCeEEEE
Confidence            999999998

>PRK14513 ATP-dependent Clp protease proteolytic subunit; Provisional

Probab=99.97  E-value=1.6e-30  Score=190.92  Aligned_cols=89  Identities=21%  Similarity=0.370  Sum_probs=83.4

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|.. +.++.++.|.|++++||++|++||+++|++++|++++++|+||+++++++||++|||||||++++|++|||+|++
T Consensus         4 ~p~~~~~~~~~~~~~d~~~~l~~~Riifl~~~i~~~~a~~ii~~Ll~L~~~~~~~~I~l~INSpGG~v~~GlaIyd~m~~   83 (201)
T PRK14513          4 IPYVIEQTGRGERMYDIYSRLLKDRIIFVGTPIESQMANTIVAQLLLLDSQNPEQEIQMYINCPGGEVYAGLAIYDTMRY   83 (201)
T ss_pred             CCcccccCCCCccccCHHHHHhhCCEEEECCEEcHHHHHHHHHHHHHhhccCCCCCEEEEEECCCCchhhHHHHHHHHHh
Confidence            4654 556667789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceeee
Q 041456           81 QISSINASEY   90 (92)
Q Consensus        81 v~~~v~t~~~   90 (92)
                      ++++|.|+|.
T Consensus        84 ~~~~V~Ti~~   93 (201)
T PRK14513         84 IKAPVSTICV   93 (201)
T ss_pred             cCCCEEEEEE
Confidence            9999999985

>PRK14514 ATP-dependent Clp protease proteolytic subunit; Provisional

Probab=99.97  E-value=1.4e-30  Score=193.52  Aligned_cols=89  Identities=25%  Similarity=0.315  Sum_probs=83.5

Q ss_pred             ccc-ccCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPF-TSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~-~~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|. ++++..+++|.|++++||++|+|||+++||+++|+++++||+||+++++++||++|||||||++++|++|||+|++
T Consensus        31 ~p~~~~~~~~~~~~~d~~~~ll~~Riifl~~~Idd~~a~~i~aqLl~L~~~~~~~~I~lyINSpGGsv~aGlaIyd~m~~  110 (221)
T PRK14514         31 NPYILEERQLNVTQMDVFSRLMMDRIIFLGTQIDDYTANTIQAQLLYLDSVDPGKDISIYINSPGGSVYAGLGIYDTMQF  110 (221)
T ss_pred             cceeeeeCCCCCcccCHHHHHhhCcEEEECCEEcHHHHHHHHHHHHHHhccCCCCCEEEEEECCCcchhhHHHHHHHHHh
Confidence            453 3566677899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceeee
Q 041456           81 QISSINASEY   90 (92)
Q Consensus        81 v~~~v~t~~~   90 (92)
                      +++||.|+|.
T Consensus       111 ~~~~V~tv~~  120 (221)
T PRK14514        111 ISSDVATICT  120 (221)
T ss_pred             cCCCEEEEEE
Confidence            9999999984

>PRK12552 ATP-dependent Clp protease-like protein; Reviewed

Probab=99.97  E-value=2.5e-30  Score=192.56  Aligned_cols=89  Identities=42%  Similarity=0.774  Sum_probs=84.7

Q ss_pred             cccccCCCCCCCCcchHHhhhcCceEEeCcccCHH----------HHHHHHHHHHHhhhcCCCCCeEEEEeCCCCc----
Q 041456            2 IPFTSGTAWEQPPPDLASYLYKNRIVYLGMSFVPS----------VRELILAEFLYLQYEDAEKPIYLYLNSTGTT----   67 (92)
Q Consensus         2 ~~~~~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~----------~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~----   67 (92)
                      +||......++.|.|++++||++|+|||+++|+++          +|+++++|||||+.+|+++||++|||||||+    
T Consensus         8 ~~~~~~~~~~~~~~d~~~~Ll~~Rii~l~~~i~~~~~~~~~~~~~~a~~iiaqLl~L~~~~~~k~I~lyINSpGGsv~~G   87 (222)
T PRK12552          8 APYYGDAVMRTPPPDLPSLLLKERIVYLGLPLFSDDDAKRQVGMDVTELIIAQLLYLEFDDPEKPIYFYINSTGTSWYTG   87 (222)
T ss_pred             ccccCCCCCCCCCcCHHHHHhhCCEEEECCeeccccccccchhHhHHHHHHHHHHHHhccCCCCCEEEEEeCCCCCcccc
Confidence            68887777888999999999999999999999999          9999999999999999999999999999988    


Q ss_pred             -----chhhhhHHHHHhhcccccceeee
Q 041456           68 -----EVGSFLCHALVFFQISSINASEY   90 (92)
Q Consensus        68 -----v~aglaIyD~m~~v~~~v~t~~~   90 (92)
                           +++|++|||+|++++++|.|+|.
T Consensus        88 ~~iG~v~~glaIyD~m~~ik~~V~Tv~~  115 (222)
T PRK12552         88 DAIGFETEAFAICDTMRYIKPPVHTICI  115 (222)
T ss_pred             ccccccccHHHHHHHHHhcCCCeEEEEE
Confidence                 67889999999999999999985

>CHL00028 clpP ATP-dependent Clp protease proteolytic subunit

Probab=99.96  E-value=5.6e-30  Score=187.45  Aligned_cols=84  Identities=21%  Similarity=0.389  Sum_probs=80.6

Q ss_pred             CCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccc
Q 041456            7 GTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSIN   86 (92)
Q Consensus         7 ~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~   86 (92)
                      .+..+.+|.|++++||++|+|||+++||+++++++++||+||+++|++++|++|||||||++++|++|||+|++++++|.
T Consensus        13 ~~~~~~~~~d~~~~l~~~Riifl~~~i~~~~a~~ii~~ll~L~~~~~~~~I~l~INSpGG~v~~g~aIyd~m~~~~~~V~   92 (200)
T CHL00028         13 PGEEDATWVDLYNRLYRERLLFLGQEVDDEIANQLIGLMVYLSIEDDTKDLYLFINSPGGSVISGLAIYDTMQFVKPDVH   92 (200)
T ss_pred             CCCCCcccccHHHHHhcCCEEEECCeecHHHHHHHHHHHHHHhccCCCCCEEEEEeCCCcchhhHHHHHHHHHhcCCCEE
Confidence            35667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeee
Q 041456           87 ASEY   90 (92)
Q Consensus        87 t~~~   90 (92)
                      |+|.
T Consensus        93 Tv~~   96 (200)
T CHL00028         93 TICL   96 (200)
T ss_pred             EEEE
Confidence            9985

>PRK12551 ATP-dependent Clp protease proteolytic subunit; Reviewed

Probab=99.96  E-value=8.6e-30  Score=186.10  Aligned_cols=89  Identities=27%  Similarity=0.423  Sum_probs=83.3

Q ss_pred             ccc-ccCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPF-TSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~-~~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|. ++.+..++.+.|++++||++|+|||+++||+++|++++++|+||+++++++||++|||||||++++|++|||+|++
T Consensus         2 ~p~~~~~~~~~~~~~d~~~~l~~~Riifl~~~i~~~~a~~ii~~Ll~l~~~~~~~~I~l~INSpGG~v~~g~aIyd~m~~   81 (196)
T PRK12551          2 IPIVIEESGRGERAFDIYSRLLRERIIFLGEPVTSDSANRIVAQLLFLEAEDPEKDIYLYINSPGGSVYDGLGIFDTMQH   81 (196)
T ss_pred             CCcccccCCCCccccCHHHHHhcCcEEEECCeecHHHHHHHHHHHHHhhccCCCCCEEEEEeCCCcchhhHHHHHHHHHh
Confidence            564 3556667788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceeee
Q 041456           81 QISSINASEY   90 (92)
Q Consensus        81 v~~~v~t~~~   90 (92)
                      ++++|.|+|.
T Consensus        82 ~~~~V~t~~~   91 (196)
T PRK12551         82 VKPDVHTVCV   91 (196)
T ss_pred             cCCCEEEEEE
Confidence            9999999984

>TIGR00493 clpP ATP-dependent Clp protease, proteolytic subunit ClpP

Probab=99.93  E-value=4.2e-26  Score=165.25  Aligned_cols=89  Identities=33%  Similarity=0.463  Sum_probs=83.4

Q ss_pred             ccc-ccCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPF-TSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~-~~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|- ++.+..++.|.|++++|+++|+|||+|+|+++++++++++|++|+.++++++|++|||||||++++|++|||+|++
T Consensus         3 ~p~~~~~~~~~~~~~d~~~~l~~~riI~l~g~I~~~~~~~ii~~L~~l~~~~~~~~i~l~InSpGG~v~~g~~I~d~l~~   82 (191)
T TIGR00493         3 IPMVIEQTGRGERSFDIYSRLLKERIIFLSGEVNDSVANLIVAQLLFLEAEDPEKDIYLYINSPGGSITAGLAIYDTMQF   82 (191)
T ss_pred             CCcccccCCCCcccccHHHHHhcCeEEEEccEEChHHHHHHHHHHHHhhccCCCCCEEEEEECCCCCHHHHHHHHHHHHh
Confidence            563 4666777899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceeee
Q 041456           81 QISSINASEY   90 (92)
Q Consensus        81 v~~~v~t~~~   90 (92)
                      .+++|.|+|.
T Consensus        83 ~~~~v~t~~~   92 (191)
T TIGR00493        83 IKPDVSTICI   92 (191)
T ss_pred             cCCCEEEEEE
Confidence            9999999985

This model for the proteolytic subunit ClpP has been rebuilt to a higher stringency. In every bacterial genome with the ClpXP machine, a ClpP protein will be found that scores with this model. In general, this ClpP member will be encoded adjacent to the clpX gene, as were all examples used in the seed alignment. A large fraction of genomes have one or more additional ClpP paralogs, sometimes encoded nearby and sometimes elsewhere. The stringency of the trusted cutoff used here excludes the more divergent ClpP paralogs from being called authentic ClpP by this model.

>PRK00277 clpP ATP-dependent Clp protease proteolytic subunit; Reviewed

Probab=99.92  E-value=3.8e-25  Score=161.05  Aligned_cols=89  Identities=29%  Similarity=0.475  Sum_probs=82.3

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|+. ......+.|.|++++|+++|+|||+|+|+++++++++++|++|+.++++++|++|||||||++++|++|||+|++
T Consensus         8 ~p~~~~~~~~~~~~~~~~~~l~~~rii~i~g~I~~~~~~~i~~~L~~l~~~~~~~~I~l~InSpGG~v~~g~~I~d~i~~   87 (200)
T PRK00277          8 VPMVIEQTSRGERSYDIYSRLLKERIIFLGGEVEDHMANLIVAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYDTMQF   87 (200)
T ss_pred             CceeeccCCCCcccccHHHHhhcCcEEEECCEECHHHHHHHHHHHHHhhccCCCCCEEEEEECCCCcHHHHHHHHHHHHh
Confidence            4654 345567899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceeee
Q 041456           81 QISSINASEY   90 (92)
Q Consensus        81 v~~~v~t~~~   90 (92)
                      ++++|.|++.
T Consensus        88 ~~~~v~t~~~   97 (200)
T PRK00277         88 IKPDVSTICI   97 (200)
T ss_pred             cCCCEEEEEE
Confidence            9999999873

>PRK12553 ATP-dependent Clp protease proteolytic subunit; Reviewed

Probab=99.90  E-value=1.5e-23  Score=153.57  Aligned_cols=89  Identities=21%  Similarity=0.319  Sum_probs=81.8

Q ss_pred             ccc-ccCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPF-TSGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~-~~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|. +.....+..+.|++++|+++|+|||+|+|+++++++++++|++++.+++.++|++|||||||++++|++|||+|+.
T Consensus        12 ~p~~~~~~~~~~~~~~~~~~l~~~r~I~l~g~I~~~~~~~i~~~L~~l~~~~~~~~I~l~INSpGG~v~~g~~I~d~i~~   91 (207)
T PRK12553         12 LPSFIERTSYGVKESDPYNKLFEERIIFLGGQVDDASANDVMAQLLVLESIDPDRDITLYINSPGGSVTAGDAIYDTIQF   91 (207)
T ss_pred             CCcccccCCCCCccccHHHHHhcCeEEEEcceECHHHHHHHHHHHHHHHhCCCCCCEEEEEeCCCCcHHHHHHHHHHHHh
Confidence            554 3445556778999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceeee
Q 041456           81 QISSINASEY   90 (92)
Q Consensus        81 v~~~v~t~~~   90 (92)
                      .+++|.|+|.
T Consensus        92 ~~~~v~t~~~  101 (207)
T PRK12553         92 IRPDVQTVCT  101 (207)
T ss_pred             cCCCcEEEEE
Confidence            9999999874

>PRK14512 ATP-dependent Clp protease proteolytic subunit; Provisional

Probab=99.90  E-value=1.3e-23  Score=153.17  Aligned_cols=83  Identities=18%  Similarity=0.265  Sum_probs=78.0

Q ss_pred             CCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccce
Q 041456            8 TAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINA   87 (92)
Q Consensus         8 ~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t   87 (92)
                      .+......+++++|+++|+|||+|+|+++++++++++|++|+.+++.++|++|||||||++++|++|||+|+++++||.|
T Consensus         7 ~~~~~~~~~~~~~l~~~r~I~i~g~I~~~~~~~i~~~L~~l~~~~~~~~I~l~INSpGG~v~ag~aI~d~i~~~~~~V~t   86 (197)
T PRK14512          7 DNKQTGIDKSLEKFLKSRSIVIAGEINKDLSELFQEKILLLEALDSKKPIFVYIDSEGGDIDAGFAIFNMIRFVKPKVFT   86 (197)
T ss_pred             ccccCCcchHHHHHhcCcEEEECCEEcHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCHHHHHHHHHHHHhCCCCEEE
Confidence            44556678999999999999999999999999999999999998889999999999999999999999999999999999


Q ss_pred             eee
Q 041456           88 SEY   90 (92)
Q Consensus        88 ~~~   90 (92)
                      +|.
T Consensus        87 ~v~   89 (197)
T PRK14512         87 IGV   89 (197)
T ss_pred             EEE
Confidence            874

>PF00574 CLP_protease: Clp protease; InterPro: IPR001907 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=99.90  E-value=6e-24  Score=150.47  Aligned_cols=79  Identities=23%  Similarity=0.345  Sum_probs=76.3

Q ss_pred             CCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceeee
Q 041456           12 QPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEY   90 (92)
Q Consensus        12 ~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~~   90 (92)
                      ..|+|++++|+++|+|||+|+||+++++.++++|++|+.++++++|++|||||||++.+|++|||+|+.++.+|.|.+.
T Consensus         4 ~~~~~i~~~l~~~r~i~l~g~I~~~~~~~~~~~L~~l~~~~~~~~i~i~INSpGG~v~~g~~i~~~i~~~~~~v~t~~~   82 (182)
T PF00574_consen    4 EEWYDIYSRLLNERIIFLNGPIDEESANRLISQLLYLENEDKNKPINIYINSPGGDVDAGLAIYDAIRSSKAPVTTVVL   82 (182)
T ss_dssp             EEEEEHHHHHHTTTEEEEESSBSHHHHHHHHHHHHHHHHHTSSSEEEEEEEECEBCHHHHHHHHHHHHHSSSEEEEEEE
T ss_pred             cEEEeHHHHHhCCeEEEECCccCHHHHHHHHHHHHHHhccCCCceEEEEEcCCCCccHHHHHHHHHHHhcCCCeEEEEe
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999999864

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S14 (ClpP endopeptidase family, clan SK). ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin []. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP [], although the P subunit alone does possess some catalytic activity. This family of sequences represent the P subunit. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 2ZL3_L 2ZL0_F 2ZL2_M 2ZL4_C 1TG6_D 2F6I_D 3V5I_b 3V5E_M 3QWD_D 2DEO_A ....

>cd07017 S14_ClpP_2 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease

Probab=99.85  E-value=3.7e-21  Score=136.32  Aligned_cols=74  Identities=35%  Similarity=0.576  Sum_probs=71.6

Q ss_pred             chHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceee
Q 041456           16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASE   89 (92)
Q Consensus        16 dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~   89 (92)
                      |++++|+++|+||++|+|+++++++++++|++++.+++.++|++|||||||++.+|++|||.|+..+.+|.|.+
T Consensus         1 ~~~~~l~~~r~i~i~g~I~~~~~~~i~~~l~~~~~~~~~~~i~l~inSpGG~v~~~~~i~~~l~~~~~~v~t~~   74 (171)
T cd07017           1 DIYSRLLKERIIFLGGPIDDEVANLIIAQLLYLESEDPKKPIYLYINSPGGSVTAGLAIYDTMQYIKPPVSTIC   74 (171)
T ss_pred             ChhHhhhcCcEEEEcCEEcHHHHHHHHHHHHHHHccCCCCceEEEEECCCCCHHHHHHHHHHHHhcCCCEEEEE
Confidence            68999999999999999999999999999999999988899999999999999999999999999999999876

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 activ

>cd07013 S14_ClpP Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease

Probab=99.78  E-value=5.4e-19  Score=124.75  Aligned_cols=65  Identities=23%  Similarity=0.281  Sum_probs=63.2

Q ss_pred             ceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceee
Q 041456           25 RIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASE   89 (92)
Q Consensus        25 RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~   89 (92)
                      |+|||+|+|++.++++++++|++|+.+++.++|.+|||||||++++|++|||+|+.++++|.|++
T Consensus         1 r~i~i~g~I~~~~~~~~~~~L~~l~~~~~~~~i~l~InSpGG~v~~~~~i~~~i~~~~~~v~~~~   65 (162)
T cd07013           1 REIMLTGEVEDISANQFAAQLLFLGAVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIKADVVTII   65 (162)
T ss_pred             CEEEEccEECcHHHHHHHHHHHHHhcCCCCCCEEEEEECCCCcHHHHHHHHHHHHhcCCCceEEE
Confidence            89999999999999999999999999999999999999999999999999999999999999875

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 proteas

>cd07016 S14_ClpP_1 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease

Probab=99.39  E-value=6e-13  Score=92.49  Aligned_cols=62  Identities=10%  Similarity=0.016  Sum_probs=56.1

Q ss_pred             ceEEeCcccCH---HHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceee
Q 041456           25 RIVYLGMSFVP---SVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASE   89 (92)
Q Consensus        25 RiifL~g~Id~---~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~   89 (92)
                      +.|+|+|+|++   .+++++.+.|.+++.+   ++|.||||||||++.+|++|+|.++.++.||.|..
T Consensus         1 ~~i~~~g~I~~~~~~~~~~~~~~l~~~~~~---~~i~l~inspGG~~~~~~~i~~~i~~~~~pvi~~v   65 (160)
T cd07016           1 AEIYIYGDIGSDWGVTAKEFKDALDALGDD---SDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKI   65 (160)
T ss_pred             CEEEEEeEeCCCcccCHHHHHHHHHhccCC---CCEEEEEECCCCCHHHHHHHHHHHHhcCCCEEEEE
Confidence            46899999999   8999999999987554   89999999999999999999999999988887754

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 a

>cd07020 Clp_protease_NfeD_1 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease

Probab=99.09  E-value=3.4e-10  Score=81.09  Aligned_cols=62  Identities=5%  Similarity=0.043  Sum_probs=55.0

Q ss_pred             eEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhccccccee
Q 041456           26 IVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINAS   88 (92)
Q Consensus        26 iifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~   88 (92)
                      +|-|.|.|++..++.+.++|..++. ++.+.|.++||||||++.++..+++.|...+.||.+.
T Consensus         3 vv~i~g~I~~~~~~~l~~~l~~a~~-~~~~~vvl~InSpGG~v~~~~~i~~~l~~~~kPvia~   64 (187)
T cd07020           3 VLEINGAITPATADYLERAIDQAEE-GGADALIIELDTPGGLLDSTREIVQAILASPVPVVVY   64 (187)
T ss_pred             EEEEeeEEChHHHHHHHHHHHHHHh-CCCCEEEEEEECCCCCHHHHHHHHHHHHhCCCCEEEE
Confidence            4678999999999999999999985 4478999999999999999999999998877777654

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 c

>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease

Probab=99.08  E-value=4.1e-10  Score=81.08  Aligned_cols=64  Identities=8%  Similarity=-0.002  Sum_probs=54.7

Q ss_pred             eEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceeee
Q 041456           26 IVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEY   90 (92)
Q Consensus        26 iifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~~   90 (92)
                      .+-+.|.|++..+..+...|-.-+ +++.++|.|+||||||++.++.+|||+|+..++||.|.++
T Consensus         3 vi~i~G~I~~~~~~~l~~~l~~A~-~~~~~~i~l~inSPGG~v~~~~~I~~~i~~~~~pvv~~v~   66 (172)
T cd07015           3 VAQIKGQITSYTYDQFDRYITIAE-QDNAEAIIIELDTPGGRADAAGNIVQRIQQSKIPVIIYVY   66 (172)
T ss_pred             EEEEeeEECHhHHHHHHHHHHHHh-cCCCCeEEEEEECCCCCHHHHHHHHHHHHhcCcCEEEEEe
Confidence            466789999988887777666543 4668999999999999999999999999999999998875

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 cle

>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease

Probab=99.05  E-value=5.5e-10  Score=77.10  Aligned_cols=64  Identities=11%  Similarity=0.123  Sum_probs=59.3

Q ss_pred             eEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceee
Q 041456           26 IVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASE   89 (92)
Q Consensus        26 iifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~   89 (92)
                      +|++.|+|++.+.+++++.|..++.+++-+.|.+++|||||++.++..++|+|+..+.||.+.+
T Consensus         1 vi~i~g~I~~~~~~~l~~~l~~a~~d~~~~~ivl~~~s~Gg~~~~~~~i~~~l~~~~kpvva~~   64 (161)
T cd00394           1 VIFINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQASRKPVIAYV   64 (161)
T ss_pred             CEEEEeEEccchHHHHHHHHHHHHhCCCCceEEEEEECCCcCHHHHHHHHHHHHHhCCCEEEEE
Confidence            5899999999999999999999998888899999999999999999999999999998877653

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 tetradec

>cd07021 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease

Probab=98.46  E-value=7e-07  Score=64.28  Aligned_cols=61  Identities=8%  Similarity=0.103  Sum_probs=50.2

Q ss_pred             eEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccce
Q 041456           26 IVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINA   87 (92)
Q Consensus        26 iifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t   87 (92)
                      .|-+.|.|++..+..+...|-.... ++-+.|.++||||||.++++..|++.+...+.||.+
T Consensus         3 vi~i~g~I~~~~~~~l~~~l~~a~~-~~~~~ivl~inspGG~v~~~~~I~~~l~~~~~pvva   63 (178)
T cd07021           3 VIPIEGEIDPGLAAFVERALKEAKE-EGADAVVLDIDTPGGRVDSALEIVDLILNSPIPTIA   63 (178)
T ss_pred             EEEEeeEECHHHHHHHHHHHHHHHh-CCCCeEEEEEECcCCCHHHHHHHHHHHHhCCCCEEE
Confidence            4668899999888877776665544 447899999999999999999999999987766544

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, preferentiall

>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad

Probab=98.01  E-value=1.6e-05  Score=57.45  Aligned_cols=65  Identities=12%  Similarity=0.040  Sum_probs=55.2

Q ss_pred             eEEeCcccC---HHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhccc-ccceeee
Q 041456           26 IVYLGMSFV---PSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQIS-SINASEY   90 (92)
Q Consensus        26 iifL~g~Id---~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~-~v~t~~~   90 (92)
                      ++.+.|+|+   ..+..++...|..++.+++-+-|.+.+|||||++.++..++++++..+. +.-+++|
T Consensus         4 vi~i~g~i~~~~~~~~~~l~~~l~~a~~d~~i~~ivl~~~s~Gg~~~~~~~i~~~i~~~~~~~kpvia~   72 (208)
T cd07023           4 VIDIEGTISDGGGIGADSLIEQLRKAREDDSVKAVVLRINSPGGSVVASEEIYREIRRLRKAKKPVVAS   72 (208)
T ss_pred             EEEEEEEEcCCCCCCHHHHHHHHHHHHhCCCCcEEEEEEECCCCCHHHHHHHHHHHHHHHhcCCcEEEE
Confidence            578899999   7899999999999988777899999999999999999999999976643 4444554

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

>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=97.71  E-value=7.5e-05  Score=57.91  Aligned_cols=58  Identities=17%  Similarity=0.083  Sum_probs=47.4

Q ss_pred             eEEeCcccCHHH-------HHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhccc
Q 041456           26 IVYLGMSFVPSV-------RELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQIS   83 (92)
Q Consensus        26 iifL~g~Id~~~-------a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~   83 (92)
                      +|.+.|.|....       .+.+.+.|-.+...++.|.|-|.||||||++.++-.|++.++-.+.
T Consensus        63 vi~~~G~I~~~~~~~~~~~~~~~~~~l~~~~~~~~vk~vvL~inSPGG~v~as~~i~~~l~~l~~  127 (317)
T COG0616          63 VIHVEGAIVAGGGPLRFIGGDDIEEILRAARADPSVKAVVLRINSPGGSVVASELIARALKRLRA  127 (317)
T ss_pred             EEEeeeeeecCCCccccccHHHHHHHHHHHhcCCCCceEEEEEECcCCchhHHHHHHHHHHHHhh
Confidence            466677777544       5666666777777788999999999999999999999999987766

>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type

Probab=97.53  E-value=0.00026  Score=51.35  Aligned_cols=61  Identities=18%  Similarity=0.063  Sum_probs=50.4

Q ss_pred             eEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc--cccce
Q 041456           26 IVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI--SSINA   87 (92)
Q Consensus        26 iifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~--~~v~t   87 (92)
                      +|.+.|.|+ ....++...|-.+...+.-+.|.|.+|||||++.++..+++.+...+  .||.+
T Consensus         4 vi~i~g~i~-~s~~~l~~~l~~a~~d~~i~~vvl~~~s~Gg~~~~~~~l~~~i~~~~~~kpvia   66 (207)
T TIGR00706         4 ILPVSGAIA-VSPEDFDKKIKRIKDDKSIKALLLRINSPGGTVVASEEIYEKLKKLKAKKPVVA   66 (207)
T ss_pred             EEEEEEEEe-cCHHHHHHHHHHHhhCCCccEEEEEecCCCCCHHHHHHHHHHHHHhcCCCCEEE
Confidence            467788887 55678888888777666678899999999999999999999999987  55543

The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.

>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type

Probab=97.29  E-value=0.00043  Score=57.74  Aligned_cols=62  Identities=16%  Similarity=0.085  Sum_probs=46.8

Q ss_pred             eEEeCcccCHH-------HHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc---cccce
Q 041456           26 IVYLGMSFVPS-------VRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI---SSINA   87 (92)
Q Consensus        26 iifL~g~Id~~-------~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~---~~v~t   87 (92)
                      +|.+.|+|.+.       ..+.+.+.|-.+..++.-|.|.|.||||||++.++..|++.+...+   .||.+
T Consensus       312 vI~~~G~I~~~~~~~~~~~~~~~~~~l~~a~~D~~VkaIVLrinSpGGs~~ase~i~~~i~~~~~~gKPVva  383 (584)
T TIGR00705       312 IVHLEGPIADGRDTEGNTGGDTVAALLRVARSDPDIKAVVLRINSPGGSVFASEIIRRELARAQARGKPVIV  383 (584)
T ss_pred             EEEEEEEEcCCCCcccccCHHHHHHHHHHHhhCCCceEEEEEecCCCCCHHHHHHHHHHHHHHHhCCCcEEE
Confidence            89999999752       2455666665554444458999999999999999999999987554   45544

E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both.

>PF01972 SDH_sah: Serine dehydrogenase proteinase; InterPro: IPR002825 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

Probab=96.94  E-value=0.0024  Score=49.70  Aligned_cols=53  Identities=13%  Similarity=0.065  Sum_probs=41.6

Q ss_pred             cccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccc
Q 041456           31 MSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSIN   86 (92)
Q Consensus        31 g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~   86 (92)
                      ..|+.+.++.+...+-   ..+++++|-|.||+|||.+.|+..|-+.++--..++.
T Consensus        70 ~~I~i~dse~v~raI~---~~~~~~~IdLii~TpGG~v~AA~~I~~~l~~~~~~v~  122 (285)
T PF01972_consen   70 RYIDIDDSEFVLRAIR---EAPKDKPIDLIIHTPGGLVDAAEQIARALREHPAKVT  122 (285)
T ss_pred             eeEcHhhHHHHHHHHH---hcCCCCceEEEEECCCCcHHHHHHHHHHHHhCCCCEE
Confidence            4577778888755554   4466789999999999999999999999986555544

The family belong to MEROPS peptidase family S49; they are mostly unassigned peptidases but include the archaean signal peptide peptidase 1 []. 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 []. ; GO: 0016021 integral to membrane

>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad

Probab=96.68  E-value=0.0057  Score=44.49  Aligned_cols=53  Identities=21%  Similarity=0.102  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc--cccce
Q 041456           35 PSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI--SSINA   87 (92)
Q Consensus        35 ~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~--~~v~t   87 (92)
                      ..+..++.+.|-.++..+.-+-|.+.+|||||++.+...+++++...+  .||.+
T Consensus        24 ~~~~~~l~~~l~~a~~d~~i~~Vvl~~~s~gg~~~~~~~l~~~l~~~~~~KpViA   78 (214)
T cd07022          24 LTSYEGIAAAIRAALADPDVRAIVLDIDSPGGEVAGVFELADAIRAARAGKPIVA   78 (214)
T ss_pred             cccHHHHHHHHHHHhhCCCCcEEEEEEeCCCCcHHHHHHHHHHHHHHhcCCCEEE
Confidence            356789999999988777778899999999999999999999998887  55443

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.

>cd07019 S49_SppA_1 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad

Probab=96.55  E-value=0.0047  Score=44.90  Aligned_cols=64  Identities=17%  Similarity=0.085  Sum_probs=45.7

Q ss_pred             EEeCcccCHHH-------HHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc-cccceeee
Q 041456           27 VYLGMSFVPSV-------RELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI-SSINASEY   90 (92)
Q Consensus        27 ifL~g~Id~~~-------a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~-~~v~t~~~   90 (92)
                      |.+.|+|.+..       ..++...|-.++.++.-+-|.|.+|||||++.+...+++.++.++ ++.-+|.|
T Consensus         5 ~~~~g~i~~~~~~~~~~~~~~l~~~l~~a~~d~~v~~ivL~~~s~Gg~~~~~~~~~~~l~~~~~~~kpVia~   76 (211)
T cd07019           5 VFANGAIVDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVS   76 (211)
T ss_pred             EEEEEEEeCCCCCCCccCHHHHHHHHHHHhhCCCceEEEEEEcCCCcCHHHHHHHHHHHHHHHhCCCCEEEE
Confidence            44555555433       367888888887666669999999999999999989999886553 34444444

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-te

>PRK10949 protease 4; Provisional

Probab=96.30  E-value=0.008  Score=50.80  Aligned_cols=62  Identities=15%  Similarity=0.127  Sum_probs=50.5

Q ss_pred             eEEeCcccCHH-------HHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc---cccce
Q 041456           26 IVYLGMSFVPS-------VRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI---SSINA   87 (92)
Q Consensus        26 iifL~g~Id~~-------~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~---~~v~t   87 (92)
                      +|.+.|.|.+.       .++.++.+|-.....+.-|-|-|-||||||++.+...|++.+...+   .||..
T Consensus       330 vi~~~G~I~~g~~~~g~~~~~~~~~~l~~a~~D~~vkaVvLrInSpGGs~~ase~i~~~i~~~r~~gKPVva  401 (618)
T PRK10949        330 VIFANGAIMDGEETPGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVV  401 (618)
T ss_pred             EEEEEEEEcCCCCcCCCcCHHHHHHHHHHHHhCCCCcEEEEEecCCCCcHHHHHHHHHHHHHHHhcCCcEEE
Confidence            67888888752       2567888888887777889999999999999999999999997664   45554

>PRK11778 putative inner membrane peptidase; Provisional

Probab=96.09  E-value=0.011  Score=46.74  Aligned_cols=54  Identities=17%  Similarity=0.110  Sum_probs=33.9

Q ss_pred             eEEeCcccCHHHHHHHHHHHHHh-hhcCCCCCeEEEEeCCCCcchhhhhHHHHHh
Q 041456           26 IVYLGMSFVPSVRELILAEFLYL-QYEDAEKPIYLYLNSTGTTEVGSFLCHALVF   79 (92)
Q Consensus        26 iifL~g~Id~~~a~~ii~~Ll~L-~~~d~~~~I~lyINSpGG~v~aglaIyD~m~   79 (92)
                      +|-+.|.|+...+..+...+..+ ....+++.|.|-||||||++.+.-.+...+.
T Consensus        94 VI~~~G~I~~~~~~~l~e~i~a~l~~A~~~~aVvLridSpGG~v~~s~~a~~~l~  148 (330)
T PRK11778         94 VLDFKGDIDASEVESLREEITAILAVAKPGDEVLLRLESPGGVVHGYGLAASQLQ  148 (330)
T ss_pred             EEEEEEEECCCcchhhHHHHHHHHHhccCCCeEEEEEeCCCCchhHHHHHHHHHH
Confidence            45677999976654443333332 2223346799999999999987444444443

>cd07014 S49_SppA Signal peptide peptidase A

Probab=95.93  E-value=0.02  Score=40.32  Aligned_cols=55  Identities=16%  Similarity=0.032  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc-cccceeeec
Q 041456           37 VRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI-SSINASEYI   91 (92)
Q Consensus        37 ~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~-~~v~t~~~~   91 (92)
                      +.+.+...+-.++..+.-+-|.|-+|||||++.....+.+.+.-.+ ++.-+|+|+
T Consensus        23 ~~~~l~~~l~~a~~d~~v~~vvl~~~~~gg~~~~~~~~~~~i~~~~~~~kpVia~v   78 (177)
T cd07014          23 SGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVASG   78 (177)
T ss_pred             CHHHHHHHHHHHhcCCCceEEEEEeeCCCcCHHHHHHHHHHHHHHHhCCCCEEEEE
Confidence            4678888888887666667899999999999988888888775443 555556553

Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is an intramembrane enzyme 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. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be ClpP-like serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain, cleaving peptide bonds in the plane of the lipid bilayer. 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 p

>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]

Probab=95.77  E-value=0.033  Score=45.69  Aligned_cols=60  Identities=8%  Similarity=0.078  Sum_probs=50.9

Q ss_pred             ceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhccccc
Q 041456           25 RIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSI   85 (92)
Q Consensus        25 RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v   85 (92)
                      ..+-+.|+|++.+++.+...|-.-+.++ -..+-+.+|.|||.+++...|-..+.-...||
T Consensus        29 ~vi~i~g~I~~~s~~~l~r~l~~A~~~~-a~~vvl~ldTPGGl~~sm~~iv~~i~~s~vPV   88 (436)
T COG1030          29 YVIEIDGAIDPASADYLQRALQSAEEEN-AAAVVLELDTPGGLLDSMRQIVRAILNSPVPV   88 (436)
T ss_pred             EEEEecCccCHHHHHHHHHHHHHHHhCC-CcEEEEEecCCCchHHHHHHHHHHHHcCCCCE
Confidence            5788999999999999998887554433 57899999999999999999999998777774

>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad

Probab=94.75  E-value=0.064  Score=39.23  Aligned_cols=60  Identities=13%  Similarity=-0.124  Sum_probs=47.1

Q ss_pred             cccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc-cccceeee
Q 041456           31 MSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI-SSINASEY   90 (92)
Q Consensus        31 g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~-~~v~t~~~   90 (92)
                      +.-+......++..|-.+...+.-+-|-|.+|||||++.+...+++.++-.+ ++.-+++|
T Consensus        24 ~~~~~~~~~~l~~~l~~a~~d~~ik~vvL~~~s~gg~~~~~~el~~~i~~~~~~~kpVia~   84 (222)
T cd07018          24 GESSELSLRDLLEALEKAAEDDRIKGIVLDLDGLSGGLAKLEELRQALERFRASGKPVIAY   84 (222)
T ss_pred             CCcCCccHHHHHHHHHHHhcCCCeEEEEEECCCCCCCHHHHHHHHHHHHHHHHhCCeEEEE
Confidence            4445667889999999887766678899999999999999999999997665 33333444

Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K 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 contain 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. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are 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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	92
3qwd_A	203	Crystal Structure Of Clpp From Staphylococcus Aureu		1e-07
3st9_A	197	Crystal Structure Of Clpp In Heptameric Form From S		1e-07
3v5i_A	203	The Crystal Structure Of The Mutant Clpp S98a (Stap		1e-07
4hnk_A	219	Crystal Structure Of An Enzyme Length = 219		3e-07
4gm2_A	205	The Crystal Structure Of A Peptidase From Plasmodiu		4e-07
3tt6_A	196	Structure Of Clpp From Bacillus Subtilis In Compres		1e-05
3kti_A	199	Structure Of Clpp In Complex With Adep1 Length = 19		1e-05
3ktg_A	199	Structure Of Clpp From Bacillus Subtilis In Monocli		1e-05
3tt7_A	197	Structure Of Clpp From Bacillus Subtilis In Complex		1e-05
2zl0_A	196	Crystal Structure Of H.Pylori Clpp Length = 196		1e-05
2zl3_A	196	Crystal Structure Of H.Pylori Clpp S99a Length = 19		2e-05
3hln_A	193	Crystal Structure Of Clpp A153c Mutant With Inter-H		2e-05
1tyf_A	193	The Structure Of Clpp At 2.3 Angstrom Resolution Su		2e-05
1yg8_A	193	The Structure Of A V6a Variant Of Clpp. Length = 19		2e-05
3mt6_R	207	Structure Of Clpp From Escherichia Coli In Complex		2e-05
1tg6_A	277	Crystallography And Mutagenesis Point To An Essenti		3e-05
3p2l_A	201	Crystal Structure Of Atp-Dependent Clp Protease Sub		4e-05

>pdb|3QWD|A Chain A, Crystal Structure Of Clpp From Staphylococcus Aureus Length = 203

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
          D+ S L K+RI+ LG     +V   I+++ L+LQ +D+EK IYLY+NS G +    F
Sbjct: 19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGF 75

>pdb|3ST9|A Chain A, Crystal Structure Of Clpp In Heptameric Form From Staphylococcus Aureus Length = 197

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
          D+ S L K+RI+ LG     +V   I+++ L+LQ +D+EK IYLY+NS G +    F
Sbjct: 21 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGF 77

>pdb|3V5I|A Chain A, The Crystal Structure Of The Mutant Clpp S98a (Staphylococcus Aureus) Length = 203

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
          D+ S L K+RI+ LG     +V   I+++ L+LQ +D+EK IYLY+NS G +    F
Sbjct: 19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGF 75

>pdb|4HNK|A Chain A, Crystal Structure Of An Enzyme Length = 219

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 42/76 (55%)
Query: 16  DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCH 75
           ++ S L   RI++L     P + E I+++ LYL+YE   KPI+LY+NSTG  +    +  
Sbjct: 34  NIPSLLLSKRIIFLSSPIYPHISEQIISQLLYLEYESKRKPIHLYINSTGDIDNNKIINL 93
Query: 76  ALVFFQISSINASEYI 91
             +   IS ++   YI
Sbjct: 94  NGITDVISIVDVINYI 109

>pdb|4GM2|A Chain A, The Crystal Structure Of A Peptidase From Plasmodium Falciparum Length = 205

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 40/73 (54%)
Query: 19 SYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALV 78
          S L   RI++L     P + E I+++ LYL+YE   KPI+LY+NSTG  +    +    +
Sbjct: 23 SLLLSKRIIFLSSPIYPHISEQIISQLLYLEYESKRKPIHLYINSTGDIDNNKIINLNGI 82
Query: 79 FFQISSINASEYI 91
             IS ++   YI
Sbjct: 83 TDVISIVDVINYI 95

>pdb|3TT6|A Chain A, Structure Of Clpp From Bacillus Subtilis In Compressed State Length = 196

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L K+RI+ LG +   +V   I+++ L+L  ED EK I LY+NS G +
Sbjct: 18 DIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLAAEDPEKEISLYINSPGGS 69

>pdb|3KTI|A Chain A, Structure Of Clpp In Complex With Adep1 Length = 199

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L K+RI+ LG +   +V   I+++ L+L  ED EK I LY+NS G +
Sbjct: 18 DIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLAAEDPEKEISLYINSPGGS 69

>pdb|3KTG|A Chain A, Structure Of Clpp From Bacillus Subtilis In Monoclinic Crystal Form Length = 199

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L K+RI+ LG +   +V   I+++ L+L  ED EK I LY+NS G +
Sbjct: 18 DIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLAAEDPEKEISLYINSPGGS 69

>pdb|3TT7|A Chain A, Structure Of Clpp From Bacillus Subtilis In Complex With Dfp Length = 197

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L K+RI+ LG +   +V   I+++ L+L  ED EK I LY+NS G +
Sbjct: 19 DIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLAAEDPEKEISLYINSPGGS 70

>pdb|2ZL0|A Chain A, Crystal Structure Of H.Pylori Clpp Length = 196

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 31/50 (62%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K+RIV L      SV   I+A+ L+L+ ED EK I LY+NS G
Sbjct: 20 DIYSRLLKDRIVLLSGEINDSVASSIVAQLLFLEAEDPEKDIGLYINSPG 69

>pdb|2ZL3|A Chain A, Crystal Structure Of H.Pylori Clpp S99a Length = 196

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 31/50 (62%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K+RIV L      SV   I+A+ L+L+ ED EK I LY+NS G
Sbjct: 20 DIYSRLLKDRIVLLSGEINDSVASSIVAQLLFLEAEDPEKDIGLYINSPG 69

>pdb|3HLN|A Chain A, Crystal Structure Of Clpp A153c Mutant With Inter-Heptamer Disulfide Bonds Length = 193

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K R+++L       +  LI+A+ L+L+ E+ EK IYLY+NS G
Sbjct: 18 DIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPG 67

>pdb|1TYF|A Chain A, The Structure Of Clpp At 2.3 Angstrom Resolution Suggests A Model For Atp-Dependent Proteolysis Length = 193

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K R+++L       +  LI+A+ L+L+ E+ EK IYLY+NS G
Sbjct: 18 DIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPG 67

>pdb|1YG8|A Chain A, The Structure Of A V6a Variant Of Clpp. Length = 193

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K R+++L       +  LI+A+ L+L+ E+ EK IYLY+NS G
Sbjct: 18 DIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPG 67

>pdb|3MT6|R Chain R, Structure Of Clpp From Escherichia Coli In Complex With Adep1 Length = 207

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K R+++L       +  LI+A+ L+L+ E+ EK IYLY+NS G
Sbjct: 32 DIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPG 81

>pdb|1TG6|A Chain A, Crystallography And Mutagenesis Point To An Essential Role For The N- Terminus Of Human Mitochondrial Clpp Length = 277

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 16  DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
           D+ S L + RIV +      SV  L++A+ L+LQ E  +KPI++Y+NS G
Sbjct: 74  DIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPG 123

>pdb|3P2L|A Chain A, Crystal Structure Of Atp-Dependent Clp Protease Subunit P From Francisella Tularensis Length = 201

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 32/56 (57%)
Query: 8  TAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNS 63
          TA  +   D+ S L K RIV+L          L++A+ L+L+ ED +K IY Y+NS
Sbjct: 14 TAGGERAFDIYSRLLKERIVFLNGEVNDHSANLVIAQLLFLESEDPDKDIYFYINS 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	92
1tg6_A	277	Putative ATP-dependent CLP protease proteolytic S;	2e-10
3p2l_A	201	ATP-dependent CLP protease proteolytic subunit; st	2e-10
1yg6_A	193	ATP-dependent CLP protease proteolytic subunit; en	2e-10
1y7o_A	218	ATP-dependent CLP protease proteolytic subunit; hy	3e-10
3qwd_A	203	ATP-dependent CLP protease proteolytic subunit; ca	4e-10
2cby_A	208	ATP-dependent CLP protease proteolytic subunit 1;	6e-10
2f6i_A	215	ATP-dependent CLP protease, putative; structural g	3e-08

>1tg6_A Putative ATP-dependent CLP protease proteolytic S; mitochondrial CLPP, CLP/HSP 100, ATP-dependent protease, HYD; HET: FME; 2.10A {Homo sapiens} SCOP: c.14.1.1 Length = 277

 Score = 54.0 bits (130), Expect = 2e-10
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 16  DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
           D+ S L + RIV +      SV  L++A+ L+LQ E  +KPI++Y+NS G
Sbjct: 74  DIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPG 123

>3p2l_A ATP-dependent CLP protease proteolytic subunit; structural genomics, center for structural genomics of infec diseases, csgid; 2.29A {Francisella tularensis subsp} Length = 201

 Score = 53.3 bits (129), Expect = 2e-10
 Identities = 21/50 (42%), Positives = 30/50 (60%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K RIV+L          L++A+ L+L+ ED +K IY Y+NS G
Sbjct: 22 DIYSRLLKERIVFLNGEVNDHSANLVIAQLLFLESEDPDKDIYFYINSPG 71

>1yg6_A ATP-dependent CLP protease proteolytic subunit; endopeptidase CLP, caseinolytic protease, protease TI, heat shock protein F21.5, hydrolase; 1.90A {Escherichia coli} SCOP: c.14.1.1 PDB: 1tyf_A 2fzs_A* 3mt6_R 1yg8_A 3hln_A 2zl2_A 2zl0_A 2zl4_A 2zl3_A 3tt7_A* 3tt6_A 3ktg_A 3kth_A 3kti_A* 3ktj_A* 3ktk_A* 3q7h_A Length = 193

 Score = 52.9 bits (128), Expect = 2e-10
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K R+++L       +  LI+A+ L+L+ E+ EK IYLY+NS G
Sbjct: 18 DIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPG 67

>1y7o_A ATP-dependent CLP protease proteolytic subunit; hydrolase; 2.51A {Streptococcus pneumoniae} SCOP: c.14.1.1 Length = 218

 Score = 53.4 bits (129), Expect = 3e-10
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K+RI+ L      ++   ++A+ L+L  +D+ K IYLY+N+ G
Sbjct: 37 DIYSRLLKDRIIMLTGPVEDNMANSVIAQLLFLDAQDSTKDIYLYVNTPG 86

>3qwd_A ATP-dependent CLP protease proteolytic subunit; caseinolytic protease, serin-protease, hydrolase; 2.10A {Staphylococcus aureus subsp} PDB: 3v5e_A 3v5i_A 3sta_V 3st9_A Length = 203

 Score = 52.9 bits (128), Expect = 4e-10
 Identities = 23/50 (46%), Positives = 34/50 (68%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K+RI+ LG     +V   I+++ L+LQ +D+EK IYLY+NS G
Sbjct: 19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPG 68

>2cby_A ATP-dependent CLP protease proteolytic subunit 1; serine protease, endopept mycobacterium tuberculosis, ATP-dependent protease; 2.6A {Mycobacterium tuberculosis} SCOP: c.14.1.1 PDB: 2c8t_A 2ce3_A Length = 208

 Score = 52.2 bits (126), Expect = 6e-10
 Identities = 18/47 (38%), Positives = 24/47 (51%)

Query: 19 SYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
            L   RI++LG      +   + A+ L L  EDA K I LY+NS G
Sbjct: 22 ERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPG 68

>2f6i_A ATP-dependent CLP protease, putative; structural genomics, structural genomics conso SGC, hydrolase; 2.45A {Plasmodium falciparum} SCOP: c.14.1.1 Length = 215

 Score = 47.6 bits (114), Expect = 3e-08
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+  + +K RI+YL         + ++++ LYL   +    I +Y+NS G
Sbjct: 31 DVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNIN-HNDIKIYINSPG 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	92
4gm2_A	205	ATP-dependent CLP protease proteolytic subunit; st	99.96
3p2l_A	201	ATP-dependent CLP protease proteolytic subunit; st	99.93
3qwd_A	203	ATP-dependent CLP protease proteolytic subunit; ca	99.93
1tg6_A	277	Putative ATP-dependent CLP protease proteolytic S;	99.93
1yg6_A	193	ATP-dependent CLP protease proteolytic subunit; en	99.91
1y7o_A	218	ATP-dependent CLP protease proteolytic subunit; hy	99.91
2f6i_A	215	ATP-dependent CLP protease, putative; structural g	99.88
2cby_A	208	ATP-dependent CLP protease proteolytic subunit 1;	99.88
3viv_A	230	441AA long hypothetical NFED protein; protein-pept	99.11
3bf0_A	593	Protease 4; bacterial, hydrolase, inner membrane,	98.62
3rst_A	240	Signal peptide peptidase SPPA; alpha/beta protein	97.16
3bf0_A	593	Protease 4; bacterial, hydrolase, inner membrane,	96.79

>4gm2_A ATP-dependent CLP protease proteolytic subunit; structural genomics, structural genomics consortium, SGC, PR hydrolase; 2.80A {Plasmodium falciparum} PDB: 4hnk_A

Probab=99.96  E-value=4.4e-30  Score=187.87  Aligned_cols=83  Identities=29%  Similarity=0.442  Sum_probs=72.0

Q ss_pred             CCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCC----------CcchhhhhHHHH
Q 041456            8 TAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG----------TTEVGSFLCHAL   77 (92)
Q Consensus         8 ~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpG----------G~v~aglaIyD~   77 (92)
                      ...+++|.|+|++||++|+|||+++||+++|+++++||++|+++||++||++||||||          |+|++|++|||+
T Consensus        12 ~~~~~~~~di~s~Ll~~Riifl~~~I~d~~a~~iiaqLl~L~~ed~~k~I~lyINSpG~~~~~~~~~~G~v~aglaIyd~   91 (205)
T 4gm2_A           12 SGRENLYFQGPSLLLSKRIIFLSSPIYPHISEQIISQLLYLEYESKRKPIHLYINSTGDIDNNKIINLNGITDVISIVDV   91 (205)
T ss_dssp             ----------CHHHHTTTEEEECSCCCHHHHHHHHHHHHHHHHHCTTCCEEEEEEECTTEETTEESCTTHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHhcCCEEEECCEEcHHHHHHHHHHHHHHHhcCCCCCEEEEEeCCCCCCcCCCCCCCCHHHHHHHHHH
Confidence            3456899999999999999999999999999999999999999999999999999999          999999999999


Q ss_pred             Hhhcccccceeee
Q 041456           78 VFFQISSINASEY   90 (92)
Q Consensus        78 m~~v~~~v~t~~~   90 (92)
                      |+++++||.|+|-
T Consensus        92 m~~~~~~V~t~~~  104 (205)
T 4gm2_A           92 INYISSDVYTYCL  104 (205)
T ss_dssp             HHHSSSCEEEEEE
T ss_pred             HHhcCCCEEEEEE
Confidence            9999999999984

>3p2l_A ATP-dependent CLP protease proteolytic subunit; structural genomics, center for structural genomics of infec diseases, csgid; 2.29A {Francisella tularensis subsp} SCOP: c.14.1.1

Probab=99.93  E-value=1.2e-26  Score=168.41  Aligned_cols=90  Identities=28%  Similarity=0.400  Sum_probs=80.9

Q ss_pred             Ccccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHh
Q 041456            1 VIPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVF   79 (92)
Q Consensus         1 ~~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~   79 (92)
                      ++|.+ ++++.+++..|+|++||++|+|||+|+|++++++.++++|++|+.+++.++|.+|||||||++.+|++|||+|+
T Consensus         6 ~~p~~~~~~~~~~~~~d~~~~l~~~riI~l~g~I~~~~a~~i~~~L~~l~~~~~~~~I~l~INSpGG~v~~~~~I~~~i~   85 (201)
T 3p2l_A            6 LVPTVIEKTAGGERAFDIYSRLLKERIVFLNGEVNDHSANLVIAQLLFLESEDPDKDIYFYINSPGGMVTAGMGVYDTMQ   85 (201)
T ss_dssp             CSSEECCC-----CCEEHHHHHHHTTEEEEESCBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHH
T ss_pred             cCCeeeeeCCCCCcccCHHHHhhCCCEEEEcCEECHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCHHHHHHHHHHHH
Confidence            36776 77888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccccceeee
Q 041456           80 FQISSINASEY   90 (92)
Q Consensus        80 ~v~~~v~t~~~   90 (92)
                      .+++||.|+|.
T Consensus        86 ~~~~~v~t~~~   96 (201)
T 3p2l_A           86 FIKPDVSTICI   96 (201)
T ss_dssp             HSSSCEEEEEE
T ss_pred             HhCCCeEEEEc
Confidence            99999999874

>3qwd_A ATP-dependent CLP protease proteolytic subunit; caseinolytic protease, serin-protease, hydrolase; 2.10A {Staphylococcus aureus subsp} SCOP: c.14.1.1 PDB: 3v5e_A 3v5i_A 3sta_V 3st9_A

Probab=99.93  E-value=2.2e-26  Score=167.24  Aligned_cols=90  Identities=30%  Similarity=0.436  Sum_probs=80.9

Q ss_pred             Ccccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHh
Q 041456            1 VIPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVF   79 (92)
Q Consensus         1 ~~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~   79 (92)
                      ++|.+ ++++.+++..|+|++||++|+|||+|+|++++++.++++|++|+.+++.++|.+|||||||++.+|++|||+|+
T Consensus         3 ~~p~~~~~~~~~~~~~d~~~~l~~~riI~l~g~I~~~~a~~i~~~L~~l~~~~~~~~I~l~InSPGG~v~~~~~I~~~i~   82 (203)
T 3qwd_A            3 LIPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQ   82 (203)
T ss_dssp             CCCEEECC-----CEEEHHHHHHHTTEEEECSCBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHH
T ss_pred             CCCeeeeecCCCCcccCHHHHHhcCCEEEEcCEECHHHHHHHHHHHHHHHhcCCCCCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            36776 77888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccccceeee
Q 041456           80 FQISSINASEY   90 (92)
Q Consensus        80 ~v~~~v~t~~~   90 (92)
                      .+++||.|+|.
T Consensus        83 ~~~~~V~t~~~   93 (203)
T 3qwd_A           83 HIKPDVQTICI   93 (203)
T ss_dssp             HSSSCEEEEEE
T ss_pred             HhcCCcEEEEe
Confidence            99999999873

>1tg6_A Putative ATP-dependent CLP protease proteolytic S; mitochondrial CLPP, CLP/HSP 100, ATP-dependent protease, HYD; HET: FME; 2.10A {Homo sapiens} SCOP: c.14.1.1

Probab=99.93  E-value=4.3e-26  Score=172.96  Aligned_cols=88  Identities=28%  Similarity=0.392  Sum_probs=76.5

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|++ +.++.+++|.|+|++||++|+|||+|+|++++++.++++|++|+.+++.|+|.||||||||++.+|++|||+|++
T Consensus        59 ~p~~~~~~~~~~~~~di~s~ll~erII~l~G~I~d~~a~~iiaqL~~l~~ed~~k~I~L~INSPGGsV~ag~aIyd~I~~  138 (277)
T 1tg6_A           59 IPIVVEQTGRGERAYDIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGLAIYDTMQY  138 (277)
T ss_dssp             CCBCC---------CBHHHHHHTTTEEEEESSBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHHH
T ss_pred             CCeeeccCCCCcccccHHHHhhcCcEEEEcCEECHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCHHHHHHHHHHHHh
Confidence            5765 666778899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceee
Q 041456           81 QISSINASE   89 (92)
Q Consensus        81 v~~~v~t~~   89 (92)
                      +++||.|+|
T Consensus       139 ~k~pV~t~v  147 (277)
T 1tg6_A          139 ILNPICTWC  147 (277)
T ss_dssp             SCSCEEEEE
T ss_pred             cCCCEEEEE
Confidence            999999987

>1yg6_A ATP-dependent CLP protease proteolytic subunit; endopeptidase CLP, caseinolytic protease, protease TI, heat shock protein F21.5, hydrolase; 1.90A {Escherichia coli} SCOP: c.14.1.1 PDB: 1tyf_A 2fzs_A* 3mt6_R 1yg8_A 3hln_A 2zl2_A 2zl0_A 2zl4_A 2zl3_A 3tt7_A* 3tt6_A 3ktg_A 3kth_A 3kti_A* 3ktj_A* 3ktk_A* 3q7h_A

Probab=99.91  E-value=2.5e-24  Score=153.85  Aligned_cols=88  Identities=27%  Similarity=0.427  Sum_probs=82.8

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|.+ +.++.++++.|++++|+++|+||++|+|++.+++.++++|++++.+++.++|.||||||||++.+|++|||+|+.
T Consensus         3 ~p~~~~~~~~~~~~~d~~~~l~~~rii~l~g~I~~~~a~~i~~~L~~l~~~~~~~~I~l~InSPGG~v~a~~~I~~~i~~   82 (193)
T 1yg6_A            3 VPMVIEQTSRGERSFDIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPGGVITAGMSIYDTMQF   82 (193)
T ss_dssp             SCBCCSSSCSSCCCCBHHHHHHTTTEEEEESSBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHHH
T ss_pred             CCeecccCCCCcchhhHHHHHhcCCEEEEcCEEcHHHHHHHHHHHHHHHhcCCCCCEEEEEECcCCCHHHHHHHHHHHHh
Confidence            6766 556667889999999999999999999999999999999999999998999999999999999999999999999


Q ss_pred             cccccceee
Q 041456           81 QISSINASE   89 (92)
Q Consensus        81 v~~~v~t~~   89 (92)
                      ++.||.|++
T Consensus        83 ~~~pV~~~v   91 (193)
T 1yg6_A           83 IKPDVSTIC   91 (193)
T ss_dssp             SSSCEEEEE
T ss_pred             cCCCEEEEE
Confidence            999999986

>1y7o_A ATP-dependent CLP protease proteolytic subunit; hydrolase; 2.51A {Streptococcus pneumoniae} SCOP: c.14.1.1

Probab=99.91  E-value=1.6e-24  Score=158.05  Aligned_cols=88  Identities=25%  Similarity=0.396  Sum_probs=77.8

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|.+ ++++.+++|.|++++|+++|+||++|+|++++++.++++|++|+.+++.++|.||||||||++.+|++|||+|+.
T Consensus        22 ~p~~~~~~~~~~~~~d~~~~l~~~rii~l~g~I~~~~a~~i~~~L~~l~~~~~~k~I~l~InSPGG~v~ag~~I~~~i~~  101 (218)
T 1y7o_A           22 IPVVIEQTSRGERSYDIYSRLLKDRIIMLTGPVEDNMANSVIAQLLFLDAQDSTKDIYLYVNTPGGSVSAGLAIVDTMNF  101 (218)
T ss_dssp             CCEECC-------CEEHHHHHHHTTEEEEESCBCHHHHHHHHHHHHHHHHHCTTSCEEEEEEECCBCHHHHHHHHHHHHH
T ss_pred             CceeeecCCCCcchhhHHHHhhcCCEEEEeCEECHHHHHHHHHHHHHHHhcCCCCCEEEEEECcCCCHHHHHHHHHHHHh
Confidence            6765 667778899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceee
Q 041456           81 QISSINASE   89 (92)
Q Consensus        81 v~~~v~t~~   89 (92)
                      +++||.|++
T Consensus       102 ~~~pV~t~v  110 (218)
T 1y7o_A          102 IKADVQTIV  110 (218)
T ss_dssp             SSSCEEEEE
T ss_pred             cCCCEEEEE
Confidence            999999986

>2f6i_A ATP-dependent CLP protease, putative; structural genomics, structural genomics conso SGC, hydrolase; 2.45A {Plasmodium falciparum} SCOP: c.14.1.1

Probab=99.88  E-value=8.8e-23  Score=148.99  Aligned_cols=82  Identities=20%  Similarity=0.344  Sum_probs=77.4

Q ss_pred             CCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccc
Q 041456            7 GTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSIN   86 (92)
Q Consensus         7 ~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~   86 (92)
                      .......|.|++++|+++|+||++|+|++++++.++++|++|+.+++ ++|.||||||||++.+|++|||+|+.+++||.
T Consensus        22 ~~~~~~~~~d~~~~l~~~riI~l~G~I~~~~a~~i~~~L~~l~~~~~-k~I~l~INSPGGsv~a~~~I~~~i~~~~~pV~  100 (215)
T 2f6i_A           22 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINH-NDIKIYINSPGGSINEGLAILDIFNYIKSDIQ  100 (215)
T ss_dssp             CCCCSCSSHHHHHHHHTTTEEEECSCBCHHHHHHHHHHHHHHHHHCC-SCEEEEEEECCBCHHHHHHHHHHHHHSSSCEE
T ss_pred             CCccccccccHHHHHhCceEEEEccEECHHHHHHHHHHHHHHHhCCC-CcEEEEEECCCCCHHHHHHHHHHHHhcCCCEE
Confidence            34455789999999999999999999999999999999999999998 99999999999999999999999999999999


Q ss_pred             eee
Q 041456           87 ASE   89 (92)
Q Consensus        87 t~~   89 (92)
                      |+|
T Consensus       101 t~v  103 (215)
T 2f6i_A          101 TIS  103 (215)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            976

>2cby_A ATP-dependent CLP protease proteolytic subunit 1; serine protease, endopept mycobacterium tuberculosis, ATP-dependent protease; 2.6A {Mycobacterium tuberculosis} SCOP: c.14.1.1 PDB: 2c8t_A 2ce3_A

Probab=99.88  E-value=5.6e-23  Score=148.63  Aligned_cols=88  Identities=23%  Similarity=0.277  Sum_probs=76.0

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      +|.+ +.++.+++|.|++++|+++|+||++|+|++.+++.++++|.+++.+++.++|.|+||||||++.+|++|||+|+.
T Consensus         4 ~p~~~~~~~~~~~~~~~~~~l~~~rii~l~G~I~~~~a~~i~~~L~~~~~~~~~k~I~l~InSPGG~v~a~~~I~~~i~~   83 (208)
T 2cby_A            4 VTDMRSNSQGLSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVL   83 (208)
T ss_dssp             -----------CHHHHHHHHHHTTTEEEECSCBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHHH
T ss_pred             CCeeeccCCCCcchhhHHHHhhcCcEEEEcCEECHHHHHHHHHHHHHHHhCCCCCCEEEEEECCCCCHHHHHHHHHHHHh
Confidence            4654 556677899999999999999999999999999999999999999988999999999999999999999999999


Q ss_pred             cccccceee
Q 041456           81 QISSINASE   89 (92)
Q Consensus        81 v~~~v~t~~   89 (92)
                      .+.||.|++
T Consensus        84 ~~~pV~~~v   92 (208)
T 2cby_A           84 APCDIATYA   92 (208)
T ss_dssp             CSSCEEEEE
T ss_pred             cCCCEEEEE
Confidence            999998876

>3viv_A 441AA long hypothetical NFED protein; protein-peptide complex, alpha / beta motif, protease, membr protein stomatin, hydrolase-protein binding complex; 2.25A {Pyrococcus horikoshii} PDB: 3bpp_A 2deo_A

Probab=99.11  E-value=1.2e-10  Score=85.84  Aligned_cols=64  Identities=6%  Similarity=-0.047  Sum_probs=58.2

Q ss_pred             ceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceee
Q 041456           25 RIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASE   89 (92)
Q Consensus        25 RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~   89 (92)
                      .+|.+.|.|++++++.+.++|..++. ++.+.|.|+||||||++.++..|||+|+..+.||.+.+
T Consensus        11 ~vI~i~g~I~~~~~~~l~~~l~~a~~-~~~~~Ivl~inspGG~v~~~~~i~~~i~~~~~PVia~v   74 (230)
T 3viv_A           11 YVAQIKGQITSYTYDQFDRYITIAEQ-DNAEAIIIELDTPGGRADAMMNIVQRIQQSKIPVIIYV   74 (230)
T ss_dssp             EEEEEESCBCHHHHHHHHHHHHHHHH-TTCSEEEEEEEBSCEEHHHHHHHHHHHHTCSSCEEEEE
T ss_pred             EEEEEeCEECHHHHHHHHHHHHHHhc-CCCCEEEEEEeCCCcCHHHHHHHHHHHHhCCCCEEEEE
Confidence            46899999999999999999999875 45899999999999999999999999999888887765

>3bf0_A Protease 4; bacterial, hydrolase, inner membrane, membrane, transmembrane; 2.55A {Escherichia coli} PDB: 3bez_A

Probab=98.62  E-value=1.2e-08  Score=82.87  Aligned_cols=74  Identities=12%  Similarity=-0.099  Sum_probs=51.9

Q ss_pred             cchHHhhhcCceEEeCccc---CHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCC-CcchhhhhHHHHHhhcccc-cceee
Q 041456           15 PDLASYLYKNRIVYLGMSF---VPSVRELILAEFLYLQYEDAEKPIYLYLNSTG-TTEVGSFLCHALVFFQISS-INASE   89 (92)
Q Consensus        15 ~dl~~~l~~~RiifL~g~I---d~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpG-G~v~aglaIyD~m~~v~~~-v~t~~   89 (92)
                      .+.+++++++   |+++++   ++..+++++++|..+..+++-+.|.|+||||| |++.++..|||+|+..++. +.+++
T Consensus        49 ~~~~~~ll~~---~~~~~~~~~~~~~~~~i~~~L~~a~~d~~ik~I~L~inspGgG~v~~~~~I~~~i~~~k~~gkpvva  125 (593)
T 3bf0_A           49 SQRFSKLSRQ---LLGASSDRLQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYA  125 (593)
T ss_dssp             ---------------------CCEEEHHHHHHHHHHHHHCTTCCCEEEECTEEEECCHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CChHHHHHhh---hccCCcccccccCHHHHHHHHHHHHhCCCceEEEEEeCCCCCCcHHHHHHHHHHHHHHHhcCCeEEE
Confidence            3556666666   677765   36789999999999988777899999999999 9999999999999999875 77777


Q ss_pred             ec
Q 041456           90 YI   91 (92)
Q Consensus        90 ~~   91 (92)
                      |.
T Consensus       126 ~~  127 (593)
T 3bf0_A          126 VG  127 (593)
T ss_dssp             EE
T ss_pred             EE
Confidence            74

>3rst_A Signal peptide peptidase SPPA; alpha/beta protein fold, signal peptide digestion, bacterial membrane, hydrolase; 2.37A {Bacillus subtilis}

Probab=97.16  E-value=0.00038  Score=50.41  Aligned_cols=57  Identities=16%  Similarity=0.039  Sum_probs=45.3

Q ss_pred             eEEeCcccCHH------------HHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc
Q 041456           26 IVYLGMSFVPS------------VRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI   82 (92)
Q Consensus        26 iifL~g~Id~~------------~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~   82 (92)
                      +|.+.|+|.+.            ..+++...|-.+..++.-+-|.|.+|||||++.++..+++.++-.+
T Consensus         7 vi~i~G~I~~~~~~~~~~~~~~~~~~~l~~~l~~a~~d~~v~~ivL~~~s~Gg~~~~~~~i~~~l~~~~   75 (240)
T 3rst_A            7 VLEVSGTIQDNGDSSSLLGADGYNHRTFLKNLERAKDDKTVKGIVLKVNSPGGGVYESAEIHKKLEEIK   75 (240)
T ss_dssp             EEEEESCBCCC---------CCCCHHHHHHHHHHHHHCTTEEEEEEEEEECCBCHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEEcCCCCcCcccccCCcCHHHHHHHHHHHHhCCCcEEEEEEecCCCCCHHHHHHHHHHHHHHH
Confidence            34555666654            3578888888887766668899999999999999999999998764

>3bf0_A Protease 4; bacterial, hydrolase, inner membrane, membrane, transmembrane; 2.55A {Escherichia coli} PDB: 3bez_A

Probab=96.79  E-value=0.00052  Score=55.70  Aligned_cols=57  Identities=18%  Similarity=0.131  Sum_probs=47.9

Q ss_pred             eEEeCcccCHH-------HHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcc
Q 041456           26 IVYLGMSFVPS-------VRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQI   82 (92)
Q Consensus        26 iifL~g~Id~~-------~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~   82 (92)
                      +|.+.+++...       .++.+.+.|-.+..++.-+-|.|.+|||||++.++..|++.++-++
T Consensus       305 vI~l~g~i~~n~~~~~~~~~~~l~~~L~~a~~d~~vkaVVL~i~spGG~~~~~~~i~~~i~~l~  368 (593)
T 3bf0_A          305 VVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAAR  368 (593)
T ss_dssp             EEEEEEEEESSSSCTTSEEHHHHHHHHHHHHHCTTEEEEEEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             EEEEeeeecCCccccchhHHHHHHHHHHHHHhCCCCCEEEEEecCCCCCHHHHHHHHHHHHHHH
Confidence            67888887544       3799999999887766678999999999999999999999887654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	92
d2cbya1	179	c.14.1.1 (A:15-193) Clp protease, ClpP subunit {My	4e-10
d2f6ia1	190	c.14.1.1 (A:177-366) Clp protease, ClpP subunit {P	3e-09
d1yg6a1	183	c.14.1.1 (A:11-193) Clp protease, ClpP subunit {Es	3e-09
d1tg6a1	193	c.14.1.1 (A:1-193) Clp protease, ClpP subunit {Hum	2e-08
d1y7oa1	192	c.14.1.1 (A:2-193) Clp protease, ClpP subunit {Str	6e-08

>d2cbya1 c.14.1.1 (A:15-193) Clp protease, ClpP subunit {Mycobacterium tuberculosis [TaxId: 1773]} Length = 179

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 51.2 bits (122), Expect = 4e-10
 Identities = 18/49 (36%), Positives = 25/49 (51%)

Query: 19 SYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
            L   RI++LG      +   + A+ L L  EDA K I LY+NS G +
Sbjct: 8  ERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGS 56

>d2f6ia1 c.14.1.1 (A:177-366) Clp protease, ClpP subunit {Plasmodium falciparum [TaxId: 5833]} Length = 190

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Plasmodium falciparum [TaxId: 5833]

 Score = 48.9 bits (116), Expect = 3e-09
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 13 PPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSF 72
             D+  + +K RI+YL         + ++++ LYL   +    I +Y+NS G +     
Sbjct: 7  MKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNIN-HNDIKIYINSPGGSINEGL 65

Query: 73 LCHALVFF 80
              +  +
Sbjct: 66 AILDIFNY 73

>d1yg6a1 c.14.1.1 (A:11-193) Clp protease, ClpP subunit {Escherichia coli [TaxId: 562]} Length = 183

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Escherichia coli [TaxId: 562]

 Score = 48.7 bits (116), Expect = 3e-09
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTG 65
          D+ S L K R+++L       +  LI+A+ L+L+ E+ EK IYLY+NS G
Sbjct: 8  DIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPG 57

>d1tg6a1 c.14.1.1 (A:1-193) Clp protease, ClpP subunit {Human (Homo sapiens), mitochondrial [TaxId: 9606]} Length = 193

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Human (Homo sapiens), mitochondrial [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 2e-08
 Identities = 21/52 (40%), Positives = 32/52 (61%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L + RIV +      SV  L++A+ L+LQ E  +KPI++Y+NS G  
Sbjct: 18 DIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPGGV 69

>d1y7oa1 c.14.1.1 (A:2-193) Clp protease, ClpP subunit {Streptococcus pneumoniae [TaxId: 1313]} Length = 192

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Streptococcus pneumoniae [TaxId: 1313]

 Score = 45.8 bits (108), Expect = 6e-08
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query: 16 DLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTT 67
          D+ S L K+RI+ L      ++   ++A+ L+L  +D+ K IYLY+N+ G +
Sbjct: 16 DIYSRLLKDRIIMLTGPVEDNMANSVIAQLLFLDAQDSTKDIYLYVNTPGGS 67

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	92
d1tg6a1	193	Clp protease, ClpP subunit {Human (Homo sapiens),	99.97
d1y7oa1	192	Clp protease, ClpP subunit {Streptococcus pneumoni	99.96
d2cbya1	179	Clp protease, ClpP subunit {Mycobacterium tubercul	99.93
d1yg6a1	183	Clp protease, ClpP subunit {Escherichia coli [TaxI	99.93
d2f6ia1	190	Clp protease, ClpP subunit {Plasmodium falciparum	99.92

>d1tg6a1 c.14.1.1 (A:1-193) Clp protease, ClpP subunit {Human (Homo sapiens), mitochondrial [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Human (Homo sapiens), mitochondrial [TaxId: 9606]

Probab=99.97  E-value=1.2e-31  Score=191.43  Aligned_cols=90  Identities=28%  Similarity=0.386  Sum_probs=78.8

Q ss_pred             Ccccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHh
Q 041456            1 VIPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVF   79 (92)
Q Consensus         1 ~~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~   79 (92)
                      +||++ |+++.++++.|+|++||++|+|||+|+||++++++++++|++|+.+++++||++|||||||++.+|++|||+|+
T Consensus         2 ~~p~~~~~~~~~~~~~Di~s~l~~~Riifl~g~I~~~~~~~~i~~l~~l~~~~~~~~I~l~InS~GG~v~~g~~i~d~i~   81 (193)
T d1tg6a1           2 LIPIVVEQTGRGERAYDIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGLAIYDTMQ   81 (193)
T ss_dssp             CCCBCC---------CBHHHHHHTTTEEEEESSBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHH
T ss_pred             CCCEEEeecCCCchhhhHhHHHhccCEEEECCEEchHHHHHHHHHHHHhcccCCCcEEEEEeecCcccHHHHHHHHHHHH
Confidence            57887 78888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccccceeee
Q 041456           80 FQISSINASEY   90 (92)
Q Consensus        80 ~v~~~v~t~~~   90 (92)
                      +++++|.|+|.
T Consensus        82 ~~~~~V~tv~~   92 (193)
T d1tg6a1          82 YILNPICTWCV   92 (193)
T ss_dssp             HSCSCEEEEEE
T ss_pred             hhcCceEEEEc
Confidence            99999999985

>d1y7oa1 c.14.1.1 (A:2-193) Clp protease, ClpP subunit {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=99.96  E-value=7.1e-31  Score=186.67  Aligned_cols=89  Identities=25%  Similarity=0.391  Sum_probs=79.1

Q ss_pred             cccc-cCCCCCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhh
Q 041456            2 IPFT-SGTAWEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFF   80 (92)
Q Consensus         2 ~~~~-~~~~~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~   80 (92)
                      ||.+ ++++.++++.|+|++||++|+|||+|+||+++++.++++|+||+.+++++||++|||||||++.+|++|||+|++
T Consensus         1 ~p~v~~~~~~~~~~~di~s~Ll~~rii~l~g~I~~~~~~~~~~~l~~l~~~~~~~~I~l~InS~GG~v~~glai~d~i~~   80 (192)
T d1y7oa1           1 IPVVIEQTSRGERSYDIYSRLLKDRIIMLTGPVEDNMANSVIAQLLFLDAQDSTKDIYLYVNTPGGSVSAGLAIVDTMNF   80 (192)
T ss_dssp             CCEECC-------CEEHHHHHHHTTEEEEESCBCHHHHHHHHHHHHHHHHHCTTSCEEEEEEECCBCHHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCcchhhhhhHHhccCEEEECCEEchHHHHHHHHHHHHhhhhcccCceeeeecCCCCCHHHHHHHHHHHHh
Confidence            5666 778888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccceeee
Q 041456           81 QISSINASEY   90 (92)
Q Consensus        81 v~~~v~t~~~   90 (92)
                      ++++|.|+|.
T Consensus        81 ~~~~v~t~~~   90 (192)
T d1y7oa1          81 IKADVQTIVM   90 (192)
T ss_dssp             SSSCEEEEEE
T ss_pred             cCcceEEEec
Confidence            9999999985

>d2cbya1 c.14.1.1 (A:15-193) Clp protease, ClpP subunit {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.93  E-value=1.5e-26  Score=162.29  Aligned_cols=76  Identities=25%  Similarity=0.349  Sum_probs=73.9

Q ss_pred             cchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceeee
Q 041456           15 PDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEY   90 (92)
Q Consensus        15 ~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~~   90 (92)
                      .++|++|+++|+|||+|+||++++++++++|++|+++++++||++|||||||++.+|++|||+|++++++|.|+|.
T Consensus         4 ~~i~~~l~~~rii~l~g~I~~~~~~~~i~~l~~l~~~~~~~~I~l~InS~GG~v~~gl~i~d~i~~~~~~v~t~~~   79 (179)
T d2cbya1           4 DSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVLAPCDIATYAM   79 (179)
T ss_dssp             HHHHHHHHTTTEEEECSCBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHHHCSSCEEEEEE
T ss_pred             cHHHHHHHhCCEEEECCEECHHHHHHHHHHHHHHhccCCCCeEEEEeeCCCCCHHHHHHHHHHHHhhccceeeehh
Confidence            4689999999999999999999999999999999999999999999999999999999999999999999999985

>d1yg6a1 c.14.1.1 (A:11-193) Clp protease, ClpP subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=2.3e-26  Score=161.12  Aligned_cols=81  Identities=27%  Similarity=0.401  Sum_probs=78.2

Q ss_pred             CCCCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceee
Q 041456           10 WEQPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASE   89 (92)
Q Consensus        10 ~~~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~   89 (92)
                      .+++..|+|++|+++|+|||+|+||+++++.++++|++|+.+++++||++|||||||++.+|++|||+|+.+++||.|+|
T Consensus         2 ~~~~~~di~s~L~~~riI~l~g~I~~~~~~~~i~~l~~l~~~~~~~~I~l~InS~GG~v~~g~~i~d~i~~~~~~v~tv~   81 (183)
T d1yg6a1           2 RGERSFDIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPGGVITAGMSIYDTMQFIKPDVSTIC   81 (183)
T ss_dssp             SSCCCCBHHHHHHTTTEEEEESSBCHHHHHHHHHHHHHHHHHCSSSCEEEEEEECCBCHHHHHHHHHHHHHSSSCEEEEE
T ss_pred             CccchhhHhHHHhccCEEEECCEECHHHHHHHHHHHHHhhhhccCCceEEEEeCCCccHHHHHHHHHHHHhCCCCEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             e
Q 041456           90 Y   90 (92)
Q Consensus        90 ~   90 (92)
                      .
T Consensus        82 ~   82 (183)
T d1yg6a1          82 M   82 (183)
T ss_dssp             E
T ss_pred             E
Confidence            5

>d2f6ia1 c.14.1.1 (A:177-366) Clp protease, ClpP subunit {Plasmodium falciparum [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Clp protease, ClpP subunit
domain: Clp protease, ClpP subunit
species: Plasmodium falciparum [TaxId: 5833]

Probab=99.92  E-value=8.2e-26  Score=160.07  Aligned_cols=78  Identities=21%  Similarity=0.401  Sum_probs=74.6

Q ss_pred             CCCcchHHhhhcCceEEeCcccCHHHHHHHHHHHHHhhhcCCCCCeEEEEeCCCCcchhhhhHHHHHhhcccccceeee
Q 041456           12 QPPPDLASYLYKNRIVYLGMSFVPSVRELILAEFLYLQYEDAEKPIYLYLNSTGTTEVGSFLCHALVFFQISSINASEY   90 (92)
Q Consensus        12 ~~~~dl~~~l~~~RiifL~g~Id~~~a~~ii~~Ll~L~~~d~~~~I~lyINSpGG~v~aglaIyD~m~~v~~~v~t~~~   90 (92)
                      ..+.|++++||++|+|||+|+||++++++++++|++|++++ .+||++|||||||++.+|++|||+|+.++++|.|+|+
T Consensus         6 ~~~~d~~~~l~~~rii~l~g~Id~~~~~~~i~~l~~l~~~~-~~~I~l~INS~GG~v~~g~ai~d~i~~~~~~v~tv~~   83 (190)
T d2f6ia1           6 DMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNIN-HNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISF   83 (190)
T ss_dssp             CSSHHHHHHHHTTTEEEECSCBCHHHHHHHHHHHHHHHHHC-CSCEEEEEEECCBCHHHHHHHHHHHHHSSSCEEEEEE
T ss_pred             cchhhHHHHHHcCcEEEECCeeCHHHHHHHHHHHHHHhccC-CCCeEEEEeCchhhhhHHHHHHHHHHhhCCceEEEEe
Confidence            45789999999999999999999999999999999999887 6799999999999999999999999999999999986