Citrus Sinensis ID: 028706

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-----
Protein Sequence
MSTYLIGQKTCMNCKTLNPQLPLQPCRCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHSPS
Secondary Structure (PSIPRED)
ccEEEEccccccccccccccccccccccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHEEEEEEEEEEEEccccccccccccccccccccccEEEEEEEEEEccccccccEEEEEccccccccEEEEEEEccccEEEcccccccEEEccccEEEEccccccccccccccccccccEEEEEEEEEccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEccccccccccccccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHccEEEccccccccccccccccccccccccEEEEEEEEEEccccccccEEEEEcccccccHHEEEEEEccccEEEEccccEEEEcccccEEEEccccccccccccccccccccEEEEEEEEEccHHHcccccccccccccccc
Coil and Loop (DISEMBL)
mstyligqktcmncktlnpqlplqpcrcilgeiSNMAAHNFLWSLTKNCFTFGLIgltvsdryasivpvrgssmsptfnpttdsfmgslsddHVLMEKFCLQkykfshgdvivfcspsnhkekHVKRIIglpgdwigtpmtndvvkvpnghcwvegdnpsssldsrsfgpiplglvkgrvthilwppqrvrhverknhqkrhsps
Flexible Loop (DISEMBL)
mstyligqktcmncktlnpQLPLQPCRCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVpvrgssmsptfnPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVthilwppqrvrhverknhqkrhsps
Low Complexity Region (SEG)
MSTYLIGQKTCMNCKTLNPQLPLQPCRCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHSPS
Disordered region (IsUnstruct)
***YLIGQKTCMNCKTLNPQLPLQPCRCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVR****************GSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEG***********FGPIPLGLVKGRVTHILWPPQ*****************
Disordered Region (DISOPRED)
***Y************************************FLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE***********
Disordered Region (DISEMBL)
MSTYLIGQKTCMNCKTLNPQLPLQPCRCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRH*************
Disordered Region (DISPRO)
*STYLIGQKTCMNCKTLNPQLPLQPCRCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE***********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTYLIGQKTCMNCKTLNPQLPLQPCRCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHSPS
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	205	2.2.26 [Sep-21-2011]
Q6AZD4	183	Mitochondrial inner membr	yes	no	0.741	0.830	0.392	2e-28
Q8BPT6	175	Mitochondrial inner membr	yes	no	0.712	0.834	0.421	2e-27
Q2KI92	177	Mitochondrial inner membr	yes	no	0.726	0.841	0.406	6e-27
Q96T52	175	Mitochondrial inner membr	yes	no	0.726	0.851	0.406	7e-27
Q5PQ63	170	Mitochondrial inner membr	N/A	no	0.726	0.876	0.394	9e-25
P46972	177	Mitochondrial inner membr	yes	no	0.629	0.728	0.433	8e-23
Q9UST2	180	Mitochondrial inner membr	yes	no	0.717	0.816	0.365	2e-19
Q9CQU8	166	Mitochondrial inner membr	no	no	0.687	0.849	0.347	4e-19
Q96LU5	166	Mitochondrial inner membr	no	no	0.687	0.849	0.341	5e-18
O74800	157	Mitochondrial inner membr	no	no	0.526	0.687	0.398	2e-16

>sp|Q6AZD4|IMP2L_DANRE Mitochondrial inner membrane protease subunit 2 OS=Danio rerio GN=immp2l PE=2 SV=1

 Score =  125 bits (315), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 93/158 (58%), Gaps = 6/158 (3%)

Query: 38  AHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLME 97
              +  +     F    + +TV DR A +  V G+SM P+ NP  +S     S D VL+ 
Sbjct: 7   GRRYFKAFVSGFFVAVPVTVTVLDRLAYVARVEGASMQPSLNPDGES-----SPDVVLLN 61

Query: 98  KFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEG 156
           ++ ++ Y    GD++   SP N ++K +KR+IG+ GD+I T    N  V+VP+GH W+EG
Sbjct: 62  RWSVRNYHVQRGDIVSVLSPKNPQQKIIKRVIGIEGDFIKTLGYKNRYVRVPDGHLWIEG 121

Query: 157 DNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
           D+   S DS +FGP+ LGLV GR +HI+WPP R + +E
Sbjct: 122 DHHGHSFDSNAFGPVSLGLVHGRASHIIWPPSRWQRIE 159

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space.
Danio rerio (taxid: 7955)
EC: 3EC: .EC: 4EC: .EC: 2EC: 1EC: .EC: -

>sp|Q8BPT6|IMP2L_MOUSE Mitochondrial inner membrane protease subunit 2 OS=Mus musculus GN=Immp2l PE=2 SV=1

 Score =  122 bits (305), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/152 (42%), Positives = 89/152 (58%), Gaps = 6/152 (3%)

Query: 44  SLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQK 103
           +  K  F    + +T  DR A +  V GSSM P+ NP      GS S D VL+  + ++ 
Sbjct: 14  AFCKGFFVAVPVAVTFLDRVACVARVEGSSMQPSLNPG-----GSQSSDVVLLNHWKVRN 68

Query: 104 YKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNPSSS 162
           ++   GD++   SP N ++K +KR+I L GD + T    N +VKVP GH WVEGD+   S
Sbjct: 69  FEVQRGDIVSLVSPKNPEQKIIKRVIALEGDIVRTIGHKNRLVKVPRGHMWVEGDHHGHS 128

Query: 163 LDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
            DS SFGP+ LGL+    THILWPP+R + +E
Sbjct: 129 FDSNSFGPVSLGLLHAHATHILWPPERWQRLE 160

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q2KI92|IMP2L_BOVIN Mitochondrial inner membrane protease subunit 2 OS=Bos taurus GN=IMMP2L PE=2 SV=1

 Score =  120 bits (301), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 63/155 (40%), Positives = 89/155 (57%), Gaps = 6/155 (3%)

Query: 41  FLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFC 100
           +  +  K  F    + +T  DR A +  V G+SM P+ NP      GS S D VL+  + 
Sbjct: 11  YFKAFCKGFFVAVPVAVTFLDRVACVARVEGASMQPSLNPG-----GSQSSDVVLLNHWK 65

Query: 101 LQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNP 159
           ++ ++   GD++   SP N ++K +KR+I L GD + T    N  VKVP GH WVEGD+ 
Sbjct: 66  VRNFEVQRGDIVSLVSPKNPEQKIIKRVIALEGDIVKTMGHKNRYVKVPRGHIWVEGDHH 125

Query: 160 SSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
             S DS SFGP+ LGL+    THILWPP+R + +E
Sbjct: 126 GHSFDSNSFGPVSLGLLHAHATHILWPPKRWQKLE 160

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q96T52|IMP2L_HUMAN Mitochondrial inner membrane protease subunit 2 OS=Homo sapiens GN=IMMP2L PE=2 SV=1

 Score =  120 bits (301), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 63/155 (40%), Positives = 90/155 (58%), Gaps = 6/155 (3%)

Query: 41  FLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFC 100
           ++ +  K  F    + +T  DR A +  V G+SM P+ NP      GS S D VL+  + 
Sbjct: 11  YIKAFCKGFFVAVPVAVTFLDRVACVARVEGASMQPSLNPG-----GSQSSDVVLLNHWK 65

Query: 101 LQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNP 159
           ++ ++   GD++   SP N ++K +KR+I L GD + T    N  VKVP GH WVEGD+ 
Sbjct: 66  VRNFEVHRGDIVSLVSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH 125

Query: 160 SSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
             S DS SFGP+ LGL+    THILWPP+R + +E
Sbjct: 126 GHSFDSNSFGPVSLGLLHAHATHILWPPERWQKLE 160

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q5PQ63|IMP2L_XENLA Mitochondrial inner membrane protease subunit 2 OS=Xenopus laevis GN=immp2l PE=2 SV=1

 Score =  113 bits (282), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 62/157 (39%), Positives = 83/157 (52%), Gaps = 8/157 (5%)

Query: 36  MAAH--NFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDH 93
           MA H   ++ +     F    + +T  DR A I  V G SM P+ NP           D 
Sbjct: 1   MAQHGRRYVRAFISGFFVAVPVTVTFLDRVACIARVEGVSMQPSLNPDARG-----ESDI 55

Query: 94  VLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHC 152
           VL+ ++  + Y    GD++   SP N ++K +KR+I L GD + T    N  VKVP GH 
Sbjct: 56  VLLNRWRARNYDVQRGDIVSLVSPKNPEQKIIKRVIALEGDIVKTLGHKNRYVKVPRGHV 115

Query: 153 WVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQR 189
           WVEGD+   S DS +FGP+ LGL+    THILWPP R
Sbjct: 116 WVEGDHHGHSFDSNAFGPVSLGLLHSHATHILWPPNR 152

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|P46972|IMP2_YEAST Mitochondrial inner membrane protease subunit 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=IMP2 PE=1 SV=1

 Score =  106 bits (265), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 59/136 (43%), Positives = 83/136 (61%), Gaps = 7/136 (5%)

Query: 57  LTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQK-YKFSHGDVIVFC 115
           LT+++    I  V+G+SM PT NP T++    L+ D VL+ KF ++     S  D+I+F 
Sbjct: 25  LTINNNVVHIAQVKGTSMQPTLNPQTET----LATDWVLLWKFGVKNPSNLSRDDIILFK 80

Query: 116 SPSNHKEKHVKRIIGLPGDWIGT--PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPL 173
           +P+N ++ + KR+ GLP D I T  P     V +P GH WVEGDN   S+DS +FGPI  
Sbjct: 81  APTNPRKVYCKRVKGLPFDTIDTKFPYPKPQVNLPRGHIWVEGDNYFHSIDSNTFGPISS 140

Query: 174 GLVKGRVTHILWPPQR 189
           GLV G+   I+WPP R
Sbjct: 141 GLVIGKAITIVWPPSR 156

Catalytic component of the mitochondrial inner membrane peptidase (IMP) complex. IMP catalyzes the removal of signal peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. The two catalytic IMP subunits seem to have non-overlapping substrate specificities. IMP2 substrates include nuclear encoded CYB2, mitochondrially encoded COX2 and cytochrome c1. Required for the stability of IMP1.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q9UST2|IMP2L_SCHPO Mitochondrial inner membrane protease subunit 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC336.13c PE=3 SV=1

 Score = 95.5 bits (236), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 86/164 (52%), Gaps = 17/164 (10%)

Query: 47  KNCFTFGLIGLT--------VSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEK 98
           K+ F   L+G+T        V     S+  + G SM P FNP T+     L  D VL+ K
Sbjct: 12  KSVFFKNLVGITLWVPVLMFVEQHVVSVGTIEGRSMKPAFNPETNM----LQRDRVLLWK 67

Query: 99  FCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT--PMTNDVVKVPNGHCWVEG 156
           +  + YK   GDV++  SP N +E  VKR++G+  D + T  P    +V VP GH WVEG
Sbjct: 68  WN-KDYK--RGDVVILRSPENPEELLVKRVLGVEYDIMKTRPPKKLSLVPVPEGHVWVEG 124

Query: 157 DNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQK 200
           D    S+DS  FGP+  GL+  +V  IL+P  R   ++ +  +K
Sbjct: 125 DEQFHSIDSNKFGPVSTGLITAKVIAILFPFSRAGRIDHEGFRK 168

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q9CQU8|IMP1L_MOUSE Mitochondrial inner membrane protease subunit 1 OS=Mus musculus GN=Immp1l PE=2 SV=1

 Score = 94.4 bits (233), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 57/164 (34%), Positives = 80/164 (48%), Gaps = 23/164 (14%)

Query: 27  RCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFM 86
           R +LG+   +A +   +    +C  F  +G         +V   G SM PT         
Sbjct: 3   RGVLGKAFRLAGYTIQYGCIAHC-AFEYVG--------GVVMCSGPSMEPTIQ------- 46

Query: 87  GSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVK 146
              + D V  E      Y    GD+++  SPS+ K    KR+IGL GD I +   +DV K
Sbjct: 47  ---NSDIVFAENLSRHFYGIQRGDIVIAKSPSDPKSNICKRVIGLEGDKILSTSPSDVFK 103

Query: 147 ----VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWP 186
               VP GH W+EGDN  +S DSR +GPIP GL++GR+   +WP
Sbjct: 104 SRSYVPTGHVWLEGDNLQNSTDSRYYGPIPYGLIRGRIFFKIWP 147

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q96LU5|IMP1L_HUMAN Mitochondrial inner membrane protease subunit 1 OS=Homo sapiens GN=IMMP1L PE=2 SV=1

 Score = 90.9 bits (224), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 56/164 (34%), Positives = 78/164 (47%), Gaps = 23/164 (14%)

Query: 27  RCILGEISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFM 86
           R +LG+   +  +   +    +C  F  +G         +V   G SM PT         
Sbjct: 3   RGVLGKTFRLVGYTIQYGCIAHC-AFEYVG--------GVVMCSGPSMEPTIQ------- 46

Query: 87  GSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVK 146
              + D V  E      Y    GD+++  SPS+ K    KR+IGL GD I T   +D  K
Sbjct: 47  ---NSDIVFAENLSRHFYGIQRGDIVIAKSPSDPKSNICKRVIGLEGDKILTTSPSDFFK 103

Query: 147 ----VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWP 186
               VP GH W+EGDN  +S DSR +GPIP GL++GR+   +WP
Sbjct: 104 SHSYVPMGHVWLEGDNLQNSTDSRCYGPIPYGLIRGRIFFKIWP 147

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|O74800|IMP1_SCHPO Mitochondrial inner membrane protease subunit 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=imp1 PE=3 SV=1

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 47/118 (39%), Positives = 68/118 (57%), Gaps = 10/118 (8%)

Query: 71  GSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIG 130
           G SM PT N   +  +  L   H    + C      S GDV+V   PS+ K+   KRIIG
Sbjct: 33  GPSMMPTLNSGGEFVL--LDKLHGRFARSC------SVGDVVVSAKPSDSKQHVCKRIIG 84

Query: 131 LPGD--WIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWP 186
           +PGD  ++    +N  + +P GH W+ GDN + SLDSR++GP+P+GL+K +V   +WP
Sbjct: 85  MPGDTIYVDPTSSNKKITIPLGHVWLAGDNIAHSLDSRNYGPVPMGLIKAKVIARVWP 142

Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

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	205
255574385	170	mitochondrial inner membrane protease su	0.829	1.0	0.747	2e-69
224140407	169	predicted protein [Populus trichocarpa]	0.819	0.994	0.711	2e-66
449439902	184	PREDICTED: mitochondrial inner membrane	0.829	0.923	0.658	4e-65
225440672	170	PREDICTED: mitochondrial inner membrane	0.785	0.947	0.695	1e-64
388512387	173	unknown [Lotus japonicus]	0.775	0.919	0.679	9e-60
116794380	170	unknown [Picea sitchensis]	0.819	0.988	0.642	2e-59
357481155	165	Mitochondrial inner membrane protease su	0.785	0.975	0.6	5e-56
351727543	170	uncharacterized protein LOC100499932 [Gl	0.775	0.935	0.610	1e-55
351722229	169	uncharacterized protein LOC100527429 [Gl	0.819	0.994	0.595	1e-55
297829426	154	signal peptidase I family protein [Arabi	0.741	0.987	0.588	1e-52

>gi|255574385|ref|XP_002528106.1| mitochondrial inner membrane protease subunit, putative [Ricinus communis] gi|223532495|gb|EEF34285.1| mitochondrial inner membrane protease subunit, putative [Ricinus communis]

 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 127/170 (74%), Positives = 142/170 (83%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           MA+ NFLWSL K  FT GLIG+T+SDRYASIVPVRG SMSPTFNP T +F GS  DD VL
Sbjct: 1   MASSNFLWSLAKKYFTVGLIGITISDRYASIVPVRGVSMSPTFNPGTSTFWGSFIDDCVL 60

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCL+KY+FSHGDV+VF SPSNHKEKH+KRIIGLPGDWIGTP   DVVKVP GHCWVE
Sbjct: 61  VEKFCLEKYRFSHGDVVVFRSPSNHKEKHIKRIIGLPGDWIGTPHAYDVVKVPEGHCWVE 120

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHSPS 205
           GDN  SS+DSR FGP+PLGL+ GRVTHI+WPPQR+  VE+K  Q R S S
Sbjct: 121 GDNLLSSMDSRYFGPVPLGLISGRVTHIVWPPQRIGEVEKKIPQGRLSSS 170

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224140407|ref|XP_002323574.1| predicted protein [Populus trichocarpa] gi|222868204|gb|EEF05335.1| predicted protein [Populus trichocarpa]

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 121/170 (71%), Positives = 144/170 (84%), Gaps = 2/170 (1%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M + + LW+LTK   T G+IGLT++DRYAS+VPVRG SMSPTFNP T++ +GSL DD VL
Sbjct: 1   MGSGSLLWNLTKKYLTVGVIGLTITDRYASVVPVRGGSMSPTFNPRTNTVLGSL-DDRVL 59

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCL KYKFSHGDV+VF SPS+HK+K +KRIIGLPGDW+GTP  NDVVK+P GHCWVE
Sbjct: 60  IEKFCLAKYKFSHGDVVVFRSPSDHKQKLIKRIIGLPGDWMGTPQ-NDVVKIPEGHCWVE 118

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHSPS 205
           GDNP+SS+DSRSFGPIPLGLV+GR T I+WPPQR+  VER+  Q R SPS
Sbjct: 119 GDNPASSMDSRSFGPIPLGLVQGRATTIVWPPQRICQVERRILQDRFSPS 168

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439902|ref|XP_004137724.1| PREDICTED: mitochondrial inner membrane protease subunit 2-like [Cucumis sativus] gi|449483475|ref|XP_004156603.1| PREDICTED: mitochondrial inner membrane protease subunit 2-like [Cucumis sativus]

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 112/170 (65%), Positives = 139/170 (81%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           MA  N +W++ K  FTFG+IG+T+SDRYAS+VP+RG+SMSPTFNP   S  G ++ D+VL
Sbjct: 1   MANRNLVWNVVKKSFTFGIIGVTISDRYASVVPIRGASMSPTFNPIATSLTGPMTGDYVL 60

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCL+KYKFS GDVIV+ SP N+KEK VKRII LPGDW+GT  T DVVKVP GHCWVE
Sbjct: 61  VEKFCLEKYKFSPGDVIVYRSPCNYKEKQVKRIIALPGDWVGTRQTYDVVKVPEGHCWVE 120

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHSPS 205
           GDNP  S+DSRSFGPIP+GL++GRV+HI+WPPQR+  VE+K  Q   +P+
Sbjct: 121 GDNPECSMDSRSFGPIPMGLIQGRVSHIVWPPQRIGAVEKKYPQGESNPT 170

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225440672|ref|XP_002279805.1| PREDICTED: mitochondrial inner membrane protease subunit 2 [Vitis vinifera] gi|297740215|emb|CBI30397.3| unnamed protein product [Vitis vinifera]

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 112/161 (69%), Positives = 131/161 (81%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M   NFLW   K CFTFGLIGLT+SDRYASI  V+G SM PTFNP   +FMGSL+DD+VL
Sbjct: 1   MGTRNFLWDFGKKCFTFGLIGLTISDRYASIAHVQGLSMYPTFNPNARTFMGSLTDDYVL 60

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCL+KYKFSHGDVI F SP+NH+EK +KRII LPGDWI  P + D +++P GHCWVE
Sbjct: 61  LEKFCLEKYKFSHGDVIAFRSPNNHREKQIKRIIALPGDWITAPHSYDALRIPEGHCWVE 120

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERK 196
           GDN +SSLDSRSFGP+PLGL  GR THI+WPPQR+  VER+
Sbjct: 121 GDNSASSLDSRSFGPVPLGLACGRATHIVWPPQRIGEVERR 161

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388512387|gb|AFK44255.1| unknown [Lotus japonicus]

 Score =  235 bits (599), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 108/159 (67%), Positives = 127/159 (79%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M    FLW+ TK   TFGLI +TVSDRY ++VPVRG SMSPTFNP T S MG +SDD V 
Sbjct: 1   MGPSGFLWNFTKKFVTFGLISVTVSDRYMTVVPVRGGSMSPTFNPKTHSLMGGVSDDCVF 60

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCLQKYKFSHGDV+VF SP NHKE H+KRII LPG+WIG     DV+K+P GHCWVE
Sbjct: 61  VEKFCLQKYKFSHGDVMVFRSPLNHKETHIKRIIALPGEWIGAHHNYDVLKIPEGHCWVE 120

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
           GDN +SSL S+SFGPIPL L++GRVTH++WPPQR+  V+
Sbjct: 121 GDNAASSLGSKSFGPIPLALIRGRVTHVVWPPQRIGAVK 159

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116794380|gb|ABK27122.1| unknown [Picea sitchensis]

 Score =  234 bits (597), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 108/168 (64%), Positives = 130/168 (77%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M A +FLW L+K   +  LIGLT+SDRYASIV V+G SM PT NP + +  GSL  D VL
Sbjct: 1   MGAWDFLWMLSKKSLSGALIGLTISDRYASIVAVQGRSMQPTLNPGSKNRFGSLKGDFVL 60

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCLQ YKFSHGDVIVF SP  H E HVKR+I LPGDWI  P T D++K+P GHCWVE
Sbjct: 61  LEKFCLQNYKFSHGDVIVFRSPYEHNEWHVKRLIALPGDWISVPGTYDILKIPEGHCWVE 120

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHS 203
           GDN  SSLDSRSFGP+PLGLV+GRVTH++WPP+RV  +E++  ++R S
Sbjct: 121 GDNAVSSLDSRSFGPVPLGLVQGRVTHVIWPPERVGAIEKQYPKERVS 168

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357481155|ref|XP_003610863.1| Mitochondrial inner membrane protease subunit [Medicago truncatula] gi|355512198|gb|AES93821.1| Mitochondrial inner membrane protease subunit [Medicago truncatula]

 Score =  223 bits (567), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 99/165 (60%), Positives = 127/165 (76%), Gaps = 4/165 (2%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M   N +W++TK   T GLI  TVSDRYA++VPVRG+SMSPTFNP T+SF    +DD+V 
Sbjct: 1   MGTRNLVWNVTKKLATIGLITFTVSDRYATVVPVRGASMSPTFNPKTNSF----TDDYVF 56

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EK CL K+KFSHGD+++F SPSN KE H+KRII LPG+W       DV+KVP GHCWVE
Sbjct: 57  VEKLCLDKFKFSHGDIVIFSSPSNFKETHIKRIIALPGEWFVNRHNQDVLKVPEGHCWVE 116

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQK 200
           GDN +SS DS+S+GP+PLGLV+GRVTH++WPPQR+  V+    ++
Sbjct: 117 GDNAASSTDSKSYGPVPLGLVRGRVTHVVWPPQRIGAVKNTTPER 161

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727543|ref|NP_001238188.1| uncharacterized protein LOC100499932 [Glycine max] gi|255627785|gb|ACU14237.1| unknown [Glycine max]

 Score =  221 bits (563), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 97/159 (61%), Positives = 124/159 (77%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M   +FLW+ TK   + G++ +TV+D + +++PVRG SMSPTFNP   S MG + DD+VL
Sbjct: 1   MGTSSFLWNCTKKFISAGIVTVTVTDLFVTVIPVRGGSMSPTFNPKAGSLMGGVFDDYVL 60

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCL  YKFSHGDV+VF SP N KE HVKRI  LPG+W GT   NDV+++P GHCWVE
Sbjct: 61  VEKFCLHSYKFSHGDVVVFRSPQNRKETHVKRIAALPGEWFGTHQKNDVIQIPLGHCWVE 120

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
           GDN +SSLDS SFGPIPLG+++GRVTH++WPPQR+  V+
Sbjct: 121 GDNTASSLDSNSFGPIPLGIIRGRVTHVVWPPQRIGAVK 159

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722229|ref|NP_001235957.1| uncharacterized protein LOC100527429 [Glycine max] gi|255632322|gb|ACU16519.1| unknown [Glycine max]

 Score =  221 bits (563), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 100/168 (59%), Positives = 127/168 (75%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M   +FLW+ TK   T G++ +TV+D + +++PVRG SMSPTFNP   S MG + DD+VL
Sbjct: 1   MGTSSFLWNCTKKFITAGIVTVTVTDHFVTVIPVRGGSMSPTFNPKAGSHMGDVFDDYVL 60

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           +EKFCL+ YKFSHGDV+VF SP NHKE HVKRI  LPG+W G    NDV+++P GHCWVE
Sbjct: 61  VEKFCLRNYKFSHGDVVVFRSPLNHKETHVKRIAALPGEWFGAHHNNDVIQIPLGHCWVE 120

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQKRHS 203
           GDN +SSLDS SFGPIPL L++GRVTH++WPPQR+  V+    Q+  S
Sbjct: 121 GDNTASSLDSNSFGPIPLALIRGRVTHVVWPPQRIGAVKSTPPQRLSS 168

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829426|ref|XP_002882595.1| signal peptidase I family protein [Arabidopsis lyrata subsp. lyrata] gi|297328435|gb|EFH58854.1| signal peptidase I family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 93/158 (58%), Positives = 125/158 (79%), Gaps = 6/158 (3%)

Query: 36  MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
           M   N LW + K  FT  +IGLT+SDR  S+VPVRG SMSPTFNP  +S++    DD+VL
Sbjct: 1   MGIQNILWQVAKKSFTGSIIGLTISDRCCSVVPVRGDSMSPTFNPQRNSYL----DDYVL 56

Query: 96  MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
           ++KFCL+ YKF+ GDV+VF SP+N  ++++KRI+G+PG+WI +  + DV++VP GHCWVE
Sbjct: 57  VDKFCLKDYKFARGDVVVFSSPTNFGDRYIKRIVGMPGEWISS--SRDVIRVPEGHCWVE 114

Query: 156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHV 193
           GDN +SSLDSR+FGPIPLGL++GRVT +LWPPQR+  +
Sbjct: 115 GDNKTSSLDSRTFGPIPLGLIQGRVTRVLWPPQRISKI 152

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	205
TAIR|locus:2095249	154	AT3G08980 [Arabidopsis thalian	0.751	1.0	0.581	5.6e-52
ZFIN|ZDB-GENE-040808-9	184	immp2l "IMP2 inner mitochondri	0.658	0.733	0.432	9.1e-29
MGI|MGI:2135611	175	Immp2l "IMP2 inner mitochondri	0.697	0.817	0.429	1e-27
UNIPROTKB|Q96T52	175	IMMP2L "Mitochondrial inner me	0.726	0.851	0.406	3.5e-27
UNIPROTKB|Q2KI92	177	IMMP2L "Mitochondrial inner me	0.697	0.807	0.422	5.7e-27
UNIPROTKB|E1BVJ0	175	IMMP2L "Uncharacterized protei	0.702	0.822	0.413	2.5e-26
FB|FBgn0034535	171	CG11110 [Drosophila melanogast	0.687	0.824	0.371	1.6e-24
CGD|CAL0002703	162	IMP2 [Candida albicans (taxid:	0.609	0.771	0.428	5.3e-24
SGD|S000004638	177	IMP2 "Catalytic subunit of mit	0.629	0.728	0.433	5.3e-24
ZFIN|ZDB-GENE-070522-4	189	immp1l "IMP1 inner mitochondri	0.619	0.671	0.404	8e-21

TAIR|locus:2095249 AT3G08980 [Arabidopsis thaliana (taxid:3702)]

 Score = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 93/160 (58%), Positives = 126/160 (78%)

Query:    36 MAAHNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVL 95
             M   N LW + K  FT  +IGLT+SDR  S+VPVRG SMSPTFNP  +S++    DD+VL
Sbjct:     1 MGIQNILWQVAKKSFTGSIIGLTISDRCCSVVPVRGDSMSPTFNPQRNSYL----DDYVL 56

Query:    96 MEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 155
             ++KFCL+ YKF+ GDV+VF SP++  ++++KRI+G+PG+WI +  + DV++VP GHCWVE
Sbjct:    57 VDKFCLKDYKFARGDVVVFSSPTHFGDRYIKRIVGMPGEWISS--SRDVIRVPEGHCWVE 114

Query:   156 GDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVER 195
             GDN +SSLDSRSFGPIPLGL++GRVT ++WPPQR+  + R
Sbjct:   115 GDNKTSSLDSRSFGPIPLGLIQGRVTRVMWPPQRISKIGR 154

GO:0005739 "mitochondrion" evidence=ISM

GO:0006508 "proteolysis" evidence=IEA;ISS

GO:0008233 "peptidase activity" evidence=ISS

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA;ISS

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0051607 "defense response to virus" evidence=RCA

ZFIN|ZDB-GENE-040808-9 immp2l "IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 61/141 (43%), Positives = 90/141 (63%)

Query:    55 IGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVF 114
             + +TV DR A +  V G+SM P+ NP  +S     S D VL+ ++ ++ Y    GD++  
Sbjct:    25 VTVTVLDRLAYVARVEGASMQPSLNPDGES-----SPDVVLLNRWSVRNYHVQRGDIVSV 79

Query:   115 CSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPL 173
              SP N ++K +KR+IG+ GD+I T    N  V+VP+GH W+EGD+   S DS +FGP+ L
Sbjct:    80 LSPKNPQQKIIKRVIGIEGDFIKTLGYKNRYVRVPDGHLWIEGDHHGHSFDSNAFGPVSL 139

Query:   174 GLVKGRVTHILWPPQRVRHVE 194
             GLV GR +HI+WPP R + +E
Sbjct:   140 GLVHGRASHIIWPPSRWQRIE 160

GO:0006508 "proteolysis" evidence=IEA

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=IEA

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:2135611 Immp2l "IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 64/149 (42%), Positives = 88/149 (59%)

Query:    47 KNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKF 106
             K  F    + +T  DR A +  V GSSM P+ NP      GS S D VL+  + ++ ++ 
Sbjct:    17 KGFFVAVPVAVTFLDRVACVARVEGSSMQPSLNPG-----GSQSSDVVLLNHWKVRNFEV 71

Query:   107 SHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNPSSSLDS 165
               GD++   SP N ++K +KR+I L GD + T    N +VKVP GH WVEGD+   S DS
Sbjct:    72 QRGDIVSLVSPKNPEQKIIKRVIALEGDIVRTIGHKNRLVKVPRGHMWVEGDHHGHSFDS 131

Query:   166 RSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
              SFGP+ LGL+    THILWPP+R + +E
Sbjct:   132 NSFGPVSLGLLHAHATHILWPPERWQRLE 160

GO:0001541 "ovarian follicle development" evidence=IMP

GO:0005739 "mitochondrion" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=ISA

GO:0006508 "proteolysis" evidence=IEA

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=IGI

GO:0007283 "spermatogenesis" evidence=IMP

GO:0008104 "protein localization" evidence=ISA

GO:0008152 "metabolic process" evidence=ISA;IMP

GO:0008233 "peptidase activity" evidence=IGI;ISA;IMP

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0030728 "ovulation" evidence=IMP

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IGI

UNIPROTKB|Q96T52 IMMP2L "Mitochondrial inner membrane protease subunit 2" [Homo sapiens (taxid:9606)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 63/155 (40%), Positives = 90/155 (58%)

Query:    41 FLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFC 100
             ++ +  K  F    + +T  DR A +  V G+SM P+ NP      GS S D VL+  + 
Sbjct:    11 YIKAFCKGFFVAVPVAVTFLDRVACVARVEGASMQPSLNPG-----GSQSSDVVLLNHWK 65

Query:   101 LQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNP 159
             ++ ++   GD++   SP N ++K +KR+I L GD + T    N  VKVP GH WVEGD+ 
Sbjct:    66 VRNFEVHRGDIVSLVSPKNPEQKIIKRVIALEGDIVRTIGHKNRYVKVPRGHIWVEGDHH 125

Query:   160 SSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
               S DS SFGP+ LGL+    THILWPP+R + +E
Sbjct:   126 GHSFDSNSFGPVSLGLLHAHATHILWPPERWQKLE 160

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0001541 "ovarian follicle development" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0030728 "ovulation" evidence=IEA

GO:0008233 "peptidase activity" evidence=ISS

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=ISS

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|Q2KI92 IMMP2L "Mitochondrial inner membrane protease subunit 2" [Bos taurus (taxid:9913)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 63/149 (42%), Positives = 87/149 (58%)

Query:    47 KNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKF 106
             K  F    + +T  DR A +  V G+SM P+ NP      GS S D VL+  + ++ ++ 
Sbjct:    17 KGFFVAVPVAVTFLDRVACVARVEGASMQPSLNPG-----GSQSSDVVLLNHWKVRNFEV 71

Query:   107 SHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTP-MTNDVVKVPNGHCWVEGDNPSSSLDS 165
               GD++   SP N ++K +KR+I L GD + T    N  VKVP GH WVEGD+   S DS
Sbjct:    72 QRGDIVSLVSPKNPEQKIIKRVIALEGDIVKTMGHKNRYVKVPRGHIWVEGDHHGHSFDS 131

Query:   166 RSFGPIPLGLVKGRVTHILWPPQRVRHVE 194
              SFGP+ LGL+    THILWPP+R + +E
Sbjct:   132 NSFGPVSLGLLHAHATHILWPPKRWQKLE 160

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IEA

GO:0030728 "ovulation" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001541 "ovarian follicle development" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0008236 "serine-type peptidase activity" evidence=IEA

UNIPROTKB|E1BVJ0 IMMP2L "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 62/150 (41%), Positives = 86/150 (57%)

Query:    41 FLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFC 100
             +L +  K  F    + +T  DR A +  V G+SM P+ NP      G  + D VL+  + 
Sbjct:    11 YLKAFFKGFFVAVPVTVTFLDRVACVARVEGASMQPSLNPG-----GRQASDVVLLNHWS 65

Query:   101 LQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNP 159
             ++ Y    GD++   SP N ++K +KR+I L GD I T       VKVP+GH WVEGD+ 
Sbjct:    66 IRNYDVQRGDIVSLVSPRNPEQKIIKRVIALEGDIIKTIGYKKKYVKVPHGHIWVEGDHH 125

Query:   160 SSSLDSRSFGPIPLGLVKGRVTHILWPPQR 189
               S DS +FGP+ LGL+  R THILWPP+R
Sbjct:   126 GHSFDSNAFGPVSLGLLHARATHILWPPKR 155

GO:0006508 "proteolysis" evidence=IEA

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0001541 "ovarian follicle development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0030728 "ovulation" evidence=IEA

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IEA

FB|FBgn0034535 CG11110 [Drosophila melanogaster (taxid:7227)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 55/148 (37%), Positives = 85/148 (57%)

Query:    55 IGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVF 114
             +G+T  D    +  V G SM P  NP  D        D+V + ++     +   GD+I  
Sbjct:    16 LGVTFLDCVGYVARVDGISMQPALNPVPDE------KDYVFLLRWGTHNSQVERGDIISL 69

Query:   115 CSPSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPL 173
              SP +  +K +KR++GL GD + T    +++V+VP GHCWVEGD+   S+DS +FGP+ L
Sbjct:    70 ISPKDPAQKIIKRVVGLQGDVVSTLGYKHEIVRVPEGHCWVEGDHTGHSMDSNTFGPVAL 129

Query:   174 GLVKGRVTHILWPPQRVRHVERKNHQKR 201
             GL+  R   I+WPP+R R +E +  ++R
Sbjct:   130 GLMSARAVAIVWPPERWRILENELPRRR 157

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=ISS

GO:0005743 "mitochondrial inner membrane" evidence=ISS

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

CGD|CAL0002703 IMP2 [Candida albicans (taxid:5476)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 57/133 (42%), Positives = 81/133 (60%)

Query:    69 VRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKY-KFSHGDVIVFCSPSNHKEKHVKR 127
             + GSSM+PTFNP T +    ++ D VL++K+ ++K    S GD+I+F SP N ++   KR
Sbjct:    33 ITGSSMTPTFNPGTST----MTKDIVLVQKYNIKKPGSLSRGDIIMFRSPENPEKLLTKR 88

Query:   128 IIGLPGDWI---GTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184
             ++G+ GD I     P     VK+P  H WVEGDN   S+DS  FGP+  GLV G+V  I+
Sbjct:    89 VVGIQGDIIRPKSPPYPKSEVKIPRNHFWVEGDNSFHSIDSNKFGPVSQGLVIGKVVTII 148

Query:   185 WPPQRVRHVERKN 197
             WPP R     ++N
Sbjct:   149 WPPSRFGSELKRN 161

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=IEA

SGD|S000004638 IMP2 "Catalytic subunit of mitochondrial inner membrane peptidase complex" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 59/136 (43%), Positives = 83/136 (61%)

Query:    57 LTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQK-YKFSHGDVIVFC 115
             LT+++    I  V+G+SM PT NP T++    L+ D VL+ KF ++     S  D+I+F 
Sbjct:    25 LTINNNVVHIAQVKGTSMQPTLNPQTET----LATDWVLLWKFGVKNPSNLSRDDIILFK 80

Query:   116 SPSNHKEKHVKRIIGLPGDWIGT--PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPL 173
             +P+N ++ + KR+ GLP D I T  P     V +P GH WVEGDN   S+DS +FGPI  
Sbjct:    81 APTNPRKVYCKRVKGLPFDTIDTKFPYPKPQVNLPRGHIWVEGDNYFHSIDSNTFGPISS 140

Query:   174 GLVKGRVTHILWPPQR 189
             GLV G+   I+WPP R
Sbjct:   141 GLVIGKAITIVWPPSR 156

GO:0004175 "endopeptidase activity" evidence=IMP;IDA

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IEA;IPI

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=IEA;IMP

GO:0008233 "peptidase activity" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

ZFIN|ZDB-GENE-070522-4 immp1l "IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 57/141 (40%), Positives = 73/141 (51%)

Query:    52 FGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDV 111
             +G I     +     V   G SM PT            + D V  E+     Y+   GD+
Sbjct:    44 YGCIAHCAFEYVGEFVSCSGPSMEPTIT----------NHDVVFSERISRHLYRIQKGDI 93

Query:   112 IVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVK----VPNGHCWVEGDNPSSSLDSRS 167
             I+  SPSN K    KR+IGL GD + T   +D+ K    VP GH W+EGDN  +S DSRS
Sbjct:    94 IIAKSPSNPKMNICKRVIGLEGDKVCTSGPSDIFKTHTYVPRGHVWLEGDNLRNSTDSRS 153

Query:   168 FGPIPLGLVKGRVTHILWPPQ 188
             +GPIP  L++GRV   LWPPQ
Sbjct:   154 YGPIPYALIRGRVCLKLWPPQ 174

GO:0006627 "protein processing involved in protein targeting to mitochondrion" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0042720 "mitochondrial inner membrane peptidase complex" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0008236 "serine-type peptidase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.21	0.691
3rd Layer	3.4.21.89	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	205
TIGR02227	163	TIGR02227, sigpep_I_bact, signal peptidase I, bact	2e-26
cd06530	85	cd06530, S26_SPase_I, The S26 Type I signal peptid	5e-23
cd06462	84	cd06462, Peptidase_S24_S26, The S24, S26 LexA/sign	1e-15
TIGR02754	90	TIGR02754, sod_Ni_protease, nickel-type superoxide	1e-07
pfam00717	69	pfam00717, Peptidase_S24, Peptidase S24-like	4e-07
COG0681	166	COG0681, LepB, Signal peptidase I [Intracellular t	2e-05
pfam10502	138	pfam10502, Peptidase_S26, Signal peptidase, peptid	2e-05
PRK10861	324	PRK10861, PRK10861, signal peptidase I; Provisiona	0.001
TIGR02771	171	TIGR02771, TraF_Ti, conjugative transfer signal pe	0.003

>gnl|CDD|233790 TIGR02227, sigpep_I_bact, signal peptidase I, bacterial type

 Score = 99.2 bits (248), Expect = 2e-26
 Identities = 51/166 (30%), Positives = 70/166 (42%), Gaps = 43/166 (25%)

Query: 50  FTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHG 109
               LI   V   Y   VP  G SM PT              D +L+ KF         G
Sbjct: 10  LLALLIRTFVFFPY--KVP--GGSMEPTLKE----------GDRILVNKFAYGTSDPKRG 55

Query: 110 DVIVFCSPSNHKEKHVKRIIGLPGDWI---------------------------GTPMTN 142
           D++VF  P ++K  ++KR+IGLPGD +                               T 
Sbjct: 56  DIVVFKDPDDNKNIYIKRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGFLDTSEFNTT 115

Query: 143 DV--VKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWP 186
           D   V VP GH +V GDN  +SLDSR FG +P+  + G+V+ + +P
Sbjct: 116 DYGPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVFYP 161

This model represents signal peptidase I from most bacteria. Eukaryotic sequences are likely organellar. Several bacteria have multiple paralogs, but these represent isozymes of signal peptidase I. Virtually all known bacteria may be presumed to A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes [Protein fate, Protein and peptide secretion and trafficking]. Length = 163

>gnl|CDD|119398 cd06530, S26_SPase_I, The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3

 Score = 87.6 bits (218), Expect = 5e-23
 Identities = 37/116 (31%), Positives = 51/116 (43%), Gaps = 31/116 (26%)

Query: 65  SIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKH 124
             V V G SM PT  P           D VL+ K      +   GDV+VF SP +  +  
Sbjct: 1   EPVVVPGGSMEPTLQP----------GDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPI 50

Query: 125 VKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV 180
           +KR+IG                      +V GDN ++SLDSR +GP+P   + G+V
Sbjct: 51  IKRVIG---------------------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85

4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa) belong to this family and they process many proteins that enter the ER for retention or for export to the Golgi apparatus, secretory vesicles, plasma membranes or vacuole. An atypical member of the S26 SPase type I family is the TraF peptidase which has the remarkable activity of producing a cyclic protein of the Pseudomonas pilin system. The type I signal peptidases are unique serine proteases that utilize a serine/lysine catalytic dyad mechanism in place of the classical serine/histidine/aspartic acid catalytic triad mechanism. Length = 85

>gnl|CDD|119396 cd06462, Peptidase_S24_S26, The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families

 Score = 68.8 bits (169), Expect = 1e-15
 Identities = 40/116 (34%), Positives = 52/116 (44%), Gaps = 32/116 (27%)

Query: 65  SIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKH 124
             + V G SM PT              D VL++K     Y+   GD++VF  P    E  
Sbjct: 1   FALRVEGDSMEPTIPD----------GDLVLVDK---SSYEPKRGDIVVFRLPGG--ELT 45

Query: 125 VKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV 180
           VKR+IGLPG+               GH ++ GDNP +S DSR  GP P   + G V
Sbjct: 46  VKRVIGLPGE---------------GHYFLLGDNP-NSPDSRIDGP-PELDIVGVV 84

The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. Length = 84

>gnl|CDD|233997 TIGR02754, sod_Ni_protease, nickel-type superoxide dismutase maturation protease

 Score = 47.5 bits (113), Expect = 1e-07
 Identities = 30/113 (26%), Positives = 45/113 (39%), Gaps = 26/113 (23%)

Query: 69  VRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRI 128
           V G SMSPT  P           D +++  +         G+V+V   P       +KR+
Sbjct: 3   VTGVSMSPTLPP----------GDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRL 52

Query: 129 IGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVT 181
                             V +   ++ GDNP +S DSR  GP+P  L+ G+V 
Sbjct: 53  AA----------------VDDNGLFLLGDNPKASTDSRQLGPVPRSLLLGKVL 89

Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad [Cellular processes, Detoxification, Protein fate, Protein modification and repair]. Length = 90

>gnl|CDD|216079 pfam00717, Peptidase_S24, Peptidase S24-like

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 16/68 (23%)

Query: 69  VRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRI 128
           V+G SM PT              D +L++K      +   GD++V     + +E  VKR+
Sbjct: 2   VKGDSMEPTIPD----------GDLLLVDKTS----EPKRGDIVVA--RLDGEEATVKRL 45

Query: 129 IGLPGDWI 136
           IGLPGD I
Sbjct: 46  IGLPGDII 53

Length = 69

>gnl|CDD|223753 COG0681, LepB, Signal peptidase I [Intracellular trafficking and secretion]

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 36/134 (26%), Positives = 54/134 (40%), Gaps = 23/134 (17%)

Query: 42  LWSLTKNCFTFG---LIGLTVSDR--YASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLM 96
           L    +   +     ++ L +  R      V V   SM PT N      +G    D VL+
Sbjct: 4   LLKFLELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLN------VG----DRVLV 53

Query: 97  EKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTND----VVKVPNGHC 152
           +KF     K    D+IV   P+  +   +KR+IGL GD +     +D    V  +P  + 
Sbjct: 54  KKFSYGFGKLKVPDIIVL--PAVVEGDLIKRVIGLRGDIV--VFKDDRLYVVPIIPRVYG 109

Query: 153 WVEGDNPSSSLDSR 166
            VE DN    +D  
Sbjct: 110 LVEKDNGKHLVDVI 123

Length = 166

>gnl|CDD|151062 pfam10502, Peptidase_S26, Signal peptidase, peptidase S26

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 22/115 (19%), Positives = 35/115 (30%), Gaps = 37/115 (32%)

Query: 107 SHGDVIVFCSPS------------NHKEKHVKRIIGLPGD--------------WIGTPM 140
             GD++  C P                   +KR++ LPG                +   +
Sbjct: 23  EVGDLVAVCPPEPAAFFAAERGYLPRGVPLLKRVLALPGQRVCIRDGLVTIDGVPVSAAL 82

Query: 141 TNDVV-----------KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184
             D              +P G  ++       S DSR FGP+P   + GR   + 
Sbjct: 83  ERDRKGRPLPPWQGCRVLPEGELFLMSVTSPDSFDSRYFGPVPASAIIGRARPVW 137

This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The active site residues take the form of a catalytic dyad that is Ser, Lys in subfamily S26A; the Ser is the nucleophile in catalysis, and the Lys is the general base. Length = 138

>gnl|CDD|182787 PRK10861, PRK10861, signal peptidase I; Provisional

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 22/76 (28%)

Query: 73  SMSPTFNPTTDSFMGSLSDDHVLMEKFCL-------QK--YKFSH---GDVIVFCSPSNH 120
           SM PT           L  D +L+EKF         Q    +  H   GD++VF  P + 
Sbjct: 91  SMMPTL----------LIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDP 140

Query: 121 KEKHVKRIIGLPGDWI 136
           K  ++KR++GLPGD +
Sbjct: 141 KLDYIKRVVGLPGDKV 156

Length = 324

>gnl|CDD|131818 TIGR02771, TraF_Ti, conjugative transfer signal peptidase TraF

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 33/117 (28%), Positives = 41/117 (35%), Gaps = 46/117 (39%)

Query: 109 GDVIVFCSPSN-------------------HKEKHVKRIIGLPGD---------WI---- 136
           GD +VFC P N                        +KR++GLPGD          I    
Sbjct: 50  GDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQL 109

Query: 137 ---GTPMTNDVV----------KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV 180
                P+  D             +P G   V   +P+S  DSR FGPI    V GRV
Sbjct: 110 LPYSKPLATDSSGRPLPPFPEGVIPPGFFVVHDTSPTS-FDSRYFGPISREQVIGRV 165

This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems. Length = 171

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
TIGR02227	163	sigpep_I_bact signal peptidase I, bacterial type.	100.0
KOG0171	176	consensus Mitochondrial inner membrane protease, s	100.0
PRK10861	324	signal peptidase I; Provisional	100.0
KOG1568	174	consensus Mitochondrial inner membrane protease, s	100.0
PRK13838	176	conjugal transfer pilin processing protease TraF;	99.89
TIGR02771	171	TraF_Ti conjugative transfer signal peptidase TraF	99.87
PRK13884	178	conjugal transfer peptidase TraF; Provisional	99.87
TIGR02754	90	sod_Ni_protease nickel-type superoxide dismutase m	99.86
PF10502	138	Peptidase_S26: Signal peptidase, peptidase S26 ; I	99.85
cd06530	85	S26_SPase_I The S26 Type I signal peptidase (SPase	99.82
TIGR02228	158	sigpep_I_arch signal peptidase I, archaeal type. T	99.78
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	99.59
COG4959	173	TraF Type IV secretory pathway, protease TraF [Pos	99.47
cd06462	84	Peptidase_S24_S26 The S24, S26 LexA/signal peptida	99.19
PF00717	70	Peptidase_S24: Peptidase S24-like peptidase classi	99.17
KOG3342	180	consensus Signal peptidase I [Intracellular traffi	99.14
cd06529	81	S24_LexA-like Peptidase S24 LexA-like proteins are	98.87
COG2932	214	Predicted transcriptional regulator [Transcription	98.81
PRK10276	139	DNA polymerase V subunit UmuD; Provisional	98.55
PRK00215	205	LexA repressor; Validated	98.43
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	98.4
PRK12423	202	LexA repressor; Provisional	98.34
COG1974	201	LexA SOS-response transcriptional repressors (RecA	97.57
COG4068	64	Uncharacterized protein containing a Zn-ribbon [Fu	92.77
TIGR02594	129	conserved hypothetical protein TIGR02594. Members	86.94
PF09889	59	DUF2116: Uncharacterized protein containing a Zn-r	85.97

>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type

Probab=100.00  E-value=1.3e-37  Score=251.27  Aligned_cols=133  Identities=35%  Similarity=0.559  Sum_probs=119.3

Q ss_pred             HHHHHHHHHHHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceE
Q 028706           46 TKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHV  125 (205)
Q Consensus        46 ~~~~~~~~lv~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~v  125 (205)
                      +..++++++++++++.+++..+.|+|+||+|||++          ||+|+++|..+...++++||+|+|+.|.++++.++
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~----------Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~i   71 (163)
T TIGR02227         2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKE----------GDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYV   71 (163)
T ss_pred             HHHHHHHHHHHHHHHhhEEEEEEECCcccccchhC----------CCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeE
Confidence            45566777888899999999999999999999999          99999999987667899999999999887788999


Q ss_pred             EEEeeeCCCeeecc------------C-----------------CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCE
Q 028706          126 KRIIGLPGDWIGTP------------M-----------------TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLV  176 (205)
Q Consensus       126 KRViglpGD~V~i~------------~-----------------~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~I  176 (205)
                      |||+|+|||+|++.            +                 ...+.+||+|+|||+|||+.+|.|||+||+|++++|
T Consensus        72 KRVig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I  151 (163)
T TIGR02227        72 KRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDI  151 (163)
T ss_pred             EEEEecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHe
Confidence            99999999999871            0                 012468999999999999999999999999999999


Q ss_pred             eEEEEEEEeCCC
Q 028706          177 KGRVTHILWPPQ  188 (205)
Q Consensus       177 iGkv~~~i~P~~  188 (205)
                      +|||++++||++
T Consensus       152 ~Gk~~~~~~p~~  163 (163)
T TIGR02227       152 IGKVSFVFYPFD  163 (163)
T ss_pred             EEEEEEEECCCC
Confidence            999999999985

A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.

>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.7e-35  Score=235.91  Aligned_cols=141  Identities=35%  Similarity=0.622  Sum_probs=125.3

Q ss_pred             HHHHHHHHHHHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceE
Q 028706           46 TKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHV  125 (205)
Q Consensus        46 ~~~~~~~~lv~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~v  125 (205)
                      ....+..+++++.+..++.++..++|.||+||+++.         ||+++.+|+++.++.+++||||++..|.++.+.++
T Consensus        15 ~~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~---------gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~c   85 (176)
T KOG0171|consen   15 FCSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDG---------GDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHIC   85 (176)
T ss_pred             hHHHHHHHHHHHHHHHHhcceeeccCCCcCceecCC---------CcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhh
Confidence            444555666778888899999999999999999996         88888899999999999999999999999999999


Q ss_pred             EEEeeeCCCeeeccC-----------CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCCccccc
Q 028706          126 KRIIGLPGDWIGTPM-----------TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE  194 (205)
Q Consensus       126 KRViglpGD~V~i~~-----------~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~~~~~~  194 (205)
                      |||+|+|||.|.+..           ...++.||+||+||+|||.++|.|||+|||||...|+||+++++||++++....
T Consensus        86 KRIva~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~  165 (176)
T KOG0171|consen   86 KRIVAMEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLI  165 (176)
T ss_pred             heeeccCCceEEEecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhcceee
Confidence            999999999776611           123579999999999999999999999999999999999999999999988765


Q ss_pred             c
Q 028706          195 R  195 (205)
Q Consensus       195 ~  195 (205)
                      -
T Consensus       166 ~  166 (176)
T KOG0171|consen  166 L  166 (176)
T ss_pred             e
Confidence            3

>PRK10861 signal peptidase I; Provisional

Probab=100.00  E-value=1.3e-33  Score=249.46  Aligned_cols=140  Identities=29%  Similarity=0.388  Sum_probs=124.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeecc------------CCCC
Q 028706           39 HNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQ------------KYKF  106 (205)
Q Consensus        39 ~~~~~~~~~~~~~~~lv~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~------------~~~~  106 (205)
                      ...+..++..++++++++++++.|+++++.|+|+||+|||..          ||+|+++|+.|.            ...+
T Consensus        57 ~~~~~~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~----------GD~IlVnK~~yg~~~p~~~~~~~~~~~p  126 (324)
T PRK10861         57 KPGWLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLI----------GDFILVEKFAYGIKDPITQTTLIETGHP  126 (324)
T ss_pred             cchHHHHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccC----------CCEEEEEEeecCccCccccccccccCCC
Confidence            344677777888888899999999999999999999999999          999999999875            2578


Q ss_pred             CcceEEEEecCCCCCcceEEEEeeeCCCeeecc---------C-------------------------------------
Q 028706          107 SHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTP---------M-------------------------------------  140 (205)
Q Consensus       107 ~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~---------~-------------------------------------  140 (205)
                      +|||||+|+.|.+++..+||||+|+|||+|++.         .                                     
T Consensus       127 ~RGDIVVF~~P~~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~  206 (324)
T PRK10861        127 KRGDIVVFKYPEDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEAT  206 (324)
T ss_pred             CCCCEEEEecCCCCCCcEEEEeeecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccc
Confidence            999999999999888999999999999999861         0                                     


Q ss_pred             ------------------C---------------------------------CCeEEecCCeEEEeeCCCCCCCCCCccc
Q 028706          141 ------------------T---------------------------------NDVVKVPNGHCWVEGDNPSSSLDSRSFG  169 (205)
Q Consensus       141 ------------------~---------------------------------~~~~~vp~g~~~v~GDN~~~S~DSR~~G  169 (205)
                                        .                                 ..+++||+|+||++|||+++|.||||||
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G  286 (324)
T PRK10861        207 SGFFQVPLNETKENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWG  286 (324)
T ss_pred             cccccccccccccccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCccc
Confidence                              0                                 0133899999999999999999999999


Q ss_pred             ccCCCCEeEEEEEEEeCCC
Q 028706          170 PIPLGLVKGRVTHILWPPQ  188 (205)
Q Consensus       170 ~V~~~~IiGkv~~~i~P~~  188 (205)
                      +||+++|+|||..++|+++
T Consensus       287 ~Vp~~~i~G~a~~i~~s~d  305 (324)
T PRK10861        287 FVPEANLVGKATAIWMSFE  305 (324)
T ss_pred             ccCHHHcEEEEEEEEEEcC
Confidence            9999999999999999986

>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]

Probab=100.00  E-value=5.8e-34  Score=226.82  Aligned_cols=156  Identities=40%  Similarity=0.693  Sum_probs=134.3

Q ss_pred             HHHHHHHHHHH--HHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCC
Q 028706           44 SLTKNCFTFGL--IGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHK  121 (205)
Q Consensus        44 ~~~~~~~~~~l--v~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~  121 (205)
                      .+.+.++.++.  +.+.+...+.....|.|.||.|||++.    .+++..|.||++|+......+.+||||+|.+|.+++
T Consensus         9 ~~~ksl~~s~~~~v~~t~~DrV~~va~v~G~smqPtlnP~----~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~   84 (174)
T KOG1568|consen    9 VFEKSLTGSLKWHVLLTFSDRVVHVAQVYGSSMQPTLNPT----MNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPD   84 (174)
T ss_pred             HHHhceeeeeeeheeeeeeeeEEEEeEEecCcCCCccCCC----cccccccEEEEEeeccccceeccCCEEEEeCCCChh
Confidence            34444444444  445566678899999999999999993    455556999999998765568899999999999999


Q ss_pred             cceEEEEeeeCCCeeec-cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCCcccccccCCCC
Q 028706          122 EKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQK  200 (205)
Q Consensus       122 ~~~vKRViglpGD~V~i-~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~~~~~~~~~~~~  200 (205)
                      +.+||||+|+|||.+.. ++....+.||+|||||+|||...|+|||.||||+...|.|+|++++||+.||+.+.+-.|..
T Consensus        85 ~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~~~~~~~  164 (174)
T KOG1568|consen   85 KVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLDKESPGR  164 (174)
T ss_pred             heeeeeeecccccEeccCCCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhhhcccCCcc
Confidence            99999999999999876 67778899999999999999999999999999999999999999999999999999877766


Q ss_pred             CCC
Q 028706          201 RHS  203 (205)
Q Consensus       201 ~~~  203 (205)
                      |..
T Consensus       165 ~~~  167 (174)
T KOG1568|consen  165 RVP  167 (174)
T ss_pred             ccc
Confidence            653

>PRK13838 conjugal transfer pilin processing protease TraF; Provisional

Probab=99.89  E-value=1.3e-22  Score=166.12  Aligned_cols=93  Identities=23%  Similarity=0.379  Sum_probs=75.4

Q ss_pred             CCeEEEEeeeccCCCCCcceEEEEecCCCC-------------------CcceEEEEeeeCCCeeecc-----------C
Q 028706           91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTP-----------M  140 (205)
Q Consensus        91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~-------------------~~~~vKRViglpGD~V~i~-----------~  140 (205)
                      .+.+.++++.+...++++||+|+|+.|.++                   ...++|||+|+|||+|++.           +
T Consensus        36 S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~  115 (176)
T PRK13838         36 SEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPS  115 (176)
T ss_pred             CCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccc
Confidence            466777777654568999999999987643                   1359999999999999871           0


Q ss_pred             C--------------CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          141 T--------------NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       141 ~--------------~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                      .              ....+||+|+|||+|||+ +|+||||||+|++++|+|+|..++
T Consensus       116 ~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi~  172 (176)
T PRK13838        116 SSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPVL  172 (176)
T ss_pred             cccccccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEEE
Confidence            0              113579999999999985 899999999999999999998764

>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF

Probab=99.87  E-value=8.1e-22  Score=160.71  Aligned_cols=80  Identities=38%  Similarity=0.659  Sum_probs=67.6

Q ss_pred             CCCCcceEEEEecCCCCC-------------------cceEEEEeeeCCCeeecc------------C------------
Q 028706          104 YKFSHGDVIVFCSPSNHK-------------------EKHVKRIIGLPGDWIGTP------------M------------  140 (205)
Q Consensus       104 ~~~~rGDIVvf~~p~~~~-------------------~~~vKRViglpGD~V~i~------------~------------  140 (205)
                      .++++||+|+|+.|.++.                   ..++|||+|+|||+|++.            +            
T Consensus        45 ~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~  124 (171)
T TIGR02771        45 KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRP  124 (171)
T ss_pred             CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCc
Confidence            389999999999875432                   279999999999999881            0            


Q ss_pred             --CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          141 --TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       141 --~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                        ...+.+||+| ||++|||+.+|+||||||+|++++|+|||..++
T Consensus       125 l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl~  169 (171)
T TIGR02771       125 LPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPLF  169 (171)
T ss_pred             cccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEeE
Confidence              0125789999 999999999999999999999999999998653

This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.

>PRK13884 conjugal transfer peptidase TraF; Provisional

Probab=99.87  E-value=2.8e-21  Score=158.50  Aligned_cols=81  Identities=21%  Similarity=0.433  Sum_probs=67.7

Q ss_pred             CCCCcceEEEEecCCCC-------------------CcceEEEEeeeCCCeeecc------------C------------
Q 028706          104 YKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTP------------M------------  140 (205)
Q Consensus       104 ~~~~rGDIVvf~~p~~~-------------------~~~~vKRViglpGD~V~i~------------~------------  140 (205)
                      .++++||+|+|+.|...                   ...++|||+|+|||+|++.            +            
T Consensus        49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~  128 (178)
T PRK13884         49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP  128 (178)
T ss_pred             CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence            37899999999977521                   1379999999999999871            0            


Q ss_pred             ----CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          141 ----TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       141 ----~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                          ....++||+|+||++|||+.+|+||||||+|++++|+|+|..++
T Consensus       129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~  176 (178)
T PRK13884        129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVI  176 (178)
T ss_pred             ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeE
Confidence                01135899999999999999999999999999999999998764

>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease

Probab=99.86  E-value=1.6e-21  Score=142.32  Aligned_cols=89  Identities=33%  Similarity=0.514  Sum_probs=78.5

Q ss_pred             EEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEe
Q 028706           68 PVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKV  147 (205)
Q Consensus        68 ~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~v  147 (205)
                      .|.|+||+|||.+          ||+|++++.......+++||+|+|+.|.+++..++||++++++              
T Consensus         2 ~V~g~SM~P~l~~----------GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~--------------   57 (90)
T TIGR02754         2 KVTGVSMSPTLPP----------GDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD--------------   57 (90)
T ss_pred             EeeCCCccCccCC----------CCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC--------------
Confidence            6899999999999          9999999854433455789999999987677899999999874              


Q ss_pred             cCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEE
Q 028706          148 PNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTH  182 (205)
Q Consensus       148 p~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~  182 (205)
                        +++|++|||+..|.|||++|+|+...|+|+|++
T Consensus        58 --~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~   90 (90)
T TIGR02754        58 --NGLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW   90 (90)
T ss_pred             --CeEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence              589999999999999999999999999999964

Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.

>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=99.85  E-value=2.7e-22  Score=158.16  Aligned_cols=92  Identities=33%  Similarity=0.621  Sum_probs=32.7

Q ss_pred             CCCCeEEEEeeeccCCCCCcceEEEEecCCC------------CCcceEEEEeeeCCCeeecc-----------------
Q 028706           89 LSDDHVLMEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGTP-----------------  139 (205)
Q Consensus        89 ~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~------------~~~~~vKRViglpGD~V~i~-----------------  139 (205)
                      ++.-+.++.+..    .+++||+|+|+.|..            .+..++|||+|+|||+|++.                 
T Consensus         9 lP~g~Y~~~~~~----~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~   84 (138)
T PF10502_consen    9 LPVGIYLIDPSD----KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLAT   84 (138)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccc----cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            334555565544    589999999999862            24689999999999999981                 


Q ss_pred             --------CCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          140 --------MTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       140 --------~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                              ......+||+|+|||+|||+.+|+||||||+|++++|+|+|..++
T Consensus        85 d~~g~~l~~~~~~~~vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~  137 (138)
T PF10502_consen   85 DSDGRPLPQFSGSGTVPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW  137 (138)
T ss_dssp             ----S-T----TEEE--TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred             ccccccccccCCceEeCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence                    112578999999999999999999999999999999999998875

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 entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.

>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3

Probab=99.82  E-value=5.6e-20  Score=132.41  Aligned_cols=84  Identities=44%  Similarity=0.698  Sum_probs=75.7

Q ss_pred             EEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeE
Q 028706           66 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV  145 (205)
Q Consensus        66 ~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~  145 (205)
                      .+.|.|+||+|++..          ||++++++.......+++||+|+|+.+.+++..++|||++               
T Consensus         2 ~~~v~g~SM~P~i~~----------gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~---------------   56 (85)
T cd06530           2 PVVVPGGSMEPTLQP----------GDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG---------------   56 (85)
T ss_pred             eeEEcCCCCcCcccC----------CCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE---------------
Confidence            578999999999999          9999999877433368999999999986556899999997               


Q ss_pred             EecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEE
Q 028706          146 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV  180 (205)
Q Consensus       146 ~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv  180 (205)
                            ||++|||+.+|.|||+||+++.++|+|++
T Consensus        57 ------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~   85 (85)
T cd06530          57 ------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV   85 (85)
T ss_pred             ------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence                  99999999999999999999999999985

4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa

>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type

Probab=99.78  E-value=2.9e-18  Score=138.15  Aligned_cols=87  Identities=30%  Similarity=0.356  Sum_probs=70.6

Q ss_pred             EEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEE
Q 028706           67 VPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVK  146 (205)
Q Consensus        67 ~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~  146 (205)
                      +.|.|+||+||+++          ||++++++...  .++++||+|+|+.|.++ +.++|||+++.++.           
T Consensus        34 v~V~g~SM~Ptl~~----------GD~vlv~~~~~--~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~~-----------   89 (158)
T TIGR02228        34 VVVLSGSMEPTFNT----------GDLILVTGADP--NDIQVGDVITYKSPGFN-TPVTHRVIEINNSG-----------   89 (158)
T ss_pred             EEEcCCCCcCCccC----------CCEEEEEeccc--CCCCCCCEEEEEECCCC-ccEEEEEEEEECCC-----------
Confidence            34999999999999          99999998543  48999999999997643 78999999997641           


Q ss_pred             ecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEE
Q 028706          147 VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTH  182 (205)
Q Consensus       147 vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~  182 (205)
                       .+-.|++.|||+ ...|   .++|+.++|+||+..
T Consensus        90 -g~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~~  120 (158)
T TIGR02228        90 -GELGFITKGDNN-PAPD---GEPVPSENVIGKYLG  120 (158)
T ss_pred             -CcEEEEEEecCC-CCCC---cccCCHHHEEEEEEE
Confidence             012488889997 4445   689999999999983

This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.

>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]

Probab=99.59  E-value=1.6e-14  Score=115.03  Aligned_cols=127  Identities=30%  Similarity=0.315  Sum_probs=99.7

Q ss_pred             HHHHHHHHHHHHHHHHHh--hheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCC
Q 028706           42 LWSLTKNCFTFGLIGLTV--SDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSN  119 (205)
Q Consensus        42 ~~~~~~~~~~~~lv~~~i--~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~  119 (205)
                      ...++..++.++++++++  ..++++++.|+|+||+|||+.          ||+|+++|.++....+..+|++  ..|..
T Consensus         7 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~----------GD~v~v~k~~~~~~~~~~~~~~--~~~~~   74 (166)
T COG0681           7 FLELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNV----------GDRVLVKKFSYGFGKLKVPDII--VLPAV   74 (166)
T ss_pred             HHHHHHHHHHHHHHhheeeeEEEEEEEEEECCCcccccccc----------CCEEEEEeccccccCCccceee--ecCCC
Confidence            345556666666667776  899999999999999999999          9999999999887778888888  55666


Q ss_pred             CCcceEEEEeeeCCCeeeccCCCC--eEEecCCeEEEeeCCC-------CCCCCCCcccccCCCCEeEEE
Q 028706          120 HKEKHVKRIIGLPGDWIGTPMTND--VVKVPNGHCWVEGDNP-------SSSLDSRSFGPIPLGLVKGRV  180 (205)
Q Consensus       120 ~~~~~vKRViglpGD~V~i~~~~~--~~~vp~g~~~v~GDN~-------~~S~DSR~~G~V~~~~IiGkv  180 (205)
                      ....++||+++.+||.|.+.....  ...+|++..++.++|.       ..+.+++.++.......+.++
T Consensus        75 ~~~~~~kr~~~~~GD~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (166)
T COG0681          75 VEGDLIKRVIGLRGDIVVFKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV  144 (166)
T ss_pred             CCcceEEEeccCCCCEEEEECCEEEeecccCcchhhhhcccccccccccccccCccccccccccccccce
Confidence            788999999999999998854322  3455666666665443       466777778877778888877

>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=99.47  E-value=3.2e-14  Score=112.99  Aligned_cols=88  Identities=28%  Similarity=0.478  Sum_probs=72.1

Q ss_pred             EEEEeeeccCCCCCcceEEEEecCCC------------CCcceEEEEeeeCCCeeec-----------------------
Q 028706           94 VLMEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGT-----------------------  138 (205)
Q Consensus        94 Vlv~k~~~~~~~~~rGDIVvf~~p~~------------~~~~~vKRViglpGD~V~i-----------------------  138 (205)
                      .-++|.+   .++.+||+|+++.|..            ....++|||.|+|||+|.+                       
T Consensus        45 yrv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR  121 (173)
T COG4959          45 YRVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGR  121 (173)
T ss_pred             EEecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCC
Confidence            3444443   4569999999999863            3467899999999999987                       


Q ss_pred             --cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          139 --PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       139 --~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                        +....+-.+-++++|+++|....|+|||||||||.++|+|.+..++
T Consensus       122 ~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPvw  169 (173)
T COG4959         122 ALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPVW  169 (173)
T ss_pred             cCCcccCCceecCCeEEEEeccCCcccccceecccCHHHcceeeeeee
Confidence              1233445588899999999999999999999999999999998873

>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families

Probab=99.19  E-value=1.6e-10  Score=81.57  Aligned_cols=83  Identities=48%  Similarity=0.753  Sum_probs=65.1

Q ss_pred             EEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeE
Q 028706           66 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV  145 (205)
Q Consensus        66 ~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~  145 (205)
                      .+.|.|+||+|++..          ||.+++++..   ..++.||+|++..+.  +..++||+...++            
T Consensus         2 ~~~v~g~SM~P~i~~----------gd~v~i~~~~---~~~~~G~iv~~~~~~--~~~~ikrl~~~~~------------   54 (84)
T cd06462           2 ALRVEGDSMEPTIPD----------GDLVLVDKSS---YEPKRGDIVVFRLPG--GELTVKRVIGLPG------------   54 (84)
T ss_pred             eeEEcCCCccCcccC----------CCEEEEEecC---CCCcCCEEEEEEcCC--CcEEEEEEEEECC------------
Confidence            468999999999999          9999999865   238999999999853  4899999998875            


Q ss_pred             EecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEE
Q 028706          146 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV  180 (205)
Q Consensus       146 ~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv  180 (205)
                         ++++++.+||+ +..+.+..+. .+..++|++
T Consensus        55 ---~~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~v   84 (84)
T cd06462          55 ---EGHYFLLGDNP-NSPDSRIDGP-PELDIVGVV   84 (84)
T ss_pred             ---CCEEEEECCCC-CCCcccccCC-CHHHEEEeC
Confidence               35899999994 5555554333 566677763

The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr

>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification

Probab=99.17  E-value=7.4e-11  Score=81.37  Aligned_cols=56  Identities=34%  Similarity=0.520  Sum_probs=44.7

Q ss_pred             EEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeec
Q 028706           68 PVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT  138 (205)
Q Consensus        68 ~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i  138 (205)
                      +|.|+||+|+|.+          ||+|++++..    .++.||+|+|..+.+. ..++||+++.+|+.+.+
T Consensus         1 ~V~GdSM~P~i~~----------Gd~v~v~~~~----~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~   56 (70)
T PF00717_consen    1 RVEGDSMEPTIKD----------GDIVLVDPSS----EPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILI   56 (70)
T ss_dssp             EEESSTTGGTSST----------TEEEEEEETS-------TTSEEEEEETTEE-SEEEEEEEEETTEEEEE
T ss_pred             CeECcCcccCeeC----------CCEEEEEEcC----CCccCeEEEEEECCce-eeEEEEEEEeCCCEEEE
Confidence            5899999999999          9999999876    8899999999985321 38999999999875443

; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. 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) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....

>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.14  E-value=3.1e-10  Score=90.25  Aligned_cols=122  Identities=22%  Similarity=0.312  Sum_probs=83.4

Q ss_pred             ccchhhhHHHHHHHHHHHHHHHHHHHhhheee------EEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCC
Q 028706           33 ISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYA------SIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKF  106 (205)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~lv~~~i~~~~~------~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~  106 (205)
                      .++|+.+..+.+.+-...++..+.++-..+.+      .++.|-++||||.++.          ||.++......  ...
T Consensus        11 ~k~mn~Rq~l~Q~ln~~mivssA~MiwK~l~vvt~seSPiVVVLSgSMePaF~R----------GDlLfL~N~~~--~p~   78 (180)
T KOG3342|consen   11 LKRMNIRQLLYQVLNFAMIVSSAYMIWKGLMVVTGSESPIVVVLSGSMEPAFHR----------GDLLFLTNRNE--DPI   78 (180)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhheeeeCCCCCEEEEEcCCcCccccc----------ccEEEEecCCC--Ccc
Confidence            44577777766665444444333333333322      3788999999999999          99999975543  367


Q ss_pred             CcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCC--eEEEeeCCCCCCCCCCc-c----cccCCCCEeEE
Q 028706          107 SHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNG--HCWVEGDNPSSSLDSRS-F----GPIPLGLVKGR  179 (205)
Q Consensus       107 ~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g--~~~v~GDN~~~S~DSR~-~----G~V~~~~IiGk  179 (205)
                      +.||||+|+.+. .+..++|||+-+-+..             +|  ++.+.|||+.  .|.|. |    --..+++|+|+
T Consensus        79 ~vGdivVf~veg-R~IPiVHRviK~he~~-------------~~~~~~LTKGDNN~--~dD~~Ly~~gq~~L~r~~Ivg~  142 (180)
T KOG3342|consen   79 RVGDIVVFKVEG-REIPIVHRVIKQHEKS-------------NGHIKFLTKGDNNA--VDDRGLYAQGQNWLERKDIVGR  142 (180)
T ss_pred             eeccEEEEEECC-ccCchhHHHHHHhccc-------------CCcEEEEecCCCCc--ccchhcccccccceeccceeeE
Confidence            899999999854 4678999999765421             23  4778899963  34442 2    13788999999


Q ss_pred             EEE
Q 028706          180 VTH  182 (205)
Q Consensus       180 v~~  182 (205)
                      |.-
T Consensus       143 ~~G  145 (180)
T KOG3342|consen  143 VRG  145 (180)
T ss_pred             Eee
Confidence            965

>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell

Probab=98.87  E-value=1.6e-08  Score=71.20  Aligned_cols=61  Identities=34%  Similarity=0.446  Sum_probs=52.9

Q ss_pred             EEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeE
Q 028706           66 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV  145 (205)
Q Consensus        66 ~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~  145 (205)
                      ...|.|+||+|+++.          ||.+++++..    .++.||++++..+   +..++||+...++            
T Consensus         2 ~~~v~g~sM~p~i~~----------gd~lii~~~~----~~~~g~i~~~~~~---~~~~ikr~~~~~~------------   52 (81)
T cd06529           2 ALRVKGDSMEPTIPD----------GDLVLVDPSD----TPRDGDIVVARLD---GELTVKRLQRRGG------------   52 (81)
T ss_pred             EEEEECCCcCCccCC----------CCEEEEcCCC----CCCCCCEEEEEEC---CEEEEEEEEECCC------------
Confidence            468999999999999          9999999765    6899999999984   4789999998874            


Q ss_pred             EecCCeEEEeeCCC
Q 028706          146 KVPNGHCWVEGDNP  159 (205)
Q Consensus       146 ~vp~g~~~v~GDN~  159 (205)
                          +.+++.++|+
T Consensus        53 ----~~~~L~s~N~   62 (81)
T cd06529          53 ----GRLRLISDNP   62 (81)
T ss_pred             ----CcEEEEeCCC
Confidence                3788889996

This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the

>COG2932 Predicted transcriptional regulator [Transcription]

Probab=98.81  E-value=3.5e-08  Score=82.65  Aligned_cols=86  Identities=26%  Similarity=0.305  Sum_probs=65.1

Q ss_pred             EEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCe
Q 028706           65 SIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDV  144 (205)
Q Consensus        65 ~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~  144 (205)
                      ....|.|+||+|++.+          ||.++|+.-.    ...+||.|++..-  .++.+|||+...+|           
T Consensus       124 ~~i~V~GDSMeP~~~~----------Gd~ilVd~~~----~~~~gd~v~v~~~--g~~~~VK~l~~~~~-----------  176 (214)
T COG2932         124 FALRVTGDSMEPTYED----------GDTLLVDPGV----NTRRGDRVYVETD--GGELYVKKLQREPG-----------  176 (214)
T ss_pred             EEEEEeCCcccccccC----------CCEEEECCCC----ceeeCCEEEEEEe--CCeEEEEEEEEecC-----------
Confidence            5689999999999999          9999998776    6678996666542  46899999998875           


Q ss_pred             EEecCCeEEEeeCCCCCCCCCCcccccCCC---CEeEEEEEEEeC
Q 028706          145 VKVPNGHCWVEGDNPSSSLDSRSFGPIPLG---LVKGRVTHILWP  186 (205)
Q Consensus       145 ~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~---~IiGkv~~~i~P  186 (205)
                           |.+.+..+|+....|--    ...+   .|||+|++..-+
T Consensus       177 -----~~~~l~S~N~~~~~~~~----~~~~~~v~iIgrVv~~~~~  212 (214)
T COG2932         177 -----GLLRLVSLNPDYYPDEI----FSEDDDVEIIGRVVWVSRL  212 (214)
T ss_pred             -----CeEEEEeCCCCCCcccc----cCccceEEEEEEEEEEeee
Confidence                 56779999985433332    2233   489999887543

>PRK10276 DNA polymerase V subunit UmuD; Provisional

Probab=98.55  E-value=8.2e-07  Score=69.82  Aligned_cols=85  Identities=22%  Similarity=0.201  Sum_probs=60.4

Q ss_pred             eEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCC
Q 028706           64 ASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN  142 (205)
Q Consensus        64 ~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~  142 (205)
                      .....|.|+||. |++.+          ||++++++-.    .++.||+|++..   .++..+||+.-.           
T Consensus        51 ~f~l~V~GdSM~~~~I~~----------GD~liVd~~~----~~~~Gdivv~~~---~g~~~vKrl~~~-----------  102 (139)
T PRK10276         51 TYFVKASGDSMIDAGISD----------GDLLIVDSAI----TASHGDIVIAAV---DGEFTVKKLQLR-----------  102 (139)
T ss_pred             EEEEEEecCCCCCCCCCC----------CCEEEEECCC----CCCCCCEEEEEE---CCEEEEEEEEEC-----------
Confidence            455899999998 68999          9999999754    678999999987   467899998742           


Q ss_pred             CeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEe
Q 028706          143 DVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW  185 (205)
Q Consensus       143 ~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~  185 (205)
                             +++++..+|+..  .....-.-..=.|+|+|++++-
T Consensus       103 -------~~~~L~s~N~~y--~~i~i~~~~~~~IiG~V~~~~~  136 (139)
T PRK10276        103 -------PTVQLIPMNSAY--SPITISSEDTLDVFGVVTHIVK  136 (139)
T ss_pred             -------CcEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEEEE
Confidence                   247788888631  1111111112269999988763

>PRK00215 LexA repressor; Validated

Probab=98.43  E-value=2.3e-06  Score=70.95  Aligned_cols=86  Identities=26%  Similarity=0.350  Sum_probs=63.4

Q ss_pred             eeEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCC
Q 028706           63 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT  141 (205)
Q Consensus        63 ~~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~  141 (205)
                      -.....|.|+||. |++.+          ||++++++..    .++.||+|++..   +++..+||+.-.          
T Consensus       117 ~~~~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivv~~~---~~~~~vKrl~~~----------  169 (205)
T PRK00215        117 EDFLLRVRGDSMIDAGILD----------GDLVIVRKQQ----TARNGQIVVALI---DDEATVKRFRRE----------  169 (205)
T ss_pred             CeEEEEEccCCCCCCCcCC----------CCEEEEeCCC----CCCCCCEEEEEE---CCEEEEEEEEEe----------
Confidence            4556889999995 79999          9999998743    678999999987   358899999754          


Q ss_pred             CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEe
Q 028706          142 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW  185 (205)
Q Consensus       142 ~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~  185 (205)
                             .|.+++..||+..  +.....+ ..-.|+|+|+..+-
T Consensus       170 -------~~~~~L~s~Np~y--~~~~~~~-~~~~IiG~Vv~~~r  203 (205)
T PRK00215        170 -------GGHIRLEPENPAY--EPIIVDP-DRVTIEGKVVGLIR  203 (205)
T ss_pred             -------CCEEEEEcCCCCC--CCEEeCC-CcEEEEEEEEEEEE
Confidence                   2478888898742  2221111 13589999988763

>TIGR00498 lexA SOS regulatory protein LexA

Probab=98.40  E-value=4.1e-06  Score=69.16  Aligned_cols=88  Identities=16%  Similarity=0.165  Sum_probs=65.5

Q ss_pred             eeEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCC
Q 028706           63 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT  141 (205)
Q Consensus        63 ~~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~  141 (205)
                      -...+.|.|+||. |++.+          ||++++++..    .++.||+|++..   .+...+||+.-.          
T Consensus       110 ~~f~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivvv~~---~~~~~vKrl~~~----------  162 (199)
T TIGR00498       110 AVFLLKVMGDSMVDAGICD----------GDLLIVRSQK----DARNGEIVAAMI---DGEVTVKRFYKD----------  162 (199)
T ss_pred             CEEEEEecCCCCCCCCCCC----------CCEEEEecCC----CCCCCCEEEEEE---CCEEEEEEEEEE----------
Confidence            4567899999996 58999          9999998653    788999999998   567899998743          


Q ss_pred             CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCC
Q 028706          142 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP  187 (205)
Q Consensus       142 ~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~  187 (205)
                             .+.+++..+|+...  ..... -..=.|+|+|+.++..+
T Consensus       163 -------~~~i~L~s~N~~y~--~i~~~-~~~~~IiG~Vv~~~r~~  198 (199)
T TIGR00498       163 -------GTKVELKPENPEFD--PIVLN-AEDVTILGKVVGVIRNF  198 (199)
T ss_pred             -------CCEEEEEcCCCCCc--CCcCC-CCcEEEEEEEEEEEEec
Confidence                   24788889987421  11111 01358999999887643

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PRK12423 LexA repressor; Provisional

Probab=98.34  E-value=4.6e-06  Score=69.47  Aligned_cols=84  Identities=18%  Similarity=0.165  Sum_probs=62.3

Q ss_pred             EEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCC
Q 028706           65 SIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTND  143 (205)
Q Consensus        65 ~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~  143 (205)
                      ....|.|+||. |+|.+          ||+|+|++-.    .++.||+|++..   .++..+||+.-..           
T Consensus       115 f~l~V~GdSM~~~~i~~----------Gd~viv~~~~----~~~~Gdivv~~~---~~~~~vKrl~~~~-----------  166 (202)
T PRK12423        115 YLLQVQGDSMIDDGILD----------GDLVGVHRSP----EARDGQIVVARL---DGEVTIKRLERSG-----------  166 (202)
T ss_pred             EEEEEecCcCCCCCcCC----------CCEEEEeCCC----cCCCCCEEEEEE---CCEEEEEEEEEeC-----------
Confidence            45899999997 79999          9999999753    778999999987   4678999987542           


Q ss_pred             eEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          144 VVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       144 ~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                            +.+++..+|+..  +...+-+-..=.|+|+|+..+
T Consensus       167 ------~~~~L~s~N~~y--~~i~~~~~~~~~I~Gvv~g~~  199 (202)
T PRK12423        167 ------DRIRLLPRNPAY--APIVVAPDQDFAIEGVFCGLI  199 (202)
T ss_pred             ------CEEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEEE
Confidence                  368888888632  222221112347999998876

>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]

Probab=97.57  E-value=0.0012  Score=55.34  Aligned_cols=89  Identities=19%  Similarity=0.214  Sum_probs=65.5

Q ss_pred             eeEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCC
Q 028706           63 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT  141 (205)
Q Consensus        63 ~~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~  141 (205)
                      -.....|.|+||. +.+.+          ||.|+|++-.    ..+.||||+...+.  ++.-+||..-..         
T Consensus       111 ~~f~L~V~GdSM~~~gi~d----------GDlvvV~~~~----~a~~GdiVvA~i~g--~e~TvKrl~~~g---------  165 (201)
T COG1974         111 ATFFLRVSGDSMIDAGILD----------GDLVVVDPTE----DAENGDIVVALIDG--EEATVKRLYRDG---------  165 (201)
T ss_pred             ceEEEEecCCccccCcCCC----------CCEEEEcCCC----CCCCCCEEEEEcCC--CcEEEEEEEEeC---------
Confidence            3556899999997 56666          9999999765    88999999999853  568899987543         


Q ss_pred             CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCC
Q 028706          142 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP  187 (205)
Q Consensus       142 ~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~  187 (205)
                              +.++++--|+..  ....+..- .-.|+|+|+.++|+.
T Consensus       166 --------~~i~L~p~Np~~--~~i~~~~~-~~~I~G~vvgv~r~~  200 (201)
T COG1974         166 --------NQILLKPENPAY--PPIPVDAD-SVTILGKVVGVIRDI  200 (201)
T ss_pred             --------CEEEEEeCCCCC--CCcccCcc-ceEEEEEEEEEEecC
Confidence                    367777777632  22222111 457999999999974

>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]

Probab=92.77  E-value=0.055  Score=36.58  Aligned_cols=28  Identities=21%  Similarity=0.476  Sum_probs=22.5

Q ss_pred             ccccccccc---cCCCCCCCccccccccccc
Q 028706            8 QKTCMNCKT---LNPQLPLQPCRCILGEISN   35 (205)
Q Consensus         8 ~~~~~~~~~---~~~~~~~~~~r~~~~~~~~   35 (205)
                      .+-|-+|++   ++.|++++.|+++++..++
T Consensus         8 H~HC~VCg~aIp~de~~CSe~C~eil~ker~   38 (64)
T COG4068           8 HRHCVVCGKAIPPDEQVCSEECGEILNKERK   38 (64)
T ss_pred             CccccccCCcCCCccchHHHHHHHHHHHHHH
Confidence            467999998   7779999999987776654

>TIGR02594 conserved hypothetical protein TIGR02594

Probab=86.94  E-value=2.6  Score=32.70  Aligned_cols=40  Identities=25%  Similarity=0.233  Sum_probs=29.9

Q ss_pred             CCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCCC
Q 028706          105 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSS  161 (205)
Q Consensus       105 ~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~~  161 (205)
                      .+++||+|+|+..   +.-+|.-+++...+              .|.++++|-|-.+
T Consensus        73 ~p~~GDiv~f~~~---~~~HVGi~~g~~~~--------------~g~i~~lgGNq~~  112 (129)
T TIGR02594        73 KPAYGCIAVKRRG---GGGHVGFVVGKDKQ--------------TGTIIVLGGNQGD  112 (129)
T ss_pred             CCCccEEEEEECC---CCCEEEEEEeEcCC--------------CCEEEEeeCCCCC
Confidence            6899999999863   34578888876654              4688999888643

Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.

>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown

Probab=85.97  E-value=0.7  Score=31.33  Aligned_cols=27  Identities=19%  Similarity=0.312  Sum_probs=18.0

Q ss_pred             cccccccc---cCCCCCCCccccccccccc
Q 028706            9 KTCMNCKT---LNPQLPLQPCRCILGEISN   35 (205)
Q Consensus         9 ~~~~~~~~---~~~~~~~~~~r~~~~~~~~   35 (205)
                      +-|-+|++   .+....+..||+.....++
T Consensus         4 kHC~~CG~~Ip~~~~fCS~~C~~~~~k~qk   33 (59)
T PF09889_consen    4 KHCPVCGKPIPPDESFCSPKCREEYRKRQK   33 (59)
T ss_pred             CcCCcCCCcCCcchhhhCHHHHHHHHHHHH
Confidence            56889987   4446777788875555443

They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	205
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	1e-06
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	3e-04

>1b12_A Signal peptidase I; serine proteinase, serine-dependant hydrolase, signal peptid processing, protein translocation; HET: 1PN; 1.95A {Escherichia coli} SCOP: b.87.1.2 PDB: 3s04_A* 1t7d_A* 3iiq_A* 1kn9_A* Length = 248

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 24/80 (30%), Positives = 33/80 (41%), Gaps = 28/80 (35%)

Query: 72  SSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFS---------------HGDVIVFCS 116
            SM PT           L  D +L+EKF    Y                   GD++VF  
Sbjct: 14  GSMMPTL----------LIGDFILVEKF---AYGIKDPIYQKTLIETGHPKRGDIVVFKY 60

Query: 117 PSNHKEKHVKRIIGLPGDWI 136
           P + K  ++KR +GLPGD +
Sbjct: 61  PEDPKLDYIKRAVGLPGDKV 80

>1b12_A Signal peptidase I; serine proteinase, serine-dependant hydrolase, signal peptid processing, protein translocation; HET: 1PN; 1.95A {Escherichia coli} SCOP: b.87.1.2 PDB: 3s04_A* 1t7d_A* 3iiq_A* 1kn9_A* Length = 248

 Score = 39.9 bits (93), Expect = 3e-04
 Identities = 16/44 (36%), Positives = 22/44 (50%)

Query: 142 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW 185
                VP G  ++ GDN  +S DSR +G +P   + GR T I  
Sbjct: 183 LATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWM 226

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	205
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	100.0
1kca_A	109	Repressor protein CI; gene regulation, DNA-binding	99.35
1umu_A	116	UMUD'; induced mutagenesis, SOS mutagenesis, DNA r	99.18
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	98.94
2hnf_A	133	Repressor protein CI101-229DM-K192A; viral protein	98.9
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	98.88
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	98.61
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	96.31

>1b12_A Signal peptidase I; serine proteinase, serine-dependant hydrolase, signal peptid processing, protein translocation; HET: 1PN; 1.95A {Escherichia coli} SCOP: b.87.1.2 PDB: 3s04_A* 1t7d_A* 3iiq_A* 1kn9_A*

Probab=100.00  E-value=5.5e-34  Score=242.55  Aligned_cols=123  Identities=32%  Similarity=0.441  Sum_probs=106.7

Q ss_pred             hhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeecc------------CCCCCcceEEEEecCCCCCcceEE
Q 028706           59 VSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQ------------KYKFSHGDVIVFCSPSNHKEKHVK  126 (205)
Q Consensus        59 i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~------------~~~~~rGDIVvf~~p~~~~~~~vK  126 (205)
                      ++.|+++++.|+|+||+|||+.          ||+|+++|..|.            ..++++||||+|+.|.+++..+||
T Consensus         1 ir~fv~~~~~v~g~SM~Ptl~~----------GD~vlv~k~~yg~r~P~~~~~l~~~~~~~rGDIvvf~~p~~~~~~~iK   70 (248)
T 1b12_A            1 VRSFIYEPFQIPSGSMMPTLLI----------GDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIK   70 (248)
T ss_dssp             -CBCCEEEEECCSCTTTTTSCT----------TEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTTCTTSEEEE
T ss_pred             CeEEEEEEEEeccccccccccC----------CCEEEEEecccCcccccccccccccCCCCCCcEEEEEeCCCCCceEEE
Confidence            4678999999999999999999          999999998753            257999999999999877889999


Q ss_pred             EEeeeCCCeeeccCC-----------------------------------------------------------------
Q 028706          127 RIIGLPGDWIGTPMT-----------------------------------------------------------------  141 (205)
Q Consensus       127 RViglpGD~V~i~~~-----------------------------------------------------------------  141 (205)
                      ||+|+|||+|++...                                                                 
T Consensus        71 RViglpGD~v~i~~~~~~l~ING~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~  150 (248)
T 1b12_A           71 RAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSE  150 (248)
T ss_dssp             EEEECTTCEEEEETTTTEEEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEE
T ss_pred             EEEeeCCCEEEEEcCceEEEECCccccccccccceeeeeeccccccccccccccccccccccccccccccccccchhhhh
Confidence            999999999976111                                                                 


Q ss_pred             --------------------------------CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCC
Q 028706          142 --------------------------------NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQR  189 (205)
Q Consensus       142 --------------------------------~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~  189 (205)
                                                      ..+++||+|+|||||||+++|.|||+||+||+++|+|||++++||+++
T Consensus       151 ~~e~l~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~VP~g~yFvmGDNR~nS~DSR~~G~Vp~~~IvGka~~i~~s~~~  230 (248)
T 1b12_A          151 RKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDK  230 (248)
T ss_dssp             EEEEETTEEEEEEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEEEEEBC-
T ss_pred             HHhhhcCccceeEecCCccccccchhcccccccccEEeCCCcEEEecCCCcccCCCCcccccCHHHeEEEEEEEEEeCCc
Confidence                                            013589999999999999999999999999999999999999999886


Q ss_pred             cc
Q 028706          190 VR  191 (205)
Q Consensus       190 ~~  191 (205)
                      ..
T Consensus       231 ~~  232 (248)
T 1b12_A          231 QE  232 (248)
T ss_dssp             --
T ss_pred             cc
Confidence            53

>1kca_A Repressor protein CI; gene regulation, DNA-binding, lambda repressor, protein oligomerization, DNA-looping; 2.91A {Enterobacteria phage lambda} SCOP: b.87.1.1

Probab=99.35  E-value=5.6e-12  Score=94.14  Aligned_cols=90  Identities=22%  Similarity=0.300  Sum_probs=71.4

Q ss_pred             EEEEEcCCCCc------cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeec
Q 028706           65 SIVPVRGSSMS------PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT  138 (205)
Q Consensus        65 ~~~~V~g~SM~------Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i  138 (205)
                      ....|.|+||+      |+|.+          ||+|++++..    .++.||+|++..+.  ++.++||++..+      
T Consensus        14 f~~~V~GdSM~~~~g~~p~i~~----------Gd~v~Vd~~~----~~~~Gdivv~~~~~--~~~~vKrl~~~~------   71 (109)
T 1kca_A           14 FWLEVEGNSMTAPTGSKPSFPD----------GMLILVDPEQ----AVEPGDFCIARLGG--DEFTFKKLIRDS------   71 (109)
T ss_dssp             EEEECCSSTTCCCTTCSSCCCT----------TCEEEEETTS----CCCTTCEEEEECST--TCEEEEEEEEET------
T ss_pred             EEEEEeCcCcCCCCCCCCeeCC----------CCEEEEecCC----cCCCCCEEEEEECC--CeEEEEEEEEeC------
Confidence            46889999999      99999          9999999754    68999999998742  478999999743      


Q ss_pred             cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCCcc
Q 028706          139 PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVR  191 (205)
Q Consensus       139 ~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~~~  191 (205)
                                 |.+++.+||+...  ....  -..-.|+|+|++.+||+..|+
T Consensus        72 -----------~~~~L~s~N~~y~--~~~~--~~~~~IiG~Vv~~~~~~~~~~  109 (109)
T 1kca_A           72 -----------GQVFLQPLNPQYP--MIPC--NESCSVVGKVIASQWPEETFG  109 (109)
T ss_dssp             -----------TEEEEECSSTTSC--CEEC--CTTCEEEEEEEEEECCGGGGC
T ss_pred             -----------CEEEEEECCCCCC--CEEc--CCCcEEEEEEEEEEeCHHHcC
Confidence                       4789999997421  1111  145679999999999987664

>1umu_A UMUD'; induced mutagenesis, SOS mutagenesis, DNA repair, beta- lactamase cleavage reaction, LEXA repressor, lambda CI; 2.50A {Escherichia coli} SCOP: b.87.1.1 PDB: 1i4v_A 1ay9_A

Probab=99.18  E-value=8.9e-11  Score=88.03  Aligned_cols=88  Identities=20%  Similarity=0.212  Sum_probs=64.6

Q ss_pred             eEEEEEcCCCCcc-ccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCC
Q 028706           64 ASIVPVRGSSMSP-TFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN  142 (205)
Q Consensus        64 ~~~~~V~g~SM~P-tl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~  142 (205)
                      .....|.|+||+| +|++          ||+|++++..    .++.||+|++..   ++..++||+...+          
T Consensus        27 ~~~~~v~GdSM~p~~i~~----------Gd~v~vd~~~----~~~~gdivv~~~---~~~~~vKr~~~~~----------   79 (116)
T 1umu_A           27 TYFVKASGDSMIDGGISD----------GDLLIVDSAI----TASHGDIVIAAV---DGEFTVKKLQLRP----------   79 (116)
T ss_dssp             EEEEECCSSTTGGGTCCT----------TCEEEEETTS----CCCTTCEEEEEE---TTEEEEEEEECSS----------
T ss_pred             EEEEEECCCCcCCCCCCC----------CCEEEEEcCC----CCCCCCEEEEEE---CCEEEEEEEEeCC----------
Confidence            4568999999999 8999          9999999754    689999999988   4578999998742          


Q ss_pred             CeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCC
Q 028706          143 DVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQ  188 (205)
Q Consensus       143 ~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~  188 (205)
                              .+++.+||+..  .......-..-.|+|+|++++..+.
T Consensus        80 --------~~~L~s~N~~y--~~~~i~~~~~~~IiG~Vv~~~r~~r  115 (116)
T 1umu_A           80 --------TVQLIPMNSAY--SPITISSEDTLDVFGVVIHVVKAAT  115 (116)
T ss_dssp             --------SCEEECSSTTS--CCEECCTTSCEEEEEEEEEEEC---
T ss_pred             --------cEEEECCCCCC--CCEEcCCCCeEEEEEEEEEEEEecC
Confidence                    57788998731  1111111123469999999876653

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=98.94  E-value=3.8e-09  Score=85.77  Aligned_cols=87  Identities=18%  Similarity=0.168  Sum_probs=65.1

Q ss_pred             eEEEEEcCCCCccc-cCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCC
Q 028706           64 ASIVPVRGSSMSPT-FNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN  142 (205)
Q Consensus        64 ~~~~~V~g~SM~Pt-l~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~  142 (205)
                      .....|.|+||+|+ |.+          ||+|++++..    .++.||+|++..   ++...+||+. .++         
T Consensus       110 ~~~~~v~GdSM~p~~i~~----------Gd~v~vd~~~----~~~~G~i~v~~~---~~~~~vKrl~-~~~---------  162 (202)
T 1jhf_A          110 DFLLRVSGMSMKDIGIMD----------GDLLAVHKTQ----DVRNGQVVVARI---DDEVTVKRLK-KQG---------  162 (202)
T ss_dssp             CEEEECCSSTTGGGTCCT----------TCEEEEEECS----CCCTTSEEEEEE---TTEEEEEEEE-EET---------
T ss_pred             EEEEEECCCCCCCCCCCC----------CCEEEEeccC----CcCCCeEEEEEE---CCEEEEEEEE-EeC---------
Confidence            35688999999999 999          9999998754    688999999987   4689999998 454         


Q ss_pred             CeEEecCCeEEEeeCCCCCCCCCCccc-ccCCCCEeEEEEEEEeC
Q 028706          143 DVVKVPNGHCWVEGDNPSSSLDSRSFG-PIPLGLVKGRVTHILWP  186 (205)
Q Consensus       143 ~~~~vp~g~~~v~GDN~~~S~DSR~~G-~V~~~~IiGkv~~~i~P  186 (205)
                             |.+++.+||+..  ....+. .-..-.|+|+|++++..
T Consensus       163 -------~~~~l~s~N~~y--~~~~~~~~~~~~~IiG~Vv~~~r~  198 (202)
T 1jhf_A          163 -------NKVELLPENSEF--KPIVVDLRQQSFTIEGLAVGVIRN  198 (202)
T ss_dssp             -------TEEEEECSSTTC--CCEEEETTTSCEEEEEEEEEEEEC
T ss_pred             -------CEEEEEECCCCC--CCEEccCCCCceEEEEEEEEEEEc
Confidence                   478888998632  111111 01223599999988764

>2hnf_A Repressor protein CI101-229DM-K192A; viral protein; 1.80A {Escherichia coli} PDB: 2ho0_A 1f39_A

Probab=98.90  E-value=5.8e-09  Score=80.00  Aligned_cols=82  Identities=20%  Similarity=0.207  Sum_probs=63.2

Q ss_pred             EEEEEcCCCCc------cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeec
Q 028706           65 SIVPVRGSSMS------PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT  138 (205)
Q Consensus        65 ~~~~V~g~SM~------Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i  138 (205)
                      ....|.|+||+      |+|.+          ||+|++++..    .++.||+|++...  .++.++||+...+      
T Consensus        45 f~~~V~GdSM~~~~g~~p~i~~----------Gd~v~vd~~~----~~~~Gdivv~~~~--~~~~~vKrl~~~~------  102 (133)
T 2hnf_A           45 FWLEVEGNSMTTPTGSKTSFPD----------GMLILVDPEQ----AVEPGDFCIARLG--GDEFTFAKLIRDS------  102 (133)
T ss_dssp             EEEECCSSTTCCC---CCCCCT----------TCEEEEETTS----CCCTTSEEEEEET--TTEEEEEEEEEET------
T ss_pred             EEEEEeCCCcCCCcCCCCccCC----------CCEEEEccCC----CCCCCCEEEEEEC--CCEEEEEEEEEeC------
Confidence            46889999999      99999          9999999753    7899999999874  2478999998643      


Q ss_pred             cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEE
Q 028706          139 PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHI  183 (205)
Q Consensus       139 ~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~  183 (205)
                                 |.+++.+||+...  .....  ..-.|+|+|++.
T Consensus       103 -----------~~~~L~s~N~~y~--~~~~~--~~~~IiG~Vv~~  132 (133)
T 2hnf_A          103 -----------GQVFLQPLNPQYP--MIPCN--ESCSVVGKVIAS  132 (133)
T ss_dssp             -----------TEEEEECSSTTSC--CEECS--TTEEEEEEEEEE
T ss_pred             -----------CeEEEEECCCCCC--CEEcC--CCCEEEEEEEEE
Confidence                       4788999997321  11111  445799999875

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=98.88  E-value=4.8e-09  Score=86.61  Aligned_cols=90  Identities=22%  Similarity=0.299  Sum_probs=69.1

Q ss_pred             EEEEEcCCCCc------cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeec
Q 028706           65 SIVPVRGSSMS------PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT  138 (205)
Q Consensus        65 ~~~~V~g~SM~------Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i  138 (205)
                      ....|.|+||+      |+|.+          ||+|+|++..    .++.||+|++...  .+..++||+...+      
T Consensus       141 ~~l~V~GdSM~~~~g~~P~i~~----------Gd~v~vd~~~----~~~~g~ivv~~~~--~~~~~vKrl~~~~------  198 (236)
T 3bdn_A          141 FWLEVEGNSMTAPTGSKPSFPD----------GMLILVDPEQ----AVEPGDFCIARLG--GDEFTFKKLIRGS------  198 (236)
T ss_dssp             EEEECCSSSSCCCSSCSSCCCS----------SCEEEECCSS----CCCTTSEEEEEST--TTCCCCEEEECCS------
T ss_pred             EEEEEeCCCcCCCCCCCCcCCC----------CCEEEECCCC----CCCCCcEEEEEEC--CCeEEEEEEEEcC------
Confidence            46789999999      99999          9999998754    6889999999872  3578999998643      


Q ss_pred             cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCCcc
Q 028706          139 PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVR  191 (205)
Q Consensus       139 ~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~~~  191 (205)
                                 |.+++..||+..  .....-  ..-.|+|+|++.+||...|+
T Consensus       199 -----------~~~~L~s~N~~y--~~~~~~--~~~~IiG~Vv~~~~~~~~~~  236 (236)
T 3bdn_A          199 -----------GQVFLQPLNPQY--PMIPCN--ESCSVVGKVIASQWPEETFG  236 (236)
T ss_dssp             -----------SSCEEECSSTTS--CCBC----CCCEEEEEEEECCCCSSSCC
T ss_pred             -----------CcEEEEeCCCCC--CCeecC--CCcEEEEEEEEEEcCHHhcC
Confidence                       467788998732  111111  34579999999999987664

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=98.61  E-value=2.7e-07  Score=74.84  Aligned_cols=84  Identities=18%  Similarity=0.195  Sum_probs=64.3

Q ss_pred             eEEEEEcCCCC-ccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCC
Q 028706           64 ASIVPVRGSSM-SPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN  142 (205)
Q Consensus        64 ~~~~~V~g~SM-~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~  142 (205)
                      .....|.|+|| +|++.+          ||+|++++..    .++.||+|++..   +++..+||+.-.           
T Consensus       109 ~f~l~v~GdSM~~p~i~~----------GD~viv~~~~----~~~~G~ivv~~~---~~~~~vKr~~~~-----------  160 (196)
T 3k2z_A          109 HFLLKVKGESMIEEHICD----------GDLVLVRRQD----WAQNGDIVAAMV---DGEVTLAKFYQR-----------  160 (196)
T ss_dssp             EEEEECCSSTTGGGTCCT----------TCEEEEEECS----CCCTTCEEEEEE---TTEEEEEEEEEE-----------
T ss_pred             EEEEEEeCCCcCCCCCCC----------CCEEEEeccC----cCCCCCEEEEEE---CCcEEEEEEEEE-----------
Confidence            45789999999 699999          9999999764    678999999987   468999999753           


Q ss_pred             CeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          143 DVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       143 ~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                            +|.+++..||+..  .....- -..-.|+|+|++++
T Consensus       161 ------~~~~~L~~~N~~y--~~i~i~-~~~~~i~G~Vv~~~  193 (196)
T 3k2z_A          161 ------GDTVELRPANREM--SSMFFR-AEKVKILGKVVGVF  193 (196)
T ss_dssp             ------TTEEEEECSCTTS--CCEEEE-GGGCEEEEEEEEEE
T ss_pred             ------CCEEEEEECCCCC--CCEEec-CCCEEEEEEEEEEE
Confidence                  3578888998732  111111 13457999999876

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=96.31  E-value=0.011  Score=46.33  Aligned_cols=65  Identities=17%  Similarity=0.165  Sum_probs=46.5

Q ss_pred             CCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCCCCCCCCcccc
Q 028706           91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGP  170 (205)
Q Consensus        91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~  170 (205)
                      ||+|+|++.     .+..|+++++..   ++..++||+.-.+|                |.+.+..||+.     ...- 
T Consensus       122 Gd~v~Vd~~-----~~~~g~i~vv~~---~g~~~vKrl~~~~~----------------~~i~L~s~N~~-----~~i~-  171 (189)
T 2fjr_A          122 GKIYFVDKQ-----ASLSDGLWLVDI---KGAISIRELTKLPG----------------RKLHVAGGKVP-----FECG-  171 (189)
T ss_dssp             TEEEEEETT-----CCSCSEEEEEEE---TTEEEEEEEEEETT----------------TEEEEESSSSC-----EEEE-
T ss_pred             CcEEEEEcC-----CccCCCEEEEEe---CCeEEEEEEEECCC----------------CEEEEEeCCCC-----eEec-
Confidence            999999864     256799999987   56899999987664                36777888861     1111 


Q ss_pred             cCCCCEeEEEEEEEe
Q 028706          171 IPLGLVKGRVTHILW  185 (205)
Q Consensus       171 V~~~~IiGkv~~~i~  185 (205)
                      ...=.|+|||++.+-
T Consensus       172 ~~~i~IiG~Vv~~~r  186 (189)
T 2fjr_A          172 IDDIKTLGRVVGVYS  186 (189)
T ss_dssp             TTSSEEEEEEEEEEE
T ss_pred             ccceEEEEEEEEEEE
Confidence            133469999998753

---

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	205
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	7e-11
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	0.001

>d1b12a_ b.87.1.2 (A:) Type 1 signal peptidase {Escherichia coli [TaxId: 562]} Length = 247

class: All beta proteins
fold: LexA/Signal peptidase
superfamily: LexA/Signal peptidase
family: Type 1 signal peptidase
domain: Type 1 signal peptidase
species: Escherichia coli [TaxId: 562]

 Score = 57.7 bits (138), Expect = 7e-11
 Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 101 LQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS 160
           L + K + GDV          +  V      PG  + T        VP G  ++ GDN  
Sbjct: 147 LSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLAT------WIVPPGQYFMMGDNRD 200

Query: 161 SSLDSRSFGPIPLGLVKGRVTHILWP 186
           +S DSR +G +P   + GR T I   
Sbjct: 201 NSADSRYWGFVPEANLVGRATAIWMS 226

>d1b12a_ b.87.1.2 (A:) Type 1 signal peptidase {Escherichia coli [TaxId: 562]} Length = 247

class: All beta proteins
fold: LexA/Signal peptidase
superfamily: LexA/Signal peptidase
family: Type 1 signal peptidase
domain: Type 1 signal peptidase
species: Escherichia coli [TaxId: 562]

 Score = 36.5 bits (83), Expect = 0.001
 Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 22/94 (23%)

Query: 69  VRGSSMSPTFNPTTDSFMGSLSDDHVLMEKF------------CLQKYKFSHGDVIVFCS 116
           +   SM PT           L  D +L+EKF             ++      GD++VF  
Sbjct: 10  IPSGSMMPTL----------LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKY 59

Query: 117 PSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNG 150
           P + K  ++KR +GLPGD +     +  + +  G
Sbjct: 60  PEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPG 93

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	205
d1b12a_	247	Type 1 signal peptidase {Escherichia coli [TaxId:	100.0
d1f39a_	101	lambda repressor C-terminal domain {Bacteriophage	99.11
d1jhfa2	126	LexA C-terminal domain {Escherichia coli [TaxId: 5	98.82
d1umua_	105	UmuD' {Escherichia coli [TaxId: 562]}	98.62

>d1b12a_ b.87.1.2 (A:) Type 1 signal peptidase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: LexA/Signal peptidase
superfamily: LexA/Signal peptidase
family: Type 1 signal peptidase
domain: Type 1 signal peptidase
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.1e-35  Score=248.99  Aligned_cols=120  Identities=32%  Similarity=0.444  Sum_probs=107.3

Q ss_pred             hheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccC------------CCCCcceEEEEecCCCCCcceEEE
Q 028706           60 SDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQK------------YKFSHGDVIVFCSPSNHKEKHVKR  127 (205)
Q Consensus        60 ~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~------------~~~~rGDIVvf~~p~~~~~~~vKR  127 (205)
                      ++|+++++.|+|+||+|||..          ||+|+|+|++|..            ..+++||+|+|..|.++...++||
T Consensus         1 R~f~~~~f~IPs~SMePTL~~----------GD~l~V~K~~Yg~r~P~~~~~~~~~~~~~rgdivvf~~p~~~~~~~ikR   70 (247)
T d1b12a_           1 RSFIYEPFQIPSGSMMPTLLI----------GDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKR   70 (247)
T ss_dssp             CBCCEEEEECCSCTTTTTSCT----------TEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTTCTTSEEEEE
T ss_pred             CEEEEEEEEeCcccccchhcc----------CCEEEEEccccCccCCccCcccccccCcccCceeeecCCCCCCcccccc
Confidence            368899999999999999999          9999999988764            355999999999999888999999


Q ss_pred             EeeeCCCeeecc--------------------------------------------------------------------
Q 028706          128 IIGLPGDWIGTP--------------------------------------------------------------------  139 (205)
Q Consensus       128 ViglpGD~V~i~--------------------------------------------------------------------  139 (205)
                      |+|+|||+|.+.                                                                    
T Consensus        71 ~ig~pGD~i~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (247)
T d1b12a_          71 AVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSER  150 (247)
T ss_dssp             EEECTTCEEEEETTTTEEEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEE
T ss_pred             ccCCCCCeEEEecccceEEecccccccceeecceeecccccCcccceeeeeeccCceeccceeeccccccccCceEeeee
Confidence            999999999750                                                                    


Q ss_pred             -----------------------------CCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCC
Q 028706          140 -----------------------------MTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQR  189 (205)
Q Consensus       140 -----------------------------~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~  189 (205)
                                                   .....++||+|+|||||||+++|.|||+||+||+++|+|||++++||+++
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Vp~~~yfvmGDNR~nS~DSR~wG~Vp~~~I~Gka~~i~~p~~~  229 (247)
T d1b12a_         151 KETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDK  229 (247)
T ss_dssp             EEEETTEEEEEEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEEEEEBC-
T ss_pred             eeccCCcceeEEecccchhcccccccCCccccceEEEeCCeEEEecCCCCCCccccccCcCCHHHeEEEEEEEEEECCC
Confidence                                         01235789999999999999999999999999999999999999999865

>d1f39a_ b.87.1.1 (A:) lambda repressor C-terminal domain {Bacteriophage lambda [TaxId: 10710]}

class: All beta proteins
fold: LexA/Signal peptidase
superfamily: LexA/Signal peptidase
family: LexA-related
domain: lambda repressor C-terminal domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=99.11  E-value=3.1e-10  Score=81.92  Aligned_cols=90  Identities=22%  Similarity=0.286  Sum_probs=69.1

Q ss_pred             EEEEEcCCCC------ccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeec
Q 028706           65 SIVPVRGSSM------SPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT  138 (205)
Q Consensus        65 ~~~~V~g~SM------~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i  138 (205)
                      ...+|.|+||      +|+|++          ||+|+|++..    .++.||+|++...  .+..++||+.-.       
T Consensus         6 F~l~V~GdSM~~~~~~ep~i~~----------Gd~viVd~~~----~~~~g~ivva~~~--~~~~~vKr~~~~-------   62 (101)
T d1f39a_           6 FWLEVEGNSMTAPTGSKPSFPD----------GMLILVDPEQ----AVEPGDFCIARLG--GDEFTFKKLIRD-------   62 (101)
T ss_dssp             EEEECCSSTTCCCTTCSSCCCT----------TCEEEEETTS----CCCTTCEEEEECT--TSCEEEEEEEEE-------
T ss_pred             EEEEEeCCccCCCcccCCCcCC----------CCEEEEEecC----ccCCCCEEEEEEC--CCeEEEEEEEEc-------
Confidence            4578999999      899999          9999999753    7899999988763  346789998754       


Q ss_pred             cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCCcc
Q 028706          139 PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVR  191 (205)
Q Consensus       139 ~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~~~  191 (205)
                                +|.+++..||+..  .....  -..-.|+|+|+..+||-..||
T Consensus        63 ----------~~~~~L~s~N~~y--~~i~~--~~~~~IiG~Vv~s~~p~~~~~  101 (101)
T d1f39a_          63 ----------SGQVFLQPLNPQY--PMIPC--NESCSVVGKVIASQWPEETFG  101 (101)
T ss_dssp             ----------TTEEEEECSSTTS--CCEEC--STTCEEEEEEEEEECCGGGGC
T ss_pred             ----------CCEEEEEECCCCC--CCCcC--CCCcEEEEEEEEEECcHHHCC
Confidence                      3578899999742  12211  135679999999999977665

>d1jhfa2 b.87.1.1 (A:73-198) LexA C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: LexA/Signal peptidase
superfamily: LexA/Signal peptidase
family: LexA-related
domain: LexA C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.82  E-value=1e-08  Score=76.34  Aligned_cols=84  Identities=18%  Similarity=0.149  Sum_probs=63.6

Q ss_pred             EEEEEcCCCCccc-cCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCC
Q 028706           65 SIVPVRGSSMSPT-FNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTND  143 (205)
Q Consensus        65 ~~~~V~g~SM~Pt-l~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~  143 (205)
                      ...+|.|+||+|+ +.+          ||++++++..    .++.||+|++..   .++..+||+.-.+           
T Consensus        39 f~lrV~GdSM~~~~i~~----------gd~viv~~~~----~~~~G~ivv~~~---~ge~~vKrl~~~~-----------   90 (126)
T d1jhfa2          39 FLLRVSGMSMKDIGIMD----------GDLLAVHKTQ----DVRNGQVVVARI---DDEVTVKRLKKQG-----------   90 (126)
T ss_dssp             EEEECCSSTTGGGTCCT----------TCEEEEEECS----CCCTTSEEEEEE---TTEEEEEEEEEET-----------
T ss_pred             EEEEEcCCcccCcccCC----------CEEEEEeccc----cccCCCEEEEEE---CCEEEEEEEEEcC-----------
Confidence            4689999999998 888          9999999754    889999999998   5689999998543           


Q ss_pred             eEEecCCeEEEeeCCCCCCCCCCccc-ccCCCCEeEEEEEEE
Q 028706          144 VVKVPNGHCWVEGDNPSSSLDSRSFG-PIPLGLVKGRVTHIL  184 (205)
Q Consensus       144 ~~~vp~g~~~v~GDN~~~S~DSR~~G-~V~~~~IiGkv~~~i  184 (205)
                            |.+++..+|+...  ...+. .=..=.|+|+|+.++
T Consensus        91 ------~~~~L~s~N~~y~--pi~~~~~~~~~~IiG~Vv~vi  124 (126)
T d1jhfa2          91 ------NKVELLPENSEFK--PIVVDLRQQSFTIEGLAVGVI  124 (126)
T ss_dssp             ------TEEEEECSSTTCC--CEEEETTTSCEEEEEEEEEEE
T ss_pred             ------CEEEEecCCcCCC--CeEccCCCCcEEEEEEEEEEE
Confidence                  5789999997422  11110 001126999999876

>d1umua_ b.87.1.1 (A:) UmuD' {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: LexA/Signal peptidase
superfamily: LexA/Signal peptidase
family: LexA-related
domain: UmuD'
species: Escherichia coli [TaxId: 562]

Probab=98.62  E-value=8.3e-08  Score=69.45  Aligned_cols=84  Identities=20%  Similarity=0.220  Sum_probs=62.5

Q ss_pred             eEEEEEcCCCC-ccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCC
Q 028706           64 ASIVPVRGSSM-SPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN  142 (205)
Q Consensus        64 ~~~~~V~g~SM-~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~  142 (205)
                      ....+|.|+|| .|.+.+          ||.+++++..    .++.||+|++..   .++..+||+.-            
T Consensus        20 ~f~~rV~GdSM~~~gI~~----------GDlliVd~~~----~~~~g~ivva~i---~ge~~vKrl~~------------   70 (105)
T d1umua_          20 TYFVKASGDSMIDGGISD----------GDLLIVDSAI----TASHGDIVIAAV---DGEFTVKKLQL------------   70 (105)
T ss_dssp             EEEEECCSSTTGGGTCCT----------TCEEEEETTS----CCCTTCEEEEEE---TTEEEEEEEEC------------
T ss_pred             eEEEEEcCCccccCccCC----------CCEEEEEccc----ccccCcEEEEEE---CCEEEEEEEEE------------
Confidence            34689999999 588999          9999999865    789999999998   57899999752            


Q ss_pred             CeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706          143 DVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL  184 (205)
Q Consensus       143 ~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i  184 (205)
                            +|..+++.+|+.  ++.....+-..=.|.|+|++++
T Consensus        71 ------~~~~~L~~~N~~--y~~i~i~~~~~~~I~GvVv~vi  104 (105)
T d1umua_          71 ------RPTVQLIPMNSA--YSPITISSEDTLDVFGVVIHVV  104 (105)
T ss_dssp             ------SSSCEEECSSTT--SCCEECCTTSCEEEEEEEEEEE
T ss_pred             ------CCcEEEECCCCC--CCCEEcCCCCCEEEEEEEEEEE
Confidence                  235667788863  2333222222335999999875